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1 #!/usr/bin/perl -w
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2
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3 # Script that simulates the result of a high throughput protocol.
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4
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5 if (@ARGV < 4)
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6 {
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7 print "Script that simulates the result of a high throughput protocol.\n";
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8 print "1st) exhaustive docking of a small representative part of the\n";
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9 print " whole library.\n";
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10 print "2nd) Store the result of sdreport -t over that exhaustive dock.\n";
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11 print " in file <sdreport_file> that will be the input of this\n";
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12 print " script.\n";
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13 print "3rd) ht_protocol_finder.pl <sdreport_file> <output_file> <thr1max>";
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14 print " <thr1min> <ns1> <ns2>\n";
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15 print " <ns1> and <ns2> are the number of steps in stage 1 and in\n";
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16 print " stage 2. If not present, the default values are 5 and 15\n";
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17 print " <thrmax> and <thrmin> setup the range of thresholds that will\n";
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18 print " be simulated in stage 1. The threshold of stage 2 depends\n";
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19 print " on the value of the threshold of stage 1.\n";
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20 print " An input of -22 -24 will try protocols:\n";
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21 print " 5 -22 15 -27\n";
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22 print " 5 -22 15 -28\n";
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23 print " 5 -22 15 -29\n";
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24 print " 5 -23 15 -28\n";
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25 print " 5 -23 15 -29\n";
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26 print " 5 -23 15 -30\n";
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27 print " 5 -24 15 -29\n";
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28 print " 5 -24 15 -30\n";
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29 print " 5 -24 15 -31\n";
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30 print " Output of the program is a 7 column values. First column\n";
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31 print " represents the time. This is a percentage of the time it\n";
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32 print " would take to do the docking in exhaustive mode, i.e. \n";
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33 print " docking each ligand 100 times. Anything\n";
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34 print " above 12 is too long.\n";
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35 print " Second column is the first percentage. Percentage of\n";
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36 print " ligands that pass the first stage.\n";
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37 print " Third column is the second percentage. Percentage of\n";
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38 print " ligands that pass the second stage.\n";
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39 print " The four last columns represent the protocol.\n";
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40 print " All the protocols tried are written at the end.\n";
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41 print " The ones for which time is less than 12%, perc1 is\n";
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42 print " less than 30% and perc2 is less than 5% but bigger than 1%\n";
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43 print " will have a series of *** after, to indicate they are good choices\n";
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44 print " WARNING! This is a simulation based in a small set.\n";
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45 print " The numbers are an indication, not factual values.\n";
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46 exit (0);
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47 }
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48 open (IFILE, $ARGV[0]) || die "cannot open $ARGV[0] for reading: $!";
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49 open (OFILE, ">$ARGV[1]") || die "cannot open $ARGV[1] for writing: $!";
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50 <IFILE>; # read first line
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51 $line = <IFILE>;
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52 $line =~ /\S+\s+(\S+)\s+\S+\s+(\S+)/;
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53 $prevname = $1;
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54 $inter = $2;
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55 push @tmp, $inter;
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56 $i = 0;
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57 while ($line = <IFILE>)
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58 {
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59 $line =~ /\S+\s+(\S+)\s+\S+\s+(\S+)/;
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60 $name = $1;
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61 $inter = $2;
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62 if ($name ne $prevname)
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63 {
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64 $prevname = $name;
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65 push @inters, [ @tmp ];
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66 $runsperligand[$i++] = @tmp;
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67 $#tmp = -1;
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68 }
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69 push @tmp, $inter;
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70 }
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71 push @inters, [ @tmp ];
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72 $runsperligand[$i++] = @tmp;
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73 $totLigands = @inters;
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74 $ta = $ARGV[2];
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75 $tb = $ARGV[3];
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76 if (@ARGV > 4)
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77 {
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78 $n1 = $ARGV[4];
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79 }
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80 else
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81 {
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82 $n1 = 5;
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83 }
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84 if (@ARGV > 5)
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85 {
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86 $n2 = $ARGV[5];
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87 }
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88 else
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89 {
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90 $n2 = 15;
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91 }
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92 printf OFILE "Command line args:\n\t";
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93 foreach $arg (@ARGV)
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94 {
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95 printf OFILE "%s\t", $arg;
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96 }
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97 printf OFILE "\n\n TIME PERC1 PERC2 N1 THR1 N2 THR2\n";
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98 for ($t1 = $ta ; $t1 >= $tb ; $t1--)
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99 {
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100 $tc = $t1 - 5;
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101 for ($t2 = $tc ; $t2 >= ($tc - 2) ; $t2--)
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102 {
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103 ($cref, $dref) =
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104 getTables($t1, $t2);
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105 @ligBelowThr1 = @$cref;
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106 @ligBelowThr2 = @$dref;
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107 ($time,$p1,$p2) = simulation($n1,$t1,$n2,$t2);
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108 if (($time < 12.0) && ($p1 < 30.0) && ($p2 < 5.0) && ($p2 > 1.0))
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109 {
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110 printf OFILE "%6.3f, %6.3f, %6.3f, %4i, %4i, %4i, %4i ***\n",
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111 $time, $p1, $p2, $n1,$t1,$n2,$t2;
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112 }
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113 else
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114 {
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115 printf OFILE "%6.3f, %6.3f, %6.3f, %4i, %4i, %4i, %4i\n",
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116 $time, $p1, $p2, $n1,$t1,$n2,$t2;
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117 }
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118 }
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119 }
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120
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121
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122 sub simulation
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123 {
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124 my(@params);
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125 my(@lt0, @lt1);
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126 my($thr1, $thr2,$ns1,$ns2,$tottime,$totnumHits,$total,$totnruns);
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127 @params = @_;
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128 $ns1 = $params[0];
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129 $thr1 = $params[1];
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130 $ns2 = $params[2];
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131 $thr2 = $params[3];
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132 $ntrials = 100;
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133 $tottime = 0;
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134 $totnumHitss1 = 0;
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135 $totnumHitss2 = 0;
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136 $total = $totLigands;
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137 $totnruns = 0;
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138 for ($i = 0 ; $i < $ntrials ; $i++)
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139 {
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140 $numHitss1 = 0;
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141 $numHitss2 = 0;
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142 $totnruns = 0;
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143 for ($j = 0 ; $j < $totLigands ; $j++)
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144 {
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145 ($passStage1, $nruns1) = stage($ns1, $ligBelowThr1[$j]);
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146 if ($passStage1)
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147 {
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148 $numHitss1++;
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149 ($passStage2, $nruns2) = stage($ns2, $ligBelowThr2[$j]);
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150 if ($passStage2)
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151 {
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152 $numHitss2++;
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153 }
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154 $totnruns += $nruns2;
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155 }
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156 $totnruns += $nruns1;
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157 }
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158 $time = $totnruns / $total;
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159 $tottime += $time;
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160 $totnumHitss1 += $numHitss1;
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161 $totnumHitss2 += $numHitss2;
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162 }
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163 $tottime /= $ntrials;
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164 $totnumHitss1 /= $ntrials;
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165 $totnumHitss2 /= $ntrials;
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166 $p1 = $totnumHitss1 * 100.0 / $totLigands;
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167 $p2 = $totnumHitss2 * 100.0 / $totLigands;
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168 return ($tottime, $p1, $p2);
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169 }
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170
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171 sub getTables
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172 {
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173 my(@params);
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174 my($totLigands, @lt1, @lt2);
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175 my($row,$inter, $belowThr1, $belowThr2);
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176 my($thr0, $thr1);
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177 @params = @_;
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178 $thr1 = $params[0];
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179 $thr2 = $params[1];
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180 $totLigands = 0;
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181 $belowThr1 = 0;
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182 $belowThr2 = 0;
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183 $totLigands = 0;
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184 for $i (0 .. $#inters)
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185 {
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186 $row = $inters[$i];
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187 for $j (0 .. $#{$row})
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188 {
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189 $inter = $row->[$j];
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190 if ($inter <= $thr1)
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191 {
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192 $belowThr1++;
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193 }
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194 if ($inter <= $thr2)
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195 {
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196 $belowThr2++;
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197 }
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198 }
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199 $lt1[$totLigands] =
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200 $belowThr1 / $runsperligand[$i];
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201 $lt2[$totLigands] =
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202 $belowThr2 / $runsperligand[$i];
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203 $totLigands++;
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204 $belowThr1 = 0;
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205 $belowThr2 = 0;
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206 }
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207 return (\@lt1, \@lt2);
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208 }
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209
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210
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211
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212 sub stage
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213 {
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214 my($nruns, $p, $i, $r);
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215 $nruns = $_[0];
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216 $p = $_[1];
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217 if ($nruns == 0)
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218 {
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219 return (1, 0);
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220 }
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221 for ($i = 0 ; $i < $nruns ; $i++)
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222 {
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223 $r = rand;
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224 if ($r < $p)
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225 {
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226 return (1, $i);
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227 }
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228 }
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229 return (0, $nruns);
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230 }
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231
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232
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