schrodinger.application.desmond.struc

Module struc

A collection of miscellaneous molecular-structure-related functions.

Functions

get_sidechain_att_atom(residue)
Given an amino acide residue 'residue' (must be a schrodinger.structure._Residue object), this function returns a tuple that is composed of two atoms (instances of the schrodinger.structure._StructureAtom class) that are the attachment atoms of the sidechain to the backbone of the given residue.

get_residue_sitename(residue)
Given a schrodinger.structure._Residue object ('residue'), this function returns a string that represents the name of the residue site.

delete_ct_property(struc, prop_name)
Deletes a property from a set of CTs, and returns the list of mutated CTs.

delete_atom_property(struc, prop_name)
Similar to the delete_ct_property, but this function deletes atom properties for all atoms.

rename_atom_property(struc, prop_name, new_name)

read_all_ct(fname)

get_fragname(fname)

Variables

[hide private]

BACKBONE_ATOM_NAME = ['H', 'HN', 'HA', 'N', 'CA', 'C', 'O']

__package__ = 'schrodinger.application.desmond'

Function Details

[hide private]

get_sidechain_att_atom(residue)

Given an amino acide residue 'residue' (must be a schrodinger.structure._Residue object), this function returns a tuple that is composed of two atoms (instances of the schrodinger.structure._StructureAtom class) that are the attachment atoms of the sidechain to the backbone of the given residue.

The first element of the returned tuple is the atom at the backbone, and the 2nd one is the atom at the sidechain.

If the attachment atoms cannot be identified, None is returned.

get_residue_sitename(residue)

Given a schrodinger.structure._Residue object ('residue'), this function returns a string that represents the name of the residue site.

The string is in the format C:RESXX[I] where C is the chain name, RES is the residue type name, XX is the residue number in the chain, and I is the insertion code. For example, a string could be "A:Tyr45[B]".

If there is no insertion code, the string will be reduced to C:RESXX, e.g. "A:Tyr45".

delete_ct_property(struc, prop_name)

Deletes a property from a set of CTs, and returns the list of mutated CTs.

The CTs are given via the 'struc' argument, which is a list of schrodinger.structure.Structure objects.

Parameters:

prop_name (string or list of strings) - The property name or names to be deleted. If a list of names is provided, all of them will be deleted.