![]() ![]() Gets the cleaned up label of atom (C2 => C, H4 = H) (0-indexed including dummies) Returns a new Molecule constructed from python dictionary.įrom_schema(molschema)įrom_string(molstr) Returns a string of Molecule formatted for mol2.įrom_arrays()Ĭonstruct Molecule from unvalidated arrays and variables. Uses the point group object obtain by calling point_group() Gets mass of atom (0-indexed including dummies) Gets the original label of the atom arg0 as given in the input file (C2, H4)(0-indexed including dummies) Sets whether to fix the Cartesian position, or to translate to the C.O.M.įix the orientation at its current frame. Gets charge of atom (0-indexed including dummies)įind_highest_point_group(self)įinds highest possible computational molecular point groupįinds computational molecular point group, user can override this with the symmetry keyword Nuclear charge of atom arg1 (0-indexed including dummies) Sets all fragments in the molecule to be inactive Gets a string re-expressing in input format the current state of the molecule.Contains Cartesian geometry info, fragmentation, charges and multiplicities, and any frame restriction. Gets whether or not center of mass is fixed Gets charge of atom (0-indexed without dummies) Gets the label of the orbital basis set on a given atom arg0Ĭomputes center of mass of molecule (does not translate molecule) Sets all fragments in the molecule to be activeĪdd_atom(self, Z, x, y, z, symbol, mass, .)Īdds to self Molecule an atom with atomic number Z, Cartesian coordinates in Bohr ( x, y, z), atomic symbol, mass, and charge, extended atomic label, and mass number A Nuclear charge of atom arg0 (0-indexed without dummies) of a molecule.ī787(ref_mol)įinds shift, rotation, and atom reordering of concern_mol that best aligns with ref_mol.ĭetect fragments among real atoms through a breadth-first search (BFS) algorithm. Class to store the elements, coordinates, fragmentation pattern, basis sets, charge, multiplicity, etc. ![]()
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