| Previous changeset 7:8029dfe04b28 (2021-02-16) Next changeset 9:5f3f7376a0e3 (2021-06-09) |
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Commit message:
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc" |
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modified:
template_parmconv.j2 |
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added:
parmconv.py |
| b |
| diff -r 8029dfe04b28 -r 04f6bb5fe7c7 parmconv.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/parmconv.py Fri Mar 12 12:32:02 2021 +0000 |
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| @@ -0,0 +1,82 @@ +import argparse +import io +import sys +from contextlib import redirect_stdout + +import parmed +from parmed import amber, gromacs +from parmed.tools.changeradii import ChRad + + +def parse_command_line(argv): + parser = argparse.ArgumentParser() + parser.add_argument('--istr', help='input structure', required=True) + parser.add_argument('--itop', help='input topology file', required=True) + parser.add_argument('--istripmask', help='stripmask') + parser.add_argument('--iradii', required=True, help='parmed radii are \ + GB_RADII amber6,bondi, mbondi, mbondi2, mbondi3') + parser.add_argument('--removedihe', action='store_true', + default=False, help='remove dihedrals with zero \ + periodicity') + parser.add_argument('--removebox', action='store_true', + default=False, help='remove periodic box info') + parser.add_argument('--o_prmtop', help='AMBER output topology', + required=True) + return parser.parse_args() + + +def get_ids(dihedrals): + """ + goes through dihedrals and looks for any with per=0. + returns a reverse sorted list of ids to be removed. + """ + indices = [] + for k, v in enumerate(dihedrals): + f = io.StringIO() + with redirect_stdout(f): + print(v) + if f.getvalue().find("per=0") != -1: + indices.append(k) + indices.sort(reverse=True) + return indices + + +args = parse_command_line(sys.argv) + +gmx_top = gromacs.GromacsTopologyFile(args.itop) +gmx_gro = gromacs.GromacsGroFile.parse(args.istr) + +if not args.removebox: + # keep box info + gmx_top.box = gmx_gro.box + gmx_top.positions = gmx_gro.positions + + +if args.removedihe: + ids_to_remove = get_ids(gmx_top.dihedrals) + print("Original number of dihedrals %i" % len(gmx_top.dihedrals)) + for i in ids_to_remove: + gmx_top.dihedrals.pop(i) + print("Update number of dihedrals %i" % len(gmx_top.dihedrals)) + +if args.istripmask is not None: + if args.istripmask == "": + pass + else: + gmx_top.strip(args.istripmask) + +radii = str(args.iradii) +parmed.tools.changeRadii(gmx_top, radii) +amb_prm = amber.AmberParm.from_structure(gmx_top) +parmed.tools.changeRadii(amb_prm, radii) + +if args.removebox: + amb_prm.pointers['IFBOX'] = 0 + +ChRad(amb_prm, radii) +for i, atom in enumerate(amb_prm.atoms): + amb_prm.parm_data['RADII'][i] = atom.solvent_radius + amb_prm.parm_data['SCREEN'][i] = atom.screen + + +amb_prm.write_parm(args.o_prmtop) |
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| diff -r 8029dfe04b28 -r 04f6bb5fe7c7 template_parmconv.j2 --- a/template_parmconv.j2 Tue Feb 16 21:56:18 2021 +0000 +++ b/template_parmconv.j2 Fri Mar 12 12:32:02 2021 +0000 |
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| @@ -2,9 +2,9 @@ {% if fmt == 'AMBER' %} parm {{ top_in }} {% elif fmt == 'GROMACS' %} -gromber {{ top_in }} {{gro_in}} +gromber {{ top_in }} {{str_in}} {% elif fmt == 'CHARMM' %} -chamber {{ top_in }} {{gro_in}} +chamber {{ top_in }} {{str_in}} {% else %} parm {{ top_in }} {% endif %} |