molsysmt.build.get_missing_bonds#

molsysmt.build.get_missing_bonds(molecular_system, selection='all', structure_index=0, max_bond_length='2 angstroms', disulfide_bonds=False, disulfide_group_names=None, pbc=True, syntax='MolSysMT', engine='MolSysMT', sorted=True, skip_digestion=False)[source]#

Identify bonds that are present in the chemical structure but absent from the topology.

This function compares the bonds inferred from residue templates and/or distance-based neighbor searches against the bonds already recorded in the topology of the molecular system and returns those that are missing. Peptidic bonds between consecutive amino acids and, optionally, disulfide bonds between cysteine residues are also detected.

Parameters:

  • molecular_system (molecular system) – Molecular system in any of the supported forms.

  • selection (str, list, tuple, or numpy.ndarray, default 'all') – Atom selection that limits the scope of the search.

  • structure_index (int, default 0) – Index of the structure frame used for distance-based bond detection.

  • max_bond_length (str or quantity, default '2 angstroms') – Maximum interatomic distance to be considered a potential bond when using distance-based inference for groups without a known template.

  • disulfide_bonds (bool, default False) – Whether to detect disulfide bonds between sulfur atoms of the specified disulfide_group_names residues.

  • disulfide_group_names (list of str, default ['CYS']) – Residue names to search for potential disulfide bond partners when disulfide_bonds is True.

  • pbc (bool, default True) – Whether to apply periodic boundary conditions when computing interatomic distances.

  • syntax (str, default 'MolSysMT') – Syntax used to interpret the selection string.

  • engine ({'MolSysMT', 'pytraj'}, default 'MolSysMT') – Backend used to perform bond detection.

  • sorted (bool, default True) – If True, each pair in the output is ordered so that the smaller atom index comes first, and the list itself is sorted lexicographically.

  • skip_digestion (bool, default False) – If True, argument digestion is skipped (intended for internal use).

Returns:

List of [atom_index_1, atom_index_2] pairs representing bonds that are present according to chemical templates or distance criteria but not yet recorded in the molecular system topology.

Return type:

list of [int, int]

Raises:

  • NotImplementedMethodError – Raised if the requested engine is not supported.

  • ArgumentChoiceError – Raised if a terminal capping group cannot be classified as N- or C-terminal.

Notes

For groups with a known template (water, ion, amino acid, terminal capping, small molecule, saccharide), intra-group bonds are taken from the corresponding template. For groups without a template, bonds are inferred by a distance-based neighbor search using max_bond_length and element-pair thresholds stored in molsysmt.element.bond.

Peptidic C–N bonds between consecutive residues are detected via a distance filter applied to the backbone C and N atoms of adjacent groups.

Added in version 1.0.0.

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