schrodinger.application.desmond.gcmc_utils module

schrodinger.application.desmond.gcmc_utils.add_ghost_solvent(model, solvent_model, num_copies=400)

Creates a new ‘ghost solvent’ ct with num_copies copies of the ct in the supplied solvent model, and adds them to the supplied model’s component and fullsystem cts.

Parameters:
  • model (cms.Cms) – the model to add ghost solvent to
  • solvent_model (cms.Cms) – a cms model containing a single solvent molecule
  • num_copies (int) – the number of copies of the ghost solvent ct to add
Returns:

the input model with solvent added
Return type:

cms.Cms
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.remove_ghost_solvent(model)

Remove ghost solvent from the full system ct and the component cts by checking for non-finite atom positions

Parameters:model (cms.Cms) – the Cms object from which to remove ghost solvent atoms
Returns:the same Cms object with its ghost solvent atoms removed
Return type: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