molsysmt.build.add_bonds#

molsysmt.build.add_bonds(molecular_system, bonded_atom_pairs, in_place=True, skip_digestion=False)[source]#

Adding covalent bonds between atom pairs in a molecular system.

This function adds new covalent bonds between pairs of atoms in a molecular system. The new bonds are defined by a list of atom index pairs. The function modifies the input molecular system in place unless otherwise specified.

Parameters:

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

  • bonded_atom_pairs (list, tuple, or numpy.ndarray of shape (n_bonds, 2)) – List or array of atom index pairs (0-based integers), where each pair defines a bond to be added.

  • in_place (bool, default True) – Whether to modify the input molecular system in place. If set to False, a copy of the molecular system is returned with the new bonds added.

  • skip_digestion (bool, default False) – If True, skips the initial validation and normalization of the input arguments. Mainly used internally.

Returns:

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

Return type:

molecular system or None

Raises:

  • NotSupportedFormError – Raised if the molecular system has a format that does not support topology editing.

  • ArgumentError – Raised if the input atom indices are invalid or improperly formatted.

Notes

  • This function only updates the topological attribute bonded_atoms.

  • No bond orders or bond types are inferred or assigned.

  • Atom indices must be valid and within the range of the molecular system’s atoms.

See also

molsysmt.build.remove_bonds()

Remove specific bonds from a molecular system.

molsysmt.build.add_missing_bonds()

Add bonds based on distance criteria and atomic types.

Examples

>>> import molsysmt as msm
>>> system = msm.convert('181L')
>>> new_bonds = [(0, 4), (5, 10)]
>>> msm.build.add_bonds(system, new_bonds)
>>> msm.get(system, bonded_atoms=True)[:5]
array([[0, 1],
       [1, 2],
       [2, 3],
       [3, 4],
       [0, 4]])

User guide

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

Added in version 1.0.0.

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