schrodinger.application.desmond.cms_utils module

Collection of util functions for cms files.

Copyright (C), Schrodinger, LLC. All rights reserved.

schrodinger.application.desmond.cms_utils.cms2pdb(cms_path: Path, pdb_path: Path)

Convert .cms file to .pdb file

Parameters:

• cms_path – path of cms file

• pdb_path – path of pdb file

schrodinger.application.desmond.cms_utils.create_empty_ffio_block(struct)

Given a structure, create an empty ffio block for it. Return structure copy and its ffio block.

Parameters:

struct (Structure) – Input structure

Return type:

Structure, ffiostructure.FFIOStructure

Returns:

Input structure copy, FFIO block

class schrodinger.application.desmond.cms_utils.MinimalFfioStructure(struct)

Bases: object

Creates a minimal-information ffio block for a given structure.

Specifically, the generated ffio block contains no OPLS-type forcefield information. Instead, only the atomic masses are set in the ffio.site sites.

__init__(struct)

Parameters:

struct (Structure) – Input structure to create a minimal ffio block for.