molsysmt.build.add_missing_bonds#

molsysmt.build.add_missing_bonds(molecular_system, max_bond_length='2 angstroms', selection='all', structure_index=0, syntax='MolSysMT', engine='MolSysMT', in_place=True, skip_digestion=False)[source]#

Adding missing covalent bonds based on atomic distances and types.

This function adds candidates returned by get_missing_bonds from group templates and distance criteria. Peptide candidates require consecutive source group indices with one identical, defined chain index. Selecting separated groups does not make them adjacent. No bond types or orders are assigned. The procedure can be applied in-place or return a modified copy; its heuristics do not certify a complete or chemically validated molecular graph.

Parameters:

  • molecular_system (molecular system) – Molecular system in any supported MolSysMT format.

  • max_bond_length (quantity or str, default='2 angstroms') – Distance cutoff for geometric candidates, with explicit length units. Defaults to ‘2 angstroms’.

  • selection (str, list, tuple, or numpy.ndarray, default='all') – Atom selection. Integer lists refer to source atom indices. Both endpoints of each added pair must belong to the selection. Defaults to ‘all’.

  • structure_index (int, default=0) – Source structure index used for distance-based candidates. Defaults to 0.

  • syntax (str, default='MolSysMT') – Selection syntax used to evaluate selection (e.g., ‘MolSysMT’, ‘MDTraj’).

  • engine (str, default='MolSysMT') – Reconstruction engine. Defaults to ‘MolSysMT’.

  • in_place (bool, default=True) – Whether to modify the source or return a modified copy. Defaults to True.

  • skip_digestion (bool, default=False) – Whether to skip MolSysMT’s internal argument digestion mechanism.

Returns:

If in_place=True, the function returns None and modifies the input molecular system. If in_place=False, a new molecular system is returned with inferred bonds added.

Return type:

molecular system or None

Raises:

  • NotSupportedFormError – Raised if the input molecular system is in a form that cannot be edited.

  • ArgumentError – Raised if any of the input arguments are invalid or inconsistent.

Notes

This method updates only the bonded_atoms attribute of the system. No bond types or orders are assigned.

This function is useful when working with coordinate files that lack bond information (e.g., .xyz, .pdb, or trajectory structures).

The list of supported molecular systems’ forms is detailed in the documentation section: User Guide > Introduction > Molecular systems > Forms

The list of supported selection syntaxes can be found here: User Guide > Introduction > Selection syntaxes

See also

molsysmt.build.get_missing_bonds()

Inspect candidates and their selection and chain constraints before adding them.

molsysmt.Topology.add_bonds()

Manually add specific bonds to a native topology.

molsysmt.Topology.remove_bonds()

Remove covalent bonds from a native topology.

molsysmt.basic.get()

Access attributes like bonded_atoms.

molsysmt.basic.convert()

Convert the system into a supported editable form.

Examples

>>> import molsysmt as msm
>>> molsys = msm.systems['alanine dipeptide']['alanine_dipeptide.h5msm']
>>> system = msm.convert(molsys)
>>> system.topology.remove_bonds('all')
>>> msm.build.add_missing_bonds(system)
>>> msm.get(system, bonded_atom_pairs=True)[:3]
[[0, 1], [1, 2], [1, 3]]

User guide

Follow this link for a tutorial on how to work with this function: User Guide > Tools > Build > Add missing bonds.

Added in version 1.0.0.

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