molsysmt.topology.get_covalent_paths#

molsysmt.topology.get_covalent_paths(molecular_system, path=None, selection='all', syntax='MolSysMT')[source]#

Finding paths of covalently bonded atoms matching an ordered pattern.

Every returned path is a walk along covalent bonds whose n-th atom satisfies the n-th selection of path. Typical uses are locating the atom quartets that define a dihedral angle, or the donor-hydrogen pairs of a hydrogen bond.

Parameters:

molecular_system (molecular system) – Molecular system in any supported MolSysMT format.
path (list, tuple, or numpy.ndarray, or None, default=None) – Ordered atom indices defining the covalent path to evaluate.
selection (str, list, tuple, or numpy.ndarray, default='all') – Selection string or boolean/integer array specifying elements.
syntax (str, default='MolSysMT') – Selection syntax used to evaluate selection (e.g., ‘MolSysMT’, ‘MDTraj’).

Returns:

Array of shape (n_paths, len(path)) with the atom indices of every path found. Order within a path follows the pattern; paths are not deduplicated by reversal.

Return type:

numpy.ndarray

Notes

“Path” is used in the graph sense: a walk over the covalent bond graph. It is unrelated to the chain element of a molecular system, which is a polymer chain. To work with those, use molsysmt.basic.get() with element=’chain’.
Only covalent bonds are traversed. See molsysmt.topology.get_bondgraph() for the graph itself.