# HG changeset patch
# User chemteam
# Date 1581036183 18000
# Node ID d540ea77b909d197e7186ff76fb213336297f941
# Parent  312f912de69ddacad97e111a214f014cf1b4b09f
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"

diff -r 312f912de69d -r d540ea77b909 distance.py
--- a/distance.py	Mon Oct 07 12:52:40 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,59 +0,0 @@
-#!/usr/bin/env python
-
-import argparse
-import sys
-
-import MDAnalysis as mda
-
-import matplotlib
-matplotlib.use('Agg')  # noqa
-import matplotlib.pyplot as plt
-
-import numpy as np
-
-
-def parse_command_line(argv):
-    parser = argparse.ArgumentParser()
-    parser.add_argument('--itraj', help='input traj')
-    parser.add_argument('--istr', help='input str')
-    parser.add_argument('--itrajext', help='input traj ext')
-    parser.add_argument('--istrext', help='input str ext')
-    parser.add_argument('--isegid1', help='segid 1')
-    parser.add_argument('--iresid1', help='resid 1')
-    parser.add_argument('--iname1', help='name 1')
-    parser.add_argument('--isegid2', help='segid 2')
-    parser.add_argument('--iresid2', help='resid 2')
-    parser.add_argument('--iname2', help='name 2')
-    parser.add_argument('--output', help='output')
-    parser.add_argument('--odistance_plot', help='odistance plot')
-    return parser.parse_args()
-
-
-args = parse_command_line(sys.argv)
-
-atom1 = "(segid %s and resid %s and name %s)" % \
-    (args.isegid1, args.iresid1, args.iname1)
-atom2 = "(segid %s and resid %s and name %s)" % \
-    (args.isegid2, args.iresid2, args.iname2)
-
-u = mda.Universe(args.istr, args.itraj,
-                 topology_format=args.istrext, format=args.itrajext)
-x = u.select_atoms(atom1)
-y = u.select_atoms(atom2)
-
-with open(args.output, 'w') as f:
-    for t in u.trajectory:
-        r = x.positions - y.positions
-        d = np.linalg.norm(r)
-        f.write(str(t.frame) + '\t ')
-        f.write(str(d) + '\n')
-
-with open(args.output) as f:
-    g = [xtmp.strip() for xtmp in f]
-    data = [tuple(map(float, xtmp.split())) for xtmp in g[0:]]
-    time = [xtmp[0] for xtmp in data]
-    distance = [xtmp[1] for xtmp in data]
-    plt.plot(time, distance)
-    plt.xlabel('Frame No.')
-    plt.ylabel(r'Distance ($\AA$)')
-    plt.savefig(args.odistance_plot, format='png')
diff -r 312f912de69d -r d540ea77b909 distance.xml
--- a/distance.xml	Mon Oct 07 12:52:40 2019 -0400
+++ b/distance.xml	Thu Feb 06 19:43:03 2020 -0500
@@ -6,33 +6,57 @@
     <expand macro="requirements" />
     <command detect_errors="exit_code">
 <![CDATA[
-     python '$__tool_directory__/distance.py' 
-        --itraj '$trajin' 
-        --istr '$strin'
-        --itrajext '$trajin.ext'
-        --istrext '$strin.ext'
-        --isegid1 '$segid1' 
-        --iresid1 '$resid1' 
-        --iname1 '$name1'
-        --isegid2 '$segid2'
-        --iresid2 '$resid2' 
-        --iname2 '$name2'
-        --output '$output'
-        --odistance_plot '$distance_plot'
-    2>&1
+    #if $inps.inps == 'one':
+        python '$__tool_directory__/distance_single.py' 
+            --isegid1 '$inps.segid1' 
+            --iresid1 '$inps.resid1' 
+            --iname1 '$inps.name1'
+            --isegid2 '$inps.segid2'
+            --iresid2 '$inps.resid2' 
+            --iname2 '$inps.name2'
+            --odistance_plot '$distance_plot'
+        2>&1
+    #elif $inps.inps == 'multiple':
+        python '$__tool_directory__/distance_multiple.py' 
+            --list1 '$inps.list1'
+            --list2 '$inps.list2'
+    #end if
+            --itraj '$trajin' 
+            --istr '$strin'
+            --itrajext '$trajin.ext'
+            --istrext '$strin.ext'
+            --output '$output'
+            $header
+
 ]]></command>
     <inputs>
         <expand macro="analysis_inputs"/>
-        <param name="segid1"  type="text" value="PRO" label="Segment ID of atom 1"/>
-        <param name="resid1"  type="text" value="212" label="Residue ID of atom 1"/>
-        <param name="name1"  type="text" value="OE2" label="Atom name of atom 1"/>
-        <param name="segid2"  type="text" value="HET" label="Segment ID of atom 2"/>
-        <param name="resid2"  type="text" value="3" label="Residue ID of atom 2"/>
-        <param name="name2"  type="text" value="C1" label="Atom name of atom 2"/>
+
+        <conditional name="inps">
+            <param argument="inps" type="select" label="Number of pairwise distances to calculate?">
+                <option value="one" selected="true">One</option>
+                <option value="multiple">Multiple</option>
+            </param>
+            <when value="one">
+                <param name="segid1"  type="text" value="PRO" label="Segment ID of atom 1"/>
+                <param name="resid1"  type="text" value="212" label="Residue ID of atom 1"/>
+                <param name="name1"  type="text" value="OE2" label="Atom name of atom 1"/>
+                <param name="segid2"  type="text" value="HET" label="Segment ID of atom 2"/>
+                <param name="resid2"  type="text" value="3" label="Residue ID of atom 2"/>
+                <param name="name2"  type="text" value="C1" label="Atom name of atom 2"/>
+            </when>
+            <when value="multiple">
+                <param name="list1"  type="data" format="text" label="Selection groups (list 1)"/>
+                <param name="list2"  type="data" format="text" label="Selection groups (list 2)"/>
+            </when>
+        </conditional>
+        <param name="header" type="boolean" truevalue="--header" falsevalue="" label="Include header in output file"/>
     </inputs>
     <outputs>
-        <data format="tabular" name="output" label="Distance Analysis raw data"/>  
-        <data format="png" name="distance_plot" label="Distance Analysis Plot"/>
+        <data format="tabular" name="output" label="Distance Analysis raw data"/>
+        <data format="png" name="distance_plot" label="Distance Analysis Plot">
+            <filter>inps == 'one'</filter>
+        </data>
     </outputs>
     <tests>
         <test>
@@ -43,6 +67,7 @@
             <param name="segid2" value="HET"/>
             <param name="resid2" value="3"/>
             <param name="name2" value="C1"/>
+            <param name="header" value="false"/>
             <output name="output" file="Distance_Analysis_raw_data.tabular" />
         </test>
         <test>
@@ -53,11 +78,27 @@
             <param name="segid2" value="SYSTEM"/>
             <param name="resid2" value="3"/>
             <param name="name2" value="C1"/>
+            <param name="header" value="false"/>
             <output name="output">
                 <assert_contents>
                     <has_n_columns n="2" />
-                    <has_line_matching expression="0\s+3.8.*" />
-                    <has_line_matching expression="14\s+3.2.*" />
+                    <has_line_matching expression="0\s+3.893.*" />
+                    <has_line_matching expression="14\s+3.262.*" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <expand macro="tests_inputs_gmx"/>
+            <param name="inps" value="multiple"/>
+            <param name="list1" value="list1.txt"/>
+            <param name="list2" value="list2.txt"/>
+            <param name="header" value="true"/>
+            <output name="output">
+                <assert_contents>
+                    <has_n_columns n="2" />
+                    <has_line_matching expression="Frame\s+resid_212_and_name_OE2-resid_3_and_name_C1" />
+                    <has_line_matching expression="0\s+3.893.*" />
+                    <has_line_matching expression="14\s+3.262.*" />
                 </assert_contents>
             </output>
         </test>
@@ -67,7 +108,9 @@
 
 **What it does**
         
-This tool calculates and plots the distance between the two atoms.
+This tool calculates and plots the distance between pairs of atoms. Two modes are 
+available: single pair mode, where distances are calculated between two specified 
+atoms, and multiple pair mode, where two lists of atoms need to be provided.
 
 _____
 
@@ -78,9 +121,27 @@
 
        - Trajectory file  (DCD).
        - PDB file.
-       - Segment IDs, Residue IDs and names of two atoms to calculate distances.
+
+In single pair mode, segment IDs, residue IDs and names of two atoms are selected. 
+Note that a MDAnalysis 'segment' is a larger organizational unit,  for example one 
+protein or all the solvent molecules or simply the whole system.
+
+In multiple pair mode, two files need to be uploaded, each with one or more atom 
+groups defined using the MDAnalysis atom selection, each on a new line. For example:
+
+::
 
-Note that a MDAnalysis 'segment' is a larger organizational unit,  for example one protein or all the solvent molecules or simply the whole system.
+    resid 163
+    resid 56
+    resid 12 and type N
+
+All possible distances between the two sets of atom groups will be calculated. For 
+example, if List 1 contains 5 atoms and List 2 contains 8 atoms, the output file will
+contain 40 columns, each with the distance between one group in List 1 and one group
+in List 2.
+
+Note that in multiple pair mode, if the group has multiple atoms, the center of mass
+will be used for the calculation.
 
 _____
 
diff -r 312f912de69d -r d540ea77b909 distance_multiple.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/distance_multiple.py	Thu Feb 06 19:43:03 2020 -0500
@@ -0,0 +1,56 @@
+import argparse
+import sys
+
+import MDAnalysis as mda
+from MDAnalysis.analysis import distances
+
+import numpy as np
+
+
+def parse_command_line(argv):
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--itraj', help='input traj')
+    parser.add_argument('--istr', help='input str')
+    parser.add_argument('--itrajext', help='input traj ext')
+    parser.add_argument('--istrext', help='input str ext')
+    parser.add_argument('--list1', help='list 2')
+    parser.add_argument('--list2', help='list 2')
+    parser.add_argument('--output', help='output')
+    parser.add_argument('--header', dest='header', action='store_true')
+    return parser.parse_args()
+
+
+args = parse_command_line(sys.argv)
+
+u = mda.Universe(args.istr, args.itraj,
+                 topology_format=args.istrext, format=args.itrajext)
+
+list1 = np.loadtxt(args.list1, dtype=str, delimiter="\t", ndmin=1)
+list2 = np.loadtxt(args.list2, dtype=str, delimiter="\t", ndmin=1)
+
+sel1 = [u.select_atoms(selection) for selection in list1]
+sel2 = [u.select_atoms(selection) for selection in list2]
+
+d = np.empty((u.trajectory.n_frames, list1.shape[0], list2.shape[0]),)
+
+for ts in u.trajectory:
+    c_o_m1 = np.array([selection.center_of_mass() for selection in sel1])
+    c_o_m2 = np.array([selection.center_of_mass() for selection in sel2])
+    distances.distance_array(c_o_m1, c_o_m2, result=d[ts.frame])
+
+d = np.hstack((
+    np.array(np.reshape(np.arange(
+        0, d.shape[0]), (d.shape[0], 1)), dtype=int),  # add column w frame
+    np.reshape(d, (d.shape[0], d.shape[1] * d.shape[2]))
+))
+
+if args.header:
+    header = 'Frame\t' + '\t'.join(
+        ['-'.join(pair) for pair in zip(
+            sum([[n, ] * len(list2) for n in list1], []),
+            list(list2) * len(list1),)]).replace(' ', '_')
+else:
+    header = ''
+
+np.savetxt(args.output, d, header=header, comments='',
+           fmt=['%d'] + ['%f'] * (d.shape[1] - 1), delimiter='\t')
diff -r 312f912de69d -r d540ea77b909 distance_single.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/distance_single.py	Thu Feb 06 19:43:03 2020 -0500
@@ -0,0 +1,62 @@
+#!/usr/bin/env python
+
+import argparse
+import sys
+
+import MDAnalysis as mda
+
+import matplotlib
+matplotlib.use('Agg')  # noqa
+import matplotlib.pyplot as plt
+
+import numpy as np
+
+
+def parse_command_line(argv):
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--itraj', help='input traj')
+    parser.add_argument('--istr', help='input str')
+    parser.add_argument('--itrajext', help='input traj ext')
+    parser.add_argument('--istrext', help='input str ext')
+    parser.add_argument('--isegid1', help='segid 1')
+    parser.add_argument('--iresid1', help='resid 1')
+    parser.add_argument('--iname1', help='name 1')
+    parser.add_argument('--isegid2', help='segid 2')
+    parser.add_argument('--iresid2', help='resid 2')
+    parser.add_argument('--iname2', help='name 2')
+    parser.add_argument('--output', help='output')
+    parser.add_argument('--odistance_plot', help='odistance plot')
+    parser.add_argument('--header',  dest='header', action='store_true')
+    return parser.parse_args()
+
+
+args = parse_command_line(sys.argv)
+
+atom1 = "(segid %s and resid %s and name %s)" % \
+    (args.isegid1, args.iresid1, args.iname1)
+atom2 = "(segid %s and resid %s and name %s)" % \
+    (args.isegid2, args.iresid2, args.iname2)
+
+u = mda.Universe(args.istr, args.itraj,
+                 topology_format=args.istrext, format=args.itrajext)
+x = u.select_atoms(atom1)
+y = u.select_atoms(atom2)
+
+with open(args.output, 'w') as f:
+    if args.header:
+        f.write('Frame\tDistance')
+    for t in u.trajectory:
+        r = x.positions - y.positions
+        d = np.linalg.norm(r)
+        f.write(str(t.frame) + '\t ')
+        f.write(str(d) + '\n')
+
+with open(args.output) as f:
+    g = [xtmp.strip() for xtmp in f]
+    data = [tuple(map(float, xtmp.split())) for xtmp in g[0:]]
+    time = [xtmp[0] for xtmp in data]
+    distance = [xtmp[1] for xtmp in data]
+    plt.plot(time, distance)
+    plt.xlabel('Frame No.')
+    plt.ylabel(r'Distance ($\AA$)')
+    plt.savefig(args.odistance_plot, format='png')
diff -r 312f912de69d -r d540ea77b909 test-data/list1.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/list1.txt	Thu Feb 06 19:43:03 2020 -0500
@@ -0,0 +1,1 @@
+resid 212 and name OE2
diff -r 312f912de69d -r d540ea77b909 test-data/list2.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/list2.txt	Thu Feb 06 19:43:03 2020 -0500
@@ -0,0 +1,1 @@
+resid 3 and name C1