# HG changeset patch # User chemteam # Date 1570467117 14400 # Node ID 36babbdd781801da1a0f4155d69bf97564830562 # Parent 49dac57d004a60369888a118cc0f1ffb70275063 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf" diff -r 49dac57d004a -r 36babbdd7818 angle.py --- a/angle.py Wed Apr 03 15:47:16 2019 -0400 +++ b/angle.py Mon Oct 07 12:51:57 2019 -0400 @@ -16,8 +16,10 @@ def parse_command_line(argv): parser = argparse.ArgumentParser() - parser.add_argument('--idcd', help='input dcd') - parser.add_argument('--ipdb', help='input pdb') + 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') @@ -52,7 +54,8 @@ return np.rad2deg(theta) -u = mda.Universe(args.ipdb, args.idcd, topology_format="PDB", format="DCD") +u = mda.Universe(args.istr, args.itraj, + topology_format=args.istrext, format=args.itrajext) data = np.array([(u.trajectory.frame, theta(u)) for ts in u.trajectory]) frame, theta = data.T diff -r 49dac57d004a -r 36babbdd7818 dihedrals.py --- a/dihedrals.py Wed Apr 03 15:47:16 2019 -0400 +++ b/dihedrals.py Mon Oct 07 12:51:57 2019 -0400 @@ -16,8 +16,10 @@ def parse_command_line(argv): parser = argparse.ArgumentParser() - parser.add_argument('--idcd', help='input dcd') - parser.add_argument('--ipdb', help='input pdb') + 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') @@ -56,7 +58,8 @@ return np.rad2deg(psi) -u = mda.Universe(args.ipdb, args.idcd, topology_format="PDB", format="DCD") +u = mda.Universe(args.istr, args.itraj, + topology_format=args.istrext, format=args.itrajext) data = np.array([(u.trajectory.frame, psi(u)) for ts in u.trajectory]) frame, psi = data.T PSI = np.concatenate(psi, axis=0) diff -r 49dac57d004a -r 36babbdd7818 distance.py --- a/distance.py Wed Apr 03 15:47:16 2019 -0400 +++ b/distance.py Mon Oct 07 12:51:57 2019 -0400 @@ -14,8 +14,10 @@ def parse_command_line(argv): parser = argparse.ArgumentParser() - parser.add_argument('--idcd', help='input dcd') - parser.add_argument('--ipdb', help='input pdb') + 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') @@ -34,7 +36,8 @@ atom2 = "(segid %s and resid %s and name %s)" % \ (args.isegid2, args.iresid2, args.iname2) -u = mda.Universe(args.ipdb, args.idcd, topology_format="PDB", format="DCD") +u = mda.Universe(args.istr, args.itraj, + topology_format=args.istrext, format=args.itrajext) x = u.select_atoms(atom1) y = u.select_atoms(atom2) diff -r 49dac57d004a -r 36babbdd7818 hbonds.py --- a/hbonds.py Wed Apr 03 15:47:16 2019 -0400 +++ b/hbonds.py Mon Oct 07 12:51:57 2019 -0400 @@ -4,6 +4,7 @@ import csv import sys +import MDAnalysis as mda import MDAnalysis.analysis.hbonds import pandas as pd @@ -11,8 +12,10 @@ def parse_command_line(argv): parser = argparse.ArgumentParser() - parser.add_argument('--idcd', help='input dcd') - parser.add_argument('--ipdb', help='input pdb') + 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('--isegid2', help='segid 2') parser.add_argument('--idistance', help='cutoff distance') @@ -31,8 +34,8 @@ distance = float(args.idistance) angle = float(args.iangle) -u = MDAnalysis.Universe( - args.ipdb, args.idcd, topology_format="PDB", format="DCD") +u = mda.Universe(args.istr, args.itraj, + topology_format=args.istrext, format=args.itrajext) h = MDAnalysis.analysis.hbonds.HydrogenBondAnalysis( u, selection1, selection2, distance=distance, angle=angle) diff -r 49dac57d004a -r 36babbdd7818 macros.xml --- a/macros.xml Wed Apr 03 15:47:16 2019 -0400 +++ b/macros.xml Mon Oct 07 12:51:57 2019 -0400 @@ -1,14 +1,14 @@ - 0.19 + 0.20 - mdanalysis + mdanalysis - - + + @@ -24,8 +24,13 @@ - - + + + + + + + diff -r 49dac57d004a -r 36babbdd7818 pca_cosine.py --- a/pca_cosine.py Wed Apr 03 15:47:16 2019 -0400 +++ b/pca_cosine.py Mon Oct 07 12:51:57 2019 -0400 @@ -12,8 +12,10 @@ def parse_command_line(argv): parser = argparse.ArgumentParser() - parser.add_argument('--idcd', help='input dcd') - parser.add_argument('--ipdb', help='input pdb') + 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('--icomponents', help='number of principle components') parser.add_argument('--iindex', help='index of the PC') parser.add_argument('--output', help='output') @@ -23,7 +25,8 @@ args = parse_command_line(sys.argv) -u = mda.Universe(args.ipdb, args.idcd, topology_format="PDB", format="DCD") +u = mda.Universe(args.istr, args.itraj, + topology_format=args.istrext, format=args.itrajext) components = int(args.icomponents) pca_index = int(args.iindex) diff -r 49dac57d004a -r 36babbdd7818 ramachandran_plots.py --- a/ramachandran_plots.py Wed Apr 03 15:47:16 2019 -0400 +++ b/ramachandran_plots.py Mon Oct 07 12:51:57 2019 -0400 @@ -19,8 +19,10 @@ def parse_command_line(argv): parser = argparse.ArgumentParser() - parser.add_argument('--idcd', help='input dcd') - parser.add_argument('--ipdb', help='input pdb') + 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') @@ -94,13 +96,16 @@ return np.rad2deg(dihe) -u = mda.Universe(args.ipdb, args.idcd, topology_format="PDB", format="DCD") +u = mda.Universe(args.istr, args.itraj, + topology_format=args.istrext, format=args.itrajext) phi_trajdata = np.array( [(u.trajectory.frame, calc_torsion(dihe_phi)) for ts in u.trajectory]) psi_trajdata = np.array( [(u.trajectory.frame, calc_torsion(dihe_psi)) for ts in u.trajectory]) +print(phi_trajdata, psi_trajdata) + phi_frame, phi_series = phi_trajdata.T psi_frame, psi_series = psi_trajdata.T diff -r 49dac57d004a -r 36babbdd7818 rdf.py --- a/rdf.py Wed Apr 03 15:47:16 2019 -0400 +++ b/rdf.py Mon Oct 07 12:51:57 2019 -0400 @@ -16,8 +16,10 @@ def parse_command_line(argv): parser = argparse.ArgumentParser() - parser.add_argument('--idcd', help='input dcd') - parser.add_argument('--ipdb', help='input pdb') + 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') @@ -42,7 +44,8 @@ start = float(args.istart) end = float(args.iend) -u = mda.Universe(args.ipdb, args.idcd, topology_format="PDB", format="DCD") +u = mda.Universe(args.istr, args.itraj, + topology_format=args.istrext, format=args.itrajext) x = u.select_atoms(atom1) y = u.select_atoms(atom2) diff -r 49dac57d004a -r 36babbdd7818 rdf.xml --- a/rdf.xml Wed Apr 03 15:47:16 2019 -0400 +++ b/rdf.xml Mon Oct 07 12:51:57 2019 -0400 @@ -1,5 +1,5 @@ - Radial Distribution Function between two atoms + - Radial Distribution Function between two atoms macros.xml @@ -7,8 +7,10 @@ - - + + - - + + - - + + @@ -58,13 +62,32 @@ + + + + + + + + + + + + + + + + + + +