schrodinger.application.desmond.struc module

A collection of miscellaneous molecular-structure-related functions.

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.application.desmond.struc.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.

schrodinger.application.desmond.struc.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”.

schrodinger.application.desmond.struc.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.
schrodinger.application.desmond.struc.delete_atom_property(struc, prop_name)

Similar to the delete_ct_property, but this function deletes atom properties for all atoms.

schrodinger.application.desmond.struc.rename_atom_property(struc, prop_name, new_name)
schrodinger.application.desmond.struc.read_all_ct(fname)
schrodinger.application.desmond.struc.get_fragname(fname)
schrodinger.application.desmond.struc.set_atom_reference_coordinates(atom: schrodinger.structure._StructureAtom, coords: List[float]) → None
Parameters:
  • atom (schrodinger.structure._StructureAtom object) – Set reference coordinates for atom
  • coords (List[float]) – [x, y, z] coordinates for atom
schrodinger.application.desmond.struc.get_atom_reference_coordinates(atom: schrodinger.structure._StructureAtom) → List[float]

Try to get reference coordinate first, if those are not defined, return regular coordinates.

Parameters:atom (schrodinger.structure._StructureAtom object) – Set reference coordinates for atom
Returns:[x, y, z], reference or current coordinates of an atom.
Return type:List[float]
schrodinger.application.desmond.struc.set_ct_reference_coordinates(ct: schrodinger.structure.Structure) → None

Set reference coordinates for all atoms in ct using current coordinates.

Parameters:ct (schrodinger.structure.Structure object) – Set reference coordinates for the structure, modified in place.
schrodinger.application.desmond.struc.get_reference_ct(ct: schrodinger.structure.Structure) → schrodinger.structure.Structure

Get reference structure. If reference coordinates are not defined, this returns the current structure.

Parameters:ct (schrodinger.structure.Structure object) – Get the reference coordinates for the structure, this is not modified.
Returns:The structure with the reference coordinates.
Return type:schrodinger.structure.Structure object
schrodinger.application.desmond.struc.hash_title(ct: schrodinger.structure.Structure) → str

Hash a structure’s title string and return the hash. :param ct: Structure to get title from.

schrodinger.application.desmond.struc.fixup_duplicate_property(cts: List[schrodinger.structure.Structure]) → List[schrodinger.structure.Structure]

Return a list of structures where the properties that only differ by the type have been deleted.

Parameters:cts – List of structures to modify.
schrodinger.application.desmond.struc.update_maestro_group(model: Cms, title: str, jobname: str) → None

Inplace modify model