molsysmt.topology.get_rigid_fragments#

molsysmt.topology.get_rigid_fragments(molecular_system, bond_indices=None, chemical_state='reference', structure_indices='all', skip_digestion=False)[source]#

Deriving rigid fragments by cutting explicitly selected covalent bonds.

Parameters:

  • molecular_system (molecular system) – Molecular system in any supported form with a complete covalent graph.

  • bond_indices (int, list, tuple or numpy.ndarray, default=None) – Source bond indices (0-based) to cut. None cuts no bonds. Repeated indices are deduplicated. Dative and ring cuts are rejected.

  • chemical_state (str, int or None, default='reference') – Chemical state supplying connectivity. ‘structure’ resolves the state assigned to the selected structures; these must agree on one state.

  • structure_indices (int, list, tuple or numpy.ndarray, default='all') – Structure indices (0-based) used only for chemical-state resolution.

  • skip_digestion (bool, default=False) – Whether to skip argument digestion. Default is False.

Returns:

Packed int64 fragment_atom_indices and fragment_offsets, a fragment index for each source atom (atom_fragment_indices), selected source bond_indices and bonded_atom_pairs, and aligned fragment_pairs. Also includes atom_indices, chemical_state_index and connectivity evidence. Fragments and their memberships are sorted by source atom index.

Return type:

dict

Raises:

  • ArgumentError – If a cut is out of range, noncovalent, or does not separate its endpoints.

  • StructuralInconsistencyError – If complete, valid chemical connectivity is unavailable.

Notes

Rigidity here means connectivity after the supplied cuts. This function does not classify chemically rotatable bonds, impose torsion angles or root a PDBQT tree. Bond orders are not needed for explicit graph cuts. Every selected bond must be a bridge in the original covalent graph; cutting multiple ring edges does not make them eligible torsions. Coordinates and the source chemical state are not modified.

See also

get_covalent_blocks

Find connected atom sets after removing atom pairs.

get_rings

Perceive a minimum cycle basis from declared connectivity.

Examples

>>> import molsysmt as msm
>>> import pandas as pd
>>> from molsysmt.native import Topology
>>> topology = Topology(n_atoms=3)
>>> topology.bonds = pd.DataFrame({'atom1_index': [0, 1],
...     'atom2_index': [1, 2], 'bond_type': ['covalent', 'covalent']})
>>> topology._chemical_states[0].connectivity_completeness = 'complete'
>>> result = msm.topology.get_rigid_fragments(topology, bond_indices=[1])
>>> result['fragment_atom_indices'].tolist(), result['fragment_offsets'].tolist()
([0, 1, 2], [0, 2, 3])

Tutorial with more examples

See Deriving rigid fragments for explicit graph cuts.

Added in version 1.0.0.

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