Mercurial > repos > chemteam > parmconv
changeset 3:2b82fc7bec67 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
| author | chemteam |
|---|---|
| date | Fri, 12 Mar 2021 12:32:24 +0000 |
| parents | b500cc25dd15 |
| children | 267a70416daf |
| files | parmconv.py parmconv.xml template_parmconv.j2 |
| diffstat | 3 files changed, 198 insertions(+), 35 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/parmconv.py Fri Mar 12 12:32:24 2021 +0000 @@ -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)
--- a/parmconv.xml Tue Feb 16 21:55:34 2021 +0000 +++ b/parmconv.xml Fri Mar 12 12:32:24 2021 +0000 @@ -1,8 +1,8 @@ <tool id="parmconv" name="Convert Parameters" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> - <description>to AMBER prmtop in preparation for MMPBSA</description> + <description>to AMBER prmtop in preparation for MMGBSA/MMPBSA</description> <macros> <import>macros.xml</import> - <token name="@GALAXY_VERSION@">0</token> + <token name="@GALAXY_VERSION@">1</token> </macros> <expand macro="requirements"> <requirement type="package" version="3.2.0">parmed</requirement> @@ -11,15 +11,53 @@ </expand> <command detect_errors="exit_code"> <![CDATA[ - python '$templating_script' '$inputs' && - PATH_TO_PARMED=\$(dirname `which parmed`) && - export AMBERHOME=\$(dirname \$PATH_TO_PARMED) && - export GMXDATA=\$AMBERHOME/share/gromacs/top/ && - parmed -i ligand.script -O && - parmed -i receptor.script -O && - parmed -i complex.script -O && - parmed -i solvatedcomplex.script -O - + #if $param_inputs.fmt == "GROMACS": + python '$__tool_directory__/parmconv.py' + --istr '$param_inputs.str_in' + --itop '$param_inputs.top_in' + $param_inputs.modbehaviour.removedihe + $param_inputs.modbehaviour.removebox + --iradii '$param_inputs.modbehaviour.radii' + --istripmask '$stripmask_ligand' + --o_prmtop '$prmtop_ligand' + 2>&1 && + python '$__tool_directory__/parmconv.py' + --istr '$param_inputs.str_in' + --itop '$param_inputs.top_in' + $param_inputs.modbehaviour.removedihe + $param_inputs.modbehaviour.removebox + --iradii '$param_inputs.modbehaviour.radii' + --istripmask '$stripmask_receptor' + --o_prmtop '$prmtop_receptor' + 2>&1 && + python '$__tool_directory__/parmconv.py' + --istr '$param_inputs.str_in' + --itop '$param_inputs.top_in' + $param_inputs.modbehaviour.removedihe + $param_inputs.modbehaviour.removebox + --iradii '$param_inputs.modbehaviour.radii' + --istripmask '$stripmask_complex' + --o_prmtop '$prmtop_complex' + 2>&1 && + python '$__tool_directory__/parmconv.py' + --istr '$param_inputs.str_in' + --itop '$param_inputs.top_in' + $param_inputs.modbehaviour.removedihe + $param_inputs.modbehaviour.removebox + --iradii '$param_inputs.modbehaviour.radii' + --istripmask '$stripmask_solvatedcomplex' + --o_prmtop '$prmtop_solvatedcomplex' + 2>&1 + #else + python '$templating_script' '$inputs' && + PATH_TO_PARMED=\$(dirname `which parmed`) && + export AMBERHOME=\$(dirname \$PATH_TO_PARMED) && + export GMXDATA=\$AMBERHOME/share/gromacs/top/ && + parmed -i ligand.script -O && + parmed -i receptor.script -O && + parmed -i complex.script -O && + parmed -i solvatedcomplex.script -O + #end if ]]> </command> <configfiles> @@ -93,7 +131,7 @@ </configfiles> <inputs> <conditional name="param_inputs"> - <param name="fmt" type="select" label="Force Field format"> + <param name="fmt" type="select" label="Input format"> <option selected="True" value="AMBER">AMBER</option> <option value="GROMACS">GROMACS</option> </param> @@ -103,46 +141,45 @@ <when value="GROMACS"> <param name="top_in" type="data" label="Input topology (top) file" format="top"/> <param name="str_in" type="data" label="Input structure (gro) file" format="gro"/> + <section name="modbehaviour" title="Modify behaviour" expanded="false"> + <param name="removedihe" type="boolean" truevalue="--removedihe" falsevalue="" checked="false" label="Remove all zero period dihedrals" help="This will remove zero period dihedrals from the generated topology"/> + <param name="removebox" type="boolean" truevalue="--removebox" falsevalue="" checked="false" label="Remove periodic box information" help="This will remove periodic information from the generated topology"/> + <param name="radii" type="select" label="Radii to use" help="Select the radii to use. Default is mbondi."> + <option selected="True" value="mbondi">mbondi</option> + <option value="mbondi2">mbondi2</option> + <option value="mbondi3">mbondi3</option> + <option value="bondi">bondi</option> + <option value="amber6">amber6</option> + </param> + </section> </when> </conditional> <param name="stripmask_ligand" type="text" label="Ligand selection" value="!:UNL" help="Define a valid AMBER stripmask that will select only the ligand"> <sanitizer> <valid initial="string.printable"> - <remove value="&"/> + <add value="&"/> </valid> - <mapping initial="none"> - <add source="&" target="__and__"/> - </mapping> </sanitizer> </param> <param name="stripmask_receptor" type="text" label="Receptor selection" value=":NA,SOL,UNL" help="Define a valid AMBER stripmask that will select only the receptor"> <sanitizer> <valid initial="string.printable"> - <remove value="&"/> + <add value="&"/> </valid> - <mapping initial="none"> - <add source="&" target="__and__"/> - </mapping> </sanitizer> </param> <param name="stripmask_complex" type="text" label="Complex selection" value=":NA,SOL" help="Define a valid AMBER stripmask that will select the complex (receptor with ligand)"> <sanitizer> <valid initial="string.printable"> - <remove value="&"/> + <add value="&"/> </valid> - <mapping initial="none"> - <add source="&" target="__and__"/> - </mapping> </sanitizer> </param> <param name="stripmask_solvatedcomplex" type="text" label="Solvated complex selection" help="Define a valid AMBER stripmask that will select the solvated complex (includes water and ions)"> <sanitizer> <valid initial="string.printable"> - <remove value="&"/> + <add value="&"/> </valid> - <mapping initial="none"> - <add source="&" target="__and__"/> - </mapping> </sanitizer> </param> </inputs> @@ -200,24 +237,68 @@ <param name="stripmask_solvatedcomplex" value=":1-500@O&!(:WAT|:LYS,ARG)"/> <output name="prmtop_ligand"> <assert_contents> - <has_text text=" 8 59"/> <has_text text="%FLAG MASS"/> <has_text text="CL"/> + <has_text text="SOLVENT_POINTERS"/> + <has_text text="BOX_DIMENSIONS"/> </assert_contents> </output> <output name="prmtop_receptor"> <assert_contents> - <has_text text=" 1960 59"/> <has_text text="%FLAG MASS"/> <has_text text="LYS VAL PHE "/> + <has_text text="SOLVENT_POINTERS"/> + <has_text text="BOX_DIMENSIONS"/> <not_has_text text="CL "/> </assert_contents> </output> <output name="prmtop_solvatedcomplex"> <assert_contents> - <has_text text=" 38265 59"/> <has_text text="%FLAG MASS"/> <has_text text="LYS VAL PHE"/> + <has_text text="SOLVENT_POINTERS"/> + <has_text text="BOX_DIMENSIONS"/> + </assert_contents> + </output> + </test> + <test> + <!-- test with removing dihedrals and periodicity --> + <param name="fmt" value="GROMACS"/> + <conditional name="param_inputs"> + <param name="top_in" value="topol_solv.top"/> + <param name="str_in" value="solv_ions.gro"/> + </conditional> + <!-- dihedrals and periodicity --> + <param name="removedihe" value="--removedihe"/> + <param name="removebox" value="--removebox"/> + <!-- pretending CL is a ligand --> + <param name="stripmask_ligand" value="!:CL"/> + <param name="stripmask_receptor" value=":NA,CL,SOL,WAT"/> + <!-- test a fairly complex selection. All backbone oxygens in residues 1-500 but not in water, lysine or arginine --> + <param name="stripmask_solvatedcomplex" value=":1-500@O&!(:WAT|:LYS,ARG)"/> + <output name="prmtop_ligand"> + <assert_contents> + <has_text text="%FLAG MASS"/> + <has_text text="CL"/> + <not_has_text text="SOLVENT_POINTERS"/> + <not_has_text text="BOX_DIMENSIONS"/> + </assert_contents> + </output> + <output name="prmtop_receptor"> + <assert_contents> + <has_text text="%FLAG MASS"/> + <has_text text="LYS VAL PHE "/> + <not_has_text text="CL "/> + <not_has_text text="SOLVENT_POINTERS"/> + <not_has_text text="BOX_DIMENSIONS"/> + </assert_contents> + </output> + <output name="prmtop_solvatedcomplex"> + <assert_contents> + <has_text text="%FLAG MASS"/> + <has_text text="LYS VAL PHE"/> + <not_has_text text="SOLVENT_POINTERS"/> + <not_has_text text="BOX_DIMENSIONS"/> </assert_contents> </output> </test> @@ -228,13 +309,13 @@ **What it does** - This tool converts parameter and topology files that represent a solvated complex into parameter files for the ligand, receptor, complex and solvated complex in AMBER prmtop format. These files are needed for MMPBSA calculations. + This tool converts parameter and topology files that represent a solvated complex into parameter files for the ligand, receptor, complex and solvated complex in AMBER prmtop format. These files are needed for MMGBSA/MMPBSA calculations. .. class:: infomark **How it works** - AmberTools ParmEd is used to strip unneeded atoms and save out the parameter files. The stripmasks are defined by the user. + AmberTools' ParmEd is used to strip unneeded atoms and save the parameter files. The stripmasks are defined by the user. .. class:: infomark
--- a/template_parmconv.j2 Tue Feb 16 21:55:34 2021 +0000 +++ b/template_parmconv.j2 Fri Mar 12 12:32:24 2021 +0000 @@ -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 %}