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)

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