molsysmt.topology.get_covalent_blocks#

molsysmt.topology.get_covalent_blocks(molecular_system, selection='all', remove_bonds=None, output_type='sets', syntax='MolSysMT')[source]#

Identifying the sets of atoms that remain covalently connected when bonds are removed.

The purpose of this function is remove_bonds: it answers which atoms would still hold together if the given bonds were cut. That is how the groups of atoms rotating around a dihedral angle are obtained, for example.

Called without remove_bonds it returns the components of the system, since a component is by definition a set of atoms mutually connected through covalent bonds. In that case it adds nothing to get(molecular_system, element=’component’), which is the ordinary way of asking for them.

Parameters:

molecular_system (molecular system) – Input system in any of the supported forms.
selection (str, list, tuple or numpy.ndarray, default 'all') – Atom selection used to build the bond graph. Atoms outside it are absent from every block, so a selection can split a block just as removing a bond does.
remove_bonds (array-like, optional) – Pairs of atom indices to remove from the bond graph before the blocks are computed. The molecular system itself is not modified: the removal is hypothetical and affects only this result.
output_type ({'sets', 'numpy.ndarray'}, default 'sets') – Output format: a list of sets of atom indices, or an array labeling each atom with the index of the block it belongs to.
syntax (str, default 'MolSysMT') – Selection syntax for string-based selections.

Returns:

Covalent blocks as sets of atom indices, or a 0-based block label per atom.

Return type:

numpy.ndarray or list

Raises:

NotImplementedMethodError – If output_type is unsupported.

Notes

Builds a bond graph with get_bondgraph and returns its connected components after removing the requested bonds.
The blocks are not the component attribute of the system unless remove_bonds is None and selection is ‘all’. With either of them the result describes a hypothetical connectivity, not the system’s own components.