Package schrodinger :: Package trajectory :: Module cmsstructure

Module cmsstructure

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

Classes

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

Functions

[hide private]

find_virtual_sites(ct, atom_index)
find all virtual sites attached to the atom (atom_index)...

match_virtual_sites(wt_vlist, mut_vlist)
match virtual sites for core atoms, by computing distances...

write_cms(filename, cst)

read_cms(filename, error_handler=None)

str, str

read_idx_file(idx_filename)
Routine to support backwards compatibility with trajectory index files.

Variables

[hide private]

__package__ = 'schrodinger.trajectory'

Function Details

[hide private]

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

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

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: str, str

absolute paths to corresponding structure file and trajectory directory