schrodinger.application.desmond.gcmc_utils module¶

schrodinger.application.desmond.gcmc_utils.add_ghost_solvent_file(ifile, solvent_file, ofile, **kwargs)¶

Opens the input file, calls add_ghost_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_ghost_solvent`

schrodinger.application.desmond.gcmc_utils.add_ghost_solvent(model, solvent_model, num_copies=1000, copy=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 ghost solvent to solvent_model – 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. :type solvent_model: cms.Cms

Parameters:	num_copies (`int`) – the number of ghost solvent molecules to add copy – whether or not to return a copy of the input structure.

Otherwise the input may be modified. :type copy: bool

Returns:	the input model with solvent added
Return type:	`cms.Cms`

schrodinger.application.desmond.gcmc_utils.merge_ghost_solvent_file(ifile, ofile)¶

Calls merge_ghost_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.merge_ghost_solvent(model, copy=False)¶

Merge the ghost solvent and solvent CTs. If no solvent CT exists, the ghost solvent will be turned into the solvent CT. This function will be left in place for 18-2 to allow users to migrate cms files with separate ghost_solvent CTs into the new single solvent CT format, but note this will only produce usable output for systems without pseudoatoms.

Parameters:	model (`cms.Cms`) – the Cms object whose CTs are to be merged copy – whether or not to return a copy of the input structure.

Otherwise the input may be modified. :type copy: bool

Returns:	the same Cms object with its ghost solvent CT merged into its

solvent CT :rtype: cms.Cms

schrodinger.application.desmond.gcmc_utils.remove_ghost_solvent_file(ifile, ofile)¶

Calls remove_ghost_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_ghost_solvent(model, copy_if_gcmc=False)¶

Remove ghost solvent from the full system CT and the component CTs such that afterward the atom_total will equal the active_total.

Parameters:	model (`cms.Cms`) – the Cms object from which to remove ghost solvent atoms copy_if_gcmc – whether or not to return a copy of the input structure

to avoid side effects (ie, the removal of ghost solvent molecules). If the input model does not contain ghost solvent, it is always returned uncopied. :type copy_if_gcmc: bool

Returns:	the same Cms object or a copy with its ghost solvent atoms removed
Return type:	`cms.Cms`

schrodinger.application.desmond.gcmc_utils.tag_gcmc_ligand_file(ifile, ofile)¶

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

schrodinger.application.desmond.gcmc_utils.tag_gcmc_ligand(model)¶

Finds the atoms of the ‘ligand molecule(s)’ and sets the ‘i_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 ‘i_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
Returns:	The modified input cms object
Return type:	`cms.Cms`

schrodinger.application.desmond.gcmc_utils.tag_gcmc_near_ligand_file(ifile, ofile, lig_file, cutoff_distance)¶

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 – atoms within this distance of any ligand atom will

be tagged :type cutoff_distance: float

schrodinger.application.desmond.gcmc_utils.tag_gcmc_near_ligand(model, ligand_model, cutoff_distance)¶

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

Parameters:	model (`cms.Cms`) – the input cms model ligand_model (`structure.Structure`) – the input ligand model cutoff_distance – solute atoms within this distance of any ligand

atom will be tagged :type cutoff_distance: float

Returns:	the modified input model
Return type:	`cms.Cms`

schrodinger.application.desmond.gcmc_utils.ffio_delete_atoms(ffio_ct, num_atoms)¶

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, other_ffio_ct)¶

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)¶

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

Note, this is currently tested in test_stage.py. That test should be moved here.

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.