schrodinger.application.watermap.watermap_inp module

This is a class that generates watermap input files and runs them through jobcontrol. This also supports all the options in GUI.

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.application.watermap.watermap_inp.print_deprecate(option, opt, value, parser)[source]
class schrodinger.application.watermap.watermap_inp.WaterMapInput(protein_st, ligand_st, **kwargs)[source]

Bases: object

__init__(protein_st, ligand_st, **kwargs)[source]

Initialize self. See help(type(self)) for accurate signature.

update(**kwargs)[source]

updates states of options

reorder_solute(st)[source]

reorder atoms so that the very first atom is located close to origin to prevent solute to be shifted to other images.

createTip4pFfio(ct)[source]
make_canonical_solvent(st)[source]

Fix atomic order to O H H

prepareStructures()[source]

Prepare -solute, -protein, -ligand.mae files.

writeMSJ() → Optional[str][source]

Write multisim file to the returned str. If there was a problem generating the msj, return None.

write(jobname, suffix='maegz', hostname=None, cpus=None)[source]

Call all write functions

Parameters
  • jobname (str) – The name of the job in the command example

  • suffix (str) – The file extension for the input file

  • hostname (str) – The name of the host in the command example

  • cpus (int) – The number of cpus in the command example

run(jobname, host, cpu)[source]

Run WaterMap Job

schrodinger.application.watermap.watermap_inp.main(opt)[source]