molsysmt.topology.get_covalent_chains

molsysmt.topology.get_covalent_chains(molecular_system, chain=None, selection='all', syntax='MolSysMT')

Building covalent chains given ordered selections for each position.

Parameters:

• molecular_system (molecular system) – Input system.

• chain (list of selections) – Ordered selections (per position) defining allowed atoms at each chain step.

• selection (str, list, tuple or numpy.ndarray, default 'all') – Global atom filter applied before chain assembly.

• syntax (str, default 'MolSysMT') – Selection syntax for string-based selections.

Returns:

Array of chains (lists of atom indices) satisfying connectivity across the positions.

Return type:

numpy.ndarray

Notes

• Uses the bond graph to walk across allowed atoms at each position.

Added in version 1.0.0.