Source code for psi4.driver.wrapper_autofrag

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__all__ = ["auto_fragments"]

from typing import List, Optional

from psi4 import core


[docs]def auto_fragments( molecule: Optional[core.Molecule] = None, seed_atoms: Optional[List[List[int]]] = None, ) -> core.Molecule: r"""Detects fragments in unfragmented molecule using BFS algorithm. Currently only used for the WebMO implementation of SAPT. Parameters ---------- molecule : :ref:`molecule <op_py_molecule>`, optional The target molecule, if not the last molecule defined. seed_atoms List of lists of atoms (0-indexed) belonging to independent fragments. Useful to prompt algorithm or to define intramolecular fragments through border atoms. Example: `[[1, 0], [2]]` Returns ------- :py:class:`~psi4.core.Molecule` |w--w| fragmented molecule in Cartesian, fixed-geom (no variable values), no dummy-atom format. Examples -------- >>> # [1] prepare unfragmented (and non-adjacent-atom) HHFF into (HF)_2 molecule ready for SAPT >>> molecule mol {\nH 0.0 0.0 0.0\nH 2.0 0.0 0.0\nF 0.0 1.0 0.0\nF 2.0 1.0 0.0\n} >>> print mol.nfragments() # 1 >>> fragmol = auto_fragments() >>> print fragmol.nfragments() # 2 """ # Make sure the molecule the user provided is the active one if molecule is None: molecule = core.get_active_molecule() molecule.update_geometry() molname = molecule.name() frag, bmol = molecule.BFS(seed_atoms=seed_atoms, return_molecule=True) bmol.set_name(molname) bmol.print_cluster() core.print_out(""" Exiting auto_fragments\n""") return bmol