Mercurial > repos > marpiech > norwich_tools_docking

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/bin/ht_protocol_finder.pl	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,232 @@
+#!/usr/bin/perl -w
+
+# Script that simulates the result of a high throughput protocol.
+
+if (@ARGV < 4)
+{
+	print "Script that simulates the result of a high throughput protocol.\n";
+	print "1st) exhaustive docking of a small representative part of the\n";
+	print "     whole library.\n";
+	print "2nd) Store the result of sdreport -t over that exhaustive dock.\n";
+	print "     in file <sdreport_file> that will be the input of this\n";
+	print "     script.\n";
+	print "3rd) ht_protocol_finder.pl <sdreport_file> <output_file> <thr1max>";
+	print " <thr1min> <ns1> <ns2>\n";
+	print "     <ns1> and <ns2> are the number of steps in stage 1 and in\n";
+	print "     stage 2. If not present, the default values are 5 and 15\n";
+	print "     <thrmax> and <thrmin> setup the range of thresholds that will\n";
+	print "     be simulated in stage 1. The threshold of stage 2 depends\n";
+	print "     on the value of the threshold of stage 1.\n";
+	print "     An input of -22 -24 will try protocols:\n";
+	print "            5	-22	15	-27\n";
+	print "            5	-22	15	-28\n";
+	print "            5	-22	15	-29\n";
+	print "            5	-23	15	-28\n";
+	print "            5	-23	15	-29\n";
+	print "            5	-23	15	-30\n";
+	print "            5	-24	15	-29\n";
+	print "            5	-24	15	-30\n";
+	print "            5	-24	15	-31\n";
+	print "     Output of the program is a 7 column values. First column\n";
+	print "     represents the time. This is a percentage of the time it\n";
+	print "     would take to do the docking in exhaustive mode, i.e. \n";
+    print "     docking each ligand 100 times. Anything\n";
+	print "     above 12 is too long.\n";
+	print "     Second column is the first percentage. Percentage of\n";
+	print "     ligands that pass the first stage.\n";
+	print "     Third column is the second percentage. Percentage of\n";
+	print "     ligands that pass the second stage.\n";
+	print "     The four last columns represent the protocol.\n";
+	print "     All the protocols tried are written at the end.\n";
+	print "     The ones for which time is less than 12%, perc1 is\n";
+	print "     less than 30% and perc2 is less than 5% but bigger than 1%\n";
+	print "     will have a series of *** after, to indicate they are good choices\n";
+	print "     WARNING! This is a simulation based in a small set.\n";
+	print "     The numbers are an indication, not factual values.\n";
+    exit (0);
+}
+open (IFILE, $ARGV[0]) || die "cannot open $ARGV[0] for reading: $!";
+open (OFILE, ">$ARGV[1]") || die "cannot open $ARGV[1] for writing: $!";
+<IFILE>;   # read first line
+$line = <IFILE>;
+$line =~ /\S+\s+(\S+)\s+\S+\s+(\S+)/;
+$prevname = $1;
+$inter = $2;
+push @tmp, $inter;
+$i = 0;
+while ($line = <IFILE>)
+{
+  $line =~ /\S+\s+(\S+)\s+\S+\s+(\S+)/;
+  $name = $1;
+  $inter = $2;
+  if ($name ne $prevname)
+  {
+      $prevname = $name;
+      push @inters, [ @tmp ];
+      $runsperligand[$i++] = @tmp;
+      $#tmp = -1;
+  }
+  push @tmp, $inter;
+}
+push @inters, [ @tmp ];
+$runsperligand[$i++] = @tmp;
+$totLigands = @inters;
+$ta = $ARGV[2];
+$tb = $ARGV[3];
+if (@ARGV > 4)
+{
+	$n1 = $ARGV[4];
+}
+else
+{
+	$n1 = 5;
+}
+if (@ARGV > 5)
+{
+	$n2 = $ARGV[5];
+}
+else
+{
+	$n2 = 15;
+}
+printf OFILE "Command line args:\n\t";
+foreach $arg (@ARGV)
+{
+	printf OFILE "%s\t", $arg;
+}
+printf OFILE "\n\n  TIME   PERC1   PERC2    N1  THR1    N2  THR2\n";
+for ($t1 = $ta ; $t1 >= $tb ; $t1--)
+{
+    $tc = $t1 - 5;
+    for ($t2 = $tc ; $t2 >= ($tc - 2) ; $t2--)
+    {
+        ($cref, $dref) =
+          getTables($t1, $t2);
+        @ligBelowThr1 = @$cref;
+        @ligBelowThr2 = @$dref;
+        ($time,$p1,$p2) = simulation($n1,$t1,$n2,$t2);
+        if (($time < 12.0) && ($p1 < 30.0) && ($p2 < 5.0) && ($p2 > 1.0))
+        {
+            printf OFILE "%6.3f, %6.3f, %6.3f, %4i, %4i, %4i, %4i ***\n",
+                         $time, $p1, $p2, $n1,$t1,$n2,$t2;
+        }
+        else
+        {
+            printf OFILE "%6.3f, %6.3f, %6.3f, %4i, %4i, %4i, %4i\n",
+                         $time, $p1, $p2, $n1,$t1,$n2,$t2;
+        }
+    }
+}
+
+
+sub simulation
+{
+  my(@params);
+  my(@lt0, @lt1);
+  my($thr1, $thr2,$ns1,$ns2,$tottime,$totnumHits,$total,$totnruns);
+  @params = @_;
+  $ns1 = $params[0];
+  $thr1 = $params[1];
+  $ns2 = $params[2];
+  $thr2 = $params[3];
+  $ntrials = 100;
+  $tottime = 0;
+  $totnumHitss1 = 0;
+  $totnumHitss2 = 0;
+  $total = $totLigands;
+  $totnruns = 0;
+  for ($i = 0 ; $i < $ntrials ; $i++)
+  {
+    $numHitss1 = 0;
+    $numHitss2 = 0;
+    $totnruns = 0;
+    for ($j = 0 ; $j < $totLigands ; $j++)
+    {
+      ($passStage1, $nruns1) = stage($ns1, $ligBelowThr1[$j]);
+      if ($passStage1)
+      {
+        $numHitss1++;
+        ($passStage2, $nruns2) = stage($ns2, $ligBelowThr2[$j]);
+        if ($passStage2)
+        {
+          $numHitss2++;
+        }
+        $totnruns += $nruns2;
+      }
+      $totnruns += $nruns1;
+    }
+    $time = $totnruns / $total;
+    $tottime += $time;
+    $totnumHitss1 += $numHitss1;
+    $totnumHitss2 += $numHitss2;
+  }
+  $tottime /= $ntrials;
+  $totnumHitss1 /= $ntrials;
+  $totnumHitss2 /= $ntrials;
+  $p1 = $totnumHitss1 * 100.0 / $totLigands;
+  $p2 = $totnumHitss2 * 100.0 / $totLigands;
+  return ($tottime, $p1, $p2);
+}
+
+sub getTables
+{
+  my(@params);
+  my($totLigands, @lt1, @lt2);
+  my($row,$inter, $belowThr1, $belowThr2);
+  my($thr0, $thr1);
+  @params = @_;
+  $thr1 = $params[0];
+  $thr2 = $params[1];
+  $totLigands = 0;
+  $belowThr1 = 0;
+  $belowThr2 = 0;
+  $totLigands = 0;
+  for $i (0 .. $#inters)
+  {
+    $row = $inters[$i];
+    for $j (0 .. $#{$row})
+    {
+      $inter = $row->[$j];
+      if ($inter <= $thr1)
+      {
+        $belowThr1++;
+      }
+      if ($inter <= $thr2)
+      {
+        $belowThr2++;
+      }
+    }
+    $lt1[$totLigands] =
+      $belowThr1 / $runsperligand[$i];
+    $lt2[$totLigands] =
+      $belowThr2 / $runsperligand[$i];
+    $totLigands++;
+    $belowThr1 = 0;
+    $belowThr2 = 0;
+  }
+  return (\@lt1, \@lt2);
+}
+
+
+
+sub stage
+{
+  my($nruns, $p, $i, $r);
+  $nruns = $_[0];
+  $p = $_[1];
+  if ($nruns == 0)
+  {
+    return (1, 0);
+  }
+  for ($i = 0 ; $i < $nruns ; $i++)
+  {
+    $r = rand;
+    if ($r < $p)
+    {
+      return (1, $i);
+    }
+  }
+  return (0, $nruns);
+}
+
+
Binary file tools/rdock/bin/libRbt.so has changed
Binary file tools/rdock/bin/libRbt.so.rDock_2013.1_src has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/bin/make_grid.csh	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,11 @@
+#!/bin/csh -f
+# Creates vdW grids for all receptor prm files listed on command line
+#
+set gridstep = 0.3
+set border = 1.0
+
+foreach grid ('vdw1' 'vdw5')
+  foreach file ($argv)
+      $RBT_ROOT/bin/rbcalcgrid -r${file} -pcalcgrid_${grid}.prm -o_${grid}.grd -g${gridstep} -b${border}
+  end
+end
Binary file tools/rdock/bin/rbcalcgrid has changed
Binary file tools/rdock/bin/rbcavity has changed
Binary file tools/rdock/bin/rbdock has changed
Binary file tools/rdock/bin/rblist has changed
Binary file tools/rdock/bin/rbmoegrid has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/bin/run_rbdock.pl	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,116 @@
+#!/usr/bin/perl
+use lib "$ENV{'RBT_ROOT'}/lib";
+require "run_rbfuncs.pl";
+
+my $rbtroot = $ENV{'RBT_ROOT'};
+my $rbthome = $ENV{'RBT_HOME'};
+my $recepDir = "$rbtroot/data/receptors";
+my $scriptDir = "$rbtroot/data/scripts";
+my $libraryDir = "$rbtroot/data/libraries";
+my $binDir = "$rbtroot/bin";
+
+#override default directories
+#Parse command line arguments
+my $nArgs = scalar(@ARGV);
+
+while (scalar(@ARGV)) {
+  my $arg = shift @ARGV;
+  if (index($arg,'-r')==0) {
+      $recepDir = substr($arg,2);
+  }
+  elsif (index($arg,'-s')==0) {
+      $scriptDir = substr($arg,2);
+  }
+  elsif (index($arg,'-l')==0) {
+      $libraryDir = substr($arg,2);
+  }
+}
+
+
+# Get the receptor, library and script tables
+my %receptor_table = get_prm_table($recepDir);
+my %script_table = get_prm_table($scriptDir);
+my %library_table = get_prm_table($libraryDir);
+
+#GET ALL THE INPUTS
+my $defFiles = "*.{sd,sdf,mol,mdl}";
+print join("\n",glob $defFiles);
+my $libFiles = get_input("\n\nEnter expression for SD files to dock",$defFiles);
+my $receptor = get_selection(\%receptor_table,"receptor");
+my $script = get_selection(\%script_table,"docking script");
+my $flags = get_input("Enter optional rbdock flags","-ap -an");
+my $runs = get_input("Enter number of runs/ligand",20);
+
+my $runRoot = get_input("Enter run name","rbdock");
+my $queueSys = get_input("Enter queuing system (NQS,CODINE,CONDOR,NONE)","CONDOR");
+my $queueName;
+$queueName = get_input("Enter NQS queue","QRBD") if ($queueSys eq "NQS");
+
+$pwd = `pwd`;
+chomp $pwd;
+
+#WRITE THE NQS SCRIPTS
+
+#GET THE LIST OF SD FILES TO DOCK
+my @libList = glob "${libFiles}";
+
+my $subFile = "submit_$runRoot.csh";
+open SUBHANDLE,">$subFile";
+print SUBHANDLE "#!/bin/csh -ef\n";
+
+my $iFile=0;
+foreach $libFile (@libList) {
+  $iFile++;
+  #Write the NQS script file
+  $runName = "${runRoot}_$iFile";
+  $nqsFile = "run_${runName}.csh";
+  my $logFile = "${runName}.log";
+
+  print "Writing $nqsFile...\n";
+
+  open NQSHANDLE,">$nqsFile";
+  print NQSHANDLE "#!/bin/csh -ef\n";
+  print NQSHANDLE "setenv RBT_ROOT $rbtroot\n";
+  print NQSHANDLE "setenv RBT_HOME $rbthome\n";
+  print NQSHANDLE "source \$RBT_ROOT/bin/setlibrbt.com\n";
+  print NQSHANDLE "cd $pwd\n";
+  print NQSHANDLE "if (-e $logFile) rm -f $logFile\n";
+  print NQSHANDLE "\$RBT_ROOT/bin/rbdock -i$libFile -o${runName} -r$receptor -p$script -n$runs $flags > $logFile\n";
+  close NQSHANDLE;
+
+  chmod 0755,$nqsFile;
+  print SUBHANDLE "qsub -q $queueName $nqsFile\n" if ($queueSys eq "NQS");
+  print SUBHANDLE "qsub -e $pwd/$runRoot/tmp/ -o $pwd/$runRoot/tmp/ $nqsFile\n" if ($queueSys eq "CODINE");
+  if ($queueSys eq "CONDOR") {
+    my $condorFile = "run_${runName}.cmd";
+    open CMDHANDLE,">$condorFile";
+    print CMDHANDLE "#CONDOR FILE WRITTEN BY run_rbscreen.pl\n";
+    print CMDHANDLE "universe        = vanilla\n";
+    print CMDHANDLE "executable      = ${nqsFile}\n";
+    print CMDHANDLE "Requirements    = CATALYST_NODE =!= True\n";
+    print CMDHANDLE "output          = ${nqsFile}.out\n";
+    print CMDHANDLE "error           = ${nqsFile}.err\n";
+    print CMDHANDLE "log             = ${nqsFile}.log\n";
+    print CMDHANDLE "queue\n";
+    close NQSHANDLE;
+    print SUBHANDLE "condor_submit $condorFile\n";
+  }
+}
+close SUBHANDLE;
+chmod 0755,$subFile;
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/bin/run_rbscreen.pl	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,416 @@
+#!/usr/bin/perl
+use File::stat;
+use lib "$ENV{'RBT_ROOT'}/lib";
+use strict;
+require "run_rbfuncs.pl";
+
+my $rbtroot = $ENV{'RBT_ROOT'};
+my $rbthome = $ENV{'RBT_HOME'};
+my $rbtligdb = $ENV{'RBT_LIGDB'};
+my $recepDir = "$rbtroot/data/receptors";
+my $scriptDir = "$rbtroot/data/scripts";
+my $filterDir = "$rbtroot/data/filters";
+my $libraryDir = "$rbtligdb/dock";
+my $binDir = "$rbtroot/bin";
+
+#override default directories
+#Parse command line arguments
+my $nArgs = scalar(@ARGV);
+
+while (scalar(@ARGV)) {
+  my $arg = shift @ARGV;
+  if (index($arg,'-r')==0) {
+      $recepDir = substr($arg,2);
+  }
+  elsif (index($arg,'-s')==0) {
+      $scriptDir = substr($arg,2);
+  }
+  elsif (index($arg,'-l')==0) {
+      $libraryDir = substr($arg,2);
+  }
+}
+
+
+# Get the receptor, library and script tables
+#my %receptor_table = get_prm_table($recepDir);
+my %receptor_table = get_prm_table($rbthome);
+my %script_table = get_prm_table($scriptDir);
+my %library_table = get_dock_table($libraryDir);
+
+#GET ALL THE INPUTS
+#my $library = get_selection(\%library_table,"library");
+my $isOK;
+my @libraries;
+my $receptor;
+my $script;
+
+do {
+  @libraries = get_multiple_selection(\%library_table,"library");
+  $isOK = get_input("\nIs this OK (Y/N)","Y");
+} until ($isOK eq "Y");
+
+do {
+  $receptor = get_selection(\%receptor_table,"receptor");
+  $isOK = get_input("\nIs this OK (Y/N)","Y");
+} until ($isOK eq "Y");
+
+# (SJ) check whether all the required files are in the dir
+# DM 7 Feb 2002 - get PSF/CRD filenames from PRM file
+print "\nLooking for all required target files in $rbthome...\n\n";
+my $prm_file = "$rbthome/".$receptor;
+my $prm_root = substr($prm_file, 0, rindex($prm_file,"."));
+my $as_file = "${prm_root}.as";
+my $vdw1_file = "${prm_root}_vdw1.grd";
+my $vdw5_file = "${prm_root}_vdw5.grd";
+
+#Set the default file names equal to their parameter names so that
+#error messages make sense if the parameters are missing completely from
+#the .prm file.
+my $psf_file = "RECEPTOR_TOPOL_FILE";
+my $crd_file = "RECEPTOR_COORD_FILE";
+my $mol2_file;
+
+# DM 12 May 2003
+# Optional target files for experimental restraints
+#
+# These default restraint suffixes and filenames should be synchronised
+# with the default parameter values in the relevant C++ class source files ($RBT_ROOT/fw/src/.cxx)
+# They are used if the user does not explicitly define the parameter in the
+# receptor .prm file
+#
+# Note: this code searches for specific SECTION names in the receptor .prm file
+# thus forcing a naming convention for the restraint terms that is not mandatory in the C++ code itself
+#
+# Pharmacophore restraint file
+# SECTION PHARMA
+# CONSTRAINTS_FILE = explicit filename
+# OPTIONAL_FILE = explicit filename
+my $ph4_filename = ".const";#synchronise with RbtPharmaSF::_CONSTRAINTS_FILE
+my $ph4_optfilename = "";
+my $has_ph4 = 0;
+# Tether restraint file
+# SECTION TETHER
+# REFERENCE_FILE = suffix to the root receptor.prm filename
+my $tether_suffix = "_reference.sd";#synchronise with RbtTetherSF::_REFERENCE_FILE
+my $has_tether = 0;
+# Nmr restraint file
+# SECTION NMR
+# FILENAME = explicit filename (not suffix)
+my $nmr_filename = "default.noe";#synchronise with RbtTetherSF::_FILENAME
+my $has_nmr = 0;
+
+open PRMHANDLE,$prm_file || die "Cannot read $prm_file";
+while (<PRMHANDLE>) {
+  my @fields = split(' ',$_);
+  my $nfields = scalar(@fields);
+  $psf_file = "$rbthome/".$fields[1] if (($fields[0] eq 'RECEPTOR_TOPOL_FILE') && ($nfields > 1));
+  $crd_file = "$rbthome/".$fields[1] if (($fields[0] eq 'RECEPTOR_COORD_FILE') && ($nfields > 1));
+  $mol2_file = "$rbthome/".$fields[1] if (($fields[0] eq 'RECEPTOR_FILE') && ($nfields > 1));
+  chomp $psf_file;
+  chomp $crd_file;
+  $has_ph4 = 1 if (($nfields > 1) && ($fields[0] eq 'SECTION') && ($fields[1] eq 'PHARMA') );
+  $ph4_filename = "$rbthome/".$fields[1] if (($nfields > 1) && ($fields[0] eq 'CONSTRAINTS_FILE') && $has_ph4);
+  $ph4_optfilename = "$rbthome/".$fields[1] if (($nfields > 1) && ($fields[0] eq 'OPTIONAL_FILE') && $has_ph4);
+  $has_tether = 1 if (($nfields > 1) && ($fields[0] eq 'SECTION') && ($fields[1] eq 'TETHER') );
+  $tether_suffix = $fields[1] if (($nfields > 1) && ($fields[0] eq 'REFERENCE_FILE') && $has_tether);
+  $has_nmr = 1 if (($nfields > 1) && ($fields[0] eq 'SECTION') && ($fields[1] eq 'NMR') );
+  $nmr_filename = "$rbthome/".$fields[1] if (($nfields > 1) && ($fields[0] eq 'FILENAME') && $has_nmr);
+}
+close PRMHANDLE;
+
+my @src_files = ($prm_file,$as_file, $vdw1_file, $vdw5_file);
+# check for either MOL2 or PSF/CRD
+if ($mol2_file ne "") {
+  push (@src_files,"$mol2_file");
+}
+else {
+  push (@src_files,"$psf_file");
+  push (@src_files,"$crd_file");
+}
+push (@src_files,"${ph4_filename}") if ($has_ph4);
+push (@src_files,"${ph4_optfilename}") if (($has_ph4) && ($ph4_optfilename ne ""));
+push (@src_files,"${prm_root}${tether_suffix}") if ($has_tether);
+push (@src_files,"${nmr_filename}") if ($has_nmr);
+
+my $is_file_missing = 0;
+foreach my $srcfile ( @src_files) {            # search through all the target files
+    if(-e $srcfile) {
+        print "Found: $srcfile";
+        my $sb = stat($srcfile);
+        #if ($sb->size < 1024) {print " WARNING size is suspiciously small ",$sb->size};
+        print "\n";
+    }
+    else {
+        print "ERROR: $srcfile is missing\n";
+        $is_file_missing    = 1;
+    }
+}
+
+if ($is_file_missing) {
+  print "\nCannot continue - please generate all required target files and place in $rbthome\n";
+  exit;
+}
+
+do {
+  $script = get_selection(\%script_table,"docking script");
+  $isOK = get_input("\nIs this OK (Y/N)","Y");
+} until ($isOK eq "Y");
+
+my $flags = get_input("Enter optional rbdock flags","-ap -an");
+my $mode;
+do
+{
+  $mode = get_input("High Throughput (HT) or Exhaustive Docking (ED)", "HT");
+}until (($mode eq "HT") || ($mode eq "ED"));
+
+my $HT;
+my $filter;
+my $FILTERFILE;
+my $nRedock;
+my $nStages;
+my @targets;
+my @runs;
+my $redockTarget;
+my $redockTargetDef = -20.0;#Default score threshold for redocking phase
+
+if ($mode eq "ED")
+{
+  $HT = 0;
+  my $run = get_input("Enter number of runs/ligand",50);
+  $flags = $flags . " -n" . $run;
+  $run--;
+  $filter = "1\nif - SCORE.NRUNS $run 0.0 -1.0,\n0\n";
+}
+else
+{
+  $HT = 1;
+  $nStages = get_input("Number of stages (excluding redocking, enter 0 for redocking only)",2);
+
+  #GET AND STORE THE TARGET SCORES AND NUMBER OF RUNS FOR EACH STAGE
+
+  if ($nStages > 0) {
+    for (my $n = 0; $n < $nStages; $n++) {
+      print "\nDOCKING STAGE $n\n";
+      my $target = get_input("Enter target score",-20.0);
+      my $run = get_input("Enter number of runs/ligand",20);
+      if ($run > 0)
+      {
+        push @targets,$target;
+        push @runs,$run;
+      }
+    }
+    $nStages = @targets;
+    print "\n";
+    #Default score threshold for redocking is equal to target score for last docking stage
+    $redockTargetDef = $targets[$nStages-1];
+  }
+
+  $nRedock = get_input("Enter number of redocking runs/ligand",0);
+  if ($nRedock > 0) {
+    $redockTarget = get_input("Enter target score for redocking",$redockTargetDef);
+  }
+  else
+  {
+    $redockTarget = $redockTargetDef;
+  }
+  my $nPhases = $nStages;
+  if ($nRedock > 0)
+  {
+    $nPhases++;
+  }
+  $filter = "$nPhases\n";
+  my $nr;
+  for (my $n = 0; $n < $nStages ; $n++)
+  {
+    $nr = $runs[$n] - 1;
+    $filter .= "if - $targets[$n] SCORE.INTER 1.0 if - SCORE.NRUNS $nr 0.0 -1.0,\n";
+  }
+  if ($nRedock > 0)
+  {
+    $nr = $nRedock - 1;
+    $filter .= "if - SCORE.NRUNS $nr 0.0 -1.0,\n";
+  }
+  my %filter_table = get_filter_table($filterDir, $redockTarget);
+  my @wfilters;
+  do {
+    print "\nSelect filters. Only the conformations that pass all the\n",
+          "filters chosen AND have SCORE.INTER lower than ", $redockTarget,
+          "\nAND SCORE.RESTR.CAVITY < 1.0 will be written down\n";
+    @wfilters = get_multiple_selection(\%filter_table,"filters");
+    $isOK = get_input("\nIs this OK (Y/N)","Y");
+  } until ($isOK eq "Y");
+
+  for (my $i = 0 ; $i < @wfilters ; $i++) # remove the no filters
+  {
+    if ($wfilters[$i] eq "1no_other_filters")
+    {
+      splice(@wfilters, $i, 1);
+    }
+  }
+
+  my $nwfilters = @wfilters + 2;
+  $filter .= "$nwfilters\n";
+  $filter .= "- SCORE.INTER $redockTarget,\n";
+  $filter .= "- SCORE.RESTR.CAVITY 1.0,\n";
+  foreach my $wfilter (@wfilters) {
+    open(FF, "$filterDir/$wfilter") || open(FF, "./$wfilter") ||
+           die "cannot open $wfilter for reading: $!";
+    my $line;
+    while ($line = <FF>){ $filter .= $line;}
+    $filter .= ",\n";
+  }
+}
+
+
+
+  my $runRoot = get_input("Enter run name","rbdock");
+
+  my $pwd = `pwd`;
+  chomp $pwd;
+
+  #Make a subdirectory for each docking stage
+  #plus a tmp directory
+  mkdir($runRoot,0755);
+  mkdir("$runRoot/tmp",0755);
+  mkdir("$runRoot/tmp/condor_logs",0755);
+  mkdir("$runRoot/log",0755);
+  mkdir("$runRoot/sd",0755);
+  mkdir("$runRoot/errors",0755);
+  chdir "$runRoot/tmp";
+
+  my $filterFile = "${runRoot}_filter.txt";
+  print "Writing $filterFile...\n";
+open FILTERHANDLE,">$filterFile";
+print FILTERHANDLE $filter;
+#WRITE THE CUSTOM DOCKING SCRIPT FOR USE BY CONDOR
+#This will be the Condor "Executable"
+#gzipped SD file to dock is passed as $1 argument
+#Run name is passed as $2 argument
+my $nqsFile = "run_${runRoot}.csh";
+print "Writing $nqsFile...\n";
+open NQSHANDLE,">$nqsFile";
+print NQSHANDLE "#!/bin/tcsh -f\n";
+print NQSHANDLE "#CONDOR EXECUTABLE SCRIPT WRITTEN BY run_rbscreen.pl\n";
+
+# DM 14 Mar 2003
+#Create a tmp runtime directory on the local disk for rDock SD and log files
+#These will be compressed before copying back to the submission directory
+#on the file server
+#There are now two tmp directories:
+# /tmp/ribodock/<version> - stores the grid files etc that are common between runs
+# /tmp/${PROG}.XXXXXX - stores the I/O SD and log files unique to each run
+
+print NQSHANDLE "set PROG = \${0:t}\n";
+print NQSHANDLE "set TMPDIR = `mktemp -d /tmp/\${PROG}.XXXXXX`\n";
+
+# synchronizing target files
+my $versionidx  = index $rbtroot,"ribodock";
+my $targetdir   = "/tmp/".substr($rbtroot,$versionidx);
+print NQSHANDLE "mkdir -pv -m0775 /tmp/ribodock\n";
+print NQSHANDLE "mkdir -pv -m0775 $targetdir\n";
+print NQSHANDLE "setenv RBT_HOME $targetdir\n";
+print NQSHANDLE "rsync -avz ".join(" ",@src_files)." $targetdir\n";
+
+# Copy the compressed sd file to the tmp directory and uncompress
+# DM 28 Feb 2002 - use the /tmp directory on the local disk instead
+# DM 14 Mar 2003 - use TMPDIR = /tmp/${PROG}.XXXXXX instead
+print NQSHANDLE "set gzfile = \$1\n";
+print NQSHANDLE "set runName = \$2\n";
+print NQSHANDLE "set copied_gzfile = \${TMPDIR}/\${gzfile:t}\n";
+print NQSHANDLE "set sdfile = \${copied_gzfile:r}\n";
+print NQSHANDLE "echo Ligand_DB : \$gzfile\n";
+print NQSHANDLE "echo Local copy: \$copied_gzfile\n";
+print NQSHANDLE "echo Unzipped  : \$sdfile\n";
+print NQSHANDLE "cp -f \$gzfile \$copied_gzfile\n";
+print NQSHANDLE "gunzip -f \$copied_gzfile\n";
+
+my $target = $redockTarget;
+print NQSHANDLE "#\n";
+print NQSHANDLE "set outRoot = \${TMPDIR}/\${runName}\n";
+print NQSHANDLE "set logFile = \${outRoot}.log\n";
+print NQSHANDLE "if (-e \$logFile) rm -f \$logFile\n";
+print NQSHANDLE "\$RBT_ROOT/bin/rbdock -i\$sdfile -o\${outRoot} -r$receptor -p$script -t$filterFile $flags > \$logFile\n";
+
+# Compress the SD and log files and copy back to submission directory
+# The ..._errors.sd files are generated by the pharmacophore restraints term for ligands that
+# do not fulfill the feature requirements
+print NQSHANDLE "if (-e \${outRoot}.sd) then\n";
+print NQSHANDLE "  gzip -9vf \${outRoot}.sd\n";
+print NQSHANDLE "  cp \${outRoot}.sd.gz ../sd\n";
+print NQSHANDLE "endif\n";
+print NQSHANDLE "if (-e \${logFile}) then\n";
+print NQSHANDLE "  gzip -9vf \${logFile}\n";
+print NQSHANDLE "  cp \${logFile}.gz ../log\n";
+print NQSHANDLE "endif\n";
+print NQSHANDLE "if (-e \${outRoot}_errors.sd) then\n";
+print NQSHANDLE "  gzip -9vf \${outRoot}_errors.sd\n";
+print NQSHANDLE "  cp \${outRoot}_errors.sd.gz ../errors\n";
+print NQSHANDLE "endif\n";
+
+print NQSHANDLE "rm -rf \${TMPDIR}\n";
+close NQSHANDLE;
+chmod 0755,$nqsFile;
+
+#PREPARE THE CONDOR JOB FILE
+my $condorFile = "run_${runRoot}.cmd";
+print "Writing $condorFile...\n";
+open CMDHANDLE,">$condorFile";
+print CMDHANDLE "#CONDOR COMMAND FILE WRITTEN BY run_rbscreen.pl\n";
+print CMDHANDLE "universe        = vanilla\n";
+print CMDHANDLE "initialdir      = $pwd/$runRoot/tmp\n";
+print CMDHANDLE "environment     = RBT_ROOT=$rbtroot;RBT_LIGDB=$rbtligdb;RBT_HOME=$rbthome;LD_LIBRARY_PATH=/usr/local/lib:$rbtroot/lib;\n";
+print CMDHANDLE "executable      = ${nqsFile}\n";
+#Stop Condor filling your mailbox
+print CMDHANDLE "Notification    = Error\n";
+print CMDHANDLE "log             = run_${runRoot}.log\n";
+# Added by DM, Enspiral Discovery, 28 Feb 2005
+# Prevent rDock jobs running on dedicated Catalyst nodes
+print CMDHANDLE "Requirements    = CATALYST_NODE =!= True\n";
+
+#GET THE LIST OF COMPRESSED SD FILES TO DOCK
+my $iFile=0;
+foreach my $library (@libraries) {
+  my @libFiles = glob "$library_table{$library}";
+  foreach my $libFile (@libFiles) {
+    $iFile++;
+    my $runName = "${runRoot}_$iFile";
+    print CMDHANDLE "output          = condor_logs/run_${runName}.out\n";
+    print CMDHANDLE "error           = condor_logs/run_${runName}.err\n";
+    print CMDHANDLE "arguments       = $libFile $runName\n";
+    print CMDHANDLE "queue\n";
+  }
+}
+close CMDHANDLE;
+
+#WRITE THE CUSTOM CLEANUP SCRIPT
+#This will be run by the user from the command line
+#after all the jobs have finished
+my $cleanFile = "clean_${runRoot}.csh";
+print "Writing $cleanFile...\n";
+open CLEANHANDLE,">$cleanFile";
+print CLEANHANDLE "#!/bin/tcsh -f\n";
+print CLEANHANDLE "#CLEANUP SCRIPT WRITTEN BY run_rbscreen.pl\n";
+print CLEANHANDLE "set sdout = ../${runRoot}_raw_hits.sd\n";
+print CLEANHANDLE "if (-e \${sdout}) then\n";
+print CLEANHANDLE "  echo ARE YOU SURE YOU WANT TO DO THIS\n";
+print CLEANHANDLE "  echo \${sdout} already exists\n";
+print CLEANHANDLE "  echo To rerun the script remove \${sdout} manually first\n";
+print CLEANHANDLE "  exit\n";
+print CLEANHANDLE "endif\n";
+print CLEANHANDLE "echo All compressed SD files in ../sd/ will be concatenated into a single compressed file \${sdout}.gz\n";
+print CLEANHANDLE "touch \${sdout}\n";
+print CLEANHANDLE "foreach file (../sd/*.sd.gz)\n";
+print CLEANHANDLE "  echo Sorting and concatenating \${file}...\n";
+print CLEANHANDLE "  zcat \${file} | \${RBT_ROOT}/bin/sdsort -n -fSCORE -s >> \${sdout}\n";
+print CLEANHANDLE "end\n";
+print CLEANHANDLE "echo Each block of consecutive records per ligand have been presorted by SCORE ";
+print CLEANHANDLE "ready for filtering\n";
+print CLEANHANDLE "echo Compressing \${sdout}...\n";
+print CLEANHANDLE "gzip -9vf \${sdout}\n";
+print CLEANHANDLE "echo DONE\n";
+print CLEANHANDLE "echo You may now safely remove the ../sd/ directory if you wish to save disk space\n";
+close CLEANHANDLE;
+chmod 0755,$cleanFile;
+
+print "To submit, cd $runRoot/tmp; condor_submit $condorFile\n";
+print "When all jobs have completed, run $runRoot/tmp/$cleanFile to concatenate the output files\n";
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/bin/sdfield	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,31 @@
+#!/usr/bin/perl
+# add extra fields to SD records
+use lib "$ENV{'RBT_ROOT'}/lib";
+use SDRecord;
+
+printHelpAndExit() if (scalar(@ARGV) == 0);
+#Parse command line arguments
+my @files;
+my $arg = shift @ARGV;
+printHelpAndExit() if ($arg eq '-h');
+#read records
+my $sdRec = new SDRecord;
+my $nRec=0;
+# if not -h, then must be the FieldName
+my $FieldName = $arg;
+my $FieldVal  = shift @ARGV; # and this must be the filed value
+# rest are the filenames
+while ($sdRec->readRec('DATA'=>1,'LINES'=>1)) {
+	$sdRec->addData('_REC' => ++$nRec);#add record# as temp data field
+	$sdRec->addData('_FILE' => $ARGV);#add filename as temp data field
+	$sdRec->addDataAndLines($FieldName => $FieldVal);
+	$sdRec->writeRec();#write record
+}
+
+sub printHelpAndExit {
+	print "\nAdding fields to SD files\n";
+	print "Usage:\n";
+	print "\tsdfield <Fieldname> <value> <infile[s]>\n";
+	print "\t-h\tthis help\n";
+	print "\t\n";
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/bin/sdfilter	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,221 @@
+#!/usr/bin/perl
+# Filters SD records by given data field                                       *
+#                                                                              *
+# Usage:  sdfilter -f'$<DataField> <Operator> <Value>'  [sdFiles]              *
+#      or sdfilter -f<filename> [sdFiles]                                      *
+#                                                                              *
+#         where <filename> contains a list of <DataField> <Operator> <Value>   *
+#         filters, one per line.                                               *
+#         Multiple filters are OR'd together (for AND, pipe to a 2nd sdfilter) *
+#                                                                              *
+#         If sdFiles not given, reads from standard input                      *
+#         Output is to standard output                                         *
+#*******************************************************************************
+use lib "$ENV{'RBT_ROOT'}/lib";
+
+use SDRecord;
+
+#keep track of the number of occurrences of each value of this key
+my $summaryKey = "Name";
+
+#list of filter strings
+#all filters in the list are OR'd together
+my @SDFILTERS;
+
+# DM 5 Dec 2000 - new option to filter on diverse_molecules.list
+# as output by C2
+# Essentially just a list of record numbers
+my $cerius2filter = 0;
+my $cerius2file = "diverse_molecules.list";
+my @cerius2recs;
+
+#Print help if no command line arguments
+printHelpAndExit() if (scalar(@ARGV) == 0);
+
+#Parse command line arguments
+my @files;
+while (scalar(@ARGV)) {
+  my $arg = shift @ARGV;
+  printHelpAndExit() if ($arg eq '-h');
+  if (index($arg,'-f')==0) {
+    $arg = substr($arg,2);
+    #try opening the argument as a file
+    if (open FILTERFILE,$arg) {
+      #get the list of filter strings from the file
+      my @strList = <FILTERFILE>;
+      close FILTERFILE;
+      chomp @strList;
+      #build the filter strings into a proper Perl expression for eval
+      #and add to the list
+      push @SDFILTERS,buildFilterList(@strList);
+    }
+    else {
+      #build the filter string into a proper Perl expression for eval
+      #and add to the list
+      push @SDFILTERS, buildFilterList($arg);
+    }
+  }
+  elsif (index($arg,'-sup')==0) {
+    my $supplier = substr($arg,4);
+    my $supplierFilter = "scalar(grep /$supplier/, \@supplierList) > 0";
+    #print "Supplier filter = $supplierFilter\n";
+    push @SDFILTERS, $supplierFilter;
+  }
+  elsif (index($arg,'-s')==0) {
+    $summaryKey = substr($arg,2);
+  }
+  #DM 05 Dec 2000 - c2 option
+  elsif (index($arg,'-c2')==0) {
+    $cerius2filter = 1;
+    $arg = substr($arg,3);
+    $cerius2file = $arg if ($arg); #argument overrides default file name
+    if (open FILTERFILE,$cerius2file) {
+      #Skip first two lines
+      my $tmp = <FILTERFILE> || die "Invalid Cerius2 file $cerius2file";
+      $tmp = <FILTERFILE> || die "Invalid Cerius2 file $cerius2file";
+      while (<FILTERFILE>) {
+	chomp;
+	push @cerius2recs,split(" ",$_);
+      }
+      close FILTERFILE;
+    }
+    die "No records in $cerius2file\n" if (scalar(@cerius2recs)==0);
+    #Sort into reverse order so we can pop the record #'s off later
+    @cerius2recs = reverse (sort {$a<=>$b} @cerius2recs);
+    #foreach $rec (@cerius2recs) {
+    #  print "$rec\n";
+    #}
+  }
+  else {
+    push @files,$arg;#must be a filename
+  }
+}
+push @ARGV,@files;#put the filenames back in the arg list
+
+#read records
+my $sdRec = new SDRecord;
+my %count;#record the number of occurrences of each value of $summaryKey
+my $nRec=0;
+#In C2 mode, just need to check record numbers so we can read the SD file
+#without parsing the data fields
+if ($cerius2filter) {
+  my $c2nextRec = pop @cerius2recs;
+  while ($sdRec->readRec('LINES'=>1)) {
+    if ((++$nRec)==$c2nextRec) {
+      $sdRec->writeRec();
+      exit if (scalar(@cerius2recs)==0);
+      $c2nextRec=pop @cerius2recs;
+    }
+  }
+}
+#Normal mode, need to parse the data fields
+else {
+  while ($sdRec->readRec('DATA'=>1,'LINES'=>1)) {
+    $sdRec->addData('_REC' => ++$nRec);#add record# as temp data field
+    $sdRec->addData('_COUNT' => ++$count{$sdRec->{'DATA'}->{$summaryKey}});#add count as temp data field
+    my @supplierList = buildSupplierList($sdRec);
+    foreach $filter (@SDFILTERS) {
+      if (eval $filter) {
+	$sdRec->writeRec();#write record if one of the filters returns true
+	last;
+      }
+    }
+  }
+}
+
+#######################################################################
+# Compose a complete SD filter string for each string in the parameter list
+# Complete strings are of the form: $sdRec->{'DATA'}->{'Name'} eq RBT162"
+# Note: the SDRecord object name is hardcoded as $sdRec
+sub buildFilterList {
+  my @strList = @_;#input list of unexpanded filter strings
+  my @filterList;#output list of expanded filter strings
+
+  #loop over each input string
+  foreach $str (@strList) {
+    my $filter;
+    my $i1 = 0;
+    my $lenstr = length($str);
+    while ($i1 < $lenstr) {
+      #print "i1=$i1\n";
+      $i2 = index($str,"\$",$i1);
+      #print "i2=$i2\n";
+      if ($i2 == -1) {
+	$filter .= substr($str,$i1);
+	last;
+      }
+      $filter .= substr($str,$i1,$i2-$i1);
+      #DM 04 Sept 2000 - allow for spaces in field names
+      #by surrounding with {} brackets
+      #e.g. ${CDD id}
+      #Check for { first, if not found assume standard format (e.g. $Name)
+      my $i3 = index($str,"{",$i2+1);
+      if ($i3 == $i2+1) {
+	my $i4 = index($str,"}",$i3+1);
+	my $var;
+	if ($i4 == -1) {
+	  $var = substr($str,$i3+1);
+	  $filter .= "\$sdRec->{'DATA'}->{'$var'}";
+	  last;
+	}
+	else {
+	  $var = substr($str,$i3+1,$i4-$i3-1);
+	  $filter .= "\$sdRec->{'DATA'}->{'$var'}";
+	}
+	$i1 = $i4+1;
+      }
+      #Standard format
+      else {
+	$i3 = index($str," ",$i2+1);
+	#print "i3=$i3\n";
+	my $var;
+	if ($i3 == -1) {
+	  $var = substr($str,$i2+1);
+	  $filter .= "\$sdRec->{'DATA'}->{'$var'}";
+	  last;
+	}
+	else {
+	  $var = substr($str,$i2+1,$i3-$i2-1);
+	  $filter .= "\$sdRec->{'DATA'}->{'$var'}";
+	}
+	$i1 = $i3;
+      }
+    }
+    #print "$filter\n";
+    push @filterList,$filter;
+  }
+  return @filterList;
+}
+
+#######################################################################
+# Extract the list of suppliers from the Cat_coden multi-line data field
+sub buildSupplierList {
+  my $rec = shift;
+  my @suppliers;
+  my $suppBase = $rec->{'DATAREF'}->{'Cat_coden'}+1;
+  my $linesRef = $rec->{'LINES'};
+  if (defined $suppBase) {
+    while ($$linesRef[$suppBase] ne "") {
+      push @suppliers,$$linesRef[$suppBase++];
+    }
+  }
+  #print "Supplier list:\n";
+  #print join("\n",@suppliers);
+  return @suppliers;
+}
+
+#######################################################################
+sub printHelpAndExit {
+  print "\nFilters SD records by data fields\n";
+  print "\nUsage:\tsdfilter -f'\$<DataField> <Operator> <Value>' [-s<DataField>] [sdFiles]\n";
+  print "or\tsdfilter -f<filename> [-s<DataField>] [sdFiles]\n\n";
+  print "Note:\tMultiple filters are allowed and are OR'd together.\n";
+  print "\tFilters can be provided in a file, one per line.\n";
+  print "\n\tStandard Perl operators should be used. e.g.\n";
+  print "\teq ne lt gt le ge for strings\n\t== != < > <= >= for numeric\n";
+  print "\n\t_REC (record #) is provided as a pseudo-data field\n";
+  print "\tif -s option is used, _COUNT (#occurrences of DataField) is provided as a pseudo-data field\n";
+  print "\n\tIf SD file list not given, reads from standard input\n";
+  print "\tOutput is to standard output\n\n";
+  exit;
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/bin/sdmodify	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,59 @@
+#!/usr/bin/perl
+# Script to set the first title line equal to a given data field
+#
+# Usage:  sdmodify -f<DataField> [sdFiles]
+#
+#         If sdFiles not given, reads from standard input
+#         Output is to standard output
+
+use lib "$ENV{'RBT_ROOT'}/lib";
+
+use SDRecord;
+
+my $SDMODKEY = "ID";
+
+#Print help if no command line arguments
+printHelpAndExit() if (scalar(@ARGV) == 0);
+
+#Parse command line arguments
+my @files;
+while (scalar(@ARGV)) {
+  my $arg = shift @ARGV;
+  printHelpAndExit() if ($arg eq '-h');
+  if (index($arg,'-f')==0) {
+    $SDMODKEY = substr($arg,2);#modification key
+  }
+  else {
+    push @files,$arg;#must be a filename
+  }
+}
+push @ARGV,@files;#put the filenames back in the arg list
+
+#read records
+my $sdRec = new SDRecord;
+my $nRec=0;
+while ($sdRec->readRec('DATA'=>1,'LINES'=>1)) {
+  $sdRec->addData('_REC' => ++$nRec);#add record# as temp data field
+  #set the first line equal to the given data field
+  my $nLines = scalar (@{$sdRec->{'LINES'}});
+  if ($nLines > 0) {
+    ${$sdRec->{'LINES'}}[0] = $sdRec->{'DATA'}->{$SDMODKEY};
+  }
+  $sdRec->writeRec();
+}
+
+#!/usr/bin/perl
+# Script to set the first title line equal to a given data field
+#
+# Usage:  sdmodify -f<DataField> [sdFiles]
+#
+#         If sdFiles not given, reads from standard input
+#         Output is to standard output
+
+sub printHelpAndExit {
+  print "\nScript to set the first title line equal to a given data field.\n";
+  print "\nUsage:\tsdmodify -f<DataField> [sdFiles]\n";
+  print "\n\tIf sdFiles not given, reads from standard input.\n";
+  print "\n\tOutput is to standard output.\n\n";
+  exit;
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/bin/sdreport	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,437 @@
+#!/usr/bin/perl
+# Produces text summaries of SD records                                        *
+#                                                                              *
+# Usage:  sdreport [-l] [-t] [-s<DataField>] [sdFiles]                         *
+#                                                                              *
+#         -l output data fields for each record as processed                   *
+#         -t tabulate Rbt.Score.* fields for each record as processed          *
+#         -s summarise data fields for all records                             *
+#         -s<DataField> summarise data fields for each unique value            *
+#                       of <DataField>                                         *
+#                                                                              *
+# Note:   If -l or -t are combined with -s, the listing/table is output        *
+#         within each ligand summary                                           *
+#         If sdFiles not given, reads from standard input                      *
+#         Output is to standard output                                         *
+#         Default is equivalent to sdfilter -l                                 *
+#*******************************************************************************
+use lib "$ENV{'RBT_ROOT'}/lib";
+
+use SDRecord;
+
+# Default field names and headings for rDock v4.00 scores
+my @defaultFields = ('SCORE','SCORE.INTER','SCORE.INTRA','SCORE.RESTR','SCORE.INTER.VDW');
+my @defaultHeadings = ('TOTAL','INTER','INTRA','RESTR','VDW');
+
+# Default field names and headings for normalised scores (score / #ligand heavy atoms)
+my @defaultNormFields = ('SCORE.norm','SCORE.INTER.norm','SCORE.INTRA.norm','SCORE.RESTR.norm','SCORE.heavy');
+my @defaultNormHeadings = ('TOTALn','INTERn','INTRAn','RESTRn','#heavy');
+
+# Default field names and headings for rDock v3.00 scores
+my @defaultOldFields = ('Rbt.Score.Corrected','Rbt.Score.Inter','Rbt.Score.Intra','Rbt.Score.IntraMin','Rbt.Score.Restraint');
+my @defaultOldHeadings = ('TOTAL','INTER','INTRA','INTRAMIN','RESTR');
+
+my $listFormat = 0;
+my $summaryFormat = 0;
+my $tableFormat = 0;
+my $supplierFormat = 0;
+my $csvFormat = 0;
+my $summaryKey = "_TITLE1";
+my $oldFields = 0;#If true, use old default field names for component scores
+my $headings = 1;#DM 21 Nov 2000, If false, don't output headings
+my @outputFields;
+my @outputHeadings;
+
+#Print help if no command line arguments
+printHelpAndExit() if (scalar(@ARGV) == 0);
+
+#Parse command line arguments
+my $nArgs = scalar(@ARGV);
+
+while (scalar(@ARGV)) {
+  my $arg = shift @ARGV;
+  printHelpAndExit() if ($arg eq '-h');
+  if (index($arg,'-l')==0) {
+    $listFormat = 1;
+  }
+  elsif (index($arg,'-o')==0) {
+    $oldFields = 1;
+  }
+  # 7 Feb 2005 (DM) Option to report normalised aggregate scores
+  elsif (index($arg,'-norm')==0) {
+    $oldFields = 2;
+  }
+  elsif (index($arg,'-sup')==0) {
+    $supplierFormat = 1;
+  }
+  elsif (index($arg,'-s')==0) {
+    $summaryFormat = 1;
+  }
+  elsif (index($arg,'-id')==0) {
+    $summaryKey = substr($arg,3);
+  }
+  elsif (index($arg,'-nh')==0) {
+    $headings = 0;
+  }
+  elsif (index($arg,'-t')==0) {
+    $tableFormat = 1;
+    push @outputFields, split(',',substr($arg,2));
+    push @outputHeadings, @outputFields;
+  }
+  elsif (index($arg,'-c')==0) {
+    $csvFormat = 1;
+    push @outputFields, split(',',substr($arg,2));
+    push @outputHeadings, @outputFields;
+  }
+  else {
+    push @files,$arg;#must be a filename
+  }
+}
+push @ARGV,@files;#put the filenames back in the arg list
+
+#use -l if neither table format is specified
+$listFormat = (!$tableFormat && !$csvFormat && !$supplierFormat);
+
+#If no output fields defined for -t or -c use the defaults (old or new)
+if (scalar(@outputFields)==0) {
+	if ($oldFields == 1) {
+		@outputFields = @defaultOldFields;
+		@outputHeadings = @defaultOldHeadings;
+	}
+	elsif ($oldFields == 2) {
+                @outputFields = @defaultNormFields;
+                @outputHeadings = @defaultNormHeadings;
+	}
+	else {
+		@outputFields = @defaultFields;
+		@outputHeadings = @defaultHeadings;
+	}
+}
+
+my $sdRec = new SDRecord;
+my %summary;#hash of SDRecord lists, indexed by user-defined summary key
+my %indexByName;
+my %indexByNum;
+my $idx = 0;
+my $nRec = 0;
+
+#Column headings for tab and csv format
+#DM 21 Nov 2000 - if $headings is false, then don't output the column headings
+if ($tableFormat && !$summaryFormat && $headings) {
+  tabHeadings($summaryKey,@outputHeadings);
+}
+if ($csvFormat && !$summaryFormat && $headings) {
+  csvHeadings($summaryKey,@outputHeadings);
+}
+
+#read records
+while ($sdRec->readRec('LINES'=>1,'DATA'=>1)) {
+  $sdRec->addData('_REC' => ++$nRec);#add record# as temp data field
+  if ($listFormat && !$summaryFormat) {
+    print "\n\nRECORD #$nRec\n";
+    $sdRec->writeData();
+  }
+  if ($tableFormat && !$summaryFormat) {
+    @recList = ($sdRec);
+    tabScores(\@recList,$summaryKey,@outputFields);
+  }
+  elsif ($csvFormat && !$summaryFormat) {
+    @recList = ($sdRec);
+    csvScores(\@recList,$summaryKey,@outputFields);
+  }
+  elsif ($supplierFormat && !$summaryFormat) {
+    @recList = ($sdRec);
+    tabulateSuppliers(\@recList,$summaryKey);
+  }
+  #add record to summary, indexed by user field value
+  #keep a separate index of unique values of user field values,
+  #indexed by number in the order the values first appear
+  #In this way we can maintain the sorted order of ligands
+  #when we come to print out the summary
+  if ($summaryFormat) {
+    my $summaryValue = $sdRec->{'DATA'}->{$summaryKey};
+    #New data field value encountered
+    if (!defined $indexByName{$summaryValue}) {
+      $idx++;#incr the number of unique values
+      #keep cross-referenced indexes (field value <-> number)
+      $indexByName{$summaryValue} = $idx;
+      $indexByNum{$idx} = $summaryValue;
+    }
+    push @{$summary{$summaryValue}},$sdRec->copy('DATA'=>1);
+  }
+}
+
+#Print summary if required
+if ($summaryFormat) {
+  print "\n===============================================================\n";
+  print "SUMMARY BY $summaryKey\n";
+  foreach $idx (sort {$a<=>$b} keys %indexByNum) {#numberic sort of index numbers
+    my $key = $indexByNum{$idx};#look up corresponding data field value
+    print "\n===============================================================\n";
+    print "$summaryKey = $key (#$idx)\n\n";
+    writeSummary($summary{$key});
+    if ($listFormat) {
+      print "\nIndividual records:\n";
+      foreach $rec (@{$summary{$key}}) {
+        print "\n";
+	      $rec->writeData();
+      }
+    }
+    if ($tableFormat) {
+      print "\nScores:\n";
+      tabHeadings($summaryKey,@outputHeadings);
+      tabScores($summary{$key},$summaryKey,@outputFields);
+    }
+    if ($csvFormat) {
+      print "\nScores:\n";
+      csvHeadings($summaryKey,@outputHeadings);
+      csvScores($summary{$key},$summaryKey,@outputFields);
+    }
+  }
+}
+
+##############################################################
+# writes a summary to STDOUT for a list of SDRecords
+# Input is a reference to an array of SDRecords
+sub writeSummary {
+  my $recListRef = shift;
+
+  #Extract the list of data values for each fieldname into a hash array
+  #(key=fieldname, value=array ref)
+  my %fields;
+  foreach $rec (@{$recListRef}) {
+    my ($key,$value);
+    while ( ($key,$value) = each %{$rec->{'DATA'}}) {
+      push @{$fields{$key}},$value;
+    }
+  }
+
+  #Look for constant fields and store separately
+  my %constFields;
+  foreach $key (keys %fields) {
+    my @values = sort  @{$fields{$key}};
+    my $nVal = scalar(@values);
+    if ($values[0] eq $values[$nVal -1]) {
+      $constFields{$key} = $values[0];#store the field name and the constant value
+      delete $fields{$key};#remove from (non-const) array
+    }
+  }
+
+  #Print constant fields
+  print "\nConstant fields:\n\n";
+  foreach $key (sort keys %constFields) {
+    printf "%-40s%s\n",$key,$constFields{$key};
+  }
+  #Print min and max value for non-const fields
+  print "\nVariable fields:\n\n";
+  foreach $key (sort keys %fields) {
+    my @values = @{$fields{$key}};
+    #Look at first value to decide whether to do text or numeric sort
+    if (isNaN($values[0])) {
+      @values = sort @values;#text sort
+    }
+    else {
+      @values = sort {$a <=> $b} @values;#numeric sort
+    }
+    my $nVal = scalar(@values);
+    printf "%-40s",$key;
+    print "Min = $values[0]\tMax = $values[$nVal-1]\t(N = $nVal)\n";
+  }
+}
+
+##############################################################
+# function isNaN equivalent to the C++, java, javascript isNaN
+# From P Vaglio, ~intranet/lib/rbt_func.pl
+sub isNaN {
+  local($_) = @_;
+  s/\s+//g;         # strip white space
+  # match +or- beginning of line 0 or 1 time
+  # then any numeric 0 or more
+  # then a decimal point
+  # then any numeric 0 or more after decimal point
+  # then possibly an e or E then + or - then any numreci at least once
+  if (/^([+-]?)(\d*)(\.(\d*))?([Ee]([+-]?\d+))?$/ && (defined $2 || defined $4)) {
+    return 0;
+  } else {
+    return 1;
+  }
+}
+
+##############################################################
+# output corresponding headings for use with tabScores
+sub tabHeadings {
+  my $summaryKey = shift;
+  my @fieldNames = @_;
+  printf("%-10s%-30s","REC",$summaryKey);
+  foreach $field (@fieldNames) {
+    printf("%10s",$field);
+  }
+  print "\n";
+}
+
+##############################################################
+# tab-delimited output of named data field values
+sub tabScores {
+  my $recListRef = shift;
+  my $summaryKey = shift;
+  my @fieldNames = @_;
+  foreach $rec (@{$recListRef}) {
+    printf("%03d\t%-30.30s",$rec->{'DATA'}->{'_REC'},$rec->{'DATA'}->{$summaryKey});
+    foreach $field (@fieldNames) {
+      my $val = $rec->{'DATA'}->{$field};
+      if (isNaN($val)) {
+        printf("%-10.12s",$val);
+      }
+      else {
+        printf("%10.3f",$val);
+      }
+    }
+    print "\n";
+  }
+}
+
+##############################################################
+# output corresponding headings for use with csvScores
+sub csvHeadings {
+  my $summaryKey = shift;
+  my @fieldNames = @_;
+  printf("%s,%s","REC",$summaryKey);
+  foreach $field (@fieldNames) {
+    printf(",%s",$field);
+  }
+  print "\n";
+}
+
+##############################################################
+# comma-delimited output of named data field values
+sub csvScores {
+  my $recListRef = shift;
+  my $summaryKey = shift;
+  my @fieldNames = @_;
+  foreach $rec (@{$recListRef}) {
+    printf("%d,%s",$rec->{'DATA'}->{'_REC'},$rec->{'DATA'}->{$summaryKey});
+    foreach $field (@fieldNames) {
+      my $val = $rec->{'DATA'}->{$field};
+      if (isNaN($val)) {
+        printf(",%s",$val);
+      }
+      else {
+        printf(",%.3f",$val);
+      }
+    }
+    print "\n";
+  }
+}
+
+
+##############################################################
+# standardised output of Catalyst supplier field
+# Input is a reference to an array of SDRecords
+# and a ligand identifier field to output in column 1 (def=Name)
+sub tabulateSuppliers {
+  my $recListRef = shift;
+  my $summaryKey = shift || 'Name';
+  foreach $rec (@{$recListRef}) {
+    my $suppBase = $rec->{'DATAREF'}->{'Supplier'}+1;
+    my $linesRef = $rec->{'LINES'};
+    my $name = $rec->{'DATA'}->{$summaryKey};
+
+    #Output some useful compound info
+    my $name = $rec->{'DATA'}->{$summaryKey};
+    my $molFormula = $rec->{'DATA'}->{'MolFormula'};
+    my $molWt = $rec->{'DATA'}->{'MolWt'};
+    my $casNum = $rec->{'DATA'}->{'CAS_num'};
+    my $mdlNum = $rec->{'DATA'}->{'MDLNUMBER'};
+    print "\n\n====================================================================================================\n";
+    printf("%-10.10s%s\n","Name:",$name);
+    printf("%-10.10s%s\n","Formula:",$molFormula);
+    printf("%-10.10s%s\n","Mol.wt:",$molWt);
+    printf("%-10.10s%s\n","CAS #:",$casNum);
+    printf("%-10.10s%s\n","MDL #:",$mdlNum);
+
+    #Get all the supplier record lines into a list
+    #Record is terminated by blank line
+    my @lines;
+    my $nLines = 0;
+    for (; $$linesRef[$suppBase+$nLines] ne ""; $nLines++) {
+      push @lines,$$linesRef[$suppBase+$nLines];
+    }
+
+    #Column headings
+    printf("\n%-20.20s%-40.40s%-40.40s\n",
+	   "Supplier",
+	   "Comment",
+	   "Price"
+	  );
+    print "----------------------------------------------------------------------------------------------------\n";
+
+    #Loop over each supplier
+    my $iLine = 0;
+    for (; $iLine < $nLines; $iLine++) {
+      #collect supplier info lines
+      my @supplierInfo = ();
+      for (; $lines[$iLine] ne "." && $iLine < $nLines; $iLine++) {
+	push @supplierInfo,$lines[$iLine];
+      }
+      #Check for incomplete record
+      if ($iLine == $nLines) {
+	print "** INCOMPLETE RECORD **\n";
+	last;
+      }
+      my $nSupplierInfo = scalar(@supplierInfo);
+      my $supplier = $supplierInfo[0];
+      #loop over each grade
+      for ($iLine++; ($lines[$iLine] ne "........................") && ($iLine < $nLines); $iLine++) {
+	#collect grade info lines
+	my @gradeInfo = ();
+	for (; index($lines[$iLine],"_") ne 0 && $iLine < $nLines; $iLine++) {
+	  push @gradeInfo,$lines[$iLine];
+	}
+	#Check for incomplete record
+	if ($iLine == $nLines) {
+	  print "** INCOMPLETE RECORD **\n";
+	  last;
+	}
+	my $grade = $gradeInfo[0];
+	#loop over each price info line
+	for (; index($lines[$iLine],".") ne 0 && $iLine < $nLines; $iLine++) {
+	  my @priceInfo = split(" ",$lines[$iLine]);
+	  my $price = join(" ",@priceInfo);
+	  printf("%-20.20s%-40.39s%-40.40s\n",
+		 $supplier,
+		 $grade,
+		 $price);
+	}
+	#Check for incomplete record
+	if ($iLine == $nLines) {
+	  print "** INCOMPLETE RECORD **\n";
+	  last;
+	}
+	last if $lines[$iLine] eq "........................";
+      }
+    }
+  }
+}
+
+
+#######################################################################
+sub printHelpAndExit {
+  print "\nProduces text summaries of SD records\n";
+  print "\nUsage:\tsdreport [-l] [-t[<FieldName,FieldName...>]] [-c<FieldName,FieldName...>] [-id<IDField>] [-nh] [-o] [-s] [-sup] [sdFiles]\n";
+  print "\n\t-l (list format) output all data fields for each record as processed\n";
+  print "\t-t (tab format) tabulate selected fields for each record as processed\n";
+  print "\t-c (csv format) comma delimited output of selected fields for each record as processed\n";
+  print "\t-s (summary format) output summary statistics for each unique value of ligand ID\n";
+  print "\t-sup (supplier format) tabulate supplier details (from Catalyst)\n";
+  print "\t-id<IDField> data field to use as ligand ID\n";
+  print "\t-nh don't output column headings in -t and -c formats\n";
+  print "\t-o use old (v3.00) score field names as default columns in -t and -c formats, else use v4.00 field names\n";
+  print "\t-norm use normalised score field names as default columns in -t and -c formats (normalised = score / #ligand heavy atoms)\n";
+  print "\nNote:\tIf -l, -t or -c are combined with -s, the listing/table is output within each ligand summary\n";
+  print "\t-sup should not be combined with other options\n";
+  print "\tDefault field names for -t and -c are rDock score field names\n";
+  print "\tDefault ID field name is Name\n";
+  print "\n\tIf sdFiles not given, reads from standard input\n";
+  print "\tOutput is to standard output\n\n";
+  exit;
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/bin/sdrmsd	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,272 @@
+#! /usr/bin/env python
+#
+# Calculate SMART RMSD with or without molecular superposition (FIT or NOFIT)
+# Script distributed under GNU LGPL 3.0 along rDock software.
+#
+# This algorithm takes into account molecular automorphism. That is, it identifies
+# molecules which are the same but might have atom orders changed and still be able to
+# match the pairs and correctly calculate the RMSD.
+#
+# Author: Daniel Alvarez-Garcia
+# Date: 08-11-2013
+
+import math
+import pybel
+import numpy as npy
+import optparse
+
+def superpose3D(ref, target, weights=None,refmask=None,targetmask=None,returnRotMat=False):
+    """superpose3D performs 3d superposition using a weighted Kabsch algorithm : http://dx.doi.org/10.1107%2FS0567739476001873 & doi: 10.1529/biophysj.105.066654
+    definition : superpose3D(ref, target, weights,refmask,targetmask)
+    @parameter 1 :  ref - xyz coordinates of the reference structure (the ligand for instance)
+    @type 1 :       float64 numpy array (nx3)
+    ---
+    @parameter 2 :  target - theoretical target positions to which we should move (does not need to be physically relevant.
+    @type 2 :       float 64 numpy array (nx3)
+    ---
+    @parameter 3:   weights - numpy array of atom weights (usuallly between 0 and 1)
+    @type 3 :       float 64 numpy array (n)
+    @parameter 4:   mask - a numpy boolean mask for designating atoms to include
+    Note ref and target positions must have the same dimensions -> n*3 numpy arrays where n is the number of points (or atoms)
+    Returns a set of new coordinates, aligned to the target state as well as the rmsd
+    """
+    if weights == None :
+        weights=1.0
+    if refmask == None :
+        refmask=npy.ones(len(ref),"bool")
+    if targetmask == None :
+        targetmask=npy.ones(len(target),"bool")
+    #first get the centroid of both states
+    ref_centroid = npy.mean(ref[refmask]*weights,axis=0)
+    #print ref_centroid
+    refCenteredCoords=ref-ref_centroid
+    #print refCenteredCoords
+    target_centroid=npy.mean(target[targetmask]*weights,axis=0)
+    targetCenteredCoords=target-target_centroid
+    #print targetCenteredCoords
+    #the following steps come from : http://www.pymolwiki.org/index.php/OptAlign#The_Code and http://en.wikipedia.org/wiki/Kabsch_algorithm
+    # Initial residual, see Kabsch.
+    E0 = npy.sum( npy.sum(refCenteredCoords[refmask] * refCenteredCoords[refmask]*weights,axis=0),axis=0) + npy.sum( npy.sum(targetCenteredCoords[targetmask] * targetCenteredCoords[targetmask]*weights,axis=0),axis=0)
+    reftmp=npy.copy(refCenteredCoords[refmask])
+    targettmp=npy.copy(targetCenteredCoords[targetmask])
+    #print refCenteredCoords[refmask]
+    #single value decomposition of the dotProduct of both position vectors
+    try:
+        dotProd = npy.dot( npy.transpose(reftmp), targettmp* weights)
+        V, S, Wt = npy.linalg.svd(dotProd )
+    except Exception:
+        try:
+            dotProd = npy.dot( npy.transpose(reftmp), targettmp)
+            V, S, Wt = npy.linalg.svd(dotProd )
+        except Exception:
+            print >> sys.stderr,"Couldn't perform the Single Value Decomposition, skipping alignment"
+        return ref, 0
+    # we already have our solution, in the results from SVD.
+    # we just need to check for reflections and then produce
+    # the rotation.  V and Wt are orthonormal, so their det's
+    # are +/-1.
+    reflect = float(str(float(npy.linalg.det(V) * npy.linalg.det(Wt))))
+    if reflect == -1.0:
+        S[-1] = -S[-1]
+        V[:,-1] = -V[:,-1]
+    rmsd = E0 - (2.0 * sum(S))
+    rmsd = npy.sqrt(abs(rmsd / len(ref[refmask])))   #get the rmsd
+    #U is simply V*Wt
+    U = npy.dot(V, Wt)  #get the rotation matrix
+    # rotate and translate the molecule
+    new_coords = npy.dot((refCenteredCoords), U)+ target_centroid  #translate & rotate
+    #new_coords=(refCenteredCoords + target_centroid)
+    #print U
+    if returnRotMat :
+        return new_coords,rmsd, U
+    return new_coords,rmsd
+
+
+def squared_distance(coordsA, coordsB):
+    """Find the squared distance between two 3-tuples"""
+    sqrdist = sum( (a-b)**2 for a, b in zip(coordsA, coordsB) )
+    return sqrdist
+
+def rmsd(allcoordsA, allcoordsB):
+    """Find the RMSD between two lists of 3-tuples"""
+    deviation = sum(squared_distance(atomA, atomB) for
+                    (atomA, atomB) in zip(allcoordsA, allcoordsB))
+    return math.sqrt(deviation / float(len(allcoordsA)))
+
+def mapToCrystal(xtal, pose):
+    """Some docking programs might alter the order of the atoms in the output (like Autodock Vina does...)
+     this will mess up the rmsd calculation with OpenBabel"""
+    query = pybel.ob.CompileMoleculeQuery(xtal.OBMol)
+    mapper=pybel.ob.OBIsomorphismMapper.GetInstance(query)
+    mappingpose = pybel.ob.vvpairUIntUInt()
+    exit=mapper.MapUnique(pose.OBMol,mappingpose)
+    return mappingpose[0]
+
+def parseArguments():
+	optparse.OptionParser.format_epilog = lambda self, formatter: self.epilog
+	epilog = """Args:
+	reference.sdf		SDF file with the reference molecule.
+	input.sdf		SDF file with the molecules to be compared to reference.\n"""
+	parser = optparse.OptionParser("usage: %prog [options] reference.sdf input.sdf", epilog=epilog)
+	parser.add_option("-f", "--fit",dest="fit", action="store_true", default=False,
+                  help="Superpose molecules before RMSD calculation")
+	parser.add_option("--threshold","-t",dest="threshold", action="store", nargs=1,
+                  help="Discard poses with RMSD < THRESHOLD with respect previous poses which where not rejected based on same principle. A Population SDField will be added to output SD with the population number.", type=float)
+	parser.add_option("-o","--out", dest="outfilename", metavar="FILE", default=False,
+                  help="If declared, write an output SDF file with the input molecules with a new sdfield <RMSD>. If molecule was fitted, the fitted molecule coordinates will be saved.")
+	(options, args) =  parser.parse_args()
+
+	#Check we have two arguments
+	if len(args) < 2:
+		parser.error("Incorrect number of arguments. Use -h or --help options to print help.")
+
+	return options, args
+
+def updateCoords(obmol, newcoords):
+    "Update OBMol coordinates. newcoords is a numpy array"
+    for i,atom in enumerate(obmol):
+        atom.OBAtom.SetVector(*newcoords[i])
+
+def getAutomorphRMSD(target, molec, fit=False):
+    """
+    Use Automorphism to reorder target coordinates to match ref coordinates atom order
+    for correct RMSD comparison. Only the lowest RMSD will be returned.
+
+    Returns:
+      If fit=False: 	bestRMSD	(float)					RMSD of the best matching mapping.
+      If fit=True:	(bestRMSD, molecCoordinates)	(float, npy.array)	RMSD of best match and its molecule fitted coordinates.
+    """
+    mappings = pybel.ob.vvpairUIntUInt()
+    bitvec = pybel.ob.OBBitVec()
+    lookup = []
+    for i, atom in enumerate(target):
+        lookup.append(i)
+    success = pybel.ob.FindAutomorphisms(target.OBMol, mappings)
+    targetcoords = [atom.coords for atom in target]
+    mappose = npy.array(mapToCrystal(target, molec))
+    mappose = mappose[npy.argsort(mappose[:,0])][:,1]
+    posecoords = npy.array([atom.coords for atom in molec])[mappose]
+    resultrmsd = 999999999999
+    for mapping in mappings:
+	automorph_coords = [None] * len(targetcoords)
+	for x, y in mapping:
+	    automorph_coords[lookup.index(x)] = targetcoords[lookup.index(y)]
+	mapping_rmsd = rmsd(posecoords, automorph_coords)
+	if mapping_rmsd < resultrmsd:
+	    resultrmsd = mapping_rmsd
+	    fitted_result = False
+	if fit:
+	    fitted_pose, fitted_rmsd = superpose3D(npy.array(automorph_coords), npy.array(posecoords))
+	    if fitted_rmsd < resultrmsd:
+		resultrmsd = fitted_rmsd
+		fitted_result = fitted_pose
+
+    if fit:
+      return (resultrmsd, fitted_pose)
+    else:
+      return resultrmsd
+
+def saveMolecWithRMSD(outsdf, molec, rmsd, population=False):
+    newData = pybel.ob.OBPairData()
+    newData.SetAttribute("RMSD")
+    newData.SetValue('%.3f'%rmsd)
+
+    if population:
+	popData = pybel.ob.OBPairData()
+	popData.SetAttribute("Population")
+	popData.SetValue('%i'%population)
+	molec.OBMol.CloneData(popData)
+
+    molec.OBMol.CloneData(newData)           # Add new data
+    outsdf.write(molec)
+
+if __name__ == "__main__":
+    import sys, os
+
+    (opts, args) = parseArguments()
+
+    xtal = args[0]
+    poses = args[1]
+
+    if not os.path.exists(xtal) or not os.path.exists(poses):
+	sys.exit("Input files not found. Please check the path given is correct.")
+
+    fit = opts.fit
+    outfname = opts.outfilename
+    threshold = opts.threshold
+
+    # Read crystal pose
+    crystal = next(pybel.readfile("sdf", xtal))
+    crystal.removeh()
+    crystalnumatoms = len(crystal.atoms)
+
+    #If outfname is defined, prepare an output SDF sink to write molecules
+    if outfname:
+	outsdf = pybel.Outputfile('sdf', outfname, overwrite=True)
+
+    # Find the RMSD between the crystal pose and each docked pose
+    dockedposes = pybel.readfile("sdf", poses)
+    if fit: print "POSE\tRMSD_FIT"
+    else: print "POSE\tRMSD_NOFIT"
+    skipped = []
+    moleclist = {}	# Save all poses with their dockid
+    population = {}	# Poses to be written
+    outlist = {}
+    for docki, dockedpose in enumerate(dockedposes):
+        dockedpose.removeh()
+	natoms = len(dockedpose.atoms)
+	if natoms != crystalnumatoms:
+		skipped.append(docki+1)
+		continue
+	if fit:
+	    resultrmsd, fitted_result = getAutomorphRMSD(crystal, dockedpose, fit=True)
+	    updateCoords(dockedpose, fitted_result)
+	else:
+	    resultrmsd = getAutomorphRMSD(crystal, dockedpose, fit=False)
+
+	if threshold:
+	    # Calculate RMSD between all previous poses
+	    # Discard if rmsd < FILTER threshold
+	    if moleclist:
+		match = None
+		bestmatchrmsd = 999999
+		for did,prevmol in moleclist.iteritems():
+		    tmprmsd = getAutomorphRMSD(prevmol, dockedpose)
+		    if tmprmsd < threshold:
+			if tmprmsd < bestmatchrmsd:
+			    bestmatchrmsd = tmprmsd
+			    match = did
+
+		if match != None:
+		    # Do not write this one
+		    # sum one up to the matching previous molecule id
+		    print >> sys.stderr, "Pose %i matches pose %i with %.3f RMSD"%(docki+1, match+1, bestmatchrmsd)
+		    population[match] += 1
+		else:
+		    # There's no match. Print info for this one and write to outsdf if needed
+		    # Save this one!
+		    if outfname: outlist[docki] = (dockedpose, resultrmsd)
+		    print "%d\t%.2f"%((docki+1),resultrmsd)
+		    moleclist[docki] = dockedpose
+		    population[docki] = 1
+	    else:
+		# First molecule in list. Append for sure
+		moleclist[docki] = dockedpose
+		population[docki] = 1
+		if outfname: outlist[docki] = (dockedpose, resultrmsd)
+	else:
+	    # Just write best rmsd found and the molecule to outsdf if demanded
+	    if outfname: saveMolecWithRMSD(outsdf, dockedpose, resultrmsd)
+	    print "%d\t%.2f"%((docki+1),resultrmsd)
+
+    if outlist:
+	# Threshold applied and outlist need to be written
+	for docki in sorted(outlist.iterkeys()):
+	    molrmsd = outlist[docki]
+	    # Get number of matchs in thresholding operation
+	    pop = population.get(docki)
+	    if not pop: pop = 1
+	    # Save molecule
+	    saveMolecWithRMSD(outsdf, molrmsd[0], molrmsd[1], pop)
+
+    if skipped: print >> sys.stderr, "SKIPPED input molecules due to number of atom missmatch: %s"%skipped
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/bin/sdsort	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,98 @@
+#!/usr/bin/perl
+# Sorts SD records by given data field
+use lib "$ENV{'RBT_ROOT'}/lib";
+
+use SDRecord;
+
+my $SDSORTKEY; # sort key
+my $SDSORTASCEND = 1;# 1 = ascending, 0 = descending
+my $SDSORTTEXT = 1;# 1 = text sort, 0 = numeric sort
+
+my $FASTFORMAT = 0;
+my $FASTKEY = "_TITLE1";
+
+#Print help if no command line arguments
+printHelpAndExit() if (scalar(@ARGV) == 0);
+
+#Parse command line arguments
+my @files;
+while (scalar(@ARGV)) {
+  $arg = shift @ARGV;
+  printHelpAndExit() if ($arg eq '-h');
+  if ($arg eq '-r') {
+    $SDSORTASCEND = 0;#descending sort requested
+  }
+  elsif ($arg eq '-n') {
+    $SDSORTTEXT = 0;;#numeric sort requested
+  }
+  elsif (index($arg,'-s')==0) {
+    $FASTFORMAT = 1;
+  }
+  elsif (index($arg,'-id')==0) {
+    $FASTKEY = substr($arg,3);
+  }
+  elsif (index($arg,'-f')==0) {
+    $SDSORTKEY = substr($arg,2);#sort key
+  }
+  else {
+    push @files,$arg;#must be a filename
+  }
+}
+push @ARGV,@files;#put the filenames back in the arg list
+
+#read records
+my $sdRec = new SDRecord;
+my @records;
+my $nRec=0;
+
+my $lastid="";
+while ($sdRec->readRec('DATA'=>1,'LINES'=>1)) {
+  $sdRec->addData('_REC' => ++$nRec);#add record# as temp data field
+  if ($FASTFORMAT) {
+    my $id = $sdRec->{'DATA'}->{$FASTKEY};
+    if (($lastid ne "") && ($lastid ne $id)) {
+      foreach $rec (sort sortSD @records) {
+	$rec->writeRec();
+      }
+      @records = ();#clear the list
+    }
+    $lastid = $id;
+  }
+  push(@records,$sdRec->copy('DATA'=>1,'LINES'=>1));
+}
+
+#write sorted records
+foreach $rec (sort sortSD @records) {
+  $rec->writeRec();
+}
+
+#######################################################
+# sort function to sort SD records by given field
+# handles text/numeric and ascending/descending sort
+sub sortSD {
+  if ($SDSORTTEXT) {
+    return $a->{'DATA'}->{$SDSORTKEY} cmp $b->{'DATA'}->{$SDSORTKEY} if ($SDSORTASCEND);
+    return $b->{'DATA'}->{$SDSORTKEY} cmp $a->{'DATA'}->{$SDSORTKEY};
+  }
+  else {
+    return $a->{'DATA'}->{$SDSORTKEY} <=> $b->{'DATA'}->{$SDSORTKEY} if ($SDSORTASCEND);
+    return $b->{'DATA'}->{$SDSORTKEY} <=> $a->{'DATA'}->{$SDSORTKEY};
+  }
+}
+
+#######################################################################
+sub printHelpAndExit {
+  print "\nSorts SD records by given data field\n";
+  print "\nUsage:\tsdsort [-n] [-r] [-f<DataField>] [sdFiles]\n\n";
+  print "\t-n\t\tnumeric sort (default is text sort)\n";
+  print "\t-r\t\tdescending sort (default is ascending sort)\n";
+  print "\t-f<DataField>\tspecifies sort field\n";
+  print "\t-s\t\tfast mode. Sorts the records for each named compound independently (must be consecutive)\n";
+  print "\t-id<NameField>\tspecifies compound name field (default = 1st title line)\n\n";
+  print "Note:\t_REC (record #) is provided as a pseudo-data field\n";
+  print "\n\tIf SD file list not given, reads from standard input\n";
+  print "\tOutput is to standard output\n";
+  print "\tFast mode can be safely used for partial sorting of huge SD files of raw docking hits\n";
+  print "\twithout running into memory problems.\n\n";
+  exit;
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/bin/sdsplit	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,72 @@
+#!/usr/bin/perl
+# Splits SD records into multiple files of equal no. of records
+use lib "$ENV{'RBT_ROOT'}/lib";
+
+use FileHandle;
+use SDRecord;
+
+# Record size to split into
+my $recSize = 1000;
+
+#output root
+my $outRoot = "tmp";
+
+#Print help if no command line arguments
+printHelpAndExit() if (scalar(@ARGV) == 0);
+
+#Parse command line arguments
+my @files;
+while (scalar(@ARGV)) {
+  my $arg = shift @ARGV;
+  printHelpAndExit() if ($arg eq '-h');
+  if (index($arg,'-o')==0) {
+    $outRoot = substr($arg,2);
+  }
+  elsif (index($arg,'-')==0) {
+    $recSize = substr($arg,1);
+  }
+  else {
+    push @files,$arg;#must be a filename
+  }
+}
+push @ARGV,@files;#put the filenames back in the arg list
+
+my $sdRec = new SDRecord;
+my $nRec=0;
+my $nFile=0;
+my $sdfh;
+
+#read records
+while ($sdRec->readRec('LINES'=>1)) {
+  #check if we need to start a new output file
+  if ($nRec % $recSize == 0) {
+    $nFile++;
+    my $outFile = $outRoot . $nFile . ".sd";
+    if (defined $sdfh) {
+      undef $sdfh;
+    }
+    $sdfh = new FileHandle ">$outFile";
+    if (!defined $sdfh) {
+      die "Can't open $outFile";
+    }
+    else {
+      print STDOUT "Opening $outFile\n";
+    }
+    $sdfh->autoflush(1);
+    select($sdfh);
+  }
+  $nRec++;
+  $sdRec->writeRec();
+}
+undef $sdfh;
+select(STDOUT);#reselect STDOUT as default
+
+#######################################################################
+sub printHelpAndExit {
+  print "\Splits SD records into multiple files of equal size\n";
+  print "\nUsage:\tsdsplit [-<RecSize>] [-o<OutputRoot>] [sdFiles]\n\n";
+  print "\t-<RecSize>\trecord size to split into (default = 1000 records)\n";
+  print "\t-o<OutputRoot>\tRoot name for output files (default = tmp)\n";
+  print "\n\tIf SD file list not given, reads from standard input\n";
+  exit;
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/bin/sdtether	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,263 @@
+#! /usr/bin/env python
+#
+# Substitute for rbtether of rDock. Will align input molecules to a reference fragment defined by a smarts string,
+# it will add a TETHERED ATOM property field to the output SDF that is correctly understood by rDock
+# rDock will restrain the matching atom positions to the reference molecule coordinates.
+#
+# Initially implemented with a conformational search algorithm to better match target coordinates.
+# But had problems with OBabel FF generating non-sense conformers. So in this version the conformer search is commented out.
+# Now if the input molecule do not have a good conformation, might not align well with the target. This effect will be
+# dimished or even vanish if the SMARTS string is defined for a rigid region (like a ring).
+# I'm still trying to incorporate somehow this conformational search.
+#
+# Script distributed under GNU LGPL 3.0 along rDock software.
+#
+# Author: Daniel Alvarez-Garcia
+# Date: 08-11-2013
+
+import math
+import pybel
+import numpy as npy
+
+def superpose3D(ref, target, weights=None,refmask=None,targetmask=None,returnRotMat=False):
+    """superpose3D performs 3d superposition using a weighted Kabsch algorithm : http://dx.doi.org/10.1107%2FS0567739476001873 & doi: 10.1529/biophysj.105.066654
+    definition : superpose3D(ref, target, weights,refmask,targetmask)
+    @parameter 1 :  ref - xyz coordinates of the reference structure (the ligand for instance)
+    @type 1 :       float64 numpy array (nx3)
+    ---
+    @parameter 2 :  target - theoretical target positions to which we should move (does not need to be physically relevant.
+    @type 2 :       float 64 numpy array (nx3)
+    ---
+    @parameter 3:   weights - numpy array of atom weights (usuallly between 0 and 1)
+    @type 3 :       float 64 numpy array (n)
+    @parameter 4:   mask - a numpy boolean mask for designating atoms to include
+    Note ref and target positions must have the same dimensions -> n*3 numpy arrays where n is the number of points (or atoms)
+    Returns a set of new coordinates, aligned to the target state as well as the rmsd
+    """
+    if weights == None :
+        weights=1.0
+    if refmask == None :
+        refmask=npy.ones(len(ref),"bool")
+    if targetmask == None :
+        targetmask=npy.ones(len(target),"bool")
+    #first get the centroid of both states
+    ref_centroid = npy.mean(ref[refmask]*weights,axis=0)
+    #print ref_centroid
+    refCenteredCoords=ref-ref_centroid
+    #print refCenteredCoords
+    target_centroid=npy.mean(target[targetmask]*weights,axis=0)
+    targetCenteredCoords=target-target_centroid
+    #print targetCenteredCoords
+    #the following steps come from : http://www.pymolwiki.org/index.php/OptAlign#The_Code and http://en.wikipedia.org/wiki/Kabsch_algorithm
+    # Initial residual, see Kabsch.
+    E0 = npy.sum( npy.sum(refCenteredCoords[refmask] * refCenteredCoords[refmask]*weights,axis=0),axis=0) + npy.sum( npy.sum(targetCenteredCoords[targetmask] * targetCenteredCoords[targetmask]*weights,axis=0),axis=0)
+    reftmp=npy.copy(refCenteredCoords[refmask])
+    targettmp=npy.copy(targetCenteredCoords[targetmask])
+    #print refCenteredCoords[refmask]
+    #single value decomposition of the dotProduct of both position vectors
+    try:
+        dotProd = npy.dot( npy.transpose(reftmp), targettmp* weights)
+        V, S, Wt = npy.linalg.svd(dotProd )
+    except Exception:
+        try:
+            dotProd = npy.dot( npy.transpose(reftmp), targettmp)
+            V, S, Wt = npy.linalg.svd(dotProd )
+        except Exception:
+            print >> sys.stderr,"Couldn't perform the Single Value Decomposition, skipping alignment"
+        return ref, 0
+    # we already have our solution, in the results from SVD.
+    # we just need to check for reflections and then produce
+    # the rotation.  V and Wt are orthonormal, so their det's
+    # are +/-1.
+    reflect = float(str(float(npy.linalg.det(V) * npy.linalg.det(Wt))))
+    if reflect == -1.0:
+        S[-1] = -S[-1]
+        V[:,-1] = -V[:,-1]
+    rmsd = E0 - (2.0 * sum(S))
+    rmsd = npy.sqrt(abs(rmsd / len(ref[refmask])))   #get the rmsd
+    #U is simply V*Wt
+    U = npy.dot(V, Wt)  #get the rotation matrix
+    # rotate and translate the molecule
+    new_coords = npy.dot((refCenteredCoords), U)+ target_centroid  #translate & rotate
+    #new_coords=(refCenteredCoords + target_centroid)
+    #print U
+    if returnRotMat :
+        return U, ref_centroid, target_centroid, rmsd
+    return new_coords,rmsd
+
+
+def squared_distance(coordsA, coordsB):
+    """Find the squared distance between two 3-tuples"""
+    sqrdist = sum( (a-b)**2 for a, b in zip(coordsA, coordsB) )
+    return sqrdist
+
+def rmsd(allcoordsA, allcoordsB):
+    """Find the RMSD between two lists of 3-tuples"""
+    deviation = sum(squared_distance(atomA, atomB) for
+                    (atomA, atomB) in zip(allcoordsA, allcoordsB))
+    return math.sqrt(deviation / float(len(allcoordsA)))
+
+def mapToCrystal(xtal, pose):
+    """Some docking programs might alter the order of the atoms in the output (like Autodock Vina does...)
+     this will mess up the rmsd calculation with OpenBabel"""
+    query = pybel.ob.CompileMoleculeQuery(xtal.OBMol)
+    mapper=pybel.ob.OBIsomorphismMapper.GetInstance(query)
+    mappingpose = pybel.ob.vvpairUIntUInt()
+    exit=mapper.MapUnique(pose.OBMol,mappingpose)
+    return mappingpose[0]
+
+def takeCoords(obmol):
+    """Take coordinates of an OBMol as a npy array"""
+    return npy.array([atom.coords for atom in obmol])
+
+def updateCoords(obmol, newcoords):
+    "Update OBMol coordinates. newcoords is a numpy array"
+    for i,atom in enumerate(obmol):
+        atom.OBAtom.SetVector(*newcoords[i])
+
+def prepareAtomString(idlist):
+    s = ""
+    n = len(idlist)
+    for i, id in enumerate(idlist):
+        s += "%i"%id
+        if (i+1) == n: s+="\n"
+        elif (i+1)%35 == 0: s+=",\n"
+        else: s+=","
+    return s
+
+
+if __name__ == "__main__":
+    import sys
+
+    if len(sys.argv) != 5:
+        sys.exit("USAGE: %s reference.sdf input.sdf output.sdf 'SMARTS'"%sys.argv[0])
+
+    refsdf = sys.argv[1]
+    molsdf = sys.argv[2]
+    outsdf = sys.argv[3]
+    smarts = pybel.Smarts(sys.argv[4])
+
+    # Read reference pose and get atom list matching smarts query
+    # if more than 1 match, take the first one
+    ref = next(pybel.readfile("sdf", refsdf))
+    refMatchIds = smarts.findall(ref)
+    numRefMatchs = len(refMatchIds)
+
+    if not numRefMatchs:
+	sys.exit("No match found in the reference structure and the SMARTS string given. Please check it.")
+
+    if numRefMatchs > 1:
+	print "More than one match in the reference molecule for the SMARTS string given. Will tether each input molecule all possible ways."
+
+    refIndxPerMatch = [npy.array(rmi) - 1 for rmi in refMatchIds]
+
+    # Take coordinates for the reference matched atoms
+    refCoords = takeCoords(ref)
+    refMatchCoords = [npy.take(refCoords, refIndx, axis=0) for refIndx in refIndxPerMatch]
+
+    # Do the same for molecule in molsdf
+    out=pybel.Outputfile('sdf', outsdf, overwrite=True)
+    molSupp = pybel.readfile("sdf", molsdf)
+    ff = pybel.ob.OBForceField_FindForceField('MMFF94')
+    for i,mol in enumerate(molSupp):
+	print "## Molecule %i"%(i+1),
+	mol.OBMol.DeleteNonPolarHydrogens()
+   	molMatchAllIds = smarts.findall(mol)
+	numMatchs = len(molMatchAllIds)
+
+	if numMatchs == 0:
+		print "No_Match",
+		continue
+	elif numMatchs ==1:
+		print "Match",
+	elif numMatchs > 1:
+                print "Multiple_Match SMART Matches for this molecule (%d)"%numMatchs,
+
+	# If more than one match, write an output of the same molecule for each match
+	# Start a default bestcoord and rmsd for later looping for each pose
+	bestCoordPerMatch = [[0 for i in range(numMatchs)] for i in range(numRefMatchs)]
+	bestRMSPerMatch = [[999 for i in range(numMatchs)] for i in range(numRefMatchs)]
+
+        # Will do a randomrotorsearch to find conformer with the lower rmsd when superposing
+        # At least 20 when possible
+        #ff.Setup(mol.OBMol)
+	#numats = mol.OBMol.NumAtoms()
+	#numrot = mol.OBMol.NumRotors()
+	#print "Atoms: %i, Rotors: %i"%(numats, numrot)
+	#geomopt = 300
+	#genconf = 100
+	# increase iterations if bigger molecule or bigger number of rotatable bonds
+	# for allowing better sampling
+	#if numats > 40 and numrot > 5:
+	#	geomopt = 300
+	#	genconf = 150
+	#if numats > 55 and numrot > 7:
+	#	genconf = 100
+	#	geomopt = 500
+        #print "\tDoing conformational search with WeightedRotorSearch (%i, %i)..."%(genconf, geomopt),
+	#ff.SteepestDescent(500, 1.0e-4)
+        #ff.WeightedRotorSearch(genconf,geomopt)
+	#ff.ConjugateGradients(500, 1.0e-6)
+	#ff.GetConformers(mol.OBMol)
+	#numconf = mol.OBMol.NumConformers()
+	numconf = 1
+	#print "%i conformers generated"%numconf
+        if numconf > 1:
+            # Doing conf search
+            #for i in range(numconf):
+            #    mol.OBMol.SetConformer(i)
+            #    confCoords = takeCoords(mol)
+	    # 	print 'coord:',confCoords[0,:]
+            #
+            #    for imatch, molMatchIds in enumerate(molMatchAllIds):
+            #        molMatchIndx = npy.array(molMatchIds) - 1
+            #        confMatchCoords = npy.take(confCoords, molMatchIndx, axis=0)
+            #
+            #        # Align: Get rotation matrix between the two sets of coords
+            #        # Apply rotation to the whole target molecule
+            #        rotMat, targetCentroid, refCentroid, rmsd = superpose3D(confMatchCoords, refMatchCoords, returnRotMat=True)
+            #        if rmsd < bestRMSPerMatch[imatch]:
+            #            newcoords = npy.dot((confCoords - targetCentroid), rotMat) + refCentroid
+            #            bestRMSPerMatch[imatch] = rmsd
+            #            bestCoordPerMatch[imatch] = newcoords
+	    #	#if bestrms < 0.01: break
+       	    pass
+        else:
+            molCoords = takeCoords(mol)
+            for imatch, molMatchIds in enumerate(molMatchAllIds):
+		    # loop in each matching way for the input molecule
+                    molMatchIndx = npy.array(molMatchIds) - 1
+                    molMatchCoords = npy.take(molCoords, molMatchIndx, axis=0)
+
+		    # Loop over the reference matches
+                    # Align: Get rotation matrix between the two sets of coords
+                    # Apply rotation to the whole target molecule
+		    for ir, refMatchCoord in enumerate(refMatchCoords):
+                    	rotMat, targetCentroid, refCentroid, rmsd = superpose3D(molMatchCoords, refMatchCoord, returnRotMat=True)
+                    	if rmsd < bestRMSPerMatch[ir][imatch]:
+                        	newcoords = npy.dot((molCoords - targetCentroid), rotMat) + refCentroid
+                        	bestRMSPerMatch[ir][imatch] = rmsd
+                        	bestCoordPerMatch[ir][imatch] = newcoords
+
+        # Finally update molecule coordinates with the best matching coordinates found
+	# change molecule coordinates, set TETHERED ATOMS property and save
+	for imatch in range(numMatchs):
+		for irefmatch in range(numRefMatchs):
+			bestCoord = bestCoordPerMatch[irefmatch][imatch]
+			bestRMS = bestRMSPerMatch[irefmatch][imatch]
+        		print "\tBest RMSD reached (match %d, refmatch %d): %s"%(imatch, irefmatch, bestRMS)
+			molMatchID = molMatchAllIds[imatch]
+        		updateCoords(mol, bestCoord)
+        		newData = pybel.ob.OBPairData()
+        		newData.SetAttribute("TETHERED ATOMS")
+        		newData.SetValue(prepareAtomString(molMatchID))
+
+			mol.OBMol.DeleteData("TETHERED ATOMS") # Remove Previous DATA
+        		mol.OBMol.CloneData(newData)	       # Add new data
+        		out.write(mol)
+
+    out.close()
+
+    print "DONE"
+    sys.stdout.close()
+    sys.stderr.close()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/bin/to_unix	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,32 @@
+#! /bin/sh -e
+#Tag 1538
+#
+# convert a DOS ASCII file to a UNIX ASCII file by removing trailing ^M at the
+# end of each line and ^Z at the end of the file
+
+#DM 23 Oct 2000 - tmp file in current directory, not /tmp
+#TMPFILE=/tmp/to_unix$$
+TMPFILE=to_unix$$
+
+if [ $# -gt 2 ]
+then
+	echo "usage: to_unix [<dos_file> [<unix_file>]]"
+	exit 1
+fi
+
+# First strip out all carriage-return and ctrl-Z's
+if [ $# -gt 0 ]
+then
+	tr -d '\015\032' < "$1" > $TMPFILE
+else
+	tr -d '\015\032' > $TMPFILE
+fi
+
+
+if [ $# -eq 2 ]
+then
+	mv -f $TMPFILE "$2"
+else
+	cat $TMPFILE
+	rm $TMPFILE
+fi
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/RbtElements.dat	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,121 @@
+RBT_ELEMENT_FILE_V1.01
+TITLE RiboTargets Elemental Data File
+VERSION $Id: //depot/dev/client3/rdock/2013.1/data/RbtElements.dat#2 $
+####################################################################
+#
+# Hydrogen-bond donor radius increment
+# Only really used for hydrogen (so gives radius of 1.1-0.6 = 0.5)
+HBOND_RADIUS_INCREMENT		-0.6
+#
+# Implicit hydrogen radius increment
+# Only used for Carbon and maybe nitrogen
+# So implicit carbon radius = 1.55+0.3 = 1.85)
+IMPLICIT_RADIUS_INCREMENT	0.3
+####################################################################
+#
+#	ATOMIC	ELEMENT	MIN	MAX	COMMON	ATOMIC	VDW
+#	NUMBER	NAME	VAL	VAL	VAL	MASS	RADIUS
+ELEMENT	0	DU	0	0	0	0.000	1.10
+ELEMENT	1	H	1	1	1	1.008	1.10
+ELEMENT	2	He	0	0	0	4.003	2.20
+ELEMENT	3	Li	-1	1	-1	6.940	1.20
+ELEMENT	4	Be	-2	2	-2	9.012	0.63
+ELEMENT	5	B	3	5	3	10.810	1.55
+ELEMENT	6	C	4	4	4	12.011	1.55
+ELEMENT	7	N	3	3	3	14.007	1.40
+ELEMENT	8	O	2	2	2	16.000	1.35
+ELEMENT	9	F	1	1	1	18.998	1.30
+ELEMENT	10	Ne	0	0	0	20.170	2.02
+ELEMENT	11	Na	-1	1	-1	22.990	1.20
+ELEMENT	12	Mg	-2	2	-2	24.305	0.74
+ELEMENT	13	Al	-3	3	-3	26.982	1.20
+ELEMENT	14	Si	4	4	4	28.086	1.20
+ELEMENT	15	P	3	5	3	30.974	1.88
+ELEMENT	16	S	2	6	2	32.060	1.81
+ELEMENT	17	Cl	1	7	1	35.453	1.75
+ELEMENT	18	Ar	0	0	0	39.948	2.77
+ELEMENT	19	K	-1	1	-1	39.102	1.20
+ELEMENT	20	Ca	-2	2	-2	40.080	1.09
+ELEMENT	21	Sc	0	0	0	44.956	1.32
+ELEMENT	22	Ti	0	0	0	47.880	1.95
+ELEMENT	23	V	0	0	0	50.040	1.06
+ELEMENT	24	Cr	0	0	0	51.996	1.13
+ELEMENT	25	Mn	0	0	0	54.938	0.63
+ELEMENT	26	Fe	0	0	0	55.847	0.71
+ELEMENT	27	Co	0	0	0	58.933	1.13
+ELEMENT	28	Ni	0	0	0	58.710	1.24
+ELEMENT	29	Cu	0	0	0	63.546	1.15
+ELEMENT	30	Zn	0	0	0	65.380	0.70
+ELEMENT	31	Ga	0	0	0	69.720	1.55
+ELEMENT	32	Ge	0	0	0	72.590	2.72
+ELEMENT	33	As	0	0	0	74.922	0.83
+ELEMENT	34	Se	0	0	0	78.960	0.90
+ELEMENT	35	Br	1	7	1	79.904	1.95
+ELEMENT	36	Kr	0	0	0	83.800	1.90
+ELEMENT	37	Rb	0	0	0	85.467	2.65
+ELEMENT	38	Sr	0	0	0	87.620	2.02
+ELEMENT	39	Y	0	0	0	88.806	1.61
+ELEMENT	40	Zr	0	0	0	91.220	1.42
+ELEMENT	41	Nb	0	0	0	92.906	1.33
+ELEMENT	42	Mo	0	0	0	95.940	1.75
+ELEMENT	43	Tc	0	0	0	98.910	1.80
+ELEMENT	44	Ru	0	0	0	101.070	1.20
+ELEMENT	45	Rh	0	0	0	102.906	1.22
+ELEMENT	46	Pd	0	0	0	106.400	1.44
+ELEMENT	47	Ag	0	0	0	107.868	1.55
+ELEMENT	48	Cd	0	0	0	112.400	1.75
+ELEMENT	49	In	0	0	0	114.820	1.46
+ELEMENT	50	Sn	0	0	0	118.690	1.67
+ELEMENT	51	Sb	0	0	0	121.750	1.12
+ELEMENT	52	Te	0	0	0	127.600	1.26
+ELEMENT	53	I	1	7	1	126.905	2.15
+ELEMENT	54	Xe	0	0	0	131.300	2.10
+ELEMENT	55	Cs	0	0	0	132.905	3.01
+ELEMENT	56	Ba	0	0	0	137.340	2.41
+ELEMENT	57	La	0	0	0	138.905	1.83
+ELEMENT	58	Ce	0	0	0	140.120	1.86
+ELEMENT	59	Pr	0	0	0	140.908	1.62
+ELEMENT	60	Nd	0	0	0	144.240	1.79
+ELEMENT	61	Pm	0	0	0	145.000	1.76
+ELEMENT	62	Sm	0	0	0	150.400	1.74
+ELEMENT	63	Eu	0	0	0	151.960	1.96
+ELEMENT	64	Gd	0	0	0	157.250	1.69
+ELEMENT	65	Tb	0	0	0	158.925	1.66
+ELEMENT	66	Dy	0	0	0	162.500	1.63
+ELEMENT	67	Ho	0	0	0	164.930	1.61
+ELEMENT	68	Er	0	0	0	167.260	1.59
+ELEMENT	69	Tm	0	0	0	168.934	1.57
+ELEMENT	70	Yb	0	0	0	173.040	1.54
+ELEMENT	71	Lu	0	0	0	174.970	1.53
+ELEMENT	72	Hf	0	0	0	178.490	1.40
+ELEMENT	73	Ta	0	0	0	180.850	1.22
+ELEMENT	74	W	0	0	0	183.850	1.26
+ELEMENT	75	Re	0	0	0	186.200	1.30
+ELEMENT	76	Os	0	0	0	190.200	1.58
+ELEMENT	77	Ir	0	0	0	192.220	1.22
+ELEMENT	78	Pt	0	0	0	195.090	1.55
+ELEMENT	79	Au	0	0	0	196.967	1.45
+ELEMENT	80	Hg	0	0	0	200.590	1.98
+ELEMENT	81	Tl	0	0	0	204.370	1.71
+ELEMENT	82	Pb	0	0	0	207.200	2.16
+ELEMENT	83	Bi	0	0	0	208.981	1.73
+ELEMENT	84	Po	0	0	0	209.000	1.21
+ELEMENT	85	At	0	0	0	210.000	1.12
+ELEMENT	86	Rn	0	0	0	222.000	2.30
+ELEMENT	87	Fr	0	0	0	223.000	3.24
+ELEMENT	88	Ra	0	0	0	226.000	2.57
+ELEMENT	89	Ac	0	0	0	227.000	2.12
+ELEMENT	90	Th	0	0	0	232.038	1.84
+ELEMENT	91	Pa	0	0	0	231.036	1.60
+ELEMENT	92	U	0	0	0	238.029	1.75
+ELEMENT	93	Np	0	0	0	237.048	1.71
+ELEMENT	94	Pu	0	0	0	244.000	1.67
+ELEMENT	95	Am	0	0	0	243.000	1.66
+ELEMENT	96	Cm	0	0	0	248.000	1.65
+ELEMENT	97	Bk	0	0	0	247.000	1.64
+ELEMENT	98	Cf	0	0	0	251.000	1.63
+ELEMENT	99	Es	0	0	0	254.000	1.62
+ELEMENT	100	Fm	0	0	0	257.000	1.61
+ELEMENT	101	Md	0	0	0	256.000	1.60
+ELEMENT	102	No	0	0	0	254.000	1.59
+ELEMENT	103	Lr	0	0	0	257.000	1.58
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/cnx.rtf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,157 @@
+*>>>>>>>>> Combined Residue Topology File for Proteins <<<<<<<<<
+*>>>>>>>>>>>>>>>>>>>> and Nucleic Acids <<<<<<<<<<<<<<<<<<<<<<<<
+*>>>>>>>>>>>>>>>>> Using All Hydrogens (ALLH) <<<<<<<<<<<<<<<<<<
+*>>>>>>>>>>>>>>>>>>>>> January 1996 <<<<<<<<<<<<<<<<<<<<<<<<<<<<
+*>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<
+*>>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu  <<<<<<<<<
+* These files are a beta release; additional parameter development
+* and testing may lead to alteration of the contents.
+*
+* $Id: //depot/dev/client3/rdock/2013.1/data/cnx.rtf#2 $
+*
+* 30 Apr 1999 (D Morley, RiboTargets)
+* Modified for RiboDock:
+* Added hybridisation state tags to comment field
+* Removed all but the MASS records (added element name)
+*
+   22     1
+!MASS     1 H      1.00800 H ! polar H (RBT::SP3)
+!MASS     2 HC     1.00800 H ! N-ter H (RBT::SP3)
+!MASS     3 HA     1.00800 H ! nonpolar H (RBT::SP3)
+MASS     4 HT     1.00800 H ! TIPS3P WATER HYDROGEN (RBT::SP3)
+MASS     5 HP     1.00800 H ! aromatic H (RBT::SP3)
+MASS     6 HB     1.00800 H ! backbone H (RBT::SP3)
+MASS     7 HR1    1.00800 H ! his he1, (+) his HG,HD2 (RBT::SP3)
+MASS     8 HR2    1.00800 H ! (+) his HE1 (RBT::SP3)
+MASS     9 HR3    1.00800 H ! neutral his HG, HD2 (RBT::SP3)
+MASS    10 HS     1.00800 H ! thiol hydrogen (RBT::SP3)
+MASS    11 HA1    1.00800 H ! for alkene; RHC=CR (RBT::SP3)
+MASS    12 HA2    1.00800 H ! for alkene; H2C=CR (RBT::SP3)
+!MASS    20 C     12.01100 C ! polar C (RBT::SP3)
+MASS    21 CA    12.01100 C ! aromatic C (RBT::SP2)
+MASS    22 CT1   12.01100 C ! aliphatic sp3 C for CH (RBT::SP3)
+MASS    23 CT2   12.01100 C ! aliphatic sp3 C for CH2 (RBT::SP3)
+MASS    24 CT3   12.01100 C ! aliphatic sp3 C for CH3 (RBT::SP3)
+MASS    25 CPH1  12.01100 C ! his CG and CD2 carbons (RBT::SP2)
+MASS    26 CPH2  12.01100 C ! his CE1 carbon (RBT::SP2)
+MASS    27 CPT   12.01100 C ! trp C between rings (RBT::SP2)
+!MASS    28 CY    12.01100 C ! TRP C in pyrrole ring (RBT::SP2)
+MASS    29 CP1   12.01100 C ! tetrahedral C (proline CA) (RBT::SP3)
+MASS    30 CP2   12.01100 C ! tetrahedral C (proline CB/CG) (RBT::SP3)
+MASS    31 CP3   12.01100 C ! tetrahedral C (proline CD) (RBT::SP3)
+MASS    32 CC    12.01100 C ! carbonyl C for sidechains asn,asp,gln,glu (RBT::SP2)
+MASS    33 CD    12.01100 C ! carbonyl C for none amides, asp,glu,cter (RBT::SP2)
+MASS    34 CPA   12.01100 C ! heme alpha-C
+MASS    35 CPB   12.01100 C ! heme beta-C
+MASS    36 CPM   12.01100 C ! heme meso-C
+MASS    37 CM    12.01100 C ! heme CO carbon (RBT::SP2)
+MASS    38 CS    12.01100 C ! thiolate carbon
+MASS    39 CE1   12.01100 C ! for alkene; RHC=CR
+MASS    40 CE2   12.01100 C ! for alkene; H2C=CR
+!MASS    50 N     14.00700 N ! proline N (RBT::SP3)
+MASS    51 NR1   14.00700 N ! neutral his protonated ring nitrogen (RBT::TRI)
+MASS    52 NR2   14.00700 N ! neutral his unprotonated ring nitrogen (RBT::SP2)
+MASS    53 NR3   14.00700 N ! charged his ring nitrogen (RBT::TRI)
+!MASS    54 NH1   14.00700 N ! peptide nitrogen (RBT::TRI)
+!MASS    55 NH2   14.00700 N ! amide nitrogen (RBT::TRI)
+!MASS    56 NH3   14.00700 N ! ammonium nitrogen (RBT::SP3)
+!MASS    57 NC2   14.00700 N ! guanidinium nitroogen (RBT::TRI)
+MASS    58 NY    14.00700 N ! TRP N in pyrrole ring (RBT::TRI)
+MASS    59 NP    14.00700 N ! Proline ring NH2+ (N-terminal) (RBT::SP3)
+MASS    60 NPH   14.00700 N ! heme pyrrole N (RBT::TRI)
+!MASS    70 O     15.99900 O ! carbonyl oxygen (RBT::SP2)
+MASS    71 OB    15.99900 O ! carbonyl oxygen in acetic acid (RBT::SP2)
+!MASS    72 OC    15.99900 O ! carboxylate oxygen (RBT::SP2)
+!MASS    73 OH1   15.99900 O ! hydroxyl oxygen (RBT::SP3)
+MASS    74 OS    15.99940 O ! ester oxygen (RBT::SP3)
+MASS    75 OT    15.99940 O ! TIPS3P WATER OXYGEN (RBT::SP3)
+MASS    76 OM    15.99900 O ! heme CO/O2 oxygen (RBT::SP2)
+MASS    81 S     32.06000 S ! sulphur (RBT::SP3)
+!MASS    82 SM    32.06000 S ! sulfur C-S-S-C type (RBT::SP3)
+MASS    83 SS    32.06000 S ! thiolate sulfur
+!
+! nucleic acid section
+!MASS 104    HT    1.008000 ! TIPS3P WATER HYDROGEN
+MASS 106    HN1   1.008000 H ! Nucleic acid amine proton (RBT::SP3)
+MASS 107    HN2   1.008000 H ! Nucleic acid ring nitrogen proton (RBT::SP3)
+MASS 108    HN3   1.008000 H ! Nucleic acid aromatic carbon proton (RBT::SP3)
+MASS 109    HN4   1.008000 H ! Nucleic acid phosphate hydroxyl proton (RBT::SP3)
+MASS 110   HN5   1.008000 H ! Nucleic acid ribose hydroxyl proton (RBT::SP3)
+MASS 111   HN6   1.008000 H ! Nucleic acid ribose aliphatic proton (RBT::SP3)
+MASS 112   HN7   1.008000 H ! Nucleic acid proton (equivalent to protein HA) (RBT::SP3)
+MASS 113   HN3B  1.008000 H ! NAD+ aromatic hydrogen (RBT::SP3)
+MASS 128   CN1  12.011000 C ! Nucleic acid carbonyl carbon (RBT::SP2)
+MASS 129   CN2  12.011000 C ! Nucleic acid aromatic carbon to amide (RBT::SP2)
+MASS 130   CN3  12.011000 C ! Nucleic acid aromatic carbon (RBT::SP2)
+MASS 131   CN4  12.011000 C ! Nucleic acid purine C8 and ADE C2 (RBT::SP2)
+MASS 132   CN5  12.011000 C ! Nucleic acid purine C4 and C5 (RBT::SP2)
+MASS 133   CN6  12.011000 C ! Nucleic acid sp3 ribose ring carbon (RBT::SP3)
+MASS 134   CN6B 12.011000 C ! Nucleic acid sp3 ribose ring carbon, C1' (RBT::SP3)
+MASS 135   CN6C 12.011000 C ! Nucleic acid sp3 deoxyribose ring carbon, C2' (RBT::SP3)
+MASS 136   CN7  12.011000 C ! Nucleic acid carbon (equivalent to protein CT1) (RBT::SP3)
+MASS 137   CN8  12.011000 C ! Nucleic acid carbon (equivalent to protein CT2) (RBT::SP3)
+MASS 138   CN9  12.011000 C ! Nucleic acid carbon (equivalent to protein CT3) (RBT::SP3)
+MASS 139   CN3A 12.011000 C ! NAD+ aromatic carbon (RBT::SP2)
+MASS 140   CN3B 12.011000 C ! NAD+ aromatic carbon (RBT::SP2)
+MASS 141   CN3C 12.011000 C ! NADH aromatic carbon (RBT::SP2)
+MASS 142   CN3D 12.011000 C ! Nucleic acid aromatic carbon for 5MC (RBT::SP2)
+MASS 143   CN1A 12.011000 C ! NAD+/NADH amide carbonyl carbon (RBT::SP2)
+MASS 150   NN1  14.007000 N ! Nucleic acid amide nitrogen (RBT::TRI)
+MASS 151   NN2  14.007000 N ! Nucleic acid protonated ring nitrogen (RBT::TRI)
+MASS 152   NN2U 14.007000 N ! Nucleic acid protonated ring nitrogen, ura N3 (RBT::TRI)
+MASS 153   NN2G 14.007000 N ! Nucleic acid protonated ring nitrogen, gua N1 (RBT::TRI)
+MASS 154   NN3  14.007000 N ! Nucleic acid unprotonated ring nitrogen (RBT::SP2)
+MASS 155   NN4  14.007000 N ! Nucleic acid purine N7 (RBT::SP2)
+MASS 156   NN5  14.007000 N ! Nucleic acid sp2 amine nitrogen (RBT::TRI)
+MASS 157   NN3A 14.007000 N ! Nucleic acid unprotonated ring nitrogen, ade N1 and N3 (RBT::SP2)
+MASS 158   NN3I 14.007000 N ! Nucleic acid unprotonated ring nitrogen, inosine N3 (RBT::SP2)
+!MASS 164   OT   15.999400 ! TIPS3P WATER OXYGEN
+MASS 165   ON1  15.999400 O ! Nucleic acid carbonyl oxygen (RBT::SP2)
+MASS 166   ON1C 15.999400 O ! Nucleic acid carbonyl oxygen, cyt O2 (RBT::SP2)
+MASS 167   ON2  15.999400 O ! Nucleic acid phosphate ester oxygen (RBT::SP3)
+MASS 168   ON3  15.999400 O ! Nucleic acid =O in phosphate (RBT::SP2)
+MASS 169   ON4  15.999400 O ! Nucleic acid phosphate hydroxyl oxygen (RBT::SP3)
+MASS 170   ON5  15.999400 O ! Nucleic acid ribose hydroxyl oxygen (RBT::SP3)
+MASS 171   ON6  15.999400 O ! Nucleic acid ribose ring oxygen (RBT::SP3)
+MASS 172   ON2b 15.999400 O ! Nucleic acid phosphate ester oxygen, tyr-phosphate (RBT::SP3)
+MASS 182   P    30.974000 P ! phosphorus (RBT::SP2)
+MASS 183   P2   30.974000 P ! pyrophosphate phosphorus
+MASS 192   SOD  22.989770 Na ! Sodium Ion
+MASS 193   MG   24.305000 Mg ! Magnesium Ion
+
+* 1 Nov 2002 (DM) Dummy atom type
+MASS   666 DUM    0.00000 DU ! Dummy atom
+!MASS 199   DUM   0.001    ! dummy atom
+
+* 9 Dec 2002 (SJ) CNX atom types
+* types with the same name but not necessarily with the same functionality
+MASS   701 H      1.00800 H ! polar H (RBT::SP3)
+MASS   702 HC     1.00800 H ! charged polar H ie in ARG,LYS (RBT::SP3)
+MASS   703 HA     1.00800 H ! apolar H (RBT::SP3)
+MASS   704 C     12.01100 C ! amide C (RBT::SP2)
+MASS   705 CH1E  12.01100 C ! Alpha-carbons with one hydrogen (RBT::SP3)
+MASS   706 CH2E  12.01100 C ! Carbon with two hydrogens (RBT::SP3)
+MASS   707 CH3E  12.01100 C ! Carbon with three hydrogens (RBT::SP3)
+MASS   708 CH2G  12.01100 C ! GLY alpha carbon (RBT::SP3)
+MASS   709 CH2P  12.01100 C ! Gamma and delta carbons in prolin (RBT::SP3)
+MASS   710 C5W   12.01100 C ! TRP gamma carbon in pyrrole ring (RBT::SP2)
+MASS   711 CW    12.01100 C ! TRP CD2 and CE2 at the fuse of the rings (RBT::SP2)
+MASS   712 CR1E  12.01100 C ! PHE aromatic deltas epss and zeta (RBT::SP2)
+MASS   713 C5    12.01100 C ! HIS gamma carbon (RBT::SP2)
+MASS   714 CRH   12.01100 C ! HIS doubly protonated CE1 (RBT::SP2)
+MASS   715 CR1H  12.01100 C ! HIS delta CD2 (RBT::SP2)
+MASS   716 CRHH  12.01100 C ! HIS epsilon CE1 (RBT::SP2)
+MASS   717 CF    12.01100 C ! PHE gamma carbon (RBT::SP2)
+MASS   718 CY    12.01100 C ! TYR CG (RBT::SP2)
+MASS   719 CY2   12.01100 C ! TYR CZ (RBT::SP2)
+MASS   720 N     14.00700 N ! PRO N (RBT::TRI)
+MASS   721 NR    14.00700 N ! HIS non-protonated ND1 (RBT::SP2)
+MASS   722 NH1   14.00700 N ! amide N (RBT::TRI)
+MASS   723 NH2   14.00700 N ! ammonium N (RBT::SP3)
+MASS   724 NH3   14.00700 N ! charged N (RBT::SP3)
+MASS   725 NC2   14.00700 N ! guanidinium charged N (RBT::TRI)
+MASS   726 O     15.99900 O ! carbonyl oxygen (RBT::SP2)
+MASS   727 OC    15.99900 O ! carboxylate oxygen (RBT::SP2)
+MASS   728 OH1   15.99900 O ! hydroxyl oxygen (RBT::SP3)
+MASS   729 SH1E  32.06000 S ! CYS SG (RBT::SP3)
+MASS   730 SM    32.06000 S ! MET SD (RBT::SP3)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/filters/gpfilter295.filter	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,15 @@
++ * log - + SCORE.INTRA.VDW SCORE.INTRA.VDW.0 0.9913
+    exp * SCORE.INTER.AROM.narom
+        * exp SCORE.INTER.POLAR.nhbd
+          LIG_POS_CHG
+- * 684
+    if SCORE.INTER.REPUL.nhba
+       LIG_NEG_CHG
+       / SCORE.INTER.VDW.nrep
+           SITE_PERC_AROMATOMS
+  if + - SCORE.INTER.POLAR.nhbd
+         + SCORE.INTRA.REPUL SCORE.INTRA.REPUL.0
+       LIG_TOT_CHG
+     SITE_NLIPOC
+     - exp SITE_NEG_CHG
+       log LIG_NHBD
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/masses.rtf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,180 @@
+* ...
+* ...
+* Copyright (c) 1986, 1987, 1988, 1989, 1990, 1991, 1992
+* Molecular Simulations Incorporated
+* Confidential and Proprietary: All Rights Reserved
+* ...
+* ....
+* TEMPLATE FOR CREATING CHARMm RTF file
+* ....
+*     (%_m) replaced by first 4 characters of molecule name
+*           in QUANTA (if used)
+* ..
+* Build RTF for %m
+* ...
+* sorted alphabetically; metals follow organics
+* Atom type numbers 201-229 are reserved for special QUANTA display atom types.
+* Last current active number is 234.
+*
+   22    0
+MASS     7 B     10.81    B  ! Boron
+MASS    14 C     12.01100 C  ! Carbonyl or Guanidinium carbon (RBT::SP2)
+MASS   190 C3    12.01100 C  ! Carbonyl carbon in 3-membered aliphatic ring (RBT::SP2)
+MASS   192 C4    12.01100 C  ! Carbonyl carbons in 4-membered aliphatic ring (RBT::SP2)
+MASS    21 C5R   12.01100 C  ! Aromatic carbon in a five membered ring (RBT::SP2)
+MASS    23 C5RE  13.01900 C  ! Extended aromatic carbon in five membered ring (RBT::SP2)
+MASS    28 C5RP  12.01100 C  ! for Aryl-Aryl bond between C5R rings (RBT::SP2)
+MASS   189 C5RQ  12.01100 C  ! for second Ar-Ar bond between C5RP rings (ortho) (RBT::SP2)
+MASS    22 C6R   12.01100 C  ! Aromatic carbon in a six  membered ring (RBT::SP2)
+MASS    24 C6RE  13.01900 C  ! Extended aromatic carbon in six membered ring (RBT::SP2)
+MASS    29 C6RP  12.01100 C  ! for Aryl-Aryl bond between C6R rings (RBT::SP2)
+MASS   194 C6RQ  12.01100 C  ! Carbon of C6RP type ortho to C6RP pair (RBT::SP2)
+MASS   230 CF1   12.01100 C  ! Carbon with one Fluorine (RBT::SP3)
+MASS   231 CF2   12.01100 C  ! Carbon with two Fluorines (RBT::SP3)
+MASS   232 CF3   12.01100 C  ! Carbons with three Fluorines (RBT::SP3)
+MASS    11 CH1E  13.01900 C  ! Extended atom carbon with one hydrogen (RBT::SP3)
+MASS    12 CH2E  14.02700 C  ! Extended atom carbon with two hydrogens (RBT::SP3)
+MASS    13 CH3E  15.03500 C  ! Extended atom carbon with three hydrogens (RBT::SP3)
+MASS    15 CM    12.01100 C  ! Carbonmonoxide, or other triply bonded, carbon (RBT::SP)
+MASS   199 CP3   12.01100 C  ! Carbon on nitrogen in proline ring (RBT::SP3)
+MASS   197 CPH1  12.01100 C  ! CG and CD2 carbons in histidine ring (RBT::SP2)
+MASS   198 CPH2  12.01100 C  ! CE1 carbon in histidine ring (RBT::SP2)
+MASS   195 CQ66  12.01100 C  ! Third adjacent pair of CR66 types in fused rings (RBT::SP2)
+MASS    25 CR55  12.01100 C  ! Aromatic carbon-merged five membered rings (RBT::SP2)
+MASS    26 CR56  12.01100 C  ! Aromatic carbon-merged five/six membered rings (RBT::SP2)
+MASS    27 CR66  12.01100 C  ! Aromatic carbon-merged six membered rings (RBT::SP2)
+MASS   196 CS66  12.01100 C  ! Second adjacent pair of CR66 types in fused rings (RBT::SP2)
+MASS    10 CT    12.01100 C  ! Aliphatic carbon (tetrahedral) (RBT::SP3)
+MASS   191 CT3   12.01100 C  ! in 3-membered aliphatic ring, usually tetrahedral (RBT::SP3)
+MASS   193 CT4   12.01100 C  ! in 4-membered aliphatic ring, usually tetrahedral (RBT::SP3)
+MASS    16 CUA1  12.01100 C  ! Carbon in double bond, first pair (RBT::SP2)
+MASS    17 CUA2  12.01100 C  ! Carbon in double bond, second conjugated pair (RBT::SP2)
+MASS    20 CUA3  12.01100 C  ! Carbon in double bond, third conjugated pair (RBT::SP2)
+MASS    18 CUY1  12.01100 C  ! Carbon in triple bond, first pair (RBT::SP)
+MASS    19 CUY2  12.01100 C  ! Carbon in triple bond, second conjugated pair (RBT::SP)
+MASS     1 H      1.00800 H  ! Hydrogen bonding hydrogen (neutral group) (RBT::SP3)
+MASS     3 HA     1.00800 H  ! Aliphatic or aromatic hydrogen (RBT::SP3)
+MASS     2 HC     1.00800 H  ! Hydrogen bonding hydrogen (charged group) (RBT::SP3)
+MASS     9 HMU    1.00800 H  ! Mu-bonded hydrogen for metals and boron-hydride (RBT::SP3)
+MASS     8 HO     1.00800 H  ! Hydrogen on an alcohol oxygen (RBT::SP3)
+MASS     4 HT     1.00800 H  ! TIPS3P water model hydrogen (RBT::SP3)
+MASS    31 N     14.00670 N  ! Nitrogen; planar-valence of 3, i.e. nitrile, etc. (RBT::TRI)
+MASS   234 N3    14.00670 N  ! Nitrogen in a three membered ring (RBT::SP3)
+MASS    34 N5R   14.00670 N  ! Nitrogen in a five membered aromatic ring (RBT::TRI)
+MASS    30 N5RP  14.00670 N  ! for Ar-Ar bond between five membered rings (RBT::TRI)
+MASS    35 N6R   14.00670 N  ! Nitrogen in a six membered aromatic ring (RBT::SP2)
+MASS    39 N6RP  14.00670 N  ! for Aryl-Aryl bond between six membered rings (RBT::SP2)
+MASS    37 NC    14.00670 N  ! Charged guanidinium-type nitrogen (RBT::TRI)
+MASS   186 NC2   14.00670 N  ! for neutral guanidinium group - Arg sidechain (RBT::SP2)
+MASS    38 NO2   14.00670 N  ! Nitrogen in nitro, or related, group (RBT::TRI)
+MASS    32 NP    14.00670 N  ! Nitrogen in peptide, amide, or related, group (RBT::TRI)
+MASS   183 NR1   14.00670 N  ! Protonated nitrogen in neutral histidine ring (RBT::TRI)
+MASS   184 NR2   14.00670 N  ! Unprotonated nitrogen in neutral histidine ring (RBT::SP2)
+MASS   185 NR3   14.00670 N  ! Nitrogens in charged histidine ring (RBT::SP2)
+MASS   182 NR55  14.00670 N  ! N at fused bond between two 5-membered aromatics (RBT::SP2)
+MASS   180 NR56  14.00670 N  ! N at fused bond between 5 and 6-membered aryls (RBT::SP2)
+MASS   181 NR66  14.00670 N  ! N at fused bond between two 6-membered aromatics (RBT::SP2)
+MASS    36 NT    14.00670 N  ! Nitrogen (tetrahedral), i.e. Amine, etc. (RBT::SP3)
+MASS    33 NX    14.00670 N  ! Proline nitrogen, or similar (RBT::TRI)
+MASS    40 O     15.99940 O  ! Carbonyl oxygen for amides, or related structures (RBT::SP2)
+MASS    56 O2M   15.99940 O  ! Oxygen in Si-O-Al or Al-O-Al bond (RBT::SP3)
+MASS    52 O5R   15.99940 O  ! Oxygen in 5 membered aromatic ring-radicals, etc. (RBT::SP3)
+MASS    53 O6R   15.99940 O  ! Oxygen in 6 membered aromatic ring-radicals, etc. (RBT::SP3)
+MASS    41 OA    15.99940 O  ! Carbonyl oxygen for aldehydes, or related (RBT::SP2)
+MASS    51 OAC   15.99940 O  ! Carbonyl oxygen for acids, or related (RBT::SP2)
+MASS    43 OC    15.99940 O  ! Charged oxygen (RBT::SP3)
+MASS    50 OE    15.99940 O  ! Ether oxygen / Acetal oxygen (RBT::SP3)
+MASS    47 OH2   15.99940 O  ! ST2  water model oxygen (RBT::SP3)
+MASS    42 OK    15.99940 O  ! Carbonyl oxygen for ketones, or related (RBT::SP2)
+MASS    48 OM    15.99940 O  ! Carbonmonoxide, or other triply bonded, oxygen
+MASS    49 OS    15.99940 O  ! Ester oxygen (RBT::TRI)
+MASS    57 OSH    0.00000 O  ! Massless O for zeolites, or related cage cmpds.
+MASS    55 OSI   15.99940 O  ! Oxygen in Si-O-Si bond (RBT::SP3)
+MASS    45 OT    15.99940 O  ! Hydroxyl oxygen (tetrahedral) or Ionizable acid (RBT::SP3)
+MASS    46 OW    15.99940 O  ! TIP3P water model oxygen (RBT::SP3)
+MASS    64 P6R   30.9738  P  ! Phosphorous in aromatic 6-membered ring (RBT::SP3)
+MASS    61 PO3   30.9738  P  ! Phosphorous bonded to three oxygens (RBT::SP2)
+MASS    62 PO4   30.9738  P  ! Phosphorous bonded to four oxygens (RBT::SP2)
+MASS    60 PT    30.9738  P  ! Phosphorous, general; usually tetrahedral (RBT::SP3)
+MASS    63 PUA1  30.9738  P  ! Phosphorous double bond
+MASS   233 PUY1  30.9738  P  ! Triple bonded phosphorus
+MASS    72 S5R   32.0600  S  ! Sulphur in a five membered aromatic ring (RBT::SP3)
+MASS    73 S6R   32.0600  S  ! Sulphur in a six membered aromatic ring (RBT::SP3)
+MASS    74 SE    32.060   S  ! Thioether sulphur (RBT::SP3)
+MASS    71 SH1E  33.06800 S  ! Extended atom sulphur with one hydrogen (RBT::SP3)
+MASS    75 SK    32.060   S  ! Thioketone sulphur (RBT::SP2)
+MASS    76 SO1   32.0600  S  ! Sulphur bonded to one oxygen (RBT::SP3)
+MASS    77 SO2   32.0600  S  ! Sulphur bonded to two oxygens (RBT::SP3)
+MASS    78 SO3   32.0600  S  ! Sulphur bonded to three oxygens (RBT::SP2)
+MASS    79 SO4   32.0600  S  ! Sulphur bonded to four oxygens (RBT::SP2)
+MASS    70 ST    32.06000 S  ! Sulphur, general; usually tetrahedral (RBT::SP3)
+MASS    94 XBR   79.904   Br ! Bromine
+MASS    93 XCL   35.45300 Cl ! Chlorine
+MASS    92 XF    18.99840 F  ! Fluorine
+MASS    95 XI   126.9045  I  ! Iodine
+MASS    91 MAL   26.9815  Al ! ALuminum
+MASS     6 MBE    9.01218 Be ! Beryllium
+MASS    84 MCA   40.080   Ca ! Calcium
+MASS    83 MK    39.098   K  ! Potassium
+MASS    80 MLI    6.941   Li ! Lithium
+MASS    82 MMG   24.305   Mg ! Magnesium
+MASS    81 MNA   22.9898  Na ! Sodium
+MASS    90 MSI   28.0855  Si ! Silicon
+MASS   177 MSIU 28.08550  Si ! Silicon when as double bond
+MASS	86 MFE   55.85    Fe ! Iron
+MASS    87 MZN  65.3800   Zn ! Zinc (Added DM 30/7/2001)
+
+* 4 Jan 1999 (DM) Added old types from
+* /darius/dsk1/progs/insightII/insight97/data/xplor/toppar/topallhdg.pro
+* just to keep rbscore happy. The numeric force field types are ficticious
+* and will not be recognised by Charmm
+MASS   301 CX    12.011   C  ! (RBT::SP2)
+MASS   302 CW    12.011   C  ! (RBT::SP2)
+MASS   303 CN    12.011   C  ! (RBT::SP2)
+MASS   304 CA    12.011   C  ! (RBT::SP2)
+MASS   305 CB    12.011   C  ! (RBT::SP2)
+MASS   306 CC    12.011   C  ! (RBT::SP2)
+MASS   307 CV    12.011   C  ! (RBT::SP2)
+MASS   308 CR    12.011   C  ! (RBT::SP2)
+MASS   309 CP    12.011   C  ! Proline carbon CG,CD (RBT::SP3)
+MASS   310 NA    14.007   N  ! (RBT::TRI)
+MASS   311 NB    14.007   N  ! (RBT::TRI)
+MASS   312 NH1   14.007   N  ! (RBT::TRI)
+MASS   313 NH2   14.007   N  ! (RBT::TRI)
+MASS   314 NH3   14.007   N  ! (RBT::SP3)
+MASS   315 OH    15.999   O  ! (RBT::SP3)
+MASS   316 S     32.060   S  ! (RBT::SP3)
+
+* 4 Jan 1999 (DM) Added old types from
+* /darius/dsk1/progs/insightII/insight97/data/xplor/toppar/topallhdg.dna
+* just to keep rbscore happy. The numeric force field types are ficticious
+* and will not be recognised by Charmm
+MASS   400 H2     1.00800 H  ! (RBT::SP3)
+MASS   401 CH    12.01100 C  ! (RBT::SP3)
+MASS   402 C2    12.01100 C  ! (RBT::SP3)
+MASS   403 CE    12.01100 C  ! (RBT::SP2)
+MASS   404 CF    12.01100 C  ! (RBT::SP2)
+MASS   405 CS    12.01100 C  ! (RBT::SP2)
+MASS   406 N2    14.00670 N  ! (RBT::TRI) Corrected DM 23/8/1999
+MASS   407 NS    14.00670 N  ! (RBT::TRI)
+MASS   408 NH2E  16.02270 N  ! (RBT::SP3)
+MASS   409 O2    15.99940 O  ! (RBT::SP3)
+MASS   411 SD    22.98980 Na !
+MASS   412 P     30.97400 P  ! (RBT::SP3)
+MASS   413 BR    79.90400 Br !
+MASS   414 MG    24.30500 Mg !
+
+* 8 Jun 1999 (DM) Added types to keep wtTARrbt158.psf happy
+MASS   450 HE     1.00800 H  ! (RBT::SP3)
+
+* 18 Jan 2001 (DM) Dummy atom type
+MASS   666 DUM    0.00000 DU ! Dummy atom
+
+* Charmm 27 additions
+MASS     5 H      1.00800 H  ! Nonpolar H prom charmm27 all-atom FF (RBT::SP3)
+MASS    54 HG     1.00800 H  ! Nonpolar H prom charmm27 all-atom FF (RBT::SP3)
+MASS    58 NE    14.00670 N  ! charmm27 N
+
+RESI  XXXX  0.0
+
+END
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CFBr.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
+ 0.200  3.0000
+ 0.400  3.0000
+ 0.600  3.0000
+ 0.800  3.0000
+ 1.000  3.0000
+ 1.200  0.0000
+ 1.400  0.0000
+ 1.600  0.0000
+ 1.800  0.0000
+ 2.000  0.0000
+ 2.200  0.0000
+ 2.400  0.0000
+ 2.600  0.0000
+ 2.800  0.0000
+ 3.000  0.0000
+ 3.200  0.0000
+ 3.400  0.0000
+ 3.600  0.0000
+ 3.800  0.0000
+ 4.000  0.0000
+ 4.200  0.0000
+ 4.400  0.0000
+ 4.600  0.0000
+ 4.800  0.0000
+ 5.000  0.0000
+ 5.200  0.0000
+ 5.400  0.0000
+ 5.600  0.0000
+ 5.800  0.0000
+ 6.000  0.0000
+ 6.200  0.0000
+ 6.400  0.0000
+ 6.600  0.0000
+ 6.800  0.0000
+ 7.000  0.0000
+ 7.200  0.0000
+ 7.400  0.0000
+ 7.600  0.0000
+ 7.800  0.0000
+ 8.000  0.0000
+ 8.200  0.0000
+ 8.400  0.0000
+ 8.600  0.0000
+ 8.800  0.0000
+ 9.000  0.0000
+ 9.200  0.0000
+ 9.400  0.0000
+ 9.600  0.0000
+ 9.800  0.0000
+10.000  0.0000
+10.200  0.0000
+10.400  0.0000
+10.600  0.0000
+10.800  0.0000
+11.000  0.0000
+11.200  0.0000
+11.400  0.0000
+11.600  0.0000
+11.800  0.0000
+12.000  0.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CFC0.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
+ 0.200  3.0000
+ 0.400  3.0000
+ 0.600  3.0000
+ 0.800  3.0000
+ 1.000  3.0000
+ 1.200  0.0000
+ 1.400  0.0000
+ 1.600  0.0000
+ 1.800  0.0000
+ 2.000  0.0000
+ 2.200  0.0000
+ 2.400  0.0000
+ 2.600  0.0000
+ 2.800  0.0000
+ 3.000  0.0000
+ 3.200  0.0000
+ 3.400  0.0000
+ 3.600  0.0000
+ 3.800  0.0000
+ 4.000  0.0000
+ 4.200  0.0000
+ 4.400  0.0000
+ 4.600  0.0000
+ 4.800  0.0000
+ 5.000  0.0000
+ 5.200  0.0000
+ 5.400  0.0000
+ 5.600  0.0000
+ 5.800  0.0000
+ 6.000  0.0000
+ 6.200  0.0000
+ 6.400  0.0000
+ 6.600  0.0000
+ 6.800  0.0000
+ 7.000  0.0000
+ 7.200  0.0000
+ 7.400  0.0000
+ 7.600  0.0000
+ 7.800  0.0000
+ 8.000  0.0000
+ 8.200  0.0000
+ 8.400  0.0000
+ 8.600  0.0000
+ 8.800  0.0000
+ 9.000  0.0000
+ 9.200  0.0000
+ 9.400  0.0000
+ 9.600  0.0000
+ 9.800  0.0000
+10.000  0.0000
+10.200  0.0000
+10.400  0.0000
+10.600  0.0000
+10.800  0.0000
+11.000  0.0000
+11.200  0.0000
+11.400  0.0000
+11.600  0.0000
+11.800  0.0000
+12.000  0.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CFC3.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
+ 0.200  3.0000
+ 0.400  3.0000
+ 0.600  3.0000
+ 0.800  3.0000
+ 1.000  3.0000
+ 1.200  3.0000
+ 1.400  2.9751
+ 1.600  3.0427
+ 1.800  3.0624
+ 2.000  2.9183
+ 2.200  2.7315
+ 2.400  2.7496
+ 2.600  2.7860
+ 2.800  2.7122
+ 3.000  2.4030
+ 3.200  1.8580
+ 3.400  1.0609
+ 3.600  0.3909
+ 3.800  0.0756
+ 4.000  -0.0327
+ 4.200  -0.1472
+ 4.400  -0.1606
+ 4.600  -0.1878
+ 4.800  -0.2021
+ 5.000  -0.2288
+ 5.200  -0.2070
+ 5.400  -0.1639
+ 5.600  -0.1349
+ 5.800  -0.1012
+ 6.000  -0.0779
+ 6.200  -0.0772
+ 6.400  -0.0651
+ 6.600  -0.0609
+ 6.800  -0.0416
+ 7.000  -0.0330
+ 7.200  -0.0197
+ 7.400  -0.0075
+ 7.600  -0.0046
+ 7.800  -0.0049
+ 8.000  -0.0095
+ 8.200  -0.0239
+ 8.400  -0.0341
+ 8.600  -0.0414
+ 8.800  -0.0372
+ 9.000  -0.0349
+ 9.200  -0.0260
+ 9.400  -0.0115
+ 9.600  0.0025
+ 9.800  0.0151
+10.000  0.0176
+10.200  0.0033
+10.400  -0.0083
+10.600  -0.0051
+10.800  0.0073
+11.000  0.0192
+11.200  0.0000
+11.400  0.0000
+11.600  0.0000
+11.800  0.0000
+12.000  0.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CFCF.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
+ 0.200  3.0000
+ 0.400  3.0000
+ 0.600  3.0000
+ 0.800  3.0000
+ 1.000  3.0000
+ 1.200  2.8892
+ 1.400  2.8387
+ 1.600  2.8842
+ 1.800  2.9750
+ 2.000  3.0500
+ 2.200  3.0468
+ 2.400  2.9158
+ 2.600  2.7876
+ 2.800  2.4875
+ 3.000  2.0639
+ 3.200  1.5614
+ 3.400  0.9736
+ 3.600  0.4618
+ 3.800  0.0978
+ 4.000  -0.1141
+ 4.200  -0.2198
+ 4.400  -0.2521
+ 4.600  -0.2238
+ 4.800  -0.2099
+ 5.000  -0.1942
+ 5.200  -0.1773
+ 5.400  -0.1562
+ 5.600  -0.1305
+ 5.800  -0.0982
+ 6.000  -0.0731
+ 6.200  -0.0441
+ 6.400  -0.0246
+ 6.600  -0.0001
+ 6.800  0.0072
+ 7.000  0.0100
+ 7.200  0.0043
+ 7.400  0.0015
+ 7.600  -0.0004
+ 7.800  0.0004
+ 8.000  0.0057
+ 8.200  0.0163
+ 8.400  0.0142
+ 8.600  0.0117
+ 8.800  -0.0030
+ 9.000  -0.0098
+ 9.200  -0.0109
+ 9.400  -0.0069
+ 9.600  0.0002
+ 9.800  -0.0036
+10.000  -0.0094
+10.200  -0.0103
+10.400  -0.0129
+10.600  -0.0109
+10.800  -0.0039
+11.000  0.0028
+11.200  0.0000
+11.400  0.0000
+11.600  0.0000
+11.800  0.0000
+12.000  0.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CFCL.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
+ 0.200  3.0000
+ 0.400  3.0000
+ 0.600  3.0000
+ 0.800  3.0000
+ 1.000  3.0000
+ 1.200  0.0000
+ 1.400  0.0000
+ 1.600  0.0000
+ 1.800  0.0000
+ 2.000  0.0000
+ 2.200  0.0000
+ 2.400  0.0000
+ 2.600  0.0000
+ 2.800  0.0000
+ 3.000  0.0000
+ 3.200  0.0000
+ 3.400  0.0000
+ 3.600  0.0000
+ 3.800  0.0000
+ 4.000  0.0000
+ 4.200  0.0000
+ 4.400  0.0000
+ 4.600  0.0000
+ 4.800  0.0000
+ 5.000  0.0000
+ 5.200  0.0000
+ 5.400  0.0000
+ 5.600  0.0000
+ 5.800  0.0000
+ 6.000  0.0000
+ 6.200  0.0000
+ 6.400  0.0000
+ 6.600  0.0000
+ 6.800  0.0000
+ 7.000  0.0000
+ 7.200  0.0000
+ 7.400  0.0000
+ 7.600  0.0000
+ 7.800  0.0000
+ 8.000  0.0000
+ 8.200  0.0000
+ 8.400  0.0000
+ 8.600  0.0000
+ 8.800  0.0000
+ 9.000  0.0000
+ 9.200  0.0000
+ 9.400  0.0000
+ 9.600  0.0000
+ 9.800  0.0000
+10.000  0.0000
+10.200  0.0000
+10.400  0.0000
+10.600  0.0000
+10.800  0.0000
+11.000  0.0000
+11.200  0.0000
+11.400  0.0000
+11.600  0.0000
+11.800  0.0000
+12.000  0.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CFCN.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
+ 0.200  3.0000
+ 0.400  3.0000
+ 0.600  3.0000
+ 0.800  3.0000
+ 1.000  3.0000
+ 1.200  3.0000
+ 1.400  3.0000
+ 1.600  3.0000
+ 1.800  3.0000
+ 2.000  2.9759
+ 2.200  3.0062
+ 2.400  3.0600
+ 2.600  3.0569
+ 2.800  2.8636
+ 3.000  2.4041
+ 3.200  1.7135
+ 3.400  0.9495
+ 3.600  0.2996
+ 3.800  -0.0990
+ 4.000  -0.3110
+ 4.200  -0.3756
+ 4.400  -0.3881
+ 4.600  -0.3713
+ 4.800  -0.3425
+ 5.000  -0.3062
+ 5.200  -0.2729
+ 5.400  -0.2267
+ 5.600  -0.1637
+ 5.800  -0.1042
+ 6.000  -0.0535
+ 6.200  0.0012
+ 6.400  0.0345
+ 6.600  0.0550
+ 6.800  0.0638
+ 7.000  0.0780
+ 7.200  0.0722
+ 7.400  0.0484
+ 7.600  0.0430
+ 7.800  0.0355
+ 8.000  0.0254
+ 8.200  0.0274
+ 8.400  0.0156
+ 8.600  -0.0024
+ 8.800  -0.0300
+ 9.000  -0.0353
+ 9.200  -0.0272
+ 9.400  -0.0213
+ 9.600  -0.0079
+ 9.800  -0.0060
+10.000  -0.0198
+10.200  -0.0216
+10.400  -0.0157
+10.600  -0.0072
+10.800  -0.0014
+11.000  0.0003
+11.200  0.0000
+11.400  0.0000
+11.600  0.0000
+11.800  0.0000
+12.000  0.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CFCO.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
+ 0.200  3.0000
+ 0.400  3.0000
+ 0.600  3.0000
+ 0.800  3.0000
+ 1.000  3.0000
+ 1.200  3.0000
+ 1.400  3.0000
+ 1.600  3.0000
+ 1.800  3.0000
+ 2.000  3.0000
+ 2.200  2.9477
+ 2.400  3.0489
+ 2.600  3.1386
+ 2.800  2.9948
+ 3.000  2.5896
+ 3.200  1.9698
+ 3.400  1.2578
+ 3.600  0.6034
+ 3.800  0.1851
+ 4.000  0.0142
+ 4.200  -0.1393
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CFCP.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CFCW.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CFF_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CFFe.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CFHL.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CFMg.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CFMn.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CFN0.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CFNA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CFNC.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CFND.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CFNP.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
+ 0.200  3.0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CFNR.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CFNS.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
+ 0.200  3.0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CFOA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CFOC.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CFOD.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CFOE.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CFOR.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
+ 0.200  3.0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CFOS.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
+ 0.200  3.0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CFP_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
+ 0.200  3.0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CFSA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CFSD.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CFV_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CFZn.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CNBr.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CNC0.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CNC3.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CNCF.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CNCL.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CNCN.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CNCO.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CNCP.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CNCW.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CNF_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CNFe.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CNHL.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CNMg.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CNMn.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CNN0.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CNNA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CNNC.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CNND.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CNNP.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CNNR.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CNNS.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CNOA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CNOC.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CNOD.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CNOE.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CNOR.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CNOS.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CNP_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CNSA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CNSD.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CNV_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CNZn.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/COBr.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/COC0.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/COC3.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/COCF.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/COCL.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/COCN.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/COCO.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/COCP.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/COCW.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/COF_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/COFe.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/COHL.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/COMg.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/COMn.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CON0.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CONA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CONC.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/COND.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CONP.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CONR.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CONS.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/COOA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/COOC.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/COOD.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/COOE.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/COOR.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/COOS.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/COP_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/COSA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/COSD.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/COV_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/COZn.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CPBr.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CPC0.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CPC3.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CPCF.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CPCL.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CPCN.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CPCO.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CPCP.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CPCW.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CPF_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CPFe.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CPHL.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CPMg.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CPMn.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CPN0.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CPNA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CPNC.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CPND.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CPNP.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CPNR.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CPNS.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CPOA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CPOC.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CPOD.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CPOE.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CPOR.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CPOS.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CPP_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CPSA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CPSD.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CPV_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/CPZn.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/HHBr.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/HHC0.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/HHC3.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/HHCF.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/HHCL.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/HHCN.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/HHCO.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/HHCP.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/HHCW.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/HHF_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/HHFe.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/HHHL.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/HHMg.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/HHMn.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/HHN0.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/HHNA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/HHNC.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/HHND.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/HHNP.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/HHNR.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/HHNS.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/HHOA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/HHOC.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/HHOD.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/HHOE.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/HHOR.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/HHOS.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
+ 0.200  3.0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/HHP_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/HHSA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/HHSD.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/HHV_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/HHZn.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NCBr.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NCC0.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NCC3.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NCCF.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NCCL.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NCCN.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NCCO.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NCCP.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NCCW.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NCF_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NCFe.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NCHL.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NCMg.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NCMn.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NCN0.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NCNA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NCNC.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NCND.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NCNP.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NCNR.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NCNS.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NCOA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NCOC.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NCOD.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NCOE.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NCOR.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NCOS.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NCP_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NCSA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NCSD.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NCV_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NCZn.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NDBr.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NDC0.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NDC3.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NDCF.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NDCL.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NDCN.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NDCO.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NDCP.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NDCW.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NDF_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NDFe.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NDHL.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NDMg.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NDMn.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NDN0.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NDNA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NDNC.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NDND.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NDNP.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NDNR.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NDNS.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NDOA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NDOC.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NDOD.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NDOE.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NDOR.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NDOS.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NDP_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NDSA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NDSD.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NDV_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NDZn.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NRBr.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NRC0.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NRC3.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NRCF.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NRCL.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NRCN.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NRCO.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NRCP.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NRCW.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NRF_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NRFe.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NRHL.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NRMg.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NRMn.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NRN0.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NRNA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NRNC.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NRND.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NRNP.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NRNR.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NRNS.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NROA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NROC.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NROD.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NROE.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NROR.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NROS.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NRP_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NRSA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NRSD.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NRV_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/NRZn.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OABr.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OAC0.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OAC3.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OACF.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OACL.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OACN.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OACO.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OACP.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OACW.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OAF_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OAFe.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OAHL.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OAMg.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OAMn.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OAN0.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OANA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OANC.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OAND.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OANP.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OANR.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OANS.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OAOA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OAOC.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OAOD.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
+ 0.200  3.0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OAOE.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
+ 0.200  3.0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OAOR.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
+ 0.200  3.0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OAOS.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
+ 0.200  3.0000
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+ 1.200  2.9425
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OAP_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OASA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OASD.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OAV_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OAZn.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OCBr.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OCC0.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OCC3.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OCCF.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OCCL.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OCCN.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OCCO.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OCCP.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OCCW.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OCF_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OCFe.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OCHL.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OCMg.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OCMn.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OCN0.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OCNA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OCNC.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OCND.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OCNP.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OCNR.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OCNS.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OCOA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OCOC.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OCOD.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OCOE.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OCOR.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OCOS.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OCP_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OCSA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OCSD.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OCV_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OCZn.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/ODBr.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/ODC0.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/ODC3.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/ODCF.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/ODCL.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/ODCN.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/ODCO.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/ODCP.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/ODCW.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/ODF_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/ODFe.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/ODHL.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/ODMg.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/ODMn.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/ODN0.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/ODNA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/ODNC.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/ODND.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/ODNP.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/ODNR.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/ODNS.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/ODOA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/ODOC.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/ODOD.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/ODOE.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/ODOR.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/ODOS.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/ODP_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/ODSA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/ODSD.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/ODV_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/ODZn.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OWBr.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OWC0.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OWC3.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OWCF.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OWCL.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OWCN.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OWCO.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OWCP.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OWCW.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OWF_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OWFe.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OWHL.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OWMg.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OWMn.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OWN0.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OWNA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OWNC.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OWND.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OWNP.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OWNR.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OWNS.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OWOA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OWOC.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OWOD.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OWOE.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OWOR.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OWOS.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OWP_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OWSA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OWSD.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OWV_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/OWZn.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SABr.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SAC0.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SAC3.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SACF.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SACL.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SACN.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SACO.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SACP.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SACW.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SAF_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SAFe.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SAHL.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SAMg.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SAMn.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SAN0.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SANA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SANC.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SAND.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SANP.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SANR.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SANS.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SAOA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SAOC.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SAOD.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SAOE.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SAOR.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SAOS.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SAP_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SASA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SASD.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SAV_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SAZn.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SDBr.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SDC0.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SDC3.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SDCF.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SDCL.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SDCN.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SDCO.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SDCP.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SDCW.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SDF_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SDFe.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SDHL.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SDMg.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SDMn.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SDN0.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SDNA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SDNC.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SDND.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SDNP.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SDNR.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SDNS.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SDOA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SDOC.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SDOD.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SDOE.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SDOR.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SDOS.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SDP_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SDSA.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SDSD.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
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+ 1.600  0.0000
+ 1.800  0.0000
+ 2.000  0.0000
+ 2.200  0.0000
+ 2.400  0.0000
+ 2.600  0.0000
+ 2.800  0.0000
+ 3.000  0.0000
+ 3.200  0.0000
+ 3.400  0.0000
+ 3.600  0.0000
+ 3.800  0.0000
+ 4.000  0.0000
+ 4.200  0.0000
+ 4.400  0.0000
+ 4.600  0.0000
+ 4.800  0.0000
+ 5.000  0.0000
+ 5.200  0.0000
+ 5.400  0.0000
+ 5.600  0.0000
+ 5.800  0.0000
+ 6.000  0.0000
+ 6.200  0.0000
+ 6.400  0.0000
+ 6.600  0.0000
+ 6.800  0.0000
+ 7.000  0.0000
+ 7.200  0.0000
+ 7.400  0.0000
+ 7.600  0.0000
+ 7.800  0.0000
+ 8.000  0.0000
+ 8.200  0.0000
+ 8.400  0.0000
+ 8.600  0.0000
+ 8.800  0.0000
+ 9.000  0.0000
+ 9.200  0.0000
+ 9.400  0.0000
+ 9.600  0.0000
+ 9.800  0.0000
+10.000  0.0000
+10.200  0.0000
+10.400  0.0000
+10.600  0.0000
+10.800  0.0000
+11.000  0.0000
+11.200  0.0000
+11.400  0.0000
+11.600  0.0000
+11.800  0.0000
+12.000  0.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SDV_.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
+ 0.200  3.0000
+ 0.400  3.0000
+ 0.600  3.0000
+ 0.800  3.0000
+ 1.000  3.0000
+ 1.200  0.0000
+ 1.400  0.0000
+ 1.600  0.0000
+ 1.800  0.0000
+ 2.000  0.0000
+ 2.200  0.0000
+ 2.400  0.0000
+ 2.600  0.0000
+ 2.800  0.0000
+ 3.000  0.0000
+ 3.200  0.0000
+ 3.400  0.0000
+ 3.600  0.0000
+ 3.800  0.0000
+ 4.000  0.0000
+ 4.200  0.0000
+ 4.400  0.0000
+ 4.600  0.0000
+ 4.800  0.0000
+ 5.000  0.0000
+ 5.200  0.0000
+ 5.400  0.0000
+ 5.600  0.0000
+ 5.800  0.0000
+ 6.000  0.0000
+ 6.200  0.0000
+ 6.400  0.0000
+ 6.600  0.0000
+ 6.800  0.0000
+ 7.000  0.0000
+ 7.200  0.0000
+ 7.400  0.0000
+ 7.600  0.0000
+ 7.800  0.0000
+ 8.000  0.0000
+ 8.200  0.0000
+ 8.400  0.0000
+ 8.600  0.0000
+ 8.800  0.0000
+ 9.000  0.0000
+ 9.200  0.0000
+ 9.400  0.0000
+ 9.600  0.0000
+ 9.800  0.0000
+10.000  0.0000
+10.200  0.0000
+10.400  0.0000
+10.600  0.0000
+10.800  0.0000
+11.000  0.0000
+11.200  0.0000
+11.400  0.0000
+11.600  0.0000
+11.800  0.0000
+12.000  0.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/SDZn.pmf	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,60 @@
+ 0.200  3.0000
+ 0.400  3.0000
+ 0.600  3.0000
+ 0.800  3.0000
+ 1.000  3.0000
+ 1.200  0.0000
+ 1.400  0.0000
+ 1.600  0.0000
+ 1.800  0.0000
+ 2.000  0.0000
+ 2.200  0.0000
+ 2.400  0.0000
+ 2.600  0.0000
+ 2.800  0.0000
+ 3.000  0.0000
+ 3.200  0.0000
+ 3.400  0.0000
+ 3.600  0.0000
+ 3.800  0.0000
+ 4.000  0.0000
+ 4.200  0.0000
+ 4.400  0.0000
+ 4.600  0.0000
+ 4.800  0.0000
+ 5.000  0.0000
+ 5.200  0.0000
+ 5.400  0.0000
+ 5.600  0.0000
+ 5.800  0.0000
+ 6.000  0.0000
+ 6.200  0.0000
+ 6.400  0.0000
+ 6.600  0.0000
+ 6.800  0.0000
+ 7.000  0.0000
+ 7.200  0.0000
+ 7.400  0.0000
+ 7.600  0.0000
+ 7.800  0.0000
+ 8.000  0.0000
+ 8.200  0.0000
+ 8.400  0.0000
+ 8.600  0.0000
+ 8.800  0.0000
+ 9.000  0.0000
+ 9.200  0.0000
+ 9.400  0.0000
+ 9.600  0.0000
+ 9.800  0.0000
+10.000  0.0000
+10.200  0.0000
+10.400  0.0000
+10.600  0.0000
+10.800  0.0000
+11.000  0.0000
+11.200  0.0000
+11.400  0.0000
+11.600  0.0000
+11.800  0.0000
+12.000  0.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/smoothed/m2pmf.awk	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,41 @@
+#!/bin/awk -f
+BEGIN{
+	true			= 1;
+	false			= !true;
+	hashmarkcount	= 0;
+	iscomment		= true;	# true for the first lines
+	i=0;
+	j=0;
+}{
+	if("#" == $1) {
+		hashmarkcount++;
+		iscomment	= true;
+	} else
+		iscomment	= false;
+	if(hashmarkcount < 6 && !iscomment ){	#get the first vector (x)
+		x[i]=$1;
+		i++;
+	}
+	else if ( !iscomment ){					# so we are at y
+		y[j]=$1;
+		j++;
+	}
+
+}END{
+	# first padding at the beginning
+	for (j=0.2;j<x[0];j+=0.2) {
+		printf("%6.3f  %6.4f\n", j,3.0);
+	}
+	# note i sould be equal to y
+	# we are considering 'i' number of data (
+	# ys without x values will be discarded, xs without y will
+	# get y value 0
+	# we are treating 'i' as the length of the vectors
+	for (j=0;j<i;j++) {
+		printf("%6.3f  %6.4f\n", x[j],y[j]);
+	}
+	# zero padding at the end
+	for(j=x[j-1]+0.2;j<=12.0;j+=0.2) {
+		printf("%6.3f  %6.4f\n", j,0.0);
+	}
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/smoothed/pmf2m.awk	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,20 @@
+#!/bin/awk -f
+{
+	a[NR]=$1;
+	b[NR]=$2;
+}END{
+	print "# name: x"
+	print "# type: matrix"
+	print "# rows: 1"
+	print "# columns: "NR
+	for(i=1;i<=NR;i++)
+		printf("%f ",a[i]);
+	print ""
+	print "# name: y"
+	print "# type: matrix"
+	print "# rows: 1"
+	print "# columns: "NR
+	for(i=1;i<=NR;i++)
+		printf("%f ",b[i]);
+	print " ";
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/pmf/smoothed/smoother.m	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,2310 @@
+## natural-cubic-spline interpolation
+## usage: yspline = spline(x,y,xspline)
+## example:
+##	x = 0:10; y = sin(x);
+##	xspline = 0:0.1:10; yspline = spline(x,y,xspline);
+##	##plot(x,y,"+",xspline,yspline);
+## Given the vectors x and y, which tabulate a function, with
+## x(1) < x(2) < x(3) <... or x(1) > x(2) > x(3) >..., and given
+## the vector xspline, this function returns a natural-cubic-spline
+## interpolated vector yspline.
+## author: Zdenek Remes, May 22, 1999
+
+
+function ynew = spline(x,y,xnew)
+[x,index]=sort(x);
+y=y(index);
+n=length(y);
+y2(1)=0.0;
+y2(n)=0.0;
+u(1)=0.0;
+for i=2:n-1
+  sig=(x(i)-x(i-1))/(x(i+1)-x(i-1));
+  p=sig*y2(i-1)+2.0;
+  y2(i)=(sig-1.0)/p;
+  u(i)=(y(i+1)-y(i))/(x(i+1)-x(i))-(y(i)-y(i-1))/(x(i)-x(i-1));
+  u(i)=(6.0*u(i)/(x(i+1)-x(i-1))-sig*u(i-1))/p;
+endfor;
+k=n-1;
+while (k >= 1)
+  y2(k)=y2(k)*y2(k+1)+u(k);
+  k--;
+endwhile;
+
+i1=1; in=length(xnew);
+
+#if (xnew(1) < x(1))
+#  error("spline: bad xspline");
+#endif;
+#if (xnew(in) > x(n))
+#  error("spline: bad xspline");
+#endif;
+
+if (xnew(1) == x(1))
+  ynew(1)=y(1);
+  i1=2;
+endif;
+if (xnew(in) == x(n))
+  ynew(in)=y(n);
+  in=in-1;
+endif;
+
+
+for i=i1:in
+  khi=n;
+  klo=1;
+  while ((khi-klo) > 1)
+    k=floor((khi+klo)/2);
+    if (x(k) > xnew(i))
+      khi=k;
+    else
+      klo=k;
+    endif;
+  endwhile;
+  h=x(khi)-x(klo);
+  a=(x(khi)-xnew(i))/h;
+  b=(xnew(i)-x(klo))/h;
+  ynew(i)=a*y(klo)+b*y(khi)+((a^3-a)*y2(klo)+(b^3-b)*y2(khi))*(h*h)/6.0;
+endfor;
+endfunction;
+
+## Savitzky-Golay smoothing filter
+## usage: [xsavgol,ysavgol]=savgol(x,y,nl,nr,m)
+## example: x=0:0.01:3;y1=sin(x.^3);y=y1+(rand(1,301)-0.5)/3;
+##	    [xsavgol,ysavgol]=savgol(x,y,10,10,2);
+##	    ##plot(x,y,"+",xsavgol,ysavgol,x,y1)
+## Given vectors x, y containing a tabulated data y=f(x) with
+## equally spaced x's this function calculates smoothed data
+## ysavgol=g(xsavgol) by Savitzky-Golay smoothing filter.
+## nl is the number of leftward (past) data points used, while
+## nr is the number of rightward (future) data points, making
+## the total number of data points used nl+nr+1. m is the order
+## of the smoothing polynomial, also equal to the highest
+## conserved moment; usual values are m=2 or m=4.
+## The idea of Savitzky-Golay filtering is to smooth the
+## underlying data y=f(x) within the moving window not by a
+## constant (whose estimate is the average), but by a poly-
+## nomial of higher order. Thus for a point y(i) the function
+## savgol fits by a least-squares method a polynomial to
+## points y(i-nl), ..., y(i+nr) in the moving window, and
+## then set g(i-nl+1) to the value of that polynomial at
+## position x(i).
+## Zdenek Remes, Mai 22, 1999
+
+function [xnew,ynew]=savgol(x,y,nl, nr, M)
+
+    if max(diff(x,2))>100*eps
+	error("The x's must be equally spaced.")
+    endif
+    for i=-nl:nr
+	for j=0:M
+	    A(i+nl+1,j+1)=i^j;
+	endfor
+    endfor
+    AA=inv(A'*A);
+    for i=-nl:nr
+	cc=0;
+	for m=0:M
+	    cc=cc+AA(1,m+1)*i^m;
+	endfor
+    c(i+nl+1)=cc;
+    endfor
+
+    nx=length(x);
+    for i=nl:nx-nr-1
+	yy=0;
+	for j=-nl:nr
+	    yy=yy+c(j+nl+1)*y(i+j+1);
+	endfor
+        xnew(i-nl+1)=x(i+1);
+	ynew(i-nl+1)=yy;
+    endfor
+endfunction
+
+## x=0:0.01:3;
+## y1=sin(x.^3);
+## y=y1+(rand(1,301)-0.5)/3;
+## [xsavgol,ysavgol]=savgol(x,y,10,10,2);
+## plot(x,y,"+",xsavgol,ysavgol,x,y1);
+## pause;
+zero=[0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ];
+##load -force CPNA.dat;
+##[xs,ys]=savgol(x,y,5,5,4);
+##save -ascii CPNA.sm xs ys;
+
+load -force CFBr.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CFBr.sm xs ys;
+printf("CFBr.sm\n");
+load -force CFC0.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CFC0.sm xs ys;
+printf("CFC0.sm\n");
+load -force CFC3.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CFC3.sm xs ys;
+printf("CFC3.sm\n");
+load -force CFCF.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CFCF.sm xs ys;
+printf("CFCF.sm\n");
+load -force CFCL.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CFCL.sm xs ys;
+printf("CFCL.sm\n");
+load -force CFCN.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CFCN.sm xs ys;
+printf("CFCN.sm\n");
+load -force CFCO.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CFCO.sm xs ys;
+printf("CFCO.sm\n");
+load -force CFCP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CFCP.sm xs ys;
+printf("CFCP.sm\n");
+load -force CFCW.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CFCW.sm xs ys;
+printf("CFCW.sm\n");
+load -force CFF_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CFF_.sm xs ys;
+printf("CFF_.sm\n");
+load -force CFFe.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CFFe.sm xs ys;
+printf("CFFe.sm\n");
+load -force CFHL.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CFHL.sm xs ys;
+printf("CFHL.sm\n");
+load -force CFMg.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CFMg.sm xs ys;
+printf("CFMg.sm\n");
+load -force CFMn.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CFMn.sm xs ys;
+printf("CFMn.sm\n");
+load -force CFN0.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CFN0.sm xs ys;
+printf("CFN0.sm\n");
+load -force CFNA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CFNA.sm xs ys;
+printf("CFNA.sm\n");
+load -force CFNC.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CFNC.sm xs ys;
+printf("CFNC.sm\n");
+load -force CFND.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CFND.sm xs ys;
+printf("CFND.sm\n");
+load -force CFNP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CFNP.sm xs ys;
+printf("CFNP.sm\n");
+load -force CFNR.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CFNR.sm xs ys;
+printf("CFNR.sm\n");
+load -force CFNS.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CFNS.sm xs ys;
+printf("CFNS.sm\n");
+load -force CFOA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CFOA.sm xs ys;
+printf("CFOA.sm\n");
+load -force CFOC.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CFOC.sm xs ys;
+printf("CFOC.sm\n");
+load -force CFOD.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CFOD.sm xs ys;
+printf("CFOD.sm\n");
+load -force CFOE.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CFOE.sm xs ys;
+printf("CFOE.sm\n");
+load -force CFOR.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CFOR.sm xs ys;
+printf("CFOR.sm\n");
+load -force CFOS.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CFOS.sm xs ys;
+printf("CFOS.sm\n");
+load -force CFP_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CFP_.sm xs ys;
+printf("CFP_.sm\n");
+load -force CFSA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CFSA.sm xs ys;
+printf("CFSA.sm\n");
+load -force CFSD.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CFSD.sm xs ys;
+printf("CFSD.sm\n");
+load -force CFV_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CFV_.sm xs ys;
+printf("CFV_.sm\n");
+load -force CFZn.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CFZn.sm xs ys;
+printf("CFZn.sm\n");
+load -force CFcF.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CFcF.sm xs ys;
+printf("CFcF.sm\n");
+load -force CFcP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CFcP.sm xs ys;
+printf("CFcP.sm\n");
+load -force CNBr.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CNBr.sm xs ys;
+printf("CNBr.sm\n");
+load -force CNC0.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CNC0.sm xs ys;
+printf("CNC0.sm\n");
+load -force CNC3.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CNC3.sm xs ys;
+printf("CNC3.sm\n");
+load -force CNCF.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CNCF.sm xs ys;
+printf("CNCF.sm\n");
+load -force CNCL.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CNCL.sm xs ys;
+printf("CNCL.sm\n");
+load -force CNCN.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CNCN.sm xs ys;
+printf("CNCN.sm\n");
+load -force CNCO.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CNCO.sm xs ys;
+printf("CNCO.sm\n");
+load -force CNCP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CNCP.sm xs ys;
+printf("CNCP.sm\n");
+load -force CNCW.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CNCW.sm xs ys;
+printf("CNCW.sm\n");
+load -force CNF_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CNF_.sm xs ys;
+printf("CNF_.sm\n");
+load -force CNFe.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CNFe.sm xs ys;
+printf("CNFe.sm\n");
+load -force CNHL.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CNHL.sm xs ys;
+printf("CNHL.sm\n");
+load -force CNMg.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CNMg.sm xs ys;
+printf("CNMg.sm\n");
+load -force CNMn.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CNMn.sm xs ys;
+printf("CNMn.sm\n");
+load -force CNN0.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CNN0.sm xs ys;
+printf("CNN0.sm\n");
+load -force CNNA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CNNA.sm xs ys;
+printf("CNNA.sm\n");
+load -force CNNC.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CNNC.sm xs ys;
+printf("CNNC.sm\n");
+load -force CNND.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CNND.sm xs ys;
+printf("CNND.sm\n");
+load -force CNNP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CNNP.sm xs ys;
+printf("CNNP.sm\n");
+load -force CNNR.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CNNR.sm xs ys;
+printf("CNNR.sm\n");
+load -force CNNS.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CNNS.sm xs ys;
+printf("CNNS.sm\n");
+load -force CNOA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CNOA.sm xs ys;
+printf("CNOA.sm\n");
+load -force CNOC.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CNOC.sm xs ys;
+printf("CNOC.sm\n");
+load -force CNOD.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CNOD.sm xs ys;
+printf("CNOD.sm\n");
+load -force CNOE.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CNOE.sm xs ys;
+printf("CNOE.sm\n");
+load -force CNOR.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CNOR.sm xs ys;
+printf("CNOR.sm\n");
+load -force CNOS.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CNOS.sm xs ys;
+printf("CNOS.sm\n");
+load -force CNP_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CNP_.sm xs ys;
+printf("CNP_.sm\n");
+load -force CNSA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CNSA.sm xs ys;
+printf("CNSA.sm\n");
+load -force CNSD.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CNSD.sm xs ys;
+printf("CNSD.sm\n");
+load -force CNV_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CNV_.sm xs ys;
+printf("CNV_.sm\n");
+load -force CNZn.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CNZn.sm xs ys;
+printf("CNZn.sm\n");
+load -force CNcF.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CNcF.sm xs ys;
+printf("CNcF.sm\n");
+load -force CNcP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CNcP.sm xs ys;
+printf("CNcP.sm\n");
+load -force COBr.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii COBr.sm xs ys;
+printf("COBr.sm\n");
+load -force COC0.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii COC0.sm xs ys;
+printf("COC0.sm\n");
+load -force COC3.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii COC3.sm xs ys;
+printf("COC3.sm\n");
+load -force COCF.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii COCF.sm xs ys;
+printf("COCF.sm\n");
+load -force COCL.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii COCL.sm xs ys;
+printf("COCL.sm\n");
+load -force COCN.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii COCN.sm xs ys;
+printf("COCN.sm\n");
+load -force COCO.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii COCO.sm xs ys;
+printf("COCO.sm\n");
+load -force COCP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii COCP.sm xs ys;
+printf("COCP.sm\n");
+load -force COCW.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii COCW.sm xs ys;
+printf("COCW.sm\n");
+load -force COF_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii COF_.sm xs ys;
+printf("COF_.sm\n");
+load -force COFe.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii COFe.sm xs ys;
+printf("COFe.sm\n");
+load -force COHL.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii COHL.sm xs ys;
+printf("COHL.sm\n");
+load -force COMg.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii COMg.sm xs ys;
+printf("COMg.sm\n");
+load -force COMn.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii COMn.sm xs ys;
+printf("COMn.sm\n");
+load -force CON0.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CON0.sm xs ys;
+printf("CON0.sm\n");
+load -force CONA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CONA.sm xs ys;
+printf("CONA.sm\n");
+load -force CONC.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CONC.sm xs ys;
+printf("CONC.sm\n");
+load -force COND.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii COND.sm xs ys;
+printf("COND.sm\n");
+load -force CONP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CONP.sm xs ys;
+printf("CONP.sm\n");
+load -force CONR.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CONR.sm xs ys;
+printf("CONR.sm\n");
+load -force CONS.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CONS.sm xs ys;
+printf("CONS.sm\n");
+load -force COOA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii COOA.sm xs ys;
+printf("COOA.sm\n");
+load -force COOC.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii COOC.sm xs ys;
+printf("COOC.sm\n");
+load -force COOD.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii COOD.sm xs ys;
+printf("COOD.sm\n");
+load -force COOE.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii COOE.sm xs ys;
+printf("COOE.sm\n");
+load -force COOR.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii COOR.sm xs ys;
+printf("COOR.sm\n");
+load -force COOS.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii COOS.sm xs ys;
+printf("COOS.sm\n");
+load -force COP_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii COP_.sm xs ys;
+printf("COP_.sm\n");
+load -force COSA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii COSA.sm xs ys;
+printf("COSA.sm\n");
+load -force COSD.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii COSD.sm xs ys;
+printf("COSD.sm\n");
+load -force COV_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii COV_.sm xs ys;
+printf("COV_.sm\n");
+load -force COZn.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii COZn.sm xs ys;
+printf("COZn.sm\n");
+load -force COcF.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii COcF.sm xs ys;
+printf("COcF.sm\n");
+load -force COcP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii COcP.sm xs ys;
+printf("COcP.sm\n");
+load -force CPBr.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CPBr.sm xs ys;
+printf("CPBr.sm\n");
+load -force CPC0.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CPC0.sm xs ys;
+printf("CPC0.sm\n");
+load -force CPC3.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CPC3.sm xs ys;
+printf("CPC3.sm\n");
+load -force CPCF.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CPCF.sm xs ys;
+printf("CPCF.sm\n");
+load -force CPCL.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CPCL.sm xs ys;
+printf("CPCL.sm\n");
+load -force CPCN.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CPCN.sm xs ys;
+printf("CPCN.sm\n");
+load -force CPCO.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CPCO.sm xs ys;
+printf("CPCO.sm\n");
+load -force CPCP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CPCP.sm xs ys;
+printf("CPCP.sm\n");
+load -force CPCW.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CPCW.sm xs ys;
+printf("CPCW.sm\n");
+load -force CPF_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CPF_.sm xs ys;
+printf("CPF_.sm\n");
+load -force CPFe.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CPFe.sm xs ys;
+printf("CPFe.sm\n");
+load -force CPHL.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CPHL.sm xs ys;
+printf("CPHL.sm\n");
+load -force CPMg.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CPMg.sm xs ys;
+printf("CPMg.sm\n");
+load -force CPMn.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CPMn.sm xs ys;
+printf("CPMn.sm\n");
+load -force CPN0.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CPN0.sm xs ys;
+printf("CPN0.sm\n");
+load -force CPNA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CPNA.sm xs ys;
+printf("CPNA.sm\n");
+load -force CPNC.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CPNC.sm xs ys;
+printf("CPNC.sm\n");
+load -force CPND.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CPND.sm xs ys;
+printf("CPND.sm\n");
+load -force CPNP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CPNP.sm xs ys;
+printf("CPNP.sm\n");
+load -force CPNR.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CPNR.sm xs ys;
+printf("CPNR.sm\n");
+load -force CPNS.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CPNS.sm xs ys;
+printf("CPNS.sm\n");
+load -force CPOA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CPOA.sm xs ys;
+printf("CPOA.sm\n");
+load -force CPOC.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CPOC.sm xs ys;
+printf("CPOC.sm\n");
+load -force CPOD.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CPOD.sm xs ys;
+printf("CPOD.sm\n");
+load -force CPOE.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CPOE.sm xs ys;
+printf("CPOE.sm\n");
+load -force CPOR.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CPOR.sm xs ys;
+printf("CPOR.sm\n");
+load -force CPOS.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CPOS.sm xs ys;
+printf("CPOS.sm\n");
+load -force CPP_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CPP_.sm xs ys;
+printf("CPP_.sm\n");
+load -force CPSA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CPSA.sm xs ys;
+printf("CPSA.sm\n");
+load -force CPSD.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CPSD.sm xs ys;
+printf("CPSD.sm\n");
+load -force CPV_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CPV_.sm xs ys;
+printf("CPV_.sm\n");
+load -force CPZn.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CPZn.sm xs ys;
+printf("CPZn.sm\n");
+load -force CPcF.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CPcF.sm xs ys;
+printf("CPcF.sm\n");
+load -force CPcP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii CPcP.sm xs ys;
+printf("CPcP.sm\n");
+load -force HHBr.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii HHBr.sm xs ys;
+printf("HHBr.sm\n");
+load -force HHC0.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii HHC0.sm xs ys;
+printf("HHC0.sm\n");
+load -force HHC3.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii HHC3.sm xs ys;
+printf("HHC3.sm\n");
+load -force HHCF.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii HHCF.sm xs ys;
+printf("HHCF.sm\n");
+load -force HHCL.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii HHCL.sm xs ys;
+printf("HHCL.sm\n");
+load -force HHCN.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii HHCN.sm xs ys;
+printf("HHCN.sm\n");
+load -force HHCO.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii HHCO.sm xs ys;
+printf("HHCO.sm\n");
+load -force HHCP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii HHCP.sm xs ys;
+printf("HHCP.sm\n");
+load -force HHCW.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii HHCW.sm xs ys;
+printf("HHCW.sm\n");
+load -force HHF_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii HHF_.sm xs ys;
+printf("HHF_.sm\n");
+load -force HHFe.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii HHFe.sm xs ys;
+printf("HHFe.sm\n");
+load -force HHHL.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii HHHL.sm xs ys;
+printf("HHHL.sm\n");
+load -force HHMg.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii HHMg.sm xs ys;
+printf("HHMg.sm\n");
+load -force HHMn.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii HHMn.sm xs ys;
+printf("HHMn.sm\n");
+load -force HHN0.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii HHN0.sm xs ys;
+printf("HHN0.sm\n");
+load -force HHNA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii HHNA.sm xs ys;
+printf("HHNA.sm\n");
+load -force HHNC.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii HHNC.sm xs ys;
+printf("HHNC.sm\n");
+load -force HHND.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii HHND.sm xs ys;
+printf("HHND.sm\n");
+load -force HHNP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii HHNP.sm xs ys;
+printf("HHNP.sm\n");
+load -force HHNR.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii HHNR.sm xs ys;
+printf("HHNR.sm\n");
+load -force HHNS.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii HHNS.sm xs ys;
+printf("HHNS.sm\n");
+load -force HHOA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii HHOA.sm xs ys;
+printf("HHOA.sm\n");
+load -force HHOC.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii HHOC.sm xs ys;
+printf("HHOC.sm\n");
+load -force HHOD.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii HHOD.sm xs ys;
+printf("HHOD.sm\n");
+load -force HHOE.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii HHOE.sm xs ys;
+printf("HHOE.sm\n");
+load -force HHOR.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii HHOR.sm xs ys;
+printf("HHOR.sm\n");
+load -force HHOS.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii HHOS.sm xs ys;
+printf("HHOS.sm\n");
+load -force HHP_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii HHP_.sm xs ys;
+printf("HHP_.sm\n");
+load -force HHSA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii HHSA.sm xs ys;
+printf("HHSA.sm\n");
+load -force HHSD.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii HHSD.sm xs ys;
+printf("HHSD.sm\n");
+load -force HHV_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii HHV_.sm xs ys;
+printf("HHV_.sm\n");
+load -force HHZn.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii HHZn.sm xs ys;
+printf("HHZn.sm\n");
+load -force HHcF.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii HHcF.sm xs ys;
+printf("HHcF.sm\n");
+load -force HHcP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii HHcP.sm xs ys;
+printf("HHcP.sm\n");
+load -force NCBr.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NCBr.sm xs ys;
+printf("NCBr.sm\n");
+load -force NCC0.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NCC0.sm xs ys;
+printf("NCC0.sm\n");
+load -force NCC3.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NCC3.sm xs ys;
+printf("NCC3.sm\n");
+load -force NCCF.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NCCF.sm xs ys;
+printf("NCCF.sm\n");
+load -force NCCL.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NCCL.sm xs ys;
+printf("NCCL.sm\n");
+load -force NCCN.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NCCN.sm xs ys;
+printf("NCCN.sm\n");
+load -force NCCO.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NCCO.sm xs ys;
+printf("NCCO.sm\n");
+load -force NCCP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NCCP.sm xs ys;
+printf("NCCP.sm\n");
+load -force NCCW.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NCCW.sm xs ys;
+printf("NCCW.sm\n");
+load -force NCF_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NCF_.sm xs ys;
+printf("NCF_.sm\n");
+load -force NCFe.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NCFe.sm xs ys;
+printf("NCFe.sm\n");
+load -force NCHL.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NCHL.sm xs ys;
+printf("NCHL.sm\n");
+load -force NCMg.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NCMg.sm xs ys;
+printf("NCMg.sm\n");
+load -force NCMn.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NCMn.sm xs ys;
+printf("NCMn.sm\n");
+load -force NCN0.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NCN0.sm xs ys;
+printf("NCN0.sm\n");
+load -force NCNA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NCNA.sm xs ys;
+printf("NCNA.sm\n");
+load -force NCNC.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NCNC.sm xs ys;
+printf("NCNC.sm\n");
+load -force NCND.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NCND.sm xs ys;
+printf("NCND.sm\n");
+load -force NCNP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NCNP.sm xs ys;
+printf("NCNP.sm\n");
+load -force NCNR.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NCNR.sm xs ys;
+printf("NCNR.sm\n");
+load -force NCNS.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NCNS.sm xs ys;
+printf("NCNS.sm\n");
+load -force NCOA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NCOA.sm xs ys;
+printf("NCOA.sm\n");
+load -force NCOC.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NCOC.sm xs ys;
+printf("NCOC.sm\n");
+load -force NCOD.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NCOD.sm xs ys;
+printf("NCOD.sm\n");
+load -force NCOE.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NCOE.sm xs ys;
+printf("NCOE.sm\n");
+load -force NCOR.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NCOR.sm xs ys;
+printf("NCOR.sm\n");
+load -force NCOS.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NCOS.sm xs ys;
+printf("NCOS.sm\n");
+load -force NCP_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NCP_.sm xs ys;
+printf("NCP_.sm\n");
+load -force NCSA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NCSA.sm xs ys;
+printf("NCSA.sm\n");
+load -force NCSD.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NCSD.sm xs ys;
+printf("NCSD.sm\n");
+load -force NCV_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NCV_.sm xs ys;
+printf("NCV_.sm\n");
+load -force NCZn.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NCZn.sm xs ys;
+printf("NCZn.sm\n");
+load -force NCcF.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NCcF.sm xs ys;
+printf("NCcF.sm\n");
+load -force NCcP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NCcP.sm xs ys;
+printf("NCcP.sm\n");
+load -force NDBr.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NDBr.sm xs ys;
+printf("NDBr.sm\n");
+load -force NDC0.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NDC0.sm xs ys;
+printf("NDC0.sm\n");
+load -force NDC3.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NDC3.sm xs ys;
+printf("NDC3.sm\n");
+load -force NDCF.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NDCF.sm xs ys;
+printf("NDCF.sm\n");
+load -force NDCL.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NDCL.sm xs ys;
+printf("NDCL.sm\n");
+load -force NDCN.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NDCN.sm xs ys;
+printf("NDCN.sm\n");
+load -force NDCO.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NDCO.sm xs ys;
+printf("NDCO.sm\n");
+load -force NDCP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NDCP.sm xs ys;
+printf("NDCP.sm\n");
+load -force NDCW.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NDCW.sm xs ys;
+printf("NDCW.sm\n");
+load -force NDF_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NDF_.sm xs ys;
+printf("NDF_.sm\n");
+load -force NDFe.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NDFe.sm xs ys;
+printf("NDFe.sm\n");
+load -force NDHL.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NDHL.sm xs ys;
+printf("NDHL.sm\n");
+load -force NDMg.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NDMg.sm xs ys;
+printf("NDMg.sm\n");
+load -force NDMn.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NDMn.sm xs ys;
+printf("NDMn.sm\n");
+load -force NDN0.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NDN0.sm xs ys;
+printf("NDN0.sm\n");
+load -force NDNA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NDNA.sm xs ys;
+printf("NDNA.sm\n");
+load -force NDNC.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NDNC.sm xs ys;
+printf("NDNC.sm\n");
+load -force NDND.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NDND.sm xs ys;
+printf("NDND.sm\n");
+load -force NDNP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NDNP.sm xs ys;
+printf("NDNP.sm\n");
+load -force NDNR.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NDNR.sm xs ys;
+printf("NDNR.sm\n");
+load -force NDNS.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NDNS.sm xs ys;
+printf("NDNS.sm\n");
+load -force NDOA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NDOA.sm xs ys;
+printf("NDOA.sm\n");
+load -force NDOC.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NDOC.sm xs ys;
+printf("NDOC.sm\n");
+load -force NDOD.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NDOD.sm xs ys;
+printf("NDOD.sm\n");
+load -force NDOE.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NDOE.sm xs ys;
+printf("NDOE.sm\n");
+load -force NDOR.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NDOR.sm xs ys;
+printf("NDOR.sm\n");
+load -force NDOS.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NDOS.sm xs ys;
+printf("NDOS.sm\n");
+load -force NDP_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NDP_.sm xs ys;
+printf("NDP_.sm\n");
+load -force NDSA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NDSA.sm xs ys;
+printf("NDSA.sm\n");
+load -force NDSD.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NDSD.sm xs ys;
+printf("NDSD.sm\n");
+load -force NDV_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NDV_.sm xs ys;
+printf("NDV_.sm\n");
+load -force NDZn.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NDZn.sm xs ys;
+printf("NDZn.sm\n");
+load -force NDcF.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NDcF.sm xs ys;
+printf("NDcF.sm\n");
+load -force NDcP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NDcP.sm xs ys;
+printf("NDcP.sm\n");
+load -force NRBr.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NRBr.sm xs ys;
+printf("NRBr.sm\n");
+load -force NRC0.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NRC0.sm xs ys;
+printf("NRC0.sm\n");
+load -force NRC3.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NRC3.sm xs ys;
+printf("NRC3.sm\n");
+load -force NRCF.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NRCF.sm xs ys;
+printf("NRCF.sm\n");
+load -force NRCL.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NRCL.sm xs ys;
+printf("NRCL.sm\n");
+load -force NRCN.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NRCN.sm xs ys;
+printf("NRCN.sm\n");
+load -force NRCO.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NRCO.sm xs ys;
+printf("NRCO.sm\n");
+load -force NRCP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NRCP.sm xs ys;
+printf("NRCP.sm\n");
+load -force NRCW.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NRCW.sm xs ys;
+printf("NRCW.sm\n");
+load -force NRF_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NRF_.sm xs ys;
+printf("NRF_.sm\n");
+load -force NRFe.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NRFe.sm xs ys;
+printf("NRFe.sm\n");
+load -force NRHL.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NRHL.sm xs ys;
+printf("NRHL.sm\n");
+load -force NRMg.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NRMg.sm xs ys;
+printf("NRMg.sm\n");
+load -force NRMn.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NRMn.sm xs ys;
+printf("NRMn.sm\n");
+load -force NRN0.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NRN0.sm xs ys;
+printf("NRN0.sm\n");
+load -force NRNA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NRNA.sm xs ys;
+printf("NRNA.sm\n");
+load -force NRNC.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NRNC.sm xs ys;
+printf("NRNC.sm\n");
+load -force NRND.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NRND.sm xs ys;
+printf("NRND.sm\n");
+load -force NRNP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NRNP.sm xs ys;
+printf("NRNP.sm\n");
+load -force NRNR.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NRNR.sm xs ys;
+printf("NRNR.sm\n");
+load -force NRNS.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NRNS.sm xs ys;
+printf("NRNS.sm\n");
+load -force NROA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NROA.sm xs ys;
+printf("NROA.sm\n");
+load -force NROC.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NROC.sm xs ys;
+printf("NROC.sm\n");
+load -force NROD.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NROD.sm xs ys;
+printf("NROD.sm\n");
+load -force NROE.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NROE.sm xs ys;
+printf("NROE.sm\n");
+load -force NROR.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NROR.sm xs ys;
+printf("NROR.sm\n");
+load -force NROS.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NROS.sm xs ys;
+printf("NROS.sm\n");
+load -force NRP_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NRP_.sm xs ys;
+printf("NRP_.sm\n");
+load -force NRSA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NRSA.sm xs ys;
+printf("NRSA.sm\n");
+load -force NRSD.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NRSD.sm xs ys;
+printf("NRSD.sm\n");
+load -force NRV_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NRV_.sm xs ys;
+printf("NRV_.sm\n");
+load -force NRZn.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NRZn.sm xs ys;
+printf("NRZn.sm\n");
+load -force NRcF.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NRcF.sm xs ys;
+printf("NRcF.sm\n");
+load -force NRcP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii NRcP.sm xs ys;
+printf("NRcP.sm\n");
+load -force OABr.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OABr.sm xs ys;
+printf("OABr.sm\n");
+load -force OAC0.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OAC0.sm xs ys;
+printf("OAC0.sm\n");
+load -force OAC3.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OAC3.sm xs ys;
+printf("OAC3.sm\n");
+load -force OACF.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OACF.sm xs ys;
+printf("OACF.sm\n");
+load -force OACL.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OACL.sm xs ys;
+printf("OACL.sm\n");
+load -force OACN.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OACN.sm xs ys;
+printf("OACN.sm\n");
+load -force OACO.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OACO.sm xs ys;
+printf("OACO.sm\n");
+load -force OACP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OACP.sm xs ys;
+printf("OACP.sm\n");
+load -force OACW.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OACW.sm xs ys;
+printf("OACW.sm\n");
+load -force OAF_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OAF_.sm xs ys;
+printf("OAF_.sm\n");
+load -force OAFe.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OAFe.sm xs ys;
+printf("OAFe.sm\n");
+load -force OAHL.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OAHL.sm xs ys;
+printf("OAHL.sm\n");
+load -force OAMg.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OAMg.sm xs ys;
+printf("OAMg.sm\n");
+load -force OAMn.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OAMn.sm xs ys;
+printf("OAMn.sm\n");
+load -force OAN0.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OAN0.sm xs ys;
+printf("OAN0.sm\n");
+load -force OANA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OANA.sm xs ys;
+printf("OANA.sm\n");
+load -force OANC.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OANC.sm xs ys;
+printf("OANC.sm\n");
+load -force OAND.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OAND.sm xs ys;
+printf("OAND.sm\n");
+load -force OANP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OANP.sm xs ys;
+printf("OANP.sm\n");
+load -force OANR.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OANR.sm xs ys;
+printf("OANR.sm\n");
+load -force OANS.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OANS.sm xs ys;
+printf("OANS.sm\n");
+load -force OAOA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OAOA.sm xs ys;
+printf("OAOA.sm\n");
+load -force OAOC.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OAOC.sm xs ys;
+printf("OAOC.sm\n");
+load -force OAOD.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OAOD.sm xs ys;
+printf("OAOD.sm\n");
+load -force OAOE.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OAOE.sm xs ys;
+printf("OAOE.sm\n");
+load -force OAOR.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OAOR.sm xs ys;
+printf("OAOR.sm\n");
+load -force OAOS.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OAOS.sm xs ys;
+printf("OAOS.sm\n");
+load -force OAP_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OAP_.sm xs ys;
+printf("OAP_.sm\n");
+load -force OASA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OASA.sm xs ys;
+printf("OASA.sm\n");
+load -force OASD.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OASD.sm xs ys;
+printf("OASD.sm\n");
+load -force OAV_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OAV_.sm xs ys;
+printf("OAV_.sm\n");
+load -force OAZn.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OAZn.sm xs ys;
+printf("OAZn.sm\n");
+load -force OAcF.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OAcF.sm xs ys;
+printf("OAcF.sm\n");
+load -force OAcP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OAcP.sm xs ys;
+printf("OAcP.sm\n");
+load -force OCBr.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OCBr.sm xs ys;
+printf("OCBr.sm\n");
+load -force OCC0.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OCC0.sm xs ys;
+printf("OCC0.sm\n");
+load -force OCC3.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OCC3.sm xs ys;
+printf("OCC3.sm\n");
+load -force OCCF.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OCCF.sm xs ys;
+printf("OCCF.sm\n");
+load -force OCCL.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OCCL.sm xs ys;
+printf("OCCL.sm\n");
+load -force OCCN.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OCCN.sm xs ys;
+printf("OCCN.sm\n");
+load -force OCCO.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OCCO.sm xs ys;
+printf("OCCO.sm\n");
+load -force OCCP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OCCP.sm xs ys;
+printf("OCCP.sm\n");
+load -force OCCW.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OCCW.sm xs ys;
+printf("OCCW.sm\n");
+load -force OCF_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OCF_.sm xs ys;
+printf("OCF_.sm\n");
+load -force OCFe.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OCFe.sm xs ys;
+printf("OCFe.sm\n");
+load -force OCHL.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OCHL.sm xs ys;
+printf("OCHL.sm\n");
+load -force OCMg.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OCMg.sm xs ys;
+printf("OCMg.sm\n");
+load -force OCMn.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OCMn.sm xs ys;
+printf("OCMn.sm\n");
+load -force OCN0.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OCN0.sm xs ys;
+printf("OCN0.sm\n");
+load -force OCNA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OCNA.sm xs ys;
+printf("OCNA.sm\n");
+load -force OCNC.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OCNC.sm xs ys;
+printf("OCNC.sm\n");
+load -force OCND.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OCND.sm xs ys;
+printf("OCND.sm\n");
+load -force OCNP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OCNP.sm xs ys;
+printf("OCNP.sm\n");
+load -force OCNR.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OCNR.sm xs ys;
+printf("OCNR.sm\n");
+load -force OCNS.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OCNS.sm xs ys;
+printf("OCNS.sm\n");
+load -force OCOA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OCOA.sm xs ys;
+printf("OCOA.sm\n");
+load -force OCOC.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OCOC.sm xs ys;
+printf("OCOC.sm\n");
+load -force OCOD.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OCOD.sm xs ys;
+printf("OCOD.sm\n");
+load -force OCOE.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OCOE.sm xs ys;
+printf("OCOE.sm\n");
+load -force OCOR.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OCOR.sm xs ys;
+printf("OCOR.sm\n");
+load -force OCOS.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OCOS.sm xs ys;
+printf("OCOS.sm\n");
+load -force OCP_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OCP_.sm xs ys;
+printf("OCP_.sm\n");
+load -force OCSA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OCSA.sm xs ys;
+printf("OCSA.sm\n");
+load -force OCSD.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OCSD.sm xs ys;
+printf("OCSD.sm\n");
+load -force OCV_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OCV_.sm xs ys;
+printf("OCV_.sm\n");
+load -force OCZn.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OCZn.sm xs ys;
+printf("OCZn.sm\n");
+load -force OCcF.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OCcF.sm xs ys;
+printf("OCcF.sm\n");
+load -force OCcP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OCcP.sm xs ys;
+printf("OCcP.sm\n");
+load -force ODBr.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii ODBr.sm xs ys;
+printf("ODBr.sm\n");
+load -force ODC0.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii ODC0.sm xs ys;
+printf("ODC0.sm\n");
+load -force ODC3.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii ODC3.sm xs ys;
+printf("ODC3.sm\n");
+load -force ODCF.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii ODCF.sm xs ys;
+printf("ODCF.sm\n");
+load -force ODCL.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii ODCL.sm xs ys;
+printf("ODCL.sm\n");
+load -force ODCN.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii ODCN.sm xs ys;
+printf("ODCN.sm\n");
+load -force ODCO.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii ODCO.sm xs ys;
+printf("ODCO.sm\n");
+load -force ODCP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii ODCP.sm xs ys;
+printf("ODCP.sm\n");
+load -force ODCW.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii ODCW.sm xs ys;
+printf("ODCW.sm\n");
+load -force ODF_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii ODF_.sm xs ys;
+printf("ODF_.sm\n");
+load -force ODFe.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii ODFe.sm xs ys;
+printf("ODFe.sm\n");
+load -force ODHL.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii ODHL.sm xs ys;
+printf("ODHL.sm\n");
+load -force ODMg.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii ODMg.sm xs ys;
+printf("ODMg.sm\n");
+load -force ODMn.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii ODMn.sm xs ys;
+printf("ODMn.sm\n");
+load -force ODN0.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii ODN0.sm xs ys;
+printf("ODN0.sm\n");
+load -force ODNA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii ODNA.sm xs ys;
+printf("ODNA.sm\n");
+load -force ODNC.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii ODNC.sm xs ys;
+printf("ODNC.sm\n");
+load -force ODND.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii ODND.sm xs ys;
+printf("ODND.sm\n");
+load -force ODNP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii ODNP.sm xs ys;
+printf("ODNP.sm\n");
+load -force ODNR.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii ODNR.sm xs ys;
+printf("ODNR.sm\n");
+load -force ODNS.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii ODNS.sm xs ys;
+printf("ODNS.sm\n");
+load -force ODOA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii ODOA.sm xs ys;
+printf("ODOA.sm\n");
+load -force ODOC.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii ODOC.sm xs ys;
+printf("ODOC.sm\n");
+load -force ODOD.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii ODOD.sm xs ys;
+printf("ODOD.sm\n");
+load -force ODOE.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii ODOE.sm xs ys;
+printf("ODOE.sm\n");
+load -force ODOR.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii ODOR.sm xs ys;
+printf("ODOR.sm\n");
+load -force ODOS.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii ODOS.sm xs ys;
+printf("ODOS.sm\n");
+load -force ODP_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii ODP_.sm xs ys;
+printf("ODP_.sm\n");
+load -force ODSA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii ODSA.sm xs ys;
+printf("ODSA.sm\n");
+load -force ODSD.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii ODSD.sm xs ys;
+printf("ODSD.sm\n");
+load -force ODV_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii ODV_.sm xs ys;
+printf("ODV_.sm\n");
+load -force ODZn.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii ODZn.sm xs ys;
+printf("ODZn.sm\n");
+load -force ODcF.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii ODcF.sm xs ys;
+printf("ODcF.sm\n");
+load -force ODcP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii ODcP.sm xs ys;
+printf("ODcP.sm\n");
+load -force OWBr.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OWBr.sm xs ys;
+printf("OWBr.sm\n");
+load -force OWC0.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OWC0.sm xs ys;
+printf("OWC0.sm\n");
+load -force OWC3.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OWC3.sm xs ys;
+printf("OWC3.sm\n");
+load -force OWCF.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OWCF.sm xs ys;
+printf("OWCF.sm\n");
+load -force OWCL.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OWCL.sm xs ys;
+printf("OWCL.sm\n");
+load -force OWCN.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OWCN.sm xs ys;
+printf("OWCN.sm\n");
+load -force OWCO.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OWCO.sm xs ys;
+printf("OWCO.sm\n");
+load -force OWCP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OWCP.sm xs ys;
+printf("OWCP.sm\n");
+load -force OWCW.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OWCW.sm xs ys;
+printf("OWCW.sm\n");
+load -force OWF_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OWF_.sm xs ys;
+printf("OWF_.sm\n");
+load -force OWFe.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OWFe.sm xs ys;
+printf("OWFe.sm\n");
+load -force OWHL.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OWHL.sm xs ys;
+printf("OWHL.sm\n");
+load -force OWMg.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OWMg.sm xs ys;
+printf("OWMg.sm\n");
+load -force OWMn.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OWMn.sm xs ys;
+printf("OWMn.sm\n");
+load -force OWN0.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OWN0.sm xs ys;
+printf("OWN0.sm\n");
+load -force OWNA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OWNA.sm xs ys;
+printf("OWNA.sm\n");
+load -force OWNC.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OWNC.sm xs ys;
+printf("OWNC.sm\n");
+load -force OWND.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OWND.sm xs ys;
+printf("OWND.sm\n");
+load -force OWNP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OWNP.sm xs ys;
+printf("OWNP.sm\n");
+load -force OWNR.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OWNR.sm xs ys;
+printf("OWNR.sm\n");
+load -force OWNS.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OWNS.sm xs ys;
+printf("OWNS.sm\n");
+load -force OWOA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OWOA.sm xs ys;
+printf("OWOA.sm\n");
+load -force OWOC.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OWOC.sm xs ys;
+printf("OWOC.sm\n");
+load -force OWOD.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OWOD.sm xs ys;
+printf("OWOD.sm\n");
+load -force OWOE.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OWOE.sm xs ys;
+printf("OWOE.sm\n");
+load -force OWOR.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OWOR.sm xs ys;
+printf("OWOR.sm\n");
+load -force OWOS.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OWOS.sm xs ys;
+printf("OWOS.sm\n");
+load -force OWP_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OWP_.sm xs ys;
+printf("OWP_.sm\n");
+load -force OWSA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OWSA.sm xs ys;
+printf("OWSA.sm\n");
+load -force OWSD.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OWSD.sm xs ys;
+printf("OWSD.sm\n");
+load -force OWV_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OWV_.sm xs ys;
+printf("OWV_.sm\n");
+load -force OWZn.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OWZn.sm xs ys;
+printf("OWZn.sm\n");
+load -force OWcF.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OWcF.sm xs ys;
+printf("OWcF.sm\n");
+load -force OWcP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii OWcP.sm xs ys;
+printf("OWcP.sm\n");
+load -force SABr.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SABr.sm xs ys;
+printf("SABr.sm\n");
+load -force SAC0.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SAC0.sm xs ys;
+printf("SAC0.sm\n");
+load -force SAC3.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SAC3.sm xs ys;
+printf("SAC3.sm\n");
+load -force SACF.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SACF.sm xs ys;
+printf("SACF.sm\n");
+load -force SACL.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SACL.sm xs ys;
+printf("SACL.sm\n");
+load -force SACN.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SACN.sm xs ys;
+printf("SACN.sm\n");
+load -force SACO.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SACO.sm xs ys;
+printf("SACO.sm\n");
+load -force SACP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SACP.sm xs ys;
+printf("SACP.sm\n");
+load -force SACW.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SACW.sm xs ys;
+printf("SACW.sm\n");
+load -force SAF_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SAF_.sm xs ys;
+printf("SAF_.sm\n");
+load -force SAFe.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SAFe.sm xs ys;
+printf("SAFe.sm\n");
+load -force SAHL.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SAHL.sm xs ys;
+printf("SAHL.sm\n");
+load -force SAMg.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SAMg.sm xs ys;
+printf("SAMg.sm\n");
+load -force SAMn.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SAMn.sm xs ys;
+printf("SAMn.sm\n");
+load -force SAN0.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SAN0.sm xs ys;
+printf("SAN0.sm\n");
+load -force SANA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SANA.sm xs ys;
+printf("SANA.sm\n");
+load -force SANC.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SANC.sm xs ys;
+printf("SANC.sm\n");
+load -force SAND.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SAND.sm xs ys;
+printf("SAND.sm\n");
+load -force SANP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SANP.sm xs ys;
+printf("SANP.sm\n");
+load -force SANR.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SANR.sm xs ys;
+printf("SANR.sm\n");
+load -force SANS.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SANS.sm xs ys;
+printf("SANS.sm\n");
+load -force SAOA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SAOA.sm xs ys;
+printf("SAOA.sm\n");
+load -force SAOC.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SAOC.sm xs ys;
+printf("SAOC.sm\n");
+load -force SAOD.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SAOD.sm xs ys;
+printf("SAOD.sm\n");
+load -force SAOE.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SAOE.sm xs ys;
+printf("SAOE.sm\n");
+load -force SAOR.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SAOR.sm xs ys;
+printf("SAOR.sm\n");
+load -force SAOS.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SAOS.sm xs ys;
+printf("SAOS.sm\n");
+load -force SAP_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SAP_.sm xs ys;
+printf("SAP_.sm\n");
+load -force SASA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SASA.sm xs ys;
+printf("SASA.sm\n");
+load -force SASD.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SASD.sm xs ys;
+printf("SASD.sm\n");
+load -force SAV_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SAV_.sm xs ys;
+printf("SAV_.sm\n");
+load -force SAZn.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SAZn.sm xs ys;
+printf("SAZn.sm\n");
+load -force SAcF.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SAcF.sm xs ys;
+printf("SAcF.sm\n");
+load -force SAcP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SAcP.sm xs ys;
+printf("SAcP.sm\n");
+load -force SDBr.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SDBr.sm xs ys;
+printf("SDBr.sm\n");
+load -force SDC0.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SDC0.sm xs ys;
+printf("SDC0.sm\n");
+load -force SDC3.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SDC3.sm xs ys;
+printf("SDC3.sm\n");
+load -force SDCF.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SDCF.sm xs ys;
+printf("SDCF.sm\n");
+load -force SDCL.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SDCL.sm xs ys;
+printf("SDCL.sm\n");
+load -force SDCN.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SDCN.sm xs ys;
+printf("SDCN.sm\n");
+load -force SDCO.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SDCO.sm xs ys;
+printf("SDCO.sm\n");
+load -force SDCP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SDCP.sm xs ys;
+printf("SDCP.sm\n");
+load -force SDCW.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SDCW.sm xs ys;
+printf("SDCW.sm\n");
+load -force SDF_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SDF_.sm xs ys;
+printf("SDF_.sm\n");
+load -force SDFe.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SDFe.sm xs ys;
+printf("SDFe.sm\n");
+load -force SDHL.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SDHL.sm xs ys;
+printf("SDHL.sm\n");
+load -force SDMg.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SDMg.sm xs ys;
+printf("SDMg.sm\n");
+load -force SDMn.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SDMn.sm xs ys;
+printf("SDMn.sm\n");
+load -force SDN0.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SDN0.sm xs ys;
+printf("SDN0.sm\n");
+load -force SDNA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SDNA.sm xs ys;
+printf("SDNA.sm\n");
+load -force SDNC.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SDNC.sm xs ys;
+printf("SDNC.sm\n");
+load -force SDND.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SDND.sm xs ys;
+printf("SDND.sm\n");
+load -force SDNP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SDNP.sm xs ys;
+printf("SDNP.sm\n");
+load -force SDNR.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SDNR.sm xs ys;
+printf("SDNR.sm\n");
+load -force SDNS.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SDNS.sm xs ys;
+printf("SDNS.sm\n");
+load -force SDOA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SDOA.sm xs ys;
+printf("SDOA.sm\n");
+load -force SDOC.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SDOC.sm xs ys;
+printf("SDOC.sm\n");
+load -force SDOD.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SDOD.sm xs ys;
+printf("SDOD.sm\n");
+load -force SDOE.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SDOE.sm xs ys;
+printf("SDOE.sm\n");
+load -force SDOR.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SDOR.sm xs ys;
+printf("SDOR.sm\n");
+load -force SDOS.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SDOS.sm xs ys;
+printf("SDOS.sm\n");
+load -force SDP_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SDP_.sm xs ys;
+printf("SDP_.sm\n");
+load -force SDSA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SDSA.sm xs ys;
+printf("SDSA.sm\n");
+load -force SDSD.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SDSD.sm xs ys;
+printf("SDSD.sm\n");
+load -force SDV_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SDV_.sm xs ys;
+printf("SDV_.sm\n");
+load -force SDZn.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SDZn.sm xs ys;
+printf("SDZn.sm\n");
+load -force SDcF.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SDcF.sm xs ys;
+printf("SDcF.sm\n");
+load -force SDcP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii SDcP.sm xs ys;
+printf("SDcP.sm\n");
+load -force cFBr.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cFBr.sm xs ys;
+printf("cFBr.sm\n");
+load -force cFC0.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cFC0.sm xs ys;
+printf("cFC0.sm\n");
+load -force cFC3.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cFC3.sm xs ys;
+printf("cFC3.sm\n");
+load -force cFCF.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cFCF.sm xs ys;
+printf("cFCF.sm\n");
+load -force cFCL.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cFCL.sm xs ys;
+printf("cFCL.sm\n");
+load -force cFCN.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cFCN.sm xs ys;
+printf("cFCN.sm\n");
+load -force cFCO.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cFCO.sm xs ys;
+printf("cFCO.sm\n");
+load -force cFCP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cFCP.sm xs ys;
+printf("cFCP.sm\n");
+load -force cFCW.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cFCW.sm xs ys;
+printf("cFCW.sm\n");
+load -force cFF_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cFF_.sm xs ys;
+printf("cFF_.sm\n");
+load -force cFFe.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cFFe.sm xs ys;
+printf("cFFe.sm\n");
+load -force cFHL.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cFHL.sm xs ys;
+printf("cFHL.sm\n");
+load -force cFMg.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cFMg.sm xs ys;
+printf("cFMg.sm\n");
+load -force cFMn.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cFMn.sm xs ys;
+printf("cFMn.sm\n");
+load -force cFN0.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cFN0.sm xs ys;
+printf("cFN0.sm\n");
+load -force cFNA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cFNA.sm xs ys;
+printf("cFNA.sm\n");
+load -force cFNC.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cFNC.sm xs ys;
+printf("cFNC.sm\n");
+load -force cFND.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cFND.sm xs ys;
+printf("cFND.sm\n");
+load -force cFNP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cFNP.sm xs ys;
+printf("cFNP.sm\n");
+load -force cFNR.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cFNR.sm xs ys;
+printf("cFNR.sm\n");
+load -force cFNS.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cFNS.sm xs ys;
+printf("cFNS.sm\n");
+load -force cFOA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cFOA.sm xs ys;
+printf("cFOA.sm\n");
+load -force cFOC.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cFOC.sm xs ys;
+printf("cFOC.sm\n");
+load -force cFOD.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cFOD.sm xs ys;
+printf("cFOD.sm\n");
+load -force cFOE.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cFOE.sm xs ys;
+printf("cFOE.sm\n");
+load -force cFOR.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cFOR.sm xs ys;
+printf("cFOR.sm\n");
+load -force cFOS.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cFOS.sm xs ys;
+printf("cFOS.sm\n");
+load -force cFP_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cFP_.sm xs ys;
+printf("cFP_.sm\n");
+load -force cFSA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cFSA.sm xs ys;
+printf("cFSA.sm\n");
+load -force cFSD.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cFSD.sm xs ys;
+printf("cFSD.sm\n");
+load -force cFV_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cFV_.sm xs ys;
+printf("cFV_.sm\n");
+load -force cFZn.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cFZn.sm xs ys;
+printf("cFZn.sm\n");
+load -force cFcF.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cFcF.sm xs ys;
+printf("cFcF.sm\n");
+load -force cFcP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cFcP.sm xs ys;
+printf("cFcP.sm\n");
+load -force cPBr.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cPBr.sm xs ys;
+printf("cPBr.sm\n");
+load -force cPC0.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cPC0.sm xs ys;
+printf("cPC0.sm\n");
+load -force cPC3.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cPC3.sm xs ys;
+printf("cPC3.sm\n");
+load -force cPCF.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cPCF.sm xs ys;
+printf("cPCF.sm\n");
+load -force cPCL.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cPCL.sm xs ys;
+printf("cPCL.sm\n");
+load -force cPCN.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cPCN.sm xs ys;
+printf("cPCN.sm\n");
+load -force cPCO.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cPCO.sm xs ys;
+printf("cPCO.sm\n");
+load -force cPCP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cPCP.sm xs ys;
+printf("cPCP.sm\n");
+load -force cPCW.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cPCW.sm xs ys;
+printf("cPCW.sm\n");
+load -force cPF_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cPF_.sm xs ys;
+printf("cPF_.sm\n");
+load -force cPFe.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cPFe.sm xs ys;
+printf("cPFe.sm\n");
+load -force cPHL.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cPHL.sm xs ys;
+printf("cPHL.sm\n");
+load -force cPMg.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cPMg.sm xs ys;
+printf("cPMg.sm\n");
+load -force cPMn.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cPMn.sm xs ys;
+printf("cPMn.sm\n");
+load -force cPN0.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cPN0.sm xs ys;
+printf("cPN0.sm\n");
+load -force cPNA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cPNA.sm xs ys;
+printf("cPNA.sm\n");
+load -force cPNC.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cPNC.sm xs ys;
+printf("cPNC.sm\n");
+load -force cPND.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cPND.sm xs ys;
+printf("cPND.sm\n");
+load -force cPNP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cPNP.sm xs ys;
+printf("cPNP.sm\n");
+load -force cPNR.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cPNR.sm xs ys;
+printf("cPNR.sm\n");
+load -force cPNS.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cPNS.sm xs ys;
+printf("cPNS.sm\n");
+load -force cPOA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cPOA.sm xs ys;
+printf("cPOA.sm\n");
+load -force cPOC.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cPOC.sm xs ys;
+printf("cPOC.sm\n");
+load -force cPOD.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cPOD.sm xs ys;
+printf("cPOD.sm\n");
+load -force cPOE.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cPOE.sm xs ys;
+printf("cPOE.sm\n");
+load -force cPOR.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cPOR.sm xs ys;
+printf("cPOR.sm\n");
+load -force cPOS.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cPOS.sm xs ys;
+printf("cPOS.sm\n");
+load -force cPP_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cPP_.sm xs ys;
+printf("cPP_.sm\n");
+load -force cPSA.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cPSA.sm xs ys;
+printf("cPSA.sm\n");
+load -force cPSD.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cPSD.sm xs ys;
+printf("cPSD.sm\n");
+load -force cPV_.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cPV_.sm xs ys;
+printf("cPV_.sm\n");
+load -force cPZn.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cPZn.sm xs ys;
+printf("cPZn.sm\n");
+load -force cPcF.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cPcF.sm xs ys;
+printf("cPcF.sm\n");
+load -force cPcP.dat;
+[xs,ys]=savgol(x,y,5,5,4);
+save -ascii cPcP.sm xs ys;
+printf("cPcP.sm\n");
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/scripts/dock.prm	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,104 @@
+RBT_PARAMETER_FILE_V1.00
+TITLE Free docking (indexed VDW)
+
+SECTION SCORE
+	INTER	 RbtInterIdxSF.prm
+    	INTRA    RbtIntraSF.prm
+	SYSTEM   RbtTargetSF.prm
+END_SECTION
+
+SECTION SETSLOPE_1
+	TRANSFORM           		RbtNullTransform
+	WEIGHT@SCORE.RESTR.CAVITY	5.0	# Dock with a high penalty for leaving the cavity
+	WEIGHT@SCORE.INTRA.DIHEDRAL	0.1	# Gradually ramp up dihedral weight from 0.1->0.5
+	ECUT@SCORE.INTER.VDW		1.0	# Gradually ramp up energy cutoff for switching to quadratic
+	USE_4_8@SCORE.INTER.VDW		TRUE	# Start docking with a 4-8 vdW potential
+	DA1MAX@SCORE.INTER.POLAR	180.0	# Broader angular dependence
+	DA2MAX@SCORE.INTER.POLAR	180.0	# Broader angular dependence
+	DR12MAX@SCORE.INTER.POLAR	1.5	# Broader distance range
+END_SECTION
+
+SECTION RANDOM_POP
+        TRANSFORM                       RbtRandPopTransform
+        POP_SIZE                        50
+	SCALE_CHROM_LENGTH		TRUE
+END_SECTION
+
+SECTION GA_SLOPE1
+	TRANSFORM			RbtGATransform
+	PCROSSOVER			0.4	# Prob. of crossover
+	XOVERMUT			TRUE	# Cauchy mutation after each crossover
+	CMUTATE				FALSE	# True = Cauchy; False = Rectang. for regular mutations
+	STEP_SIZE			1.0	# Max translational mutation
+END_SECTION
+
+SECTION SETSLOPE_3
+	TRANSFORM           		RbtNullTransform
+	WEIGHT@SCORE.INTRA.DIHEDRAL	0.2
+	ECUT@SCORE.INTER.VDW		5.0
+	DA1MAX@SCORE.INTER.POLAR	140.0
+	DA2MAX@SCORE.INTER.POLAR	140.0
+	DR12MAX@SCORE.INTER.POLAR	1.2
+END_SECTION
+
+SECTION GA_SLOPE3
+	TRANSFORM			RbtGATransform
+	PCROSSOVER			0.4	# Prob. of crossover
+	XOVERMUT			TRUE	# Cauchy mutation after each crossover
+	CMUTATE				FALSE	# True = Cauchy; False = Rectang. for regular mutations
+	STEP_SIZE			1.0	# Max torsional mutation
+END_SECTION
+
+SECTION SETSLOPE_5
+	TRANSFORM           		RbtNullTransform
+	WEIGHT@SCORE.INTRA.DIHEDRAL	0.3
+	ECUT@SCORE.INTER.VDW		25.0
+	USE_4_8@SCORE.INTER.VDW		FALSE	# Now switch to a convential 6-12 for final GA, MC, minimisation
+	DA1MAX@SCORE.INTER.POLAR	120.0
+	DA2MAX@SCORE.INTER.POLAR	120.0
+	DR12MAX@SCORE.INTER.POLAR	0.9
+END_SECTION
+
+SECTION GA_SLOPE5
+	TRANSFORM			RbtGATransform
+	PCROSSOVER			0.4	# Prob. of crossover
+	XOVERMUT			TRUE	# Cauchy mutation after each crossover
+	CMUTATE				FALSE	# True = Cauchy; False = Rectang. for regular mutations
+	STEP_SIZE			1.0	# Max torsional mutation
+END_SECTION
+
+SECTION SETSLOPE_10
+	TRANSFORM           		RbtNullTransform
+	WEIGHT@SCORE.INTRA.DIHEDRAL	0.5	# Final dihedral weight matches SF file
+	ECUT@SCORE.INTER.VDW		120.0	# Final ECUT matches SF file
+	DA1MAX@SCORE.INTER.POLAR	80.0
+	DA2MAX@SCORE.INTER.POLAR	100.0
+	DR12MAX@SCORE.INTER.POLAR	0.6
+END_SECTION
+
+SECTION MC_10K
+	TRANSFORM           		RbtSimAnnTransform
+	START_T             		10.0
+	FINAL_T             		10.0
+	NUM_BLOCKS          		5
+	STEP_SIZE          		0.1
+	MIN_ACC_RATE            	0.25
+	PARTITION_DIST          	8.0
+	PARTITION_FREQ          	50
+	HISTORY_FREQ            	0
+END_SECTION
+
+SECTION SIMPLEX
+	TRANSFORM			RbtSimplexTransform
+	MAX_CALLS			200
+	NCYCLES				20
+	STOPPING_STEP_LENGTH		10e-4
+	PARTITION_DIST			8.0
+        STEP_SIZE			1.0
+	CONVERGENCE			0.001
+END_SECTION
+
+SECTION FINAL
+	TRANSFORM           		RbtNullTransform
+	WEIGHT@SCORE.RESTR.CAVITY	1.0	# revert to standard cavity penalty
+END_SECTION
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/scripts/dock_grid.prm	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,96 @@
+RBT_PARAMETER_FILE_V1.00
+TITLE Free docking (grid-based VDW)
+
+SECTION SCORE
+    	INTER    RbtInterGridSF.prm
+    	INTRA    RbtIntraSF.prm
+	SYSTEM   RbtTargetSF.prm
+END_SECTION
+
+SECTION SETSLOPE_1
+	TRANSFORM           		RbtNullTransform
+	WEIGHT@SCORE.RESTR.CAVITY	5.0	# Dock with a high penalty for leaving the cavity
+	WEIGHT@SCORE.INTRA.DIHEDRAL	0.1	# Gradually ramp up dihedral weight from 0.1->0.5
+        ENABLED@SCORE.INTER.VDW1	TRUE	# Enable vdW grid with ECUT=1
+        ENABLED@SCORE.INTER.VDW5       	FALSE	# Disable vdW grid with ECUT=5
+        ENABLED@SCORE.INTER.VDW        	FALSE	# Disable indexed vdW
+END_SECTION
+
+SECTION RANDOM_POP
+        TRANSFORM                       RbtRandPopTransform
+        POP_SIZE                        50
+	SCALE_CHROM_LENGTH		TRUE
+END_SECTION
+
+SECTION GA_SLOPE1
+	TRANSFORM			RbtGATransform
+	PCROSSOVER			0.4	# Prob. of crossover
+	XOVERMUT			TRUE	# Cauchy mutation after each crossover
+	CMUTATE				FALSE	# True = Cauchy; False = Rectang. for regular mutations
+	STEP_SIZE			1.0	# Max translational mutation
+END_SECTION
+
+SECTION SETSLOPE_3
+	TRANSFORM           		RbtNullTransform
+	WEIGHT@SCORE.INTRA.DIHEDRAL	0.2
+        ENABLED@SCORE.INTER.VDW1       	FALSE	# Disable vdW grid with ECUT=1
+        ENABLED@SCORE.INTER.VDW5       	TRUE	# Enable vdW grid with ECUT=5
+END_SECTION
+
+SECTION GA_SLOPE3
+	TRANSFORM			RbtGATransform
+	PCROSSOVER			0.4	# Prob. of crossover
+	XOVERMUT			TRUE	# Cauchy mutation after each crossover
+	CMUTATE				FALSE	# True = Cauchy; False = Rectang. for regular mutations
+	STEP_SIZE			1.0	# Max torsional mutation
+END_SECTION
+
+SECTION SETSLOPE_5
+	TRANSFORM           		RbtNullTransform
+	WEIGHT@SCORE.INTRA.DIHEDRAL	0.3
+        ENABLED@SCORE.INTER.VDW5       	FALSE	# Disable vdW grid with ECUT=5
+        ENABLED@SCORE.INTER.VDW		TRUE	# Enable indexed vdW
+	ECUT@SCORE.INTER.VDW		25.0
+END_SECTION
+
+SECTION GA_SLOPE5
+	TRANSFORM			RbtGATransform
+	PCROSSOVER			0.4	# Prob. of crossover
+	XOVERMUT			TRUE	# Cauchy mutation after each crossover
+	CMUTATE				FALSE	# True = Cauchy; False = Rectang. for regular mutations
+	STEP_SIZE			1.0	# Max torsional mutation
+END_SECTION
+
+SECTION SETSLOPE_10
+	TRANSFORM           		RbtNullTransform
+	WEIGHT@SCORE.INTRA.DIHEDRAL	0.5	# Final dihedral weight matches SF file
+	ECUT@SCORE.INTER.VDW		120.0	# Final ECUT matches SF file
+END_SECTION
+
+SECTION MC_10K
+	TRANSFORM           		RbtSimAnnTransform
+	START_T             		10.0
+	FINAL_T             		10.0
+	NUM_BLOCKS          		5
+	STEP_SIZE          		0.1
+	MIN_ACC_RATE            	0.25
+	PARTITION_DIST          	8.0
+	PARTITION_FREQ          	50
+	HISTORY_FREQ            	0
+END_SECTION
+
+SECTION SIMPLEX
+	TRANSFORM			RbtSimplexTransform
+	MAX_CALLS			200
+	NCYCLES				20
+	STOPPING_STEP_LENGTH		10e-4
+	PARTITION_DIST			8.0
+        STEP_SIZE			1.0
+	CONVERGENCE			0.001
+END_SECTION
+
+SECTION FINAL
+	TRANSFORM           		RbtNullTransform
+	WEIGHT@SCORE.RESTR.CAVITY	1.0	# revert to standard cavity penalty
+END_SECTION
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/scripts/dock_solv.prm	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,104 @@
+RBT_PARAMETER_FILE_V1.00
+TITLE Free docking (with SOLVATION, indexed VDW)
+
+SECTION SCORE
+    	INTER    RbtSolvIdxSF.prm
+    	INTRA    RbtIntraSF.prm
+	SYSTEM   RbtTargetSF.prm
+END_SECTION
+
+SECTION SETSLOPE_1
+	TRANSFORM           		RbtNullTransform
+	WEIGHT@SCORE.RESTR.CAVITY	5.0	# Dock with a high penalty for leaving the cavity
+	WEIGHT@SCORE.INTRA.DIHEDRAL	0.1	# Gradually ramp up dihedral weight from 0.1->0.5
+	ECUT@SCORE.INTER.VDW		1.0	# Gradually ramp up energy cutoff for switching to quadratic
+	USE_4_8@SCORE.INTER.VDW		TRUE	# Start docking with a 4-8 vdW potential
+	DA1MAX@SCORE.INTER.POLAR	180.0	# Broader angular dependence
+	DA2MAX@SCORE.INTER.POLAR	180.0	# Broader angular dependence
+	DR12MAX@SCORE.INTER.POLAR	1.5	# Broader distance range
+END_SECTION
+
+SECTION RANDOM_POP
+        TRANSFORM                       RbtRandPopTransform
+        POP_SIZE                        50
+	SCALE_CHROM_LENGTH		TRUE
+END_SECTION
+
+SECTION GA_SLOPE1
+	TRANSFORM			RbtGATransform
+	PCROSSOVER			0.4	# Prob. of crossover
+	XOVERMUT			TRUE	# Cauchy mutation after each crossover
+	CMUTATE				FALSE	# True = Cauchy; False = Rectang. for regular mutations
+	STEP_SIZE			1.0	# Max translational mutation
+END_SECTION
+
+SECTION SETSLOPE_3
+	TRANSFORM           		RbtNullTransform
+	WEIGHT@SCORE.INTRA.DIHEDRAL	0.2
+	ECUT@SCORE.INTER.VDW		5.0
+	DA1MAX@SCORE.INTER.POLAR	140.0
+	DA2MAX@SCORE.INTER.POLAR	140.0
+	DR12MAX@SCORE.INTER.POLAR	1.2
+END_SECTION
+
+SECTION GA_SLOPE3
+	TRANSFORM			RbtGATransform
+	PCROSSOVER			0.4	# Prob. of crossover
+	XOVERMUT			TRUE	# Cauchy mutation after each crossover
+	CMUTATE				FALSE	# True = Cauchy; False = Rectang. for regular mutations
+	STEP_SIZE			1.0	# Max torsional mutation
+END_SECTION
+
+SECTION SETSLOPE_5
+	TRANSFORM           		RbtNullTransform
+	WEIGHT@SCORE.INTRA.DIHEDRAL	0.3
+	ECUT@SCORE.INTER.VDW		25.0
+	USE_4_8@SCORE.INTER.VDW		FALSE	# Now switch to a convential 6-12 for final GA, MC, minimisation
+	DA1MAX@SCORE.INTER.POLAR	120.0
+	DA2MAX@SCORE.INTER.POLAR	120.0
+	DR12MAX@SCORE.INTER.POLAR	0.9
+END_SECTION
+
+SECTION GA_SLOPE5
+	TRANSFORM			RbtGATransform
+	PCROSSOVER			0.4	# Prob. of crossover
+	XOVERMUT			TRUE	# Cauchy mutation after each crossover
+	CMUTATE				FALSE	# True = Cauchy; False = Rectang. for regular mutations
+	STEP_SIZE			1.0	# Max torsional mutation
+END_SECTION
+
+SECTION SETSLOPE_10
+	TRANSFORM           		RbtNullTransform
+	WEIGHT@SCORE.INTRA.DIHEDRAL	0.5	# Final dihedral weight matches SF file
+	ECUT@SCORE.INTER.VDW		120.0	# Final ECUT matches SF file
+	DA1MAX@SCORE.INTER.POLAR	80.0
+	DA2MAX@SCORE.INTER.POLAR	100.0
+	DR12MAX@SCORE.INTER.POLAR	0.6
+END_SECTION
+
+SECTION MC_10K
+	TRANSFORM           		RbtSimAnnTransform
+	START_T             		10.0
+	FINAL_T             		10.0
+	NUM_BLOCKS          		5
+	STEP_SIZE          		0.1
+	MIN_ACC_RATE            	0.25
+	PARTITION_DIST          	8.0
+	PARTITION_FREQ          	50
+	HISTORY_FREQ            	0
+END_SECTION
+
+SECTION SIMPLEX
+	TRANSFORM			RbtSimplexTransform
+	MAX_CALLS			200
+	NCYCLES				20
+	STOPPING_STEP_LENGTH		10e-4
+	PARTITION_DIST			8.0
+        STEP_SIZE			1.0
+	CONVERGENCE			0.001
+END_SECTION
+
+SECTION FINAL
+	TRANSFORM           		RbtNullTransform
+	WEIGHT@SCORE.RESTR.CAVITY	1.0	# revert to standard cavity penalty
+END_SECTION
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/scripts/dock_solv_grid.prm	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,96 @@
+RBT_PARAMETER_FILE_V1.00
+TITLE Free docking (with SOLVATION, grid-based VDW)
+
+SECTION SCORE
+    	INTER    RbtSolvGridSF.prm
+    	INTRA    RbtIntraSF.prm
+	SYSTEM   RbtTargetSF.prm
+END_SECTION
+
+SECTION SETSLOPE_1
+	TRANSFORM           		RbtNullTransform
+	WEIGHT@SCORE.RESTR.CAVITY	5.0	# Dock with a high penalty for leaving the cavity
+	WEIGHT@SCORE.INTRA.DIHEDRAL	0.1	# Gradually ramp up dihedral weight from 0.1->0.5
+        ENABLED@SCORE.INTER.VDW1	TRUE	# Enable vdW grid with ECUT=1
+        ENABLED@SCORE.INTER.VDW5       	FALSE	# Disable vdW grid with ECUT=5
+        ENABLED@SCORE.INTER.VDW        	FALSE	# Disable indexed vdW
+END_SECTION
+
+SECTION RANDOM_POP
+        TRANSFORM                       RbtRandPopTransform
+        POP_SIZE                        50
+	SCALE_CHROM_LENGTH		TRUE
+END_SECTION
+
+SECTION GA_SLOPE1
+	TRANSFORM			RbtGATransform
+	PCROSSOVER			0.4	# Prob. of crossover
+	XOVERMUT			TRUE	# Cauchy mutation after each crossover
+	CMUTATE				FALSE	# True = Cauchy; False = Rectang. for regular mutations
+	STEP_SIZE			1.0	# Max translational mutation
+END_SECTION
+
+SECTION SETSLOPE_3
+	TRANSFORM           		RbtNullTransform
+	WEIGHT@SCORE.INTRA.DIHEDRAL	0.2
+        ENABLED@SCORE.INTER.VDW1       	FALSE	# Disable vdW grid with ECUT=1
+        ENABLED@SCORE.INTER.VDW5       	TRUE	# Enable vdW grid with ECUT=5
+END_SECTION
+
+SECTION GA_SLOPE3
+	TRANSFORM			RbtGATransform
+	PCROSSOVER			0.4	# Prob. of crossover
+	XOVERMUT			TRUE	# Cauchy mutation after each crossover
+	CMUTATE				FALSE	# True = Cauchy; False = Rectang. for regular mutations
+	STEP_SIZE			1.0	# Max torsional mutation
+END_SECTION
+
+SECTION SETSLOPE_5
+	TRANSFORM           		RbtNullTransform
+	WEIGHT@SCORE.INTRA.DIHEDRAL	0.3
+        ENABLED@SCORE.INTER.VDW5       	FALSE	# Disable vdW grid with ECUT=5
+        ENABLED@SCORE.INTER.VDW		TRUE	# Enable indexed vdW
+	ECUT@SCORE.INTER.VDW		25.0
+END_SECTION
+
+SECTION GA_SLOPE5
+	TRANSFORM			RbtGATransform
+	PCROSSOVER			0.4	# Prob. of crossover
+	XOVERMUT			TRUE	# Cauchy mutation after each crossover
+	CMUTATE				FALSE	# True = Cauchy; False = Rectang. for regular mutations
+	STEP_SIZE			1.0	# Max torsional mutation
+END_SECTION
+
+SECTION SETSLOPE_10
+	TRANSFORM           		RbtNullTransform
+	WEIGHT@SCORE.INTRA.DIHEDRAL	0.5	# Final dihedral weight matches SF file
+	ECUT@SCORE.INTER.VDW		120.0	# Final ECUT matches SF file
+END_SECTION
+
+SECTION MC_10K
+	TRANSFORM           		RbtSimAnnTransform
+	START_T             		10.0
+	FINAL_T             		10.0
+	NUM_BLOCKS          		5
+	STEP_SIZE          		0.1
+	MIN_ACC_RATE            	0.25
+	PARTITION_DIST          	8.0
+	PARTITION_FREQ          	50
+	HISTORY_FREQ            	0
+END_SECTION
+
+SECTION SIMPLEX
+	TRANSFORM			RbtSimplexTransform
+	MAX_CALLS			200
+	NCYCLES				20
+	STOPPING_STEP_LENGTH		10e-4
+	PARTITION_DIST			8.0
+        STEP_SIZE			1.0
+	CONVERGENCE			0.001
+END_SECTION
+
+SECTION FINAL
+	TRANSFORM           		RbtNullTransform
+	WEIGHT@SCORE.RESTR.CAVITY	1.0	# revert to standard cavity penalty
+END_SECTION
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/scripts/minimise.prm	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,22 @@
+RBT_PARAMETER_FILE_V1.00
+TITLE Simplex minimisation
+
+SECTION SCORE
+	INTER	RbtInterIdxSF.prm
+	INTRA	RbtIntraSF.prm
+	SYSTEM	RbtTargetSF.prm
+END_SECTION
+
+SECTION SIMPLEX
+	TRANSFORM			RbtSimplexTransform
+	MAX_CALLS			200
+	NCYCLES				20
+	STOPPING_STEP_LENGTH		10e-4
+	PARTITION_DIST			8.0
+        STEP_SIZE			1.0
+	CONVERGENCE			0.001
+END_SECTION
+
+SECTION FINAL
+	TRANSFORM			RbtNullTransform
+END_SECTION
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/scripts/minimise_solv.prm	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,22 @@
+RBT_PARAMETER_FILE_V1.00
+TITLE Simplex minimisation (with SOLVATION)
+
+SECTION SCORE
+	INTER	RbtSolvIdxSF.prm
+	INTRA	RbtIntraSF.prm
+	SYSTEM	RbtTargetSF.prm
+END_SECTION
+
+SECTION SIMPLEX
+	TRANSFORM			RbtSimplexTransform
+	MAX_CALLS			200
+	NCYCLES				20
+	STOPPING_STEP_LENGTH		10e-4
+	PARTITION_DIST			8.0
+        STEP_SIZE			1.0
+	CONVERGENCE			0.001
+END_SECTION
+
+SECTION FINAL
+	TRANSFORM			RbtNullTransform
+END_SECTION
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/scripts/score.prm	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,12 @@
+RBT_PARAMETER_FILE_V1.00
+TITLE Score only
+
+SECTION SCORE
+	INTER	RbtInterIdxSF.prm
+	INTRA	RbtIntraSF.prm
+ 	SYSTEM	RbtTargetSF.prm
+END_SECTION
+
+SECTION FINAL
+	TRANSFORM			RbtNullTransform
+END_SECTION
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/scripts/score_pmf.prm	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,12 @@
+RBT_PARAMETER_FILE_V1.00
+TITLE Score only (PMF)
+
+SECTION SCORE
+	INTER	RbtPMFIdxSF.prm
+	INTRA	RbtIntraSF.prm
+ 	TARGET	RbtTargetSF.prm
+END_SECTION
+
+SECTION FINAL
+	TRANSFORM			RbtNullTransform
+END_SECTION
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/scripts/score_solv.prm	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,12 @@
+RBT_PARAMETER_FILE_V1.00
+TITLE Score only (with SOLVATION)
+
+SECTION SCORE
+	INTER	RbtSolvIdxSF.prm
+	INTRA	RbtIntraSF.prm
+ 	SYSTEM	RbtTargetSF.prm
+END_SECTION
+
+SECTION FINAL
+	TRANSFORM			RbtNullTransform
+END_SECTION
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/sf/RbtInterGridSF.prm	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,139 @@
+RBT_PARAMETER_FILE_V1.00
+TITLE Intermolecular scoring function (without SOLVATION, grid-based VDW)
+VERSION $Id: //depot/dev/client3/rdock/2013.1/data/sf/RbtInterGridSF.prm#2 $
+
+################################################################################
+# Constant scoring function
+# Represents loss of translation, rotational entropy of ligand
+SECTION CONST
+	SCORING_FUNCTION	RbtConstSF
+	WEIGHT			+5.4
+END_SECTION
+
+################################################################################
+# Rotational scoring function
+# Represents loss of torsional entropy of ligand
+SECTION ROT
+	SCORING_FUNCTION	RbtRotSF
+	WEIGHT			+1.0
+END_SECTION
+
+################################################################################
+# Pseudo SFs for setting up atomic attributes for polar and lipo atoms
+SECTION SETUP_POLAR
+	SCORING_FUNCTION	RbtSetupPolarSF
+	RADIUS			5.0
+	NORM			25
+	POWER			0.5
+	CHGFACTOR		0.5
+	GUANFACTOR		0.5
+END_SECTION
+
+################################################################################
+# Hydrogen-bond scoring function (also Metal-acceptor, C.cat - acceptor)
+SECTION POLAR
+	SCORING_FUNCTION	RbtPolarIdxSF
+	WEIGHT			3.4
+	R12FACTOR		1.0
+	R12INCR			0.05
+	DR12MIN		 	0.25
+	DR12MAX		 	0.6
+	A1			180.0
+	DA1MIN			30.0
+	DA1MAX			80.0
+	A2			180.0
+	DA2MIN			60.0
+	DA2MAX			100.0
+	INCMETAL		TRUE
+	INCHBD			TRUE
+	INCHBA			TRUE
+	INCGUAN			TRUE
+	GUAN_PLANE		TRUE
+	ABS_DR12		TRUE
+	GRIDSTEP		0.5
+	RANGE			4.41
+	INCR			2.46
+	ATTR			TRUE
+	LP_OSP2			TRUE
+	LP_PHI			45
+	LP_DPHIMIN		15
+	LP_DPHIMAX		30
+	LP_DTHETAMIN		20
+	LP_DTHETAMAX		60
+END_SECTION
+
+################################################################################
+# Repulsive polar scoring function (donor-donor, acceptor-acceptor, metal-donor, C.cat-donor etc)
+SECTION REPUL
+	SCORING_FUNCTION	RbtPolarIdxSF
+	WEIGHT			5.0
+	R12FACTOR		1.0
+	R12INCR			0.6
+	DR12MIN			0.25
+	DR12MAX			1.1
+	A1			180.0
+	DA1MIN			30.0
+	DA1MAX			60.0
+	A2			180.0
+	DA2MIN			30.0
+	DA2MAX			60.0
+	INCMETAL		TRUE
+	INCHBD			TRUE
+	INCHBA			TRUE
+	INCGUAN			TRUE
+	GUAN_PLANE		FALSE
+	ABS_DR12		FALSE
+	GRIDSTEP		0.5
+	RANGE			5.32
+	INCR			3.51
+	ATTR			FALSE
+	LP_OSP2			FALSE
+END_SECTION
+
+################################################################################
+# Aromatic (pi-pi) scoring function, also used for cation-pi
+#SECTION AROM
+#	SCORING_FUNCTION	RbtAromIdxSF
+#	WEIGHT			-1.8
+#	R12 			3.5
+#	DR12MIN		 	0.25
+#	DR12MAX 		0.6
+#	DAMIN			20.0
+#	DAMAX			30.0
+#	GRIDSTEP		0.5
+#	RANGE			4.1
+#	INCR			4.1
+#END_SECTION
+
+################################################################################
+#
+# VDW SCORING FUNCTIONS
+# Two precalculated grids are loaded with different values of ECUT
+# Each is initially disabled
+# We also load an indexed-grid version which is enabled
+#
+SECTION VDW1
+	SCORING_FUNCTION	RbtVdwGridSF
+	WEIGHT			1.0
+        GRID		        _vdw1.grd
+	SMOOTHED		FALSE
+        ENABLED			FALSE
+END_SECTION
+
+SECTION VDW5
+	SCORING_FUNCTION	RbtVdwGridSF
+	WEIGHT			1.0
+        GRID		        _vdw5.grd
+	SMOOTHED		FALSE
+        ENABLED			FALSE
+END_SECTION
+
+SECTION VDW
+	SCORING_FUNCTION	RbtVdwIdxSF
+	WEIGHT			1.0
+	USE_4_8			FALSE
+	USE_TRIPOS		FALSE
+	RMAX			1.5
+	ECUT			120.0
+	E0			1.5
+END_SECTION
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/sf/RbtInterIdxSF.prm	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,126 @@
+RBT_PARAMETER_FILE_V1.00
+TITLE Intermolecular scoring function (without SOLVATION, indexed VDW)
+VERSION $Id: //depot/dev/client3/rdock/2013.1/data/sf/RbtInterIdxSF.prm#3 $
+
+################################################################################
+# Constant scoring function
+# Represents loss of translation, rotational entropy of ligand
+# DM 14 June 2006 - also calculates solvent penalty for all enabled solvent
+# SOLVENT_PENALTY is defined as a fraction of the ligand binding penalty
+# i.e. ligand binding penalty = 1.0 * WEIGHT
+# solvent binding penalty = N(enabled solvent) * SOLVENT_PENALTY * WEIGHT
+# 0.37 * 5.4 = 2.0 kJ/mol, which corresponds to GOLD Chemscore penalty
+# Verdonk et al, J. Med. Chem. 2005 (48) 6504-6515
+SECTION CONST
+	SCORING_FUNCTION	RbtConstSF
+	SOLVENT_PENALTY		0.37
+	WEIGHT			+5.4
+END_SECTION
+
+################################################################################
+# Rotational scoring function
+# Represents loss of torsional entropy of ligand
+SECTION ROT
+	SCORING_FUNCTION	RbtRotSF
+	WEIGHT			+1.0
+END_SECTION
+
+################################################################################
+# Pseudo SFs for setting up atomic attributes for polar and lipo atoms
+SECTION SETUP_POLAR
+	SCORING_FUNCTION	RbtSetupPolarSF
+	RADIUS			5.0
+	NORM			25
+	POWER			0.5
+	CHGFACTOR		0.5
+	GUANFACTOR		0.5
+END_SECTION
+
+################################################################################
+# Hydrogen-bond scoring function (also Metal-acceptor, C.cat - acceptor)
+SECTION POLAR
+	SCORING_FUNCTION	RbtPolarIdxSF
+	WEIGHT			3.4
+	R12FACTOR		1.0
+	R12INCR			0.05
+	DR12MIN		 	0.25
+	DR12MAX		 	0.6
+	A1			180.0
+	DA1MIN			30.0
+	DA1MAX			80.0
+	A2			180.0
+	DA2MIN			60.0
+	DA2MAX			100.0
+	INCMETAL		TRUE
+	INCHBD			TRUE
+	INCHBA			TRUE
+	INCGUAN			TRUE
+	GUAN_PLANE		TRUE
+	ABS_DR12		TRUE
+	GRIDSTEP		0.5
+	RANGE			5.31
+	INCR			3.36
+	ATTR			TRUE
+	LP_OSP2			TRUE
+	LP_PHI			45
+	LP_DPHIMIN		15
+	LP_DPHIMAX		30
+	LP_DTHETAMIN		20
+	LP_DTHETAMAX		60
+END_SECTION
+
+################################################################################
+# Repulsive polar scoring function (donor-donor, acceptor-acceptor, metal-donor, C.cat-donor etc)
+SECTION REPUL
+	SCORING_FUNCTION	RbtPolarIdxSF
+	WEIGHT			5.0
+	R12FACTOR		1.0
+	R12INCR			0.6
+	DR12MIN			0.25
+	DR12MAX			1.1
+	A1			180.0
+	DA1MIN			30.0
+	DA1MAX			60.0
+	A2			180.0
+	DA2MIN			30.0
+	DA2MAX			60.0
+	INCMETAL		TRUE
+	INCHBD			TRUE
+	INCHBA			TRUE
+	INCGUAN			TRUE
+	GUAN_PLANE		FALSE
+	ABS_DR12		FALSE
+	GRIDSTEP		0.5
+	RANGE			5.32
+	INCR			3.51
+	ATTR			FALSE
+	LP_OSP2			FALSE
+END_SECTION
+
+################################################################################
+# Aromatic (pi-pi) scoring function, also used for cation-pi
+#SECTION AROM
+#	SCORING_FUNCTION	RbtAromIdxSF
+#	WEIGHT			-1.8
+#	R12 			3.5
+#	DR12MIN		 	0.25
+#	DR12MAX 		0.6
+#	DAMIN			20.0
+#	DAMAX			30.0
+#	GRIDSTEP		0.5
+#	RANGE			4.1
+#	INCR			4.1
+#END_SECTION
+
+################################################################################
+# Van der Waals scoring function
+SECTION VDW
+	SCORING_FUNCTION	RbtVdwIdxSF
+	WEIGHT			1.0
+	USE_4_8			FALSE
+	USE_TRIPOS		FALSE
+	RMAX			1.5
+	ECUT			120.0
+	E0			1.5
+	FAST_SOLVENT		TRUE
+END_SECTION
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/sf/RbtIntraSF.prm	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,73 @@
+RBT_PARAMETER_FILE_V1.00
+TITLE Intra-ligand scoring function
+VERSION $Id: //depot/dev/client3/rdock/2013.1/data/sf/RbtIntraSF.prm#2 $
+
+SECTION VDW
+	SCORING_FUNCTION	RbtVdwIntraSF
+	WEIGHT			1.0
+	USE_4_8			FALSE
+	USE_TRIPOS		TRUE
+	RMAX			1.5
+	ECUT			120
+	E0			1.5
+END_SECTION
+
+SECTION POLAR
+	SCORING_FUNCTION	RbtPolarIntraSF
+	WEIGHT			3.4
+	R12FACTOR		1.0
+	R12INCR			0.05
+	DR12MIN		 	0.25
+	DR12MAX		 	0.6
+	A1			180.0
+	DA1MIN			30.0
+	DA1MAX			80.0
+	A2			180.0
+	DA2MIN			60.0
+	DA2MAX			100.0
+	INCMETAL		TRUE
+	INCHBD			TRUE
+	INCHBA			TRUE
+	INCGUAN			TRUE
+	GUAN_PLANE		TRUE
+	ABS_DR12		TRUE
+	RANGE			4.41
+	ATTR			TRUE
+	TRACE			0
+	LP_OSP2			TRUE
+	LP_PHI			45
+	LP_DPHIMIN		15
+	LP_DPHIMAX		30
+	LP_DTHETAMIN		20
+	LP_DTHETAMAX		60
+END_SECTION
+
+SECTION REPUL
+	SCORING_FUNCTION	RbtPolarIntraSF
+	WEIGHT			5.0
+	R12FACTOR		1.0
+	R12INCR			0.6
+	DR12MIN			0.25
+	DR12MAX			1.1
+	A1			180.0
+	DA1MIN			30.0
+	DA1MAX			60.0
+	A2			180.0
+	DA2MIN			30.0
+	DA2MAX			60.0
+	INCMETAL		TRUE
+	INCHBD			TRUE
+	INCHBA			TRUE
+	INCGUAN			TRUE
+	GUAN_PLANE		FALSE
+	ABS_DR12		FALSE
+	RANGE			5.32
+	ATTR			FALSE
+	LP_OSP2			FALSE
+END_SECTION
+
+SECTION DIHEDRAL
+	SCORING_FUNCTION	RbtDihedralIntraSF
+	WEIGHT			0.5
+	IMPL_H_CORR		TRUE
+END_SECTION
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/sf/RbtIonicAtoms.prm	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,197 @@
+RBT_PARAMETER_FILE_V1.00
+TITLE Receptor ionic atom definitions
+VERSION $Id: //depot/dev/client3/rdock/2013.1/data/sf/RbtIonicAtoms.prm#2 $
+################################################################################
+#
+# Revision history:
+#
+# 21 Nov 2001 (DM) Added Heme Fe entries
+# 19 Oct 2001 (DM) Extended list of metal ions
+# 13 Jun 2000 (DM) Branched from RbtRNAScoringFunction.prm
+#                  New format for ionic atoms (separate section for each residue)
+#
+################################################################################
+# Formal charges for RNA atoms
+#
+# A/ADE
+#
+SECTION A
+	O1P		-0.5
+	O2P		-0.5
+END_SECTION
+
+SECTION ADE
+	O1P		-0.5
+	O2P		-0.5
+END_SECTION
+#
+# C/CYT
+#
+SECTION C
+	O1P		-0.5
+	O2P		-0.5
+END_SECTION
+
+SECTION CYT
+	O1P		-0.5
+	O2P		-0.5
+END_SECTION
+#
+# G/GUA
+#
+SECTION G
+	O1P		-0.5
+	O2P		-0.5
+END_SECTION
+
+SECTION GUA
+	O1P		-0.5
+	O2P		-0.5
+END_SECTION
+#
+# U/URA
+#
+SECTION U
+	O1P		-0.5
+	O2P		-0.5
+END_SECTION
+
+SECTION URA
+	O1P		-0.5
+	O2P		-0.5
+END_SECTION
+
+#################################################################################
+# Formal charges for amino acids
+#
+# LYS+
+#
+SECTION LYS
+	HZ1		+0.333
+	HZ2		+0.333
+	HZ3		+0.333
+END_SECTION
+#
+# ARG+
+#
+SECTION ARG
+	HE		+0.167
+	HH11		+0.167
+	HH12		+0.167
+	HH21		+0.167
+	HH22		+0.167
+	CZ		+0.167
+END_SECTION
+#
+# HSP+
+#
+SECTION HSP
+	HD1		+0.333
+	HE2		+0.333
+	CE1		+0.333
+END_SECTION
+
+SECTION HIS
+	MANDATORY	HD1,HE2
+	HD1             +0.333
+        HE2             +0.333
+        CE1             +0.333
+END_SECTION
+#
+# ASP-
+#
+SECTION ASP
+	FORBIDDEN	HD1,HD2
+	OD1		-0.5
+	OD2		-0.5
+END_SECTION
+#
+# GLU-
+#
+SECTION GLU
+	FORBIDDEN	HE1,HE2
+	OE1		-0.5
+	OE2		-0.5
+END_SECTION
+
+#################################################################################
+# Formal charges for metal cations
+#
+SECTION NA
+	NA		+1.0
+END_SECTION
+
+SECTION MG
+	MG		+1.0
+END_SECTION
+
+SECTION K
+	K		+1.0
+END_SECTION
+
+SECTION CA
+	CA		+1.0
+END_SECTION
+
+SECTION V
+	V		+1.0
+END_SECTION
+
+SECTION MN
+	MN		+1.0
+END_SECTION
+
+SECTION FE
+	FE		+1.0
+END_SECTION
+
+# Specific entries for GOLD PDB test set
+SECTION FS4
+	FE1		+1.0
+	FE2		+1.0
+	FE3		+1.0
+	FE4		+1.0
+END_SECTION
+
+SECTION HEM
+	FE		+1.0
+END_SECTION
+
+SECTION NI
+	NI		+1.0
+END_SECTION
+
+SECTION ZN
+	ZN		+1.0
+END_SECTION
+
+# Specific entries for ASTEX MOL2 test set
+SECTION HG
+	HG		+1.0
+END_SECTION
+
+SECTION CD
+	CD		+1.0
+END_SECTION
+
+SECTION FS
+	FE1		+1.0
+	FE2		+1.0
+	FE3		+1.0
+	FE4		+1.0
+END_SECTION
+
+SECTION CO
+	CO		+1.0
+END_SECTION
+
+#These metals occur in undefined residues
+SECTION UNK
+	MG		+1.0
+	MN		+1.0
+	ZN		+1.0
+	FE1		+1.0
+	FE2             +1.0
+	FE3             +1.0
+	FE4             +1.0
+END_SECTION
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/sf/RbtPMFIdxSF.prm	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,46 @@
+RBT_PARAMETER_FILE_V1.00
+TITLE Protein-ligand PMF (indexed version)
+VERSION $Id: //depot/dev/client3/rdock/2013.1/data/sf/RbtPMFIdxSF.prm#2 $
+################################################################################
+#
+# Revision history:
+#
+# References:
+#
+################################################################################
+# Constant scoring function
+# Represents loss of translation, rotational entropy of ligand
+SECTION CONST
+	SCORING_FUNCTION	RbtConstSF
+	WEIGHT			+5.4	# Free-energy weighting
+END_SECTION
+
+################################################################################
+# Rotational scoring function
+# Represents loss of torsional entropy of ligand
+SECTION ROT
+	SCORING_FUNCTION	RbtRotSF
+	WEIGHT			+1.0	# Free-energy weighting
+END_SECTION
+
+################################################################################
+# Setup PMF atom types
+SECTION SETUP_PMF
+    	SCORING_FUNCTION    	RbtSetupPMFSF
+END_SECTION
+
+################################################################################
+# Intermolecular PMF
+SECTION PMF
+        SCORING_FUNCTION        RbtPMFIdxSF
+        SLOPE                   -3.0		# slope of the repulsive short-range linear term
+        CC_CUTOFF                6.0		# count only shorter C_receptor - C_ligand interactions
+        WEIGHT                   1.0
+        GRIDSTEP                 1.0		# indexed grid distance (need not be dense)
+        BORDER                   1.0		#
+        PMFDIR                   data/pmf	# ${RBT_ROOT/}data/pmf where the .pmfs are
+END_SECTION
+###############################################################################
+#        OVERALL_CUTOFF           9.0		# value of overall cutoff (similar to C cutoff but for all types)
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/sf/RbtSolvGridSF.prm	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,104 @@
+RBT_PARAMETER_FILE_V1.00
+TITLE Intermolecular scoring function (with SOLVATION, grid-based VDW)
+VERSION $Id: //depot/dev/client3/rdock/2013.1/data/sf/RbtSolvGridSF.prm#3 $
+
+################################################################################
+# Constant scoring function
+# Represents loss of translation, rotational entropy of ligand
+SECTION CONST
+	SCORING_FUNCTION	RbtConstSF
+	WEIGHT			+5.4
+END_SECTION
+
+################################################################################
+# Rotational scoring function
+# Represents loss of torsional entropy of ligand
+SECTION ROT
+	SCORING_FUNCTION	RbtRotSF
+	WEIGHT			+1.0
+END_SECTION
+
+################################################################################
+# Pseudo SFs for setting up atomic attributes for polar and lipo atoms
+SECTION SETUP_POLAR
+	SCORING_FUNCTION	RbtSetupPolarSF
+	RADIUS			5.0
+	NORM			25
+	POWER			0.5
+	CHGFACTOR		0.5
+	GUANFACTOR		0.5
+END_SECTION
+
+################################################################################
+# Hydrogen-bond scoring function (also Metal-acceptor, C.cat - acceptor)
+SECTION POLAR
+	SCORING_FUNCTION	RbtPolarIdxSF
+	WEIGHT			5.0
+	R12FACTOR		1.0
+	R12INCR			0.05
+	DR12MIN		 	0.25
+	DR12MAX		 	0.6
+	A1			180.0
+	DA1MIN			30.0
+	DA1MAX			80.0
+	A2			180.0
+	DA2MIN			60.0
+	DA2MAX			100.0
+	INCMETAL		TRUE
+	INCHBD			TRUE
+	INCHBA			TRUE
+	INCGUAN			TRUE
+	GUAN_PLANE		TRUE
+	ABS_DR12		TRUE
+	GRIDSTEP		0.5
+	RANGE			4.41
+	INCR			2.46
+	ATTR			TRUE
+	LP_OSP2			TRUE
+	LP_PHI			45
+	LP_DPHIMIN		15
+	LP_DPHIMAX		30
+	LP_DTHETAMIN		20
+	LP_DTHETAMAX		60
+END_SECTION
+
+################################################################################
+#
+# VDW SCORING FUNCTIONS
+# Two precalculated grids are loaded with different values of ECUT
+# Each is initially disabled
+# We also load an indexed-grid version which is enabled
+#
+SECTION VDW1
+	SCORING_FUNCTION	RbtVdwGridSF
+	WEIGHT			1.5
+        GRID		        _vdw1.grd
+	SMOOTHED		FALSE
+        ENABLED			FALSE
+END_SECTION
+
+SECTION VDW5
+	SCORING_FUNCTION	RbtVdwGridSF
+	WEIGHT			1.5
+        GRID		        _vdw5.grd
+	SMOOTHED		FALSE
+        ENABLED			FALSE
+END_SECTION
+
+SECTION VDW
+	SCORING_FUNCTION	RbtVdwIdxSF
+	WEIGHT			1.5
+	USE_4_8			FALSE
+	USE_TRIPOS		FALSE
+	RMAX			1.5
+	ECUT			120.0
+	E0			1.5
+END_SECTION
+
+################################################################################
+# Desolvation scoring function
+SECTION SOLV
+        SCORING_FUNCTION        RbtSAIdxSF
+	WEIGHT			0.5
+	GRIDSTEP		0.5
+END_SECTION
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/sf/RbtSolvIdxSF.prm	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,90 @@
+RBT_PARAMETER_FILE_V1.00
+TITLE Intermolecular scoring function (with SOLVATION, indexed VDW)
+VERSION $Id: //depot/dev/client3/rdock/2013.1/data/sf/RbtSolvIdxSF.prm#3 $
+
+################################################################################
+# Constant scoring function
+# Represents loss of translation, rotational entropy of ligand
+# DM 14 June 2006 - also calculates solvent penalty for all enabled solvent
+# SOLVENT_PENALTY is defined as a fraction of the ligand binding penalty
+# i.e. ligand binding penalty = 1.0 * WEIGHT
+# solvent binding penalty = N(enabled solvent) * SOLVENT_PENALTY * WEIGHT
+# 0.37 * 5.4 = 2.0 kJ/mol, which corresponds to GOLD Chemscore penalty
+# Verdonk et al, J. Med. Chem. 2005 (48) 6504-6515
+SECTION CONST
+        SCORING_FUNCTION        RbtConstSF
+        SOLVENT_PENALTY         0.37
+        WEIGHT                  +5.4
+END_SECTION
+
+################################################################################
+# Rotational scoring function
+# Represents loss of torsional entropy of ligand
+SECTION ROT
+	SCORING_FUNCTION	RbtRotSF
+	WEIGHT			+1.0
+END_SECTION
+
+################################################################################
+# Pseudo SFs for setting up atomic attributes for polar and lipo atoms
+SECTION SETUP_POLAR
+	SCORING_FUNCTION	RbtSetupPolarSF
+	RADIUS			5.0
+	NORM			25
+	POWER			0.5
+	CHGFACTOR		0.5
+	GUANFACTOR		0.5
+END_SECTION
+
+################################################################################
+# Hydrogen-bond scoring function (also Metal-acceptor, C.cat - acceptor)
+SECTION POLAR
+	SCORING_FUNCTION	RbtPolarIdxSF
+	WEIGHT			5.0
+	R12FACTOR		1.0
+	R12INCR			0.05
+	DR12MIN		 	0.25
+	DR12MAX		 	0.6
+	A1			180.0
+	DA1MIN			30.0
+	DA1MAX			80.0
+	A2			180.0
+	DA2MIN			60.0
+	DA2MAX			100.0
+	INCMETAL		TRUE
+	INCHBD			TRUE
+	INCHBA			TRUE
+	INCGUAN			TRUE
+	GUAN_PLANE		TRUE
+	ABS_DR12		TRUE
+	GRIDSTEP		0.5
+	RANGE			5.31
+	INCR			3.36
+	ATTR			TRUE
+	LP_OSP2			TRUE
+	LP_PHI			45
+	LP_DPHIMIN		15
+	LP_DPHIMAX		30
+	LP_DTHETAMIN		20
+	LP_DTHETAMAX		60
+END_SECTION
+
+################################################################################
+# Van der Waals scoring function
+SECTION VDW
+	SCORING_FUNCTION	RbtVdwIdxSF
+	WEIGHT			1.5
+	USE_4_8			FALSE
+	USE_TRIPOS		FALSE
+	RMAX			1.5
+	ECUT			120.0
+	E0			1.5
+END_SECTION
+
+################################################################################
+# Desolvation scoring function
+SECTION SOLV
+        SCORING_FUNCTION        RbtSAIdxSF
+	WEIGHT			0.5
+	GRIDSTEP		0.5
+END_SECTION
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/sf/RbtTargetSF.prm	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,9 @@
+RBT_PARAMETER_FILE_V1.00
+TITLE Intra-target scoring function
+VERSION $Id: //depot/dev/client3/rdock/2013.1/data/sf/RbtTargetSF.prm#2 $
+
+SECTION DIHEDRAL
+	SCORING_FUNCTION	RbtDihedralTargetSF
+	WEIGHT			0.5
+	IMPL_H_CORR		TRUE
+END_SECTION
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/sf/Tripos52_dihedrals.prm	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,247 @@
+RBT_PARAMETER_FILE_V1.00
+TITLE Dihedral parameters from Tripos 5.2 forcefield
+VERSION $Id: //depot/dev/client3/rdock/2013.1/data/sf/Tripos52_dihedrals.prm#2 $
+################################################################################
+#
+# Revision history:
+#
+# 05 Dec 2003 (DM) Added extra params by analogy, and from COSMIC(90)!
+#                  to cover all GOLD/FLEXX/NA ligands (except sulphonamide params)
+# 09 May 2002 (DM) Initial version from J Comp Chem, 10 (1989) 982-1012
+################################################################################
+#
+DEFAULT			0.200,+3
+
+SECTION C.1_C.1
+	*_*		0.000,+1
+END_SECTION
+
+SECTION C.1_C.2
+	*_*		0.000,+1
+END_SECTION
+
+SECTION C.2_C.2
+	*_*		1.424,-2
+END_SECTION
+
+SECTION C.1_C.3
+	*_*		0.000,+1
+END_SECTION
+
+SECTION C.2_C.3
+	*_*		0.120,-3
+	*_C.2		0.126,+3
+	*_C.3		0.126,+3
+	*_H		0.274,+3
+	O.2_C.3		0.700,-3
+	C.2_C.2		0.126,-3
+	C.2_H		0.273,-3
+	C.3_C.2		0.126,+3
+	C.3_C.3		0.126,+3
+	C.3_H		0.274,+3
+	H_C.2		0.274,+3
+	H_C.3		0.274,+3
+	H_H		0.274,+3
+	C.2_*		0.126,-3
+	H_*		0.274,+3
+	C.2_C.3		0.126,-3
+END_SECTION
+
+SECTION C.3_C.3
+	*_*		0.200,+3
+	C.2_C.2		0.040,+3
+	C.2_C.3		0.126,+3
+	C.3_C.2		0.126,+3
+	C.3_C.3		0.500,+3
+	*_H		0.320,+3
+	H_*		0.320,+3
+END_SECTION
+
+SECTION C.1_C.ar
+	*_*		0.000,+1
+END_SECTION
+
+SECTION C.2_C.ar
+	*_*		1.600,-2
+END_SECTION
+
+SECTION C.cat_C.ar
+	*_*		1.600,-2
+END_SECTION
+
+SECTION C.3_C.ar
+	*_*		0.120,-3
+END_SECTION
+
+SECTION C.ar_C.ar
+	*_*		0.600,-2
+END_SECTION
+
+SECTION C.1_N.2
+	*_*		0.000,+1
+END_SECTION
+
+SECTION C.2_N.2
+	*_*		12.00,-2
+END_SECTION
+
+SECTION C.3_N.2
+	*_*		0.400,-3
+END_SECTION
+
+SECTION C.ar_N.2
+	*_*		1.600,-2
+END_SECTION
+
+SECTION N.2_N.2
+	*_*		1.600,-2
+END_SECTION
+
+SECTION C.2_N.3
+	*_*		0.120,-3
+END_SECTION
+
+SECTION C.3_N.3
+	*_*		0.200,+3
+END_SECTION
+
+SECTION C.3_N.4
+	*_*		0.200,+3
+END_SECTION
+
+SECTION C.ar_N.3
+	*_*		0.120,-3
+END_SECTION
+
+SECTION C.ar_N.4
+	*_*		0.120,-3
+END_SECTION
+
+SECTION N.3_N.3
+	*_*		0.200,+3
+END_SECTION
+
+SECTION C.2_N.am
+	*_*		6.460,-2
+END_SECTION
+
+SECTION C.3_N.am
+	*_*		0.200,+3
+END_SECTION
+
+SECTION C.ar_N.am
+	*_*		1.600,-2
+END_SECTION
+
+SECTION N.2_N.am
+	*_*		1.600,-2
+END_SECTION
+
+SECTION N.3_N.am
+	*_*		0.120,-3
+END_SECTION
+
+SECTION N.4_N.am
+	*_*		0.120,-3
+END_SECTION
+
+SECTION N.am_N.am
+	*_*		1.600,-2
+END_SECTION
+
+SECTION C.2_N.pl3
+	*_*		12.00,-2
+END_SECTION
+
+SECTION C.3_N.pl3
+	*_*		0.400,-3
+END_SECTION
+
+SECTION C.ar_N.pl3
+	*_*		1.600,-2
+END_SECTION
+
+SECTION N.2_N.pl3
+	*_*		1.600,-2
+END_SECTION
+
+SECTION N.pl3_N.pl3
+	*_*		1.600,-2
+END_SECTION
+
+SECTION C.2_O.3
+	*_*		5.800,-2
+END_SECTION
+
+SECTION C.3_O.3
+	*_*		1.200,+3
+END_SECTION
+
+SECTION C.ar_O.3
+	*_*		1.200,-2
+END_SECTION
+
+SECTION N.2_O.3
+	*_*		1.000,+2
+END_SECTION
+
+SECTION N.3_O.3
+	*_*		0.200,+3
+END_SECTION
+
+SECTION N.am_O.3
+	*_*		1.000,-2
+END_SECTION
+
+SECTION N.pl3_O.3
+	*_*		1.000,-2
+END_SECTION
+
+SECTION C.2_P.3
+	*_*		1.000,-2
+END_SECTION
+
+SECTION C.3_P.3
+	*_*		0.400,+3
+END_SECTION
+
+SECTION C.ar_P.3
+	*_*		1.000,+3
+END_SECTION
+
+SECTION O.3_P.3
+	*_*		0.400,+3
+END_SECTION
+
+SECTION C.2_S.2
+	*_*		1.000,-2
+END_SECTION
+
+SECTION C.3_S.2
+	*_*		0.400,+3
+END_SECTION
+
+SECTION C.ar_S.2
+	*_*		1.000,+3
+END_SECTION
+
+SECTION N.3_S.2
+	*_*		0.400,+3
+END_SECTION
+
+SECTION C.2_S.3
+	*_*		1.000,-2
+END_SECTION
+
+SECTION C.3_S.3
+	*_*		0.400,+3
+END_SECTION
+
+SECTION C.ar_S.3
+	*_*		1.000,+3
+END_SECTION
+
+SECTION S.3_S.3
+	*_*		4.000,+3
+END_SECTION
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/sf/Tripos52_vdw.prm	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,324 @@
+RBT_PARAMETER_FILE_V1.00
+TITLE vdW parameters from Tripos 5.2 forcefield and GOLD paper
+VERSION $Id: //depot/dev/client3/rdock/2013.1/data/sf/Tripos52_vdw.prm#2 $
+################################################################################
+#
+# Revision history:
+#
+# 15 May 2002 (DM) Added extended types (carbons with implicit Hs,
+#                  plus polar H)
+# 13 May 2002 (DM) Initial version from J Comp Chem, 10 (1989) 982-1012
+#                  and J Mol Biol, 267 (1997) 727-748
+################################################################################
+#
+# Hydrogen
+#
+SECTION H
+	R	1.500
+	K	0.042
+	IP	13.60
+	POL	 4.00
+END_SECTION
+
+SECTION H.P
+	R	1.200
+	K	0.042
+	IP	13.60
+	POL	 4.00
+	isHBD	TRUE
+END_SECTION
+#
+# Carbon
+#
+SECTION C.cat
+	R	1.700
+	K	0.107
+	IP	15.62
+	POL	13.80
+END_SECTION
+
+SECTION C.3
+	R	1.700
+	K	0.107
+	IP	14.61
+	POL	13.80
+END_SECTION
+#
+# Increment R by 0.1 for each implicit hydrogen
+# Need to adjust POL to maintain same well depth
+# Leave K untouched for now
+
+
+SECTION C.3.H1
+	R	1.800
+	K	0.107
+	IP	14.61
+	POL	16.38
+END_SECTION
+
+SECTION C.3.H2
+	R	1.900
+	K	0.107
+	IP	14.61
+	POL	19.27
+END_SECTION
+
+SECTION C.3.H3
+	R	2.000
+	K	0.107
+	IP	14.61
+	POL	22.47
+END_SECTION
+
+SECTION C.2
+	R	1.700
+	K	0.107
+	IP	15.62
+	POL	13.80
+END_SECTION
+
+SECTION C.2.H1
+	R	1.800
+	K	0.107
+	IP	15.62
+	POL	16.38
+END_SECTION
+
+SECTION C.2.H2
+	R	1.900
+	K	0.107
+	IP	15.62
+	POL	19.27
+END_SECTION
+
+SECTION C.ar
+	R	1.700
+	K	0.107
+	IP	15.62
+	POL	13.80
+END_SECTION
+
+SECTION C.ar.H1
+	R	1.800
+	K	0.107
+	IP	15.62
+	POL	16.38
+END_SECTION
+
+SECTION C.1
+	R	1.700
+	K	0.107
+	IP	17.47
+	POL	13.80
+END_SECTION
+
+SECTION C.1.H1
+	R	1.800
+	K	0.107
+	IP	17.47
+	POL	16.38
+END_SECTION
+#
+# Nitrogen
+#
+SECTION N.4
+	R	1.550
+	K	0.095
+	IP	33.29
+	POL	 8.40
+END_SECTION
+
+SECTION N.3
+	R	1.550
+	K	0.095
+	IP	18.93
+	POL	 8.40
+	isHBA	TRUE
+END_SECTION
+
+SECTION N.pl3
+	R	1.550
+	K	0.095
+	IP	19.72
+	POL	 8.40
+END_SECTION
+
+SECTION N.am
+	R	1.550
+	K	0.095
+	IP	19.72
+	POL	 8.40
+END_SECTION
+
+SECTION N.2
+	R	1.550
+	K	0.095
+	IP	22.10
+	POL	 8.40
+	isHBA	TRUE
+END_SECTION
+
+SECTION N.ar
+	R	1.550
+	K	0.095
+	IP	22.10
+	POL	 8.40
+	isHBA	TRUE
+END_SECTION
+
+SECTION N.1
+	R	1.550
+	K	0.095
+	IP	23.91
+	POL	 8.40
+	isHBA	TRUE
+END_SECTION
+#
+# Oxygen
+#
+SECTION O.co2
+	R	1.520
+	K	0.116
+	IP	35.12
+	POL	5.4
+	isHBA	TRUE
+END_SECTION
+
+SECTION O.3
+	R	1.520
+	K	0.116
+	IP	24.39
+	POL	 5.40
+	isHBA	TRUE
+END_SECTION
+
+SECTION O.2
+	R	1.520
+	K	0.116
+	IP	26.65
+	POL	 5.40
+	isHBA	TRUE
+END_SECTION
+#
+# Sulphur
+#
+SECTION S.3
+	R	1.800
+	K	0.314
+	IP	15.50
+	POL	29.40
+END_SECTION
+
+SECTION S.o
+	R	1.700
+	K	0.314
+	IP	15.50
+	POL	29.40
+END_SECTION
+
+SECTION S.o2
+	R	1.700
+	K	0.314
+	IP	15.50
+	POL	29.40
+END_SECTION
+
+SECTION S.2
+	R	1.800
+	K	0.314
+	IP	17.78
+	POL	29.40
+END_SECTION
+#
+# Phosphorous
+#
+SECTION P.3
+	R	1.800
+	K	0.314
+	IP	16.78
+	POL	40.6
+END_SECTION
+#
+# Halides
+#
+SECTION F
+	R	1.470
+	K	0.109
+	IP	20.86
+	POL	 3.70
+END_SECTION
+
+SECTION Cl
+	R	1.750
+	K	0.314
+	IP	15.03
+	POL	21.80
+END_SECTION
+
+SECTION Br
+	R	1.850
+	K	0.434
+	IP	13.10
+	POL	31.20
+END_SECTION
+
+SECTION I
+	R	1.980
+	K	0.623
+	IP	12.67
+	POL	49.00
+END_SECTION
+#
+# Metals
+#
+SECTION Na
+	R	1.200
+	K	0.400
+END_SECTION
+
+SECTION K
+	R	1.200
+	K	0.400
+END_SECTION
+
+SECTION Ca
+	R	1.200
+	K	0.600
+END_SECTION
+
+SECTION Mg
+	R	1.200
+	K	0.600
+END_SECTION
+
+SECTION Li
+	R	1.200
+	K	0.400
+END_SECTION
+
+SECTION Al
+	R	1.200
+	K	0.042
+END_SECTION
+
+SECTION Si
+	R	1.200
+	K	0.042
+END_SECTION
+#
+# Undefined types
+#
+SECTION UNDEFINED
+	R	1.200
+	K	0.600
+END_SECTION
+
+SECTION Du
+	R	1.200
+	K	0.042
+END_SECTION
+
+SECTION LP
+	R	1.200
+	K	0.042
+END_SECTION
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/sf/Tripos52_vdw.prm.old	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,319 @@
+RBT_PARAMETER_FILE_V1.00
+TITLE vdW parameters from Tripos 5.2 forcefield and GOLD paper
+VERSION $Id: //depot/dev/client3/rdock/2013.1/data/sf/Tripos52_vdw.prm#2 $
+################################################################################
+#
+# Revision history:
+#
+# 15 May 2002 (DM) Added extended types (carbons with implicit Hs,
+#                  plus polar H)
+# 13 May 2002 (DM) Initial version from J Comp Chem, 10 (1989) 982-1012
+#                  and J Mol Biol, 267 (1997) 727-748
+################################################################################
+#
+# Hydrogen
+#
+SECTION H
+	R	1.500
+	K	0.042
+	IP	13.60
+	POL	 4.00
+END_SECTION
+
+SECTION H.P
+	R	1.200
+	K	0.042
+	IP	13.60
+	POL	 4.00
+	isHBD	TRUE
+END_SECTION
+#
+# Carbon
+#
+SECTION C.cat
+	R	1.700
+	K	0.107
+	IP	15.62
+	POL	13.80
+END_SECTION
+
+SECTION C.3
+	R	1.700
+	K	0.107
+	IP	14.61
+	POL	13.80
+END_SECTION
+#
+# Increment R by 0.1 for each implicit hydrogen
+# Need to adjust POL to maintain same well depth
+# Leave K untouched for now
+
+
+SECTION C.3.H1
+	R	1.800
+	K	0.107
+	IP	14.61
+	POL	16.38
+END_SECTION
+
+SECTION C.3.H2
+	R	1.900
+	K	0.107
+	IP	14.61
+	POL	19.27
+END_SECTION
+
+SECTION C.3.H3
+	R	2.000
+	K	0.107
+	IP	14.61
+	POL	22.47
+END_SECTION
+
+SECTION C.2
+	R	1.700
+	K	0.107
+	IP	15.62
+	POL	13.80
+END_SECTION
+
+SECTION C.2.H1
+	R	1.800
+	K	0.107
+	IP	15.62
+	POL	16.38
+END_SECTION
+
+SECTION C.2.H2
+	R	1.900
+	K	0.107
+	IP	15.62
+	POL	19.27
+END_SECTION
+
+SECTION C.ar
+	R	1.700
+	K	0.107
+	IP	15.62
+	POL	13.80
+END_SECTION
+
+SECTION C.ar.H1
+	R	1.800
+	K	0.107
+	IP	15.62
+	POL	16.38
+END_SECTION
+
+SECTION C.1
+	R	1.700
+	K	0.107
+	IP	17.47
+	POL	13.80
+END_SECTION
+
+SECTION C.1.H1
+	R	1.800
+	K	0.107
+	IP	17.47
+	POL	16.38
+END_SECTION
+#
+# Nitrogen
+#
+SECTION N.4
+	R	1.550
+	K	0.095
+	IP	33.29
+	POL	 8.40
+END_SECTION
+
+SECTION N.3
+	R	1.550
+	K	0.095
+	IP	18.93
+	POL	 8.40
+	isHBA	TRUE
+END_SECTION
+
+SECTION N.pl3
+	R	1.550
+	K	0.095
+	IP	19.72
+	POL	 8.40
+END_SECTION
+
+SECTION N.am
+	R	1.550
+	K	0.095
+	IP	19.72
+	POL	 8.40
+END_SECTION
+
+SECTION N.2
+	R	1.550
+	K	0.095
+	IP	22.10
+	POL	 8.40
+	isHBA	TRUE
+END_SECTION
+
+SECTION N.ar
+	R	1.550
+	K	0.095
+	IP	22.10
+	POL	 8.40
+	isHBA	TRUE
+END_SECTION
+
+SECTION N.1
+	R	1.550
+	K	0.095
+	IP	23.91
+	POL	 8.40
+	isHBA	TRUE
+END_SECTION
+#
+# Oxygen
+#
+SECTION O.co2
+	R	1.520
+	K	0.116
+	IP	35.12
+	POL	5.4
+	isHBA	TRUE
+END_SECTION
+
+SECTION O.3
+	R	1.520
+	K	0.116
+	IP	24.39
+	POL	 5.40
+	isHBA	TRUE
+END_SECTION
+
+SECTION O.2
+	R	1.520
+	K	0.116
+	IP	26.65
+	POL	 5.40
+	isHBA	TRUE
+END_SECTION
+#
+# Sulphur
+#
+SECTION S.3
+	R	1.800
+	K	0.314
+	IP	15.50
+	POL	29.40
+END_SECTION
+
+SECTION S.o
+	R	1.700
+	K	0.314
+	IP	15.50
+	POL	29.40
+END_SECTION
+
+SECTION S.o2
+	R	1.700
+	K	0.314
+	IP	15.50
+	POL	29.40
+END_SECTION
+
+SECTION S.2
+	R	1.800
+	K	0.314
+	IP	17.78
+	POL	29.40
+END_SECTION
+#
+# Phosphorous
+#
+SECTION P.3
+	R	1.800
+	K	0.314
+	IP	16.78
+	POL	40.6
+END_SECTION
+#
+# Halides
+#
+SECTION F
+	R	1.470
+	K	0.109
+	IP	20.86
+	POL	 3.70
+END_SECTION
+
+SECTION Cl
+	R	1.750
+	K	0.314
+	IP	15.03
+	POL	21.80
+END_SECTION
+
+SECTION Br
+	R	1.850
+	K	0.434
+	IP	13.10
+	POL	31.20
+END_SECTION
+
+SECTION I
+	R	1.980
+	K	0.623
+	IP	12.67
+	POL	49.00
+END_SECTION
+#
+# Metals
+#
+SECTION Na
+	R	1.200
+	K	0.400
+END_SECTION
+
+SECTION K
+	R	1.200
+	K	0.400
+END_SECTION
+
+SECTION Ca
+	R	1.200
+	K	0.600
+END_SECTION
+
+SECTION Li
+	R	1.200
+	K	0.400
+END_SECTION
+
+SECTION Al
+	R	1.200
+	K	0.042
+END_SECTION
+
+SECTION Si
+	R	1.200
+	K	0.042
+END_SECTION
+#
+# Undefined types
+#
+SECTION UNDEFINED
+	R	1.200
+	K	0.042
+END_SECTION
+
+SECTION Du
+	R	1.200
+	K	0.042
+END_SECTION
+
+SECTION LP
+	R	1.200
+	K	0.042
+END_SECTION
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/sf/calcgrid_vdw1.prm	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,14 @@
+RBT_PARAMETER_FILE_V1.00
+TITLE vdw potential (4-8 functional form, ECUT=1.0)
+VERSION $Id: //depot/dev/client3/rdock/2013.1/data/sf/calcgrid_vdw1.prm#2 $
+
+SECTION VDW_1
+	SCORING_FUNCTION	RbtVdwIdxSF
+	WEIGHT			1.0	# Free-energy weighting
+	USE_4_8			TRUE	# TRUE = Use 4-8 potential (Ref (16))
+	USE_TRIPOS		FALSE	# FALSE = IP/POL method for kij
+	RMAX			1.5	# Truncate at RMAX*rmin
+	ECUT			1.0	# Switch to quadratic at E=ECUT*kij
+	E0			1.5	# At r=0, E=E0*ECUT*kij
+	TRACE			0
+END_SECTION
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/sf/calcgrid_vdw5.prm	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,14 @@
+RBT_PARAMETER_FILE_V1.00
+TITLE vdw potential (4-8 functional form, ECUT=5.0)
+VERSION $Id: //depot/dev/client3/rdock/2013.1/data/sf/calcgrid_vdw5.prm#2 $
+
+SECTION VDW_5
+	SCORING_FUNCTION	RbtVdwIdxSF
+	WEIGHT			1.0	# Free-energy weighting
+	USE_4_8			TRUE	# TRUE = Use 4-8 potential (Ref (16))
+	USE_TRIPOS		FALSE	# FALSE = IP/POL method for kij
+	RMAX			1.5	# Truncate at RMAX*rmin
+	ECUT			5.0	# Switch to quadratic at E=ECUT*kij
+	E0			1.5	# At r=0, E=E0*ECUT*kij
+	TRACE			0
+END_SECTION
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/sf/solvation_asp.prm	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,353 @@
+RBT_PARAMETER_FILE_V1.00
+TITLE Params for quick SASA calculation and ASP solvation
+VERSION $Id: //depot/dev/client3/rdock/2013.1/data/sf/solvation_asp.prm#2 $
+
+SECTION UNDEFINED
+	R	1.200
+	P	1.000
+	ASP	0.000
+END_SECTION
+#
+# Carbon
+#
+SECTION C_sp3
+	R	1.700
+	P	2.149
+	ASP	0.8438
+END_SECTION
+
+SECTION CH_sp3
+	R	1.800
+	P	1.276
+	ASP	0.0114
+END_SECTION
+
+SECTION CH2_sp3
+	R	1.900
+	P	1.045
+	ASP	0.0046
+END_SECTION
+
+SECTION CH3_sp3
+	R	2.000
+	P	0.880
+	ASP	0.0064
+END_SECTION
+
+SECTION C_sp2
+	R	1.720
+	P	1.554
+	ASP	0.0789
+END_SECTION
+
+SECTION CH_sp2
+	R	1.800
+	P	1.073
+	ASP	-0.0014
+END_SECTION
+
+SECTION CH2_sp2
+	R	1.800
+	P	0.961
+	ASP	0.0095
+END_SECTION
+
+SECTION C_sp2p
+	R	1.720
+	P	1.554
+#	ASP	-2.3757
+#	ASP	-1.18785
+	ASP	-0.7919
+	CHG_SCALING	TRUE
+END_SECTION
+
+SECTION C_ar
+	R	1.720
+	P	1.554
+	ASP	0.0170
+END_SECTION
+
+SECTION CH_ar
+	R	1.800
+	P	1.073
+	ASP	-0.0143
+END_SECTION
+
+SECTION C_sp
+	R	1.780
+	P	0.737
+	ASP	-0.0052
+END_SECTION
+
+SECTION C_sp3_P
+	R	1.700
+	P	2.149
+	ASP	-0.0473
+END_SECTION
+
+SECTION CH_sp3_P
+	R	1.800
+	P	1.276
+	ASP	-0.0394
+END_SECTION
+
+SECTION CH2_sp3_P
+	R	1.900
+	P	1.045
+	ASP	-0.0078
+END_SECTION
+
+SECTION CH3_sp3_P
+	R	2.000
+	P	0.880
+	ASP	0.0033
+END_SECTION
+
+SECTION C_sp2_P
+	R	1.720
+	P	1.554
+	ASP	-0.2609
+END_SECTION
+
+SECTION CH_sp2_P
+	R	1.800
+	P	1.073
+	ASP	-0.0227
+END_SECTION
+
+SECTION CH2_sp2_P
+	R	1.800
+	P	0.961
+	ASP	-0.0050
+END_SECTION
+
+SECTION C_ar_P
+	R	1.720
+	P	1.554
+	ASP	0.0759
+END_SECTION
+
+SECTION CH_ar_P
+	R	1.800
+	P	1.073
+	ASP	-0.0015
+END_SECTION
+#
+# Hydrogen
+#
+SECTION H
+	R	1.200
+	P	1.000
+	ASP	0.000
+END_SECTION
+
+SECTION HO
+	R	1.000
+	P	0.944
+	ASP	0.0499
+END_SECTION
+
+SECTION HN
+	R	1.100
+	P	1.128
+	ASP	-0.0242
+END_SECTION
+
+SECTION HNp
+	R	1.200
+	P	1.049
+#	ASP	-5.854
+#	ASP	-2.927
+	ASP	-1.951333
+	CHG_SCALING	TRUE
+END_SECTION
+
+SECTION HS
+	R	1.200
+	P	0.928
+	ASP	0.0487
+END_SECTION
+#
+# Oxygen
+#
+SECTION O_sp3
+	R	1.520
+	P	1.080
+	ASP	-0.1380
+END_SECTION
+
+SECTION OH_sp3
+	R	1.520
+	P	1.080
+	ASP	-0.2720
+END_SECTION
+
+# DM 17 Jan 2006 - new type for water oxygen
+# ASP value is undetermined at present
+SECTION OW
+	R	1.520
+	P	1.080
+	ASP	0.000
+END_SECTION
+
+SECTION O_tri
+	R	1.520
+	P	1.080
+	ASP	0.0965
+END_SECTION
+
+SECTION OH_tri
+	R	1.520
+	P	1.080
+	ASP	-0.0985
+END_SECTION
+
+SECTION O_sp2
+	R	1.500
+	P	0.926
+	ASP	-0.1122
+END_SECTION
+
+SECTION ON
+	R	1.500
+	P	0.926
+	ASP	-0.0055
+END_SECTION
+
+SECTION Om
+	R	1.700
+	P	0.922
+#	ASP	-2.1509
+#	ASP	-1.07545
+	ASP	-0.71696667
+	CHG_SCALING	TRUE
+END_SECTION
+#
+# Nitrogen
+#
+SECTION N_sp3
+	R	1.600
+	P	1.215
+	ASP	-0.6249
+END_SECTION
+
+SECTION NH_sp3
+	R	1.600
+	P	1.215
+	ASP	-0.3960
+END_SECTION
+
+SECTION NH2_sp3
+	R	1.600
+	P	1.215
+	ASP	-0.2150
+END_SECTION
+
+SECTION N_sp3p
+	R	1.600
+	P	1.215
+	ASP	-0.1186
+END_SECTION
+
+SECTION N_tri
+	R	1.550
+	P	1.028
+	ASP	-0.2300
+END_SECTION
+
+SECTION NH_tri
+	R	1.550
+	P	1.028
+	ASP	-0.4149
+END_SECTION
+
+SECTION NH2_tri
+	R	1.550
+	P	1.028
+	ASP	-0.1943
+END_SECTION
+
+SECTION N_sp2
+	R	1.550
+	P	1.413
+	ASP	-0.0768
+END_SECTION
+
+SECTION N_sp2p
+	R	1.550
+	P	1.413
+	ASP	-0.2744
+END_SECTION
+
+SECTION N_ar
+	R	1.550
+	P	1.413
+	ASP	-0.5310
+END_SECTION
+
+# P value is nominal, not in HHS paper
+SECTION N_sp
+	R	1.550
+	P	1.000
+	ASP	-0.1208
+END_SECTION
+#
+# Sulphur
+#
+SECTION S_sp3
+	R	1.800
+	P	1.121
+	ASP	-0.0685
+END_SECTION
+
+SECTION S_sp2
+	R	1.800
+	P	1.121
+	ASP	-0.0314
+END_SECTION
+#
+# Phosphorous
+#
+SECTION P
+	R	1.800
+	P	1.589
+	ASP	-1.2750
+END_SECTION
+#
+# Halides
+#
+SECTION F
+	R	1.470
+	P	0.906
+	ASP	0.0043
+END_SECTION
+
+SECTION Cl
+	R	1.750
+	P	0.906
+	ASP	-0.0096
+END_SECTION
+
+SECTION Br
+	R	1.850
+	P	0.898
+	ASP	-0.0194
+END_SECTION
+
+SECTION I
+	R	1.980
+	P	0.876
+	ASP	-0.0189
+END_SECTION
+#
+# Single type for metals at present
+#
+SECTION Metal
+#	R	1.200
+	R	0.700
+	P	1.000
+#	ASP	-5.000
+#	ASP	-2.500
+	ASP	-1.6667
+	CHG_SCALING	TRUE
+END_SECTION
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/data/top_all22_prot_na.inp	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,124 @@
+*>>>>>>>>> Combined Residue Topology File for Proteins <<<<<<<<<
+*>>>>>>>>>>>>>>>>>>>> and Nucleic Acids <<<<<<<<<<<<<<<<<<<<<<<<
+*>>>>>>>>>>>>>>>>> Using All Hydrogens (ALLH) <<<<<<<<<<<<<<<<<<
+*>>>>>>>>>>>>>>>>>>>>> January 1996 <<<<<<<<<<<<<<<<<<<<<<<<<<<<
+*>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<
+*>>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu  <<<<<<<<<
+* These files are a beta release; additional parameter development
+* and testing may lead to alteration of the contents.
+*
+* $Id: //depot/dev/client3/rdock/2013.1/data/top_all22_prot_na.inp#2 $
+*
+* 30 Apr 1999 (D Morley, RiboTargets)
+* Modified for RiboDock:
+* Added hybridisation state tags to comment field
+* Removed all but the MASS records (added element name)
+*
+   22     1
+MASS     1 H      1.00800 H ! polar H (RBT::SP3)
+MASS     2 HC     1.00800 H ! N-ter H (RBT::SP3)
+MASS     3 HA     1.00800 H ! nonpolar H (RBT::SP3)
+MASS     4 HT     1.00800 H ! TIPS3P WATER HYDROGEN (RBT::SP3)
+MASS     5 HP     1.00800 H ! aromatic H (RBT::SP3)
+MASS     6 HB     1.00800 H ! backbone H (RBT::SP3)
+MASS     7 HR1    1.00800 H ! his he1, (+) his HG,HD2 (RBT::SP3)
+MASS     8 HR2    1.00800 H ! (+) his HE1 (RBT::SP3)
+MASS     9 HR3    1.00800 H ! neutral his HG, HD2 (RBT::SP3)
+MASS    10 HS     1.00800 H ! thiol hydrogen (RBT::SP3)
+MASS    11 HA1    1.00800 H ! for alkene; RHC=CR (RBT::SP3)
+MASS    12 HA2    1.00800 H ! for alkene; H2C=CR (RBT::SP3)
+MASS    20 C     12.01100 C ! polar C (RBT::SP2)
+MASS    21 CA    12.01100 C ! aromatic C (RBT::SP2)
+MASS    22 CT1   12.01100 C ! aliphatic sp3 C for CH (RBT::SP3)
+MASS    23 CT2   12.01100 C ! aliphatic sp3 C for CH2 (RBT::SP3)
+MASS    24 CT3   12.01100 C ! aliphatic sp3 C for CH3 (RBT::SP3)
+MASS    25 CPH1  12.01100 C ! his CG and CD2 carbons (RBT::SP2)
+MASS    26 CPH2  12.01100 C ! his CE1 carbon (RBT::SP2)
+MASS    27 CPT   12.01100 C ! trp C between rings (RBT::SP2)
+MASS    28 CY    12.01100 C ! TRP C in pyrrole ring (RBT::SP2)
+MASS    29 CP1   12.01100 C ! tetrahedral C (proline CA) (RBT::SP3)
+MASS    30 CP2   12.01100 C ! tetrahedral C (proline CB/CG) (RBT::SP3)
+MASS    31 CP3   12.01100 C ! tetrahedral C (proline CD) (RBT::SP3)
+MASS    32 CC    12.01100 C ! carbonyl C for sidechains asn,asp,gln,glu (RBT::SP2)
+MASS    33 CD    12.01100 C ! carbonyl C for none amides, asp,glu,cter (RBT::SP2)
+MASS    34 CPA   12.01100 C ! heme alpha-C
+MASS    35 CPB   12.01100 C ! heme beta-C
+MASS    36 CPM   12.01100 C ! heme meso-C
+MASS    37 CM    12.01100 C ! heme CO carbon (RBT::SP2)
+MASS    38 CS    12.01100 C ! thiolate carbon
+MASS    39 CE1   12.01100 C ! for alkene; RHC=CR
+MASS    40 CE2   12.01100 C ! for alkene; H2C=CR
+MASS    50 N     14.00700 N ! proline N (RBT::TRI)
+MASS    51 NR1   14.00700 N ! neutral his protonated ring nitrogen (RBT::TRI)
+MASS    52 NR2   14.00700 N ! neutral his unprotonated ring nitrogen (RBT::SP2)
+MASS    53 NR3   14.00700 N ! charged his ring nitrogen (RBT::TRI)
+MASS    54 NH1   14.00700 N ! peptide nitrogen (RBT::TRI)
+MASS    55 NH2   14.00700 N ! amide nitrogen (RBT::TRI)
+MASS    56 NH3   14.00700 N ! ammonium nitrogen (RBT::SP3)
+MASS    57 NC2   14.00700 N ! guanidinium nitroogen (RBT::TRI)
+MASS    58 NY    14.00700 N ! TRP N in pyrrole ring (RBT::TRI)
+MASS    59 NP    14.00700 N ! Proline ring NH2+ (N-terminal) (RBT::SP3)
+MASS    60 NPH   14.00700 N ! heme pyrrole N (RBT::TRI)
+MASS    70 O     15.99900 O ! carbonyl oxygen (RBT::SP2)
+MASS    71 OB    15.99900 O ! carbonyl oxygen in acetic acid (RBT::SP2)
+MASS    72 OC    15.99900 O ! carboxylate oxygen (RBT::SP2)
+MASS    73 OH1   15.99900 O ! hydroxyl oxygen (RBT::SP3)
+MASS    74 OS    15.99940 O ! ester oxygen (RBT::SP3)
+MASS    75 OT    15.99940 O ! TIPS3P WATER OXYGEN (RBT::SP3)
+MASS    76 OM    15.99900 O ! heme CO/O2 oxygen (RBT::SP2)
+MASS    81 S     32.06000 S ! sulphur (RBT::SP3)
+MASS    82 SM    32.06000 S ! sulfur C-S-S-C type (RBT::SP3)
+MASS    83 SS    32.06000 S ! thiolate sulfur
+!
+! nucleic acid section
+!MASS 104    HT    1.008000 ! TIPS3P WATER HYDROGEN
+MASS 106    HN1   1.008000 H ! Nucleic acid amine proton (RBT::SP3)
+MASS 107    HN2   1.008000 H ! Nucleic acid ring nitrogen proton (RBT::SP3)
+MASS 108    HN3   1.008000 H ! Nucleic acid aromatic carbon proton (RBT::SP3)
+MASS 109    HN4   1.008000 H ! Nucleic acid phosphate hydroxyl proton (RBT::SP3)
+MASS 110   HN5   1.008000 H ! Nucleic acid ribose hydroxyl proton (RBT::SP3)
+MASS 111   HN6   1.008000 H ! Nucleic acid ribose aliphatic proton (RBT::SP3)
+MASS 112   HN7   1.008000 H ! Nucleic acid proton (equivalent to protein HA) (RBT::SP3)
+MASS 113   HN3B  1.008000 H ! NAD+ aromatic hydrogen (RBT::SP3)
+MASS 128   CN1  12.011000 C ! Nucleic acid carbonyl carbon (RBT::SP2)
+MASS 129   CN2  12.011000 C ! Nucleic acid aromatic carbon to amide (RBT::SP2)
+MASS 130   CN3  12.011000 C ! Nucleic acid aromatic carbon (RBT::SP2)
+MASS 131   CN4  12.011000 C ! Nucleic acid purine C8 and ADE C2 (RBT::SP2)
+MASS 132   CN5  12.011000 C ! Nucleic acid purine C4 and C5 (RBT::SP2)
+MASS 133   CN6  12.011000 C ! Nucleic acid sp3 ribose ring carbon (RBT::SP3)
+MASS 134   CN6B 12.011000 C ! Nucleic acid sp3 ribose ring carbon, C1' (RBT::SP3)
+MASS 135   CN6C 12.011000 C ! Nucleic acid sp3 deoxyribose ring carbon, C2' (RBT::SP3)
+MASS 136   CN7  12.011000 C ! Nucleic acid carbon (equivalent to protein CT1) (RBT::SP3)
+MASS 137   CN8  12.011000 C ! Nucleic acid carbon (equivalent to protein CT2) (RBT::SP3)
+MASS 138   CN9  12.011000 C ! Nucleic acid carbon (equivalent to protein CT3) (RBT::SP3)
+MASS 139   CN3A 12.011000 C ! NAD+ aromatic carbon (RBT::SP2)
+MASS 140   CN3B 12.011000 C ! NAD+ aromatic carbon (RBT::SP2)
+MASS 141   CN3C 12.011000 C ! NADH aromatic carbon (RBT::SP2)
+MASS 142   CN3D 12.011000 C ! Nucleic acid aromatic carbon for 5MC (RBT::SP2)
+MASS 143   CN1A 12.011000 C ! NAD+/NADH amide carbonyl carbon (RBT::SP2)
+MASS 150   NN1  14.007000 N ! Nucleic acid amide nitrogen (RBT::TRI)
+MASS 151   NN2  14.007000 N ! Nucleic acid protonated ring nitrogen (RBT::TRI)
+MASS 152   NN2U 14.007000 N ! Nucleic acid protonated ring nitrogen, ura N3 (RBT::TRI)
+MASS 153   NN2G 14.007000 N ! Nucleic acid protonated ring nitrogen, gua N1 (RBT::TRI)
+MASS 154   NN3  14.007000 N ! Nucleic acid unprotonated ring nitrogen (RBT::SP2)
+MASS 155   NN4  14.007000 N ! Nucleic acid purine N7 (RBT::SP2)
+MASS 156   NN5  14.007000 N ! Nucleic acid sp2 amine nitrogen (RBT::TRI)
+MASS 157   NN3A 14.007000 N ! Nucleic acid unprotonated ring nitrogen, ade N1 and N3 (RBT::SP2)
+MASS 158   NN3I 14.007000 N ! Nucleic acid unprotonated ring nitrogen, inosine N3 (RBT::SP2)
+!MASS 164   OT   15.999400 ! TIPS3P WATER OXYGEN
+MASS 165   ON1  15.999400 O ! Nucleic acid carbonyl oxygen (RBT::SP2)
+MASS 166   ON1C 15.999400 O ! Nucleic acid carbonyl oxygen, cyt O2 (RBT::SP2)
+MASS 167   ON2  15.999400 O ! Nucleic acid phosphate ester oxygen (RBT::SP3)
+MASS 168   ON3  15.999400 O ! Nucleic acid =O in phosphate (RBT::SP2)
+MASS 169   ON4  15.999400 O ! Nucleic acid phosphate hydroxyl oxygen (RBT::SP3)
+MASS 170   ON5  15.999400 O ! Nucleic acid ribose hydroxyl oxygen (RBT::SP3)
+MASS 171   ON6  15.999400 O ! Nucleic acid ribose ring oxygen (RBT::SP3)
+MASS 172   ON2b 15.999400 O ! Nucleic acid phosphate ester oxygen, tyr-phosphate (RBT::SP3)
+MASS 182   P    30.974000 P ! phosphorus (RBT::SP2)
+MASS 183   P2   30.974000 P ! pyrophosphate phosphorus
+MASS 192   SOD  22.989770 Na ! Sodium Ion
+MASS 193   MG   24.305000 Mg ! Magnesium Ion
+
+* 1 Nov 2002 (DM) Dummy atom type
+MASS   666 DUM    0.00000 DU ! Dummy atom
+!MASS 199   DUM   0.001    ! dummy atom
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/lib/SDRecord.pm	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,227 @@
+package SDRecord;
+# Perl module for reading/writing SD records from/to STDIN/STDOUT
+# Methods:  new
+#           readRec
+#           writeRec
+#           writeData
+#           copy
+#           addData
+#
+# Data:     LINES    - reference to array of record text lines
+#           DATA     - reference to hash array of record data fields
+#           DATAREF  - reference to hash array of line numbers for data fields
+
+my $LINES = 'LINES';
+my $DATA = 'DATA';
+#DM 27 Sept 1999 - also store line number of beginning each data field
+#so we can extract multi-line fields more easily from the LINES array
+my $DATAREF = 'DATAREF';
+
+############################################################
+# Constructor
+sub new {
+  my $this = {};
+  bless $this;
+  return $this;
+}
+
+############################################################
+# readRec() - read next SD record from STDIN
+# Input params:
+#   'LINES' => any value - save lines
+#   'DATA'  => any value - save data
+sub readRec {
+  my $this = shift;
+  my %params = @_;#input parameters
+  my @lines;#array for storing all text lines
+  my %data;#hash array for storing all data key,value pairs
+  my %dataref;#hash array for storing line number references for each data field
+  my ($fieldName,$ob,$cb);
+
+  #clear current data
+  delete $this->{$LINES};
+  delete $this->{$DATA};
+  delete $this->{$DATAREF};
+
+  #read lines from STDIN to the next record delimiter
+  #store in @lines array
+  #DM 16 Nov 1999 - can now cope with DOS text files directly
+  $/ = "\n";#Default Unix line separator
+  while (<>) {
+    chomp;#Get rid of Unix line separator
+    $/ = "\r";
+    chomp;#Get rid of DOS line separator
+    $/ = "\n";#Reset to normal Unix
+    last if ($_ eq '$$$$');#end of record
+    push @lines,$_;
+    #print "$_\n";
+  }
+
+  #check if we read anything
+  if (scalar(@lines) > 0) {
+    #store ref to @lines if required
+    $this->{$LINES} = \@lines if (defined $params{$LINES});
+    #search for data fields if required
+    if (defined $params{$DATA}) {
+      $fieldName = '';
+      my $lineNum = 0;
+      foreach $line (@lines) {
+	$lineNum++;
+	#DM 12 Jul 1999 - include the first three title lines as
+	#pseudo data fields
+	if ($lineNum <= 3) {
+	  $data{"_TITLE$lineNum"} = $line;
+	  #DM 20 Dec 1999 - include dimensionality (2D/3D) as pseudo data field
+	  if ($lineNum == 2) {
+	    $data{"_NDIM"} = substr($line,20,1);
+	  }
+	}
+	#DM 05 Aug 1999 - include number of atoms as pseudo data field
+	elsif ($lineNum == 4) {
+	  my @fields = split(" ",$line);
+	  $data{"_NATOMS"} = $fields[0] if (scalar(@fields)>0);
+	}
+	if (index($line,'>') == 0) {#found a data field
+	  $ob = index($line,'<');#first open bracket
+	  $cb = rindex($line,'>');#last close bracket
+	  if (($ob != -1) && ($cb != -1)) { #save field name
+	    $fieldName = substr($line,$ob+1,$cb-$ob-1);
+	    $dataref{$fieldName} = $lineNum-1;#store ref to line number
+	  }
+	}
+	#if field name defined, then store first line of value
+	elsif ($fieldName ne '') {
+	  $data{$fieldName} = $line;
+	  $fieldName = '';#clear field name
+	}
+      }
+      #store ref to %data in $this
+      $this->{$DATA} = \%data;
+      $this->{$DATAREF} = \%dataref;
+    }
+    return 1;
+  }
+  else {
+    return 0;
+  }
+}
+
+############################################################
+# writeRec() - write current record to STDOUT (mol + data)
+sub writeRec {
+  my $this = shift;
+  if (defined $this->{$LINES}) {
+    foreach $line (@{$this->{$LINES}}) {
+      print "$line\n";
+    }
+    print "\$\$\$\$\n";
+  }
+}
+
+############################################################
+# writeMol() - write current mol record to STDOUT
+sub writeMol {
+  my $this = shift;
+  if (defined $this->{$LINES}) {
+    foreach $line (@{$this->{$LINES}}) {
+      print "$line\n";
+      last if ($line eq "M  END");
+    }
+  }
+}
+
+############################################################
+# writeData() - list data field/values to STDOUT
+sub writeData {
+  my $this = shift;
+  my ($keys ,$value, $lineNum );
+  if (defined $this->{$DATA}) {
+    foreach $key (sort keys %{$this->{$DATA}}) {
+      $value = $this->{$DATA}->{$key};
+      $lineNum = $this->{$DATAREF}->{$key};
+      #print "$key eq $value (line $lineNum)\n";
+      print "\$$key eq \"$value\"\n";
+    }
+  }
+}
+
+############################################################
+# copy() - create deep copy of SDRecord
+# Input params:
+#   'LINES' = any value - deep copy of lines
+#   'DATA'  = any value - deep copy of data and dataref
+
+sub copy {
+  my $this = shift;
+  my %params = @_;#input parameters
+  my $clone = new SDRecord;
+  if ((defined $params{$LINES}) && (defined $this->{$LINES})) {
+    my @lines = @{$this->{$LINES}};
+    $clone->{$LINES} = \@lines;
+  }
+  if (defined $params{$DATA}) {
+    if (defined $this->{$DATA}) {
+      my %data = %{$this->{$DATA}};
+      $clone->{$DATA} = \%data;
+    }
+    # DM 24 Jul 2001 - DATAREF was missing from deep copy
+    # We copy the dataref array using the same DATA input parameter
+    # i.e. if the data is copied then so is dataref
+    if (defined $this->{$DATAREF}) {
+      my %dataref = %{$this->{$DATAREF}};
+      $clone->{$DATAREF} = \%dataref;
+    }
+  }
+  return $clone;
+}
+
+############################################################
+# addData() - adds data to data hash array
+sub addData {
+  my $this = shift;
+  my %params = @_;#input parameters
+  #if the array is already defined then add to it
+  if (defined $this->{$DATA}) {
+    my ($keys ,$value );
+    while (($key, $value) = each (%params)) {
+      $this->{$DATA}->{$key} = $value;
+    }
+  }
+  #if not defined, then create it
+  else {
+    $this->{$DATA} = \%params;
+  }
+}
+
+############################################################
+# addDataAndLines() - adds data to data hash array,
+# and adds corresponding lines also so that record may be
+# rewritten with the new fields
+sub addDataAndLines {
+  my $this = shift;
+  my %params = @_;#input parameters
+
+  while (($key, $value) = each (%params)) {
+    #DM 23 Oct 2000
+    #Check if data field already exists, if so replace value
+    #Note: this only works for single line data fields
+    if (defined $this->{$DATA}->{$key}) {
+      my $keyRef = $this->{$DATAREF}->{$key};
+      ${$this->{$LINES}}[$keyRef+1] = $value;
+    }
+    #else add the corresponding lines to the lines arrays
+    else {
+      my $keyRef = scalar(@{$this->{$LINES}});
+      $this->{$DATAREF}->{$key} = $keyRef;
+      push @{$this->{$LINES}},">  <$key>";
+      push @{$this->{$LINES}},"$value";
+      push @{$this->{$LINES}},"";
+    }
+  }
+
+  #DM 23 Oct 2000 - add data after adding the lines
+  $this->addData(%params);
+
+}
+
+1;
Binary file tools/rdock/lib/libRbt.so has changed
Binary file tools/rdock/lib/libRbt.so.rDock_2013.1_src has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rdock/lib/run_rbfuncs.pl	Mon Aug 29 08:23:52 2016 -0400
@@ -0,0 +1,296 @@
+#!/usr/bin/perl
+# Perl functions for the run_rb* collection of automated docking scripts
+
+use strict;
+
+################################################################################
+# sub get_prm_table
+#
+# Purpose: return a hash table of
+# key=parameter file name, value = file title
+# for all .prm files in a directory
+#
+# Usage: %prm_table = get_prm_table($dir)
+#
+# Arguments:
+# $prmDir - directory to search for .prm files
+#
+# Return parameters:
+# %prm_table - hash table
+#
+sub get_prm_table {
+#Arguments
+  my $prm_dir = shift;
+
+#Local variables
+  my @prm_list;
+  my %prm_table;
+  my $TITLEREC = "TITLE ";
+  my $file;
+  my $title;
+  my @titleLines;
+
+#Get the list of files ending in .prm
+  @prm_list = glob "$prm_dir/*.prm";
+
+#Read each file and extract the title record
+  foreach $file (@prm_list) {
+    open PRMHANDLE,$file;
+    @titleLines = grep /^$TITLEREC/,<PRMHANDLE>;
+    close PRMHANDLE;
+#Extract just the file name from the full path
+    my $prmName = substr($file, rindex($file,"/")+1);
+#Check if a title record was found
+    if (scalar @titleLines) {
+      $title = substr $titleLines[0],length($TITLEREC);
+      chomp $title;
+      $prm_table{$prmName} = $title;
+    }
+    else {
+      $prm_table{$prmName} = "No title";
+    }
+  }
+  return %prm_table;
+}
+################################################################################
+# sub get_dock_table
+#
+# Purpose: Modified version of get_prm_table
+# specific for the RBT_LIGDB docking database
+# Return a hash table of
+# key=docking library, value = expression for all sd files in that library
+#
+# Assumes that all subdirs within $db_dir are separate vendor libraries,
+# and that each subdir contains a set of compressed .sd.gz files
+#
+# Usage: %dock_table = get_dock_table($dir)
+#
+# Arguments:
+# $db_dir - directory to search for docking libraries
+#
+# Return parameters:
+# %dock_table - hash table#
+#
+sub get_dock_table {
+#Arguments
+  my $db_dir = shift;
+
+#Local variables
+  my ($lib,$sdfiles);
+  my (@lib_list,@sd_list);
+  my %dock_table;
+
+  opendir DBDIR,$db_dir;
+  @lib_list = readdir DBDIR;
+  closedir DBDIR;
+
+  foreach $lib (sort @lib_list) {
+    if (-d "$db_dir/$lib") {
+      $sdfiles = "$db_dir/$lib/*.sd*";
+      @sd_list = glob $sdfiles;
+      my $n = scalar(@sd_list);
+      if ($n > 0) {
+        $dock_table{"$lib ($n files)"} = $sdfiles;
+      }
+    }
+  }
+
+  return %dock_table;
+}
+#
+################################################################################
+# sub get_selection
+#
+# Purpose: allow a user to select from
+# a list of parameter files.
+#
+# Usage: $receptor = get_selection(\%prm_table,"receptor")
+#
+# Arguments:
+# $prm_table_ref - reference to hash table returned by get_prm_table
+# $name          - descriptive name for items (e.g. "receptor" or "script"
+#
+# Return parameters:
+# $item - selected items (key into %prm_table)
+#
+sub get_selection {
+#Arguments
+  my $prm_table_ref = shift;
+  my $name = shift;
+
+#Local variables
+  my @items = sort keys %$prm_table_ref;
+  my $nItems = scalar @items;
+  my ($i,$itemNum,$item);
+  my $inRange;
+
+  print "\n\n$name selection:\n\n";
+  $i=1;
+  foreach $item (@items) {
+    print "$i\t$item\t$$prm_table_ref{$item}\n";
+    $i++;
+  }
+  do {
+    print "\nEnter the $name number: ";
+    $itemNum = <STDIN>;
+    chomp $itemNum;
+    print "\n";
+    $inRange = (($itemNum >= 1) && ($itemNum <= $nItems));
+    print "$itemNum is out of range\n" if (!$inRange);
+  } until ($inRange);
+
+  print "\nYou have selected the following $name\n";
+  $item = $items[$itemNum-1];
+  print "$itemNum\t$item\t$$prm_table_ref{$item}\n";
+  return $item;
+}
+
+################################################################################
+# sub get_multiple_selection
+#
+# Purpose: allow a user to multiply select from the docking library list
+#
+# Usage: $receptor = get_selection(\%prm_table,"receptor")
+#
+# Arguments:
+# $prm_table_ref - reference to hash table returned by get_prm_table
+# $name          - descriptive name for items (e.g. "receptor" or "script"
+#
+# Return parameters:
+# $item - selected items (key into %prm_table)
+#
+sub get_multiple_selection {
+#Arguments
+  my $prm_table_ref = shift;
+  my $name = shift;
+
+#Local variables
+  my @items = sort keys %$prm_table_ref;
+  my $nItems = scalar @items;
+  my ($i,$idstring,$itemNum,$item);
+  my @itemNums;
+  my @selectedItems;
+  my $inRange;
+  my $allInRange;
+
+  print "\n\n$name selection:\n\n";
+  $i=1;
+  foreach $item (@items) {
+    print "$i\t$item\t$$prm_table_ref{$item}\n";
+    $i++;
+  }
+  do {
+    print "\nEnter the $name number(s): ";
+    my $idstring = <STDIN>;
+    chomp $idstring;
+    @itemNums = get_ids($idstring);
+    print "\n";
+    $allInRange = 1;
+    foreach $itemNum (@itemNums) {
+      $inRange = (($itemNum >= 1) && ($itemNum <= $nItems));
+      print "$itemNum is out of range\n" if (!$inRange);
+      $allInRange = $allInRange && $inRange;
+    }
+  } until ($allInRange);
+
+  print "\nYou have selected the following $name(s)\n";
+  foreach $itemNum (@itemNums) {
+    $item = $items[$itemNum-1];
+    push @selectedItems,$item;
+    print "$itemNum\t$item\t$$prm_table_ref{$item}\n";
+  }
+  return @selectedItems;
+}
+
+################################################################################
+# sub get_input
+#
+# Purpose: get user input, or returns default if no response given
+#
+# Usage: $nRuns = get_input("Enter no. of runs per ligand",10)
+#
+# Arguments:
+# $question    - text of question to ask
+# $defResponse - default answer
+#
+# Return parameters:
+# $response - user response, or default
+
+sub get_input {
+#Arguments
+  my $question = shift;
+  my $defResponse = shift;
+  print "$question [$defResponse]: ";
+  my $response = <STDIN>;
+  chomp $response;
+  $response = $defResponse if ($response eq "");
+  return $response;
+}
+
+# Based on //depot/intranet/1.0/lib/rbt_func.pl#1
+# this function converts a list of ids in one string
+# in the format 1,2,4-6,8,15-20
+# and returns an @array with the unique ids
+sub get_ids {
+  my $idstring = shift;
+  my %ids;
+
+  foreach my $id (split (',',$idstring)){
+    if ( grep (/-/,$id)){
+      (my $low, my $up) = split ('-',$id);
+      for ( my $co = $low; $co <= $up; $co++ ){
+	$ids{$co}=$co;
+      }
+    }
+    else {
+      $ids{$id}=$id;
+    }
+  }
+
+  return (sort {$a<=>$b} keys %ids);
+}
+################################################################################
+# sub get_filter_table
+#
+# Purpose: return a hash table of
+# key=filter file name, value = file title
+# for all .filter files in a directory
+#
+# Usage: %filter_table = get_filter_table($dir)
+#
+# Arguments:
+# $filterDir - directory to search for .filter files
+# $tmp - temperature for first filter
+# Note:
+# The first two filters are not in a file, but are created here
+#
+# Return parameters:
+# %filter_table - hash table
+#
+sub get_filter_table {
+#Arguments
+  my $filter_dir = shift;
+  my $tmp = shift;
+
+#Local variables
+  my $pwd = $ENV{"PWD"};
+  my @filter_list;
+  my %filter_table;
+  my $file;
+
+#Get the list of files ending in .filter
+  @filter_list = ((glob "$pwd/*.filter"), (glob "$filter_dir/*.filter"));
+  $filter_table{"1no_other_filters"} = "";
+  # $filter_table{"1threshold"} = "\tSCORE.INTER < $tmp";
+  # $filter_table{"2cavity"} = "\t\tSCORE.RESTR.CAVITY < 1 ";
+
+#Read each file and extract the title record
+  foreach $file (@filter_list) {
+#Extract just the file name from the full path
+    my $filterName = substr($file, rindex($file,"/")+1);
+#Check if a title record was found
+    $filter_table{$filterName} = "No title";
+  }
+  return %filter_table;
+}
+1;
Binary file tools/smina/smina.static has changed