schrodinger.trajectory.cmsstructure module

A core class (CmsStructure) that is a complete description of the Desmond model system.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.trajectory.cmsstructure.CmsStructure(full_ct, comp_ffsts, error_handler=None, matched_virtuals=set([]))

Bases: schrodinger.structure.Structure

CmsStructure represents a complete description of Desmond model system, which includes one full ct and several component cts.

charge

charges of individual atoms in the structure

find_trajectory_directory(base_directory=None)

Locate the trajectory directory. This directory name should be stored directly in a structure property, but the method allows for backwards- compatibility with a trajectory index file.

Parameters:base_directory (str) – path to look for trajectory file

mass

Mass of individual atoms in this structure

total_mass

Mass of all atoms in this structure

trajectory_directory

Directory location of correspondingDesmond simulation trajectory

writeCms(filename, frame=None)

Write out a cms file for a particular frame.

schrodinger.trajectory.cmsstructure.find_virtual_sites(ct, atom_index)

find all virtual sites attached to the atom (atom_index) input ct: desmond.ffiostructure structure atom_index: atom index starting from 1 return: list of list [ffio_index, atom_index, [x_coord, y_coord, z_coord], pseudo_index]

ffio_index: index of virtual in ffio_sites block pseudo_index: index of virtual in ffio_pseudo block

schrodinger.trajectory.cmsstructure.match_virtual_sites(wt_vlist, mut_vlist)

match virtual sites for core atoms, by computing distances wt_vlist, mut_vlist: virtual site lists returned by find_virtual_sites

matched core atom pair

return: set of tuples of matching pseudo indices

schrodinger.trajectory.cmsstructure.read_cms(filename, error_handler=None)

schrodinger.trajectory.cmsstructure.read_idx_file(idx_filename)

Routine to support backwards compatibility with trajectory index files.

Read a trajectory index file, extracting the CMS structure filename and the trajectory directory path. Make sure both exist and are readable. The file should only contain two lines, in the following format:

structure = XXX-out.cms trajectory = XXX_trj

Parameters:idx_filename (str) – the trajectory index file path Returns:absolute paths to corresponding structure file and trajectory directory Return type:str, str

schrodinger.trajectory.cmsstructure.write_cms(filename, cst)