schrodinger.application.desmond.gcmc_utils module

schrodinger.application.desmond.gcmc_utils.add_inactive_solvent_file(ifile: str, solvent_file: str, ofile: str, **kwargs)

Opens the input file, calls add_inactive_solvent, and writes the result to a new file.

Parameters

  • ifile (str) – the input filename

  • solvent_file (str) – the solvent filename

  • ofile (str) – the output filename

  • kwargs – keyword arguments passed to add_inactive_solvent

schrodinger.application.desmond.gcmc_utils.add_inactive_solvent(model: schrodinger.application.desmond.cms.Cms, solvent_model: schrodinger.application.desmond.cms.Cms, num_copies: int = 2000, copy: bool = False)

Appends num_copies copies of the molecules in the supplied solvent model to either system’s solvent CT if it exists or otherwise a new solvent CT. These changes are propagated to the fullsystem CT as well.

Parameters

  • model (cms.Cms) – the model to add inactive solvent to

  • solvent_model (cms.Cms) – a cms model containing a solvent CT, can be the same as model. NOTE - if solvent_model contains different PBC’s than model, these PBC’s will not be honored, which could lead to ‘broken’ molecules.

  • num_copies (int) – the number of inactive solvent molecules to add

  • copy (bool) – whether or not to return a copy of the input structure. Otherwise the input may be modified.

Returns

the input model with solvent added

Return type

cms.Cms

schrodinger.application.desmond.gcmc_utils.remove_inactive_solvent_file(ifile: str, ofile: str)

Calls remove_inactive_solvent on a file and writes the result to a new file

Parameters

  • ifile (str) – the input filename

  • ofile (str) – the output filename

schrodinger.application.desmond.gcmc_utils.remove_inactive_solvent(model: schrodinger.application.desmond.cms.Cms, copy_if_gcmc: bool = False)

Remove inactive solvent from the full system CT and the component CTs such that afterward the comp_atom_total will equal the active_total

Parameters

  • model (cms.Cms) – the Cms object from which to remove inactive solvent atoms

  • copy_if_gcmc (bool) – whether or not to return a copy of the input structure to avoid side effects (ie, the removal of inactive solvent molecules). If the input model does not contain inactive solvent, it is always returned uncopied.

Returns

the same Cms object or a copy with its inactive solvent atoms removed

Return type

cms.Cms

schrodinger.application.desmond.gcmc_utils.tag_gcmc_ligand_file(ifile: str, ofile: str, **kwargs)

Calls tag_gcmc_ligand on the input file and writes the results to the output file.

Parameters

  • ifile (str) – the input filename

  • ofile (str) – the output filename

  • kwargs – keyword arguments passed to tag_gcmc_ligand

schrodinger.application.desmond.gcmc_utils.tag_gcmc_ligand(model: schrodinger.application.desmond.cms.Cms, tag_only_mutated: bool = False)

Finds the atoms of the ‘ligand molecule(s)’ and sets the GCMC_LIGAND property to 1. The ‘ligand molecule(s)’ is(are) defined as the molecule containing the first atom of the ligand ct(s), in order to exclude alchemical ions/water. If no ligand is found, or if atoms in the system contain the GCMC_LIGAND property already, the system is returned unchanged. For FEP systems, both the reference and mutant ligands are tagged.

Parameters

  • model (cms.Cms) – The input cms object

  • tag_only_mutated – If false (default), all atoms in the cms model’s FEP cts are tagged. Otherwise, only atoms in the FEP cts which are mapped to dummy atoms are tagged. The case of mutated atoms that map to each other rather than to dummy atoms is not supported.

Returns

The modified input cms object

Return type

cms.Cms

schrodinger.application.desmond.gcmc_utils.tag_gcmc_near_ligand_file(ifile: str, ofile: str, lig_file: str, cutoff_distance: float)

Calls tag_gcmc_near_ligand on the input file and writes it to the output file, using the given ligand file and cutoff distance.

Parameters

  • ifile (str) – the input file

  • ofile (str) – the output file

  • lig_file (str) – the file containing the ligand model

  • cutoff_distance (float) – atoms within this distance of any ligand atom will be tagged

schrodinger.application.desmond.gcmc_utils.tag_gcmc_near_ligand(model: schrodinger.application.desmond.cms.Cms, ligand_model: schrodinger.application.desmond.cms.Cms, cutoff_distance: float)

Tags solute atoms in the model that are within the cutoff distance of any atom in the ligand model by setting the GCMC_LIGAND atom property to 1.

Parameters

  • model (cms.Cms) – the input cms model

  • ligand_model (structure.Structure) – the input ligand model

  • cutoff_distance (float) – solute atoms within this distance of any ligand atom will be tagged

Returns

the modified input model

Return type

cms.Cms

schrodinger.application.desmond.gcmc_utils.ffio_delete_atoms(ffio_ct: schrodinger.application.desmond.ffiostructure.FFIOStructure, num_atoms: int)

Deletes the given number of atoms and a proportional number of pseudoatoms from the input CT.

Parameters

  • ffio_ct (cms.ffiostructure.FFIOStructure) – The input ffio CT

  • num_atoms (int) – the number of atoms to delete

schrodinger.application.desmond.gcmc_utils.ffio_extend_ct(ffio_ct: schrodinger.application.desmond.ffiostructure.FFIOStructure, other_ffio_ct: schrodinger.application.desmond.ffiostructure.FFIOStructure)

Extends an ffio CT with the atoms and pseudoatoms of another ffio CT. The CTs should each only contain copies of the same single molecule.

Parameters

  • ffio_ct (cms.ffiostructure.FFIOStructure) – The input ffio CT

  • other_ffio_ct (cms.ffiostructure.FFIOStructure) – The ffio CT to extend the input CT with

schrodinger.application.desmond.gcmc_utils.equalize_number_waters(struc_files: List[str])

Deletes the waters from the marked component CTs of the structure files until each has the same number of waters.

Parameters

struc_files ({str: (int, int)}) – a dictionary mapping the filenames of cms files to a tuple containing the index of their solvent CT and the total number of atoms in the system.