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_structure_properties(structures, property_keys)

For a supplied list of structures and structure property keys, delete the property values associated with those keys from each structure if possible.

Parameters:

• structures (list(structure.Structure) or structure.Structure) – a list of structure (or a single structure) from which to delete the specified properties
• property_keys (list(str) or str) – a list of structure property keys (or a single structure property keys) that should be deleted from the supplied structures

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

Similar to delete_structure_properties(), 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.hash_str(str_to_hash: str) → str

Return the hash.

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

schrodinger.application.desmond.struc.get_res_ct_and_atom_idx(res: schrodinger.structure._Residue, cap=False) → Tuple[schrodinger.structure.Structure, Dict[int, int]]

Given a structure._Residue object, extract the residue structure and a map of from the original atom index to the residue fragment atom index.

Parameters:

• res – Residue to extract
• cap – Set to True to add capping groups, default is False. These atoms are not included in the atom index.

schrodinger.application.desmond.struc.align_cap(ct0: schrodinger.structure.Structure, ct1: schrodinger.structure.Structure) → None

Given two capped peptides, set the coordinates for the cap groups in ct1 to match those of ct1.

Parameters:

• ct0 – The reference structure.
• ct1 – The structure to modify in place.