utils.indices

Functions

get_backbone_indices(atom_list)	Returns list of protein backbone indices.
get_residue_indices(atom_list[, name, ...])	Returns a list of indices that correspond to a given residue in the crd file.

utils.indices.get_residue_indices(atom_list: openmm.app.internal.charmm.topologyobjects.AtomList, name: List[str] = ['ala', 'arg', 'asn', 'asp', 'cys', 'gln', 'glu', 'gly', 'his', 'ile', 'leu', 'lys', 'met', 'phe', 'pro', 'pyl', 'ser', 'sec', 'thr', 'trp', 'tyr', 'val', 'asx', 'glx', 'xaa', 'xle'], include_hydrogens: bool = True) → List[int]

Returns a list of indices that correspond to a given residue in the crd file. If you do not give a residue name, the indices of all the protein atoms are given.

Args:

atom_list (app.internal.charmm.topologyobjects.AtomList): atom list that should be searched for indices. name (List[str]orstr, optional): residue name to be searched for. if none is given, the atom list is searched for amino acid residues. Defaults to AA.

Returns:

List[int]: list of indices in the crd file.

utils.indices.get_backbone_indices(atom_list: openmm.app.internal.charmm.topologyobjects.AtomList) → List[int]

Returns list of protein backbone indices.

Args:

atom_list (app.internal.charmm.topologyobjects.AtomList): [description]

Returns:

List[int]: [description]