changeset 5:62ce73c9d737 draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
author chemteam
date Thu, 06 Feb 2020 19:41:27 -0500
parents e7d0075052c9
children 7c5fd4117a07
files distance.py distance_multiple.py distance_single.py test-data/list1.txt test-data/list2.txt
diffstat 5 files changed, 120 insertions(+), 59 deletions(-) [+]
line wrap: on
line diff
--- a/distance.py	Mon Oct 07 12:51:05 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')
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/distance_multiple.py	Thu Feb 06 19:41:27 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')
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/distance_single.py	Thu Feb 06 19:41:27 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')
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/list1.txt	Thu Feb 06 19:41:27 2020 -0500
@@ -0,0 +1,1 @@
+resid 212 and name OE2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/list2.txt	Thu Feb 06 19:41:27 2020 -0500
@@ -0,0 +1,1 @@
+resid 3 and name C1