Mercurial > repos > chemteam > ambertools_parmchk2

annotate parmconv.py @ 10:75cf92df2580 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit aa5e1ad9fb06855dddc66b6cdfa2e5724c251c53"
author chemteam
date Wed, 14 Jul 2021 11:28:29 +0000
parents 7afe7044a2aa
children
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8
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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1 import argparse
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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2 import io
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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3 import sys
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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4 from contextlib import redirect_stdout
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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5
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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6 import parmed
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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7 from parmed import amber, gromacs
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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8 from parmed.tools.changeradii import ChRad
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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9
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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10
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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11 def parse_command_line(argv):
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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12 parser = argparse.ArgumentParser()
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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13 parser.add_argument('--istr', help='input structure', required=True)
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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14 parser.add_argument('--itop', help='input topology file', required=True)
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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15 parser.add_argument('--istripmask', help='stripmask')
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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16 parser.add_argument('--iradii', required=True, help='parmed radii are \
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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17 GB_RADII amber6,bondi, mbondi, mbondi2, mbondi3')
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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18 parser.add_argument('--removedihe', action='store_true',
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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19 default=False, help='remove dihedrals with zero \
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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20 periodicity')
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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21 parser.add_argument('--removebox', action='store_true',
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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22 default=False, help='remove periodic box info')
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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23 parser.add_argument('--o_prmtop', help='AMBER output topology',
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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24 required=True)
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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25 return parser.parse_args()
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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26
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27
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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28 def get_ids(dihedrals):
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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29 """
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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30 goes through dihedrals and looks for any with per=0.
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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31 returns a reverse sorted list of ids to be removed.
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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32 """
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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33 indices = []
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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34 for k, v in enumerate(dihedrals):
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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35 f = io.StringIO()
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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36 with redirect_stdout(f):
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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37 print(v)
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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38 if f.getvalue().find("per=0") != -1:
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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39 indices.append(k)
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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40 indices.sort(reverse=True)
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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41 return indices
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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42
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43
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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44 args = parse_command_line(sys.argv)
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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45
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46 gmx_top = gromacs.GromacsTopologyFile(args.itop)
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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47 gmx_gro = gromacs.GromacsGroFile.parse(args.istr)
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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48
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49 if not args.removebox:
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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50 # keep box info
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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51 gmx_top.box = gmx_gro.box
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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52 gmx_top.positions = gmx_gro.positions
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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53
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54
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55 if args.removedihe:
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56 ids_to_remove = get_ids(gmx_top.dihedrals)
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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57 print("Original number of dihedrals %i" % len(gmx_top.dihedrals))
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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58 for i in ids_to_remove:
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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59 gmx_top.dihedrals.pop(i)
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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60 print("Update number of dihedrals %i" % len(gmx_top.dihedrals))
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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61
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62 if args.istripmask is not None:
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63 if args.istripmask == "":
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64 pass
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65 else:
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66 gmx_top.strip(args.istripmask)
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67
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68 radii = str(args.iradii)
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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69 parmed.tools.changeRadii(gmx_top, radii)
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70 amb_prm = amber.AmberParm.from_structure(gmx_top)
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71 parmed.tools.changeRadii(amb_prm, radii)
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72
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73 if args.removebox:
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74 amb_prm.pointers['IFBOX'] = 0
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75
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76 ChRad(amb_prm, radii)
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77 for i, atom in enumerate(amb_prm.atoms):
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78 amb_prm.parm_data['RADII'][i] = atom.solvent_radius
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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79 amb_prm.parm_data['SCREEN'][i] = atom.screen
7afe7044a2aa "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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80
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81
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82 amb_prm.write_parm(args.o_prmtop)