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 analyzes the atomic coordinates and element types in a molecular system to infer and add covalent bonds between atoms that are close enough based on standard bonding distances. The new bonds are added to the bonded_atoms attribute. No bond types or orders are assigned. The procedure can be applied in-place or return a modified copy.

Parameters:

  • molecular_system (molecular system) – Molecular system in any of the supported forms to which new covalent bonds will be added.

  • max_bond_length (str or float with unit, default '2 angstroms') – Maximum distance between two atoms for a bond to be considered. Atoms further than this value will not be bonded. If a string is passed, it must include units (e.g., ‘0.19 nm’).

  • selection (tuple, list, numpy.ndarray or str, default 'all') – Selection of atoms to which the method applies. The selection can be given by a list, tuple or numpy array of atom indices (0-based integers), or by a query string following any of the selection syntaxes parsable by MolSysMT.

  • structure_index (int, default 0) – Structure index (0-based) to use when the molecular system contains multiple structures. The bond detection is based on the atomic positions at this structure.

  • syntax (str, default 'MolSysMT') – Supported syntax used in the selection argument (in case it is a string).

  • engine ({'MolSysMT'}, default 'MolSysMT') – Engine used to infer bonds. Currently only the native ‘MolSysMT’ engine is supported.

  • in_place (bool, default True) – If True, the input molecular system is modified directly. If False, a new system with the added bonds is returned.

  • skip_digestion (bool, default False) – If True, skips initial validation of input arguments. Used internally.

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 frames).

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.add_bonds()

Manually add specific bonds to a molecular system.

molsysmt.build.remove_bonds()

Remove covalent bonds from a molecular system.

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)
>>> msm.build.remove_bonds(system)
>>> msm.build.add_missing_bonds(system)
>>> msm.get(system, bonded_atoms=True)[:3]
array([[0, 1],
       [1, 2],
       [2, 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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