Molecule¶

class psi4.core.Molecule¶

Bases: pybind11_builtins.pybind11_object

Class to store the elements, coordinates, fragmentation pattern, basis sets, charge, multiplicity, etc. of a molecule.

Methods Summary

`B787`(ref_mol[, do_plot, verbose, atoms_map, …])	Finds shift, rotation, and atom reordering of concern_mol that best aligns with ref_mol.
`BFS`([seed_atoms, bond_threshold, …])	Detect fragments among real atoms through a breadth-first search (BFS) algorithm.
`Z`(self, arg0)	Nuclear charge of atom arg0 (0-indexed without dummies)
`activate_all_fragments`(self)	Sets all fragments in the molecule to be active
`add_atom`(self, Z, x, y, z, symbol, mass, …)	Adds 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
`atom_at_position`(args, *kwargs)	Overloaded function.
`basis_on_atom`(self, arg0)	Gets the label of the orbital basis set on a given atom arg0
`center_of_mass`(self)	Computes center of mass of molecule (does not translate molecule)
`charge`(self, atom)	Gets charge of atom (0-indexed without dummies)
`clone`(self)	Returns a new Molecule identical to arg1
`com_fixed`(self)	Gets whether or not center of mass is fixed
`comment`(self)	Gets molecule comment
`connectivity`(self)	Gets molecule connectivity
`create_psi4_string_from_molecule`(self)	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.
`deactivate_all_fragments`(self)	Sets all fragments in the molecule to be inactive
`distance_matrix`(self)	Returns Matrix of interatom distances
`extract_subsets`(args, *kwargs)	Overloaded function.
`fZ`(self, arg0)	Nuclear charge of atom arg1 (0-indexed including dummies)
`fcharge`(self, atom)	Gets charge of atom (0-indexed including dummies)
`find_highest_point_group`(self, tolerance)	Finds highest possible computational molecular point group
`find_point_group`(self, tolerance)	Finds computational molecular point group, user can override this with the symmetry keyword
`fix_com`(self, arg0)	Sets whether to fix the Cartesian position, or to translate to the C.O.M.
`fix_orientation`(self, arg0)	Fix the orientation at its current frame
`flabel`(self, atom)	Gets the original label of the atom arg0 as given in the input file (C2, H4)(0-indexed including dummies)
`fmass`(self, atom)	Gets mass of atom (0-indexed including dummies)
`form_symmetry_information`(self, arg0)	Uses the point group object obtain by calling point_group()
`format_molecule_for_mol`()	Returns a string of Molecule formatted for mol2.
`from_arrays`([geom, elea, elez, elem, mass, …])	Construct Molecule from unvalidated arrays and variables.
`from_dict`(arg0)	Returns a new Molecule constructed from python dictionary.
`from_schema`(molschema[, return_dict, verbose])	Construct Molecule from non-Psi4 schema.
`from_string`(molstr[, dtype, name, fix_com, …])
`fsymbol`(self, atom)	Gets the cleaned up label of atom (C2 => C, H4 = H) (0-indexed including dummies)
`ftrue_atomic_number`(self, atom)	Gets atomic number of atom from element (0-indexed including dummies)
`full_geometry`(self)	Gets the geometry [Bohr] as a (Natom X 3) matrix of coordinates (including dummies)
`full_pg_n`(self)	Gets n in Cnv, etc.; If there is no n (e.g.
`fx`(self, arg0)	x position of atom arg0 (0-indexed including dummies in Bohr)
`fy`(self, arg0)	y position of atom arg0 (0-indexed including dummies in Bohr)
`fz`(self, arg0)	z position of atom arg0 (0-indexed including dummies in Bohr)
`geometry`(self)	Gets the geometry [Bohr] as a (Natom X 3) matrix of coordinates (excluding dummies)
`get_fragment_charges`(self)	Gets the charge of each fragment
`get_fragment_multiplicities`(self)	Gets the multiplicity of each fragment
`get_fragment_types`(self)	Returns a list describing how to handle each fragment {Real, Ghost, Absent}
`get_fragments`(self)	Returns list of pairs of atom ranges defining each fragment from parent molecule(fragments[frag_ind] = <Afirst,Alast+1>)
`get_full_point_group`(self)	Gets point group name such as C3v or S8
`get_full_point_group_with_n`(self)	Gets point group name such as Cnv or Sn
`get_variable`(self, arg0)	Returns the value of variable arg0 in the structural variables list
`inertia_tensor`(self)	Returns intertial tensor
`input_units_to_au`(self)	Returns unit conversion to [a0] for geometry
`irrep_labels`(self)	Returns Irreducible Representation symmetry labels
`is_variable`(self, arg0)	Checks if variable arg0 is in the structural variables list
`label`(self, atom)	Gets the original label of the atom as given in the input file (C2, H4)(0-indexed without dummies)
`mass`(self, atom)	Returns mass of atom (0-indexed)
`mass_number`(self, arg0)	Mass number (A) of atom if known, else -1
`molecular_charge`(self)	Gets the molecular charge
`move_to_com`(self)	Moves molecule to center of mass
`multiplicity`(self)	Gets the multiplicity (defined as 2Ms + 1)
`nallatom`(self)	Number of real and dummy atoms
`name`(self)	Gets molecule name
`natom`(self)	Number of real atoms
`nfragments`(self)	Gets the number of fragments in the molecule
`nuclear_dipole`(args, *kwargs)	Overloaded function.
`nuclear_repulsion_energy`(self, dipole_field, …)	Computes nuclear repulsion energy
`nuclear_repulsion_energy_deriv1`(self, …)	Returns first derivative of nuclear repulsion energy as a matrix (natom, 3)
`nuclear_repulsion_energy_deriv2`(self)	Returns second derivative of nuclear repulsion energy as a matrix (natom X 3, natom X 3)
`orientation_fixed`(self)	Get whether or not orientation is fixed
`point_group`(self)	Returns the current point group object
`print_bond_angles`(self)	Print the bond angle geometrical parameters
`print_cluster`(self)	Prints the molecule in Cartesians in input units adding fragment separators
`print_distances`(self)	Print the interatomic distance geometrical parameters
`print_in_input_format`(self)	Prints the molecule as Cartesian or ZMatrix entries, just as inputted.
`print_out`(self)	Prints the molecule in Cartesians in input units to output file
`print_out_in_angstrom`(self)	Prints the molecule in Cartesians in Angstroms to output file
`print_out_in_bohr`(self)	Prints the molecule in Cartesians in Bohr to output file
`print_out_of_planes`(self)	Print the out-of-plane angle geometrical parameters to output file
`print_rotational_constants`(self)	Print the rotational constants to output file
`provenance`(self)	Gets molecule provenance
`reinterpret_coordentry`(self, arg0)	Do reinterpret coordinate entries during update_geometry().
`reset_point_group`(self, arg0)	Overrides symmetry from outside the molecule string
`rotational_constants`(self)	Returns the rotational constants [cm^-1] of the molecule
`rotational_symmetry_number`(self)	Returns number of unique orientations of the rigid molecule that only interchange identical atoms
`rotor_type`(self)	Returns rotor type, e.g.
`run_dftd3`([func, dashlvl, dashparam, …])	Compute dispersion correction via Grimme’s DFTD3 program.
`run_gcp`([func, dertype, verbose])	Function to call Grimme’s GCP program https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/gcp/gcp to compute an a posteriori geometrical BSSE correction to self for several HF, generic DFT, and specific HF-3c and PBEh-3c method/basis combinations, func.
`save_string_xyz`(self)	Saves the string of an XYZ file to arg2
`save_string_xyz_file`(self)	Saves an XYZ file to arg2
`save_xyz_file`(self, arg0, arg1)	Saves an XYZ file to arg0
`schoenflies_symbol`(self)	Returns the Schoenflies symbol
`scramble`([do_shift, do_rotate, do_resort, …])	Tester for B787 by shifting, rotating, and atom shuffling ref_mol and checking that the aligner returns the opposite transformation.
`set_active_fragment`(self, arg0)	Sets the specified fragment arg0 to be Real
`set_active_fragments`(self, arg0)	Sets the specified list arg0 of fragments to be Real
`set_basis_all_atoms`(self, arg0, arg1)	Sets basis set arg0 to all atoms
`set_basis_by_label`(self, arg0, arg1, arg2)	Sets basis set arg1 to all atoms with label (e.g., H4) arg0
`set_basis_by_symbol`(self, arg0, arg1, arg2)	Sets basis set arg1 to all atoms with symbol (e.g., H) arg0
`set_comment`(self, arg0)	Sets molecule comment
`set_connectivity`(self, arg0, int, float]])	Sets molecule connectivity
`set_full_geometry`(self, arg0)	Sets the geometry, given a (Natom X 3) matrix arg0 of coordinates (in Bohr) (including dummies
`set_geometry`(self, arg0)	Sets the geometry, given a (Natom X 3) matrix arg0 of coordinates [a0] (excluding dummies)
`set_ghost_fragment`(self, arg0)	Sets the specified fragment arg0 to be Ghost
`set_ghost_fragments`(self, arg0)	Sets the specified list arg0 of fragments to be Ghost
`set_input_units_to_au`(self, arg0)	Sets unit conversion to [a0] for geometry
`set_mass`(self, atom, mass)	Sets mass of atom (0-indexed) to mass (good for isotopic substitutions)
`set_molecular_charge`(self, arg0)	Change the overall molecular charge.
`set_multiplicity`(self, arg0)	Change the multiplicity (defined as 2S + 1).
`set_name`(self, arg0)	Sets molecule name
`set_nuclear_charge`(self, arg0, arg1)	Set the nuclear charge of the given atom arg0 to the value arg1 (primarily for ECP).
`set_point_group`(self, arg0)	Sets the molecular point group to the point group object arg0
`set_provenance`(self, arg0, str])	Sets molecule provenance
`set_units`(self, arg0)	Sets units (Angstrom or Bohr) used to define the geometry.
`set_variable`(self, arg0, arg1)	Sets the value arg1 to the variable arg0 in the list of structure variables, then calls update_geometry()
`symbol`(self, atom)	Gets the cleaned up label of atom (C2 => C, H4 = H) (0-indexed without dummies)
`symmetrize`(self, arg0)	Finds the highest point Abelian point group within the specified tolerance, and forces the geometry to have that symmetry.
`symmetry_from_input`(self)	Returns the symmetry specified in the input
`to_arrays`([dummy, ghost_as_dummy])	Exports coordinate info into NumPy arrays.
`to_dict`([force_c1, force_units, np_out])	Serializes instance into Molecule dictionary.
`to_schema`(dtype[, units])	Serializes instance into dictionary according to schema dtype.
`to_string`(dtype[, units, atom_format, …])	Format a string representation of QM molecule.
`translate`(self, arg0)	Translates molecule by arg0
`true_atomic_number`(self, atom)	Gets atomic number of atom from element (0-indexed without dummies)
`units`(self)	Returns units used to define the geometry, i.e.
`update_geometry`(self)	Reevaluates the geometry with current variable values, orientation directives, etc.
`x`(self, arg0)	x position [Bohr] of atom arg0 (0-indexed without dummies)
`xyz`(self, i)	Return the Vector3 for atom i (0-indexed without dummies)
`y`(self, arg0)	y position [Bohr] of atom arg0 (0-indexed without dummies)
`z`(self, arg0)	z position [Bohr] of atom arg0 (0-indexed without dummies)

Methods Documentation

B787(ref_mol, do_plot=False, verbose=1, atoms_map=False, run_resorting=False, mols_align=False, run_to_completion=False, uno_cutoff=0.001, run_mirror=False)[source]¶

Finds shift, rotation, and atom reordering of concern_mol that best aligns with ref_mol.

Wraps qcdb.align.B787() for qcdb.Molecule or psi4.core.Molecule. Employs the Kabsch, Hungarian, and Uno algorithms to exhaustively locate the best alignment for non-oriented, non-ordered structures.

Parameters:	concern_mol (qcdb.Molecule or psi4.core.Molecule) – Molecule of concern, to be shifted, rotated, and reordered into best coincidence with ref_mol. ref_mol (qcdb.Molecule or psi4.core.Molecule) – Molecule to match. atoms_map (bool, optional) – Whether atom1 of ref_mol corresponds to atom1 of concern_mol, etc. If true, specifying True can save much time. mols_align (bool, optional) – Whether ref_mol and concern_mol have identical geometries by eye (barring orientation or atom mapping) and expected final RMSD = 0. If True, procedure is truncated when RMSD condition met, saving time. do_plot (bool, optional) – Pops up a mpl plot showing before, after, and ref geometries. run_to_completion (bool, optional) – Run reorderings to completion (past RMSD = 0) even if unnecessary because mols_align=True. Used to test worst-case timings. run_resorting (bool, optional) – Run the resorting machinery even if unnecessary because atoms_map=True. uno_cutoff (float, optional) – TODO run_mirror (bool, optional) – Run alternate geometries potentially allowing best match to ref_mol from mirror image of concern_mol. Only run if system confirmed to be nonsuperimposable upon mirror reflection.
Returns:	First item is RMSD [A] between ref_mol and the optimally aligned geometry computed. Second item is a AlignmentMill namedtuple with fields (shift, rotation, atommap, mirror) that prescribe the transformation from concern_mol and the optimally aligned geometry. Third item is a crude charge-, multiplicity-, fragment-less Molecule at optimally aligned (and atom-ordered) geometry. Return type determined by concern_mol type.
Return type:	float, tuple, qcdb.Molecule or psi4.core.Molecule

BFS(seed_atoms=None, bond_threshold=1.2, return_arrays=False, return_molecules=False, return_molecule=False)[source]¶

Detect fragments among real atoms through a breadth-first search (BFS) algorithm.

Parameters:

self (qcdb.Molecule or psi4.core.Molecule) –
seed_atoms (list, optional) – 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]]
bond_threshold (float, optional) – Factor beyond average of covalent radii to determine bond cutoff.
return_arrays (bool, optional) – If True, also return fragments as list of arrays.
return_molecules (bool, optional) – If True, also return fragments as list of Molecules.
return_molecule (bool, optional) – If True, also return one big Molecule with fragmentation encoded.

Returns:

bfs_map (list of lists) – Array of atom indices (0-indexed) of detected fragments.
bfs_arrays (tuple of lists of ndarray, optional) – geom, mass, elem info per-fragment. Only provided if return_arrays is True.
bfs_molecules (list of qcdb.Molecule or psi4.core.Molecule, optional) – List of molecules, each built from one fragment. Center and orientation of fragments is fixed so orientation info from self is not lost. Loses chgmult and ghost/dummy info from self and contains default chgmult. Only provided if return_molecules is True. Returned are of same type as self.
bfs_molecule (qcdb.Molecule or psi4.core.Molecule, optional) – Single molecule with same number of real atoms as self with atoms reordered into adjacent fragments and fragment markers inserted. Loses ghost/dummy info from self; keeps total charge but not total mult. Only provided if return_molecule is True. Returned is of same type as self.

Notes

Relies upon van der Waals radii and so faulty for close (especially: hydrogen-bonded) fragments. See seed_atoms.

Any existing fragmentation info/chgmult encoded in self is lost.

Original code from Michael S. Marshall, linear-scaling algorithm from Trent M. Parker, revamped by Lori A. Burns

Z(self: psi4.core.Molecule, arg0: int) → float¶: Nuclear charge of atom arg0 (0-indexed without dummies)

activate_all_fragments(self: psi4.core.Molecule) → None¶: Sets all fragments in the molecule to be active

add_atom(self: psi4.core.Molecule, Z: float, x: float, y: float, z: float, symbol: str, mass: float, charge: float, label: str, A: int) → None¶: Adds 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

atom_at_position(*args, **kwargs)¶

Overloaded function.

atom_at_position(self: psi4.core.Molecule, coord: float, tol: float) -> int

Tests to see if an atom is at the position coord with a given tolerance tol

atom_at_position(self: psi4.core.Molecule, coord: List[float[3]], tol: float) -> int

Tests to see if an atom is at the position coord with a given tolerance tol

basis_on_atom(self: psi4.core.Molecule, arg0: int) → str¶: Gets the label of the orbital basis set on a given atom arg0

center_of_mass(self: psi4.core.Molecule) → psi4.core.Vector3¶: Computes center of mass of molecule (does not translate molecule)

charge(self: psi4.core.Molecule, atom: int) → float¶: Gets charge of atom (0-indexed without dummies)

clone(self: psi4.core.Molecule) → psi4.core.Molecule¶: Returns a new Molecule identical to arg1

com_fixed(self: psi4.core.Molecule) → bool¶: Gets whether or not center of mass is fixed

comment(self: psi4.core.Molecule) → str¶: Gets molecule comment

connectivity(self: psi4.core.Molecule) → List[Tuple[int, int, float]]¶: Gets molecule connectivity

create_psi4_string_from_molecule(self: psi4.core.Molecule) → str¶: 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.

deactivate_all_fragments(self: psi4.core.Molecule) → None¶: Sets all fragments in the molecule to be inactive

distance_matrix(self: psi4.core.Molecule) → psi4.core.Matrix¶: Returns Matrix of interatom distances

extract_subsets(*args, **kwargs)¶

Overloaded function.

extract_subsets(self: psi4.core.Molecule, arg0: List[int], arg1: List[int]) -> psi4.core.Molecule

Returns copy of self with arg0 fragments Real and arg1 fragments Ghost

extract_subsets(self: psi4.core.Molecule, arg0: List[int], arg1: int) -> psi4.core.Molecule

Returns copy of self with arg0 fragments Real and arg1 fragment Ghost

extract_subsets(self: psi4.core.Molecule, arg0: int, arg1: List[int]) -> psi4.core.Molecule

Returns copy of self with arg0 fragment Real and arg1 fragments Ghost

extract_subsets(self: psi4.core.Molecule, arg0: int, arg1: int) -> psi4.core.Molecule

Returns copy of self with arg0 fragment Real and arg1 fragment Ghost

extract_subsets(self: psi4.core.Molecule, arg0: List[int]) -> psi4.core.Molecule

Returns copy of self with arg0 fragments Real

extract_subsets(self: psi4.core.Molecule, arg0: int) -> psi4.core.Molecule

Returns copy of self with arg0 fragment Real

fZ(self: psi4.core.Molecule, arg0: int) → float¶: Nuclear charge of atom arg1 (0-indexed including dummies)

fcharge(self: psi4.core.Molecule, atom: int) → float¶: Gets charge of atom (0-indexed including dummies)

find_highest_point_group(self: psi4.core.Molecule, tolerance: float=1e-08) → psi4.core.PointGroup¶: Finds highest possible computational molecular point group

find_point_group(self: psi4.core.Molecule, tolerance: float=1e-08) → psi4.core.PointGroup¶: Finds computational molecular point group, user can override this with the symmetry keyword

fix_com(self: psi4.core.Molecule, arg0: bool) → None¶: Sets whether to fix the Cartesian position, or to translate to the C.O.M.

fix_orientation(self: psi4.core.Molecule, arg0: bool) → None¶: Fix the orientation at its current frame

flabel(self: psi4.core.Molecule, atom: int) → str¶: Gets the original label of the atom arg0 as given in the input file (C2, H4)(0-indexed including dummies)

fmass(self: psi4.core.Molecule, atom: int) → float¶: Gets mass of atom (0-indexed including dummies)

form_symmetry_information(self: psi4.core.Molecule, arg0: float) → None¶: Uses the point group object obtain by calling point_group()

format_molecule_for_mol()¶

Returns a string of Molecule formatted for mol2.

Written by Trent M. Parker 9 Jun 2014

classmethod from_arrays(geom=None, elea=None, elez=None, elem=None, mass=None, real=None, elbl=None, name=None, units='Angstrom', input_units_to_au=None, fix_com=None, fix_orientation=None, fix_symmetry=None, fragment_separators=None, fragment_charges=None, fragment_multiplicities=None, molecular_charge=None, molecular_multiplicity=None, comment=None, provenance=None, connectivity=None, missing_enabled_return='error', tooclose=0.1, zero_ghost_fragments=False, nonphysical=False, mtol=0.001, verbose=1, return_dict=False)¶

Construct Molecule from unvalidated arrays and variables.

Light wrapper around from_arrays() that is a full-featured constructor to dictionary representa- tion of Molecule. This follows one step further to return Molecule instance.

:param See from_arrays().:

Returns:
Return type:	`psi4.core.Molecule`

from_dict(arg0: dict) → psi4.core.Molecule¶: Returns a new Molecule constructed from python dictionary. In progress: name and capabilities should not be relied upon

classmethod from_schema(molschema, return_dict=False, verbose=1)¶

Construct Molecule from non-Psi4 schema.

Light wrapper around from_arrays().

Parameters:

molschema (dict) – Dictionary form of Molecule following known schema.
return_dict (bool, optional) – Additionally return Molecule dictionary intermediate.
verbose (int, optional) – Amount of printing.

Returns:

mol (psi4.core.Molecule)
molrec (dict, optional) – Dictionary representation of instance. Only provided if return_dict is True.

classmethod from_string(molstr, dtype=None, name=None, fix_com=None, fix_orientation=None, fix_symmetry=None, return_dict=False, enable_qm=True, enable_efp=True, missing_enabled_return_qm='none', missing_enabled_return_efp='none', verbose=1)¶

fsymbol(self: psi4.core.Molecule, atom: int) → str¶: Gets the cleaned up label of atom (C2 => C, H4 = H) (0-indexed including dummies)

ftrue_atomic_number(self: psi4.core.Molecule, atom: int) → int¶: Gets atomic number of atom from element (0-indexed including dummies)

full_geometry(self: psi4.core.Molecule) → psi4.core.Matrix¶: Gets the geometry [Bohr] as a (Natom X 3) matrix of coordinates (including dummies)

full_pg_n(self: psi4.core.Molecule) → int¶: Gets n in Cnv, etc.; If there is no n (e.g. Td) it’s the highest-order rotation axis

fx(self: psi4.core.Molecule, arg0: int) → float¶: x position of atom arg0 (0-indexed including dummies in Bohr)

fy(self: psi4.core.Molecule, arg0: int) → float¶: y position of atom arg0 (0-indexed including dummies in Bohr)

fz(self: psi4.core.Molecule, arg0: int) → float¶: z position of atom arg0 (0-indexed including dummies in Bohr)

geometry(self: psi4.core.Molecule) → psi4.core.Matrix¶: Gets the geometry [Bohr] as a (Natom X 3) matrix of coordinates (excluding dummies)

get_fragment_charges(self: psi4.core.Molecule) → List[int]¶: Gets the charge of each fragment

get_fragment_multiplicities(self: psi4.core.Molecule) → List[int]¶: Gets the multiplicity of each fragment

get_fragment_types(self: psi4.core.Molecule) → List[str]¶: Returns a list describing how to handle each fragment {Real, Ghost, Absent}

get_fragments(self: psi4.core.Molecule) → List[Tuple[int, int]]¶: Returns list of pairs of atom ranges defining each fragment from parent molecule(fragments[frag_ind] = <Afirst,Alast+1>)

get_full_point_group(self: psi4.core.Molecule) → str¶: Gets point group name such as C3v or S8

get_full_point_group_with_n(self: psi4.core.Molecule) → str¶: Gets point group name such as Cnv or Sn

get_variable(self: psi4.core.Molecule, arg0: str) → float¶: Returns the value of variable arg0 in the structural variables list

inertia_tensor(self: psi4.core.Molecule) → psi4.core.Matrix¶: Returns intertial tensor

input_units_to_au(self: psi4.core.Molecule) → float¶: Returns unit conversion to [a0] for geometry

irrep_labels(self: psi4.core.Molecule) → List[str]¶: Returns Irreducible Representation symmetry labels

is_variable(self: psi4.core.Molecule, arg0: str) → bool¶: Checks if variable arg0 is in the structural variables list

label(self: psi4.core.Molecule, atom: int) → str¶: Gets the original label of the atom as given in the input file (C2, H4)(0-indexed without dummies)

mass(self: psi4.core.Molecule, atom: int) → float¶: Returns mass of atom (0-indexed)

mass_number(self: psi4.core.Molecule, arg0: int) → int¶: Mass number (A) of atom if known, else -1

molecular_charge(self: psi4.core.Molecule) → int¶: Gets the molecular charge

move_to_com(self: psi4.core.Molecule) → None¶: Moves molecule to center of mass

multiplicity(self: psi4.core.Molecule) → int¶: Gets the multiplicity (defined as 2Ms + 1)

nallatom(self: psi4.core.Molecule) → int¶: Number of real and dummy atoms

name(self: psi4.core.Molecule) → str¶: Gets molecule name

natom(self: psi4.core.Molecule) → int¶: Number of real atoms

nfragments(self: psi4.core.Molecule) → int¶: Gets the number of fragments in the molecule

nuclear_dipole(*args, **kwargs)¶

Overloaded function.

nuclear_dipole(self: psi4.core.Molecule, arg0: psi4.core.Vector3) -> psi4.core.Vector3

Gets the nuclear contribution to the dipole, with respect to a specified origin atg0

nuclear_dipole(self: psi4.core.Molecule) -> psi4.core.Vector3

Gets the nuclear contribution to the dipole, with respect to the origin

nuclear_repulsion_energy(self: psi4.core.Molecule, dipole_field: List[float[3]]=[0.0, 0.0, 0.0]) → float¶: Computes nuclear repulsion energy

nuclear_repulsion_energy_deriv1(self: psi4.core.Molecule, dipole_field: List[float[3]]=[0.0, 0.0, 0.0]) → psi4.core.Matrix¶: Returns first derivative of nuclear repulsion energy as a matrix (natom, 3)

nuclear_repulsion_energy_deriv2(self: psi4.core.Molecule) → psi4.core.Matrix¶: Returns second derivative of nuclear repulsion energy as a matrix (natom X 3, natom X 3)

orientation_fixed(self: psi4.core.Molecule) → bool¶: Get whether or not orientation is fixed

point_group(self: psi4.core.Molecule) → psi4.core.PointGroup¶: Returns the current point group object

print_bond_angles(self: psi4.core.Molecule) → None¶: Print the bond angle geometrical parameters

print_cluster(self: psi4.core.Molecule) → None¶: Prints the molecule in Cartesians in input units adding fragment separators

print_distances(self: psi4.core.Molecule) → None¶: Print the interatomic distance geometrical parameters

print_in_input_format(self: psi4.core.Molecule) → None¶: Prints the molecule as Cartesian or ZMatrix entries, just as inputted.

print_out(self: psi4.core.Molecule) → None¶: Prints the molecule in Cartesians in input units to output file

print_out_in_angstrom(self: psi4.core.Molecule) → None¶: Prints the molecule in Cartesians in Angstroms to output file

print_out_in_bohr(self: psi4.core.Molecule) → None¶: Prints the molecule in Cartesians in Bohr to output file

print_out_of_planes(self: psi4.core.Molecule) → None¶: Print the out-of-plane angle geometrical parameters to output file

print_rotational_constants(self: psi4.core.Molecule) → None¶: Print the rotational constants to output file

provenance(self: psi4.core.Molecule) → Dict[str, str]¶: Gets molecule provenance

reinterpret_coordentry(self: psi4.core.Molecule, arg0: bool) → None¶: Do reinterpret coordinate entries during update_geometry().

reset_point_group(self: psi4.core.Molecule, arg0: str) → None¶: Overrides symmetry from outside the molecule string

rotational_constants(self: psi4.core.Molecule) → psi4.core.Vector¶: Returns the rotational constants [cm^-1] of the molecule

rotational_symmetry_number(self: psi4.core.Molecule) → int¶: Returns number of unique orientations of the rigid molecule that only interchange identical atoms

rotor_type(self: psi4.core.Molecule) → str¶: Returns rotor type, e.g. ‘RT_ATOM’ or ‘RT_SYMMETRIC_TOP’

run_dftd3(func=None, dashlvl=None, dashparam=None, dertype=None, verbose=1)[source]¶

Compute dispersion correction via Grimme’s DFTD3 program.

Parameters:

func (str, optional) – Name of functional (func only, func & disp, or disp only) for which to compute dispersion (e.g., blyp, BLYP-D2, blyp-d3bj, blyp-d3(bj), hf+d). Any or all parameters initialized from dashcoeff[dashlvl][func] can be overwritten via dashparam.
dashlvl (str, optional) – Name of dispersion correction to be applied (e.g., d, D2, d3(bj), das2010). Must be key in dashcoeff or “alias” or “formal” to one.
dashparam (dict, optional) – Values for the same keys as dashcoeff[dashlvl][‘default’] used to override any or all values initialized by func. Extra parameters will error.
dertype (int or str, optional) – Maximum derivative level at which to run DFTD3. For large molecules, energy-only calculations can be significantly more efficient. Influences return values, see below.
verbose (int, optional) – Amount of printing.

Returns:

energy (float) – When dertype=0, energy [Eh].
gradient (ndarray) – When dertype=1, (nat, 3) gradient [Eh/a0].
(energy, gradient) (tuple of float and ndarray) – When dertype=None, both energy [Eh] and (nat, 3) gradient [Eh/a0].

run_gcp(func=None, dertype=None, verbose=False)¶: Function to call Grimme’s GCP program https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/gcp/gcp to compute an a posteriori geometrical BSSE correction to self for several HF, generic DFT, and specific HF-3c and PBEh-3c method/basis combinations, func. Returns energy if dertype is 0, gradient if dertype is 1, else tuple of energy and gradient if dertype unspecified. The gcp executable must be independently compiled and found in PATH or PSIPATH. self may be either a qcdb.Molecule (sensibly) or a psi4.Molecule (works b/c psi4.Molecule has been extended by this method py-side and only public interface fns used) or a string that can be instantiated into a qcdb.Molecule.

save_string_xyz(self: psi4.core.Molecule) → str¶: Saves the string of an XYZ file to arg2

save_string_xyz_file(self: psi4.core.Molecule) → str¶: Saves an XYZ file to arg2

save_xyz_file(self: psi4.core.Molecule, arg0: str, arg1: bool) → None¶: Saves an XYZ file to arg0

schoenflies_symbol(self: psi4.core.Molecule) → str¶: Returns the Schoenflies symbol

scramble(do_shift=True, do_rotate=True, do_resort=True, deflection=1.0, do_mirror=False, do_plot=False, run_to_completion=False, run_resorting=False, verbose=1)[source]¶

Tester for B787 by shifting, rotating, and atom shuffling ref_mol and checking that the aligner returns the opposite transformation.

Parameters:	ref_mol (qcdb.Molecule or psi4.core.Molecule) – Molecule to perturb. do_shift (bool or array-like, optional) – Whether to generate a random atom shift on interval [-3, 3) in each dimension (True) or leave at current origin. To shift by a specified vector, supply a 3-element list. do_rotate (bool or array-like, optional) – Whether to generate a random 3D rotation according to algorithm of Arvo. To rotate by a specified matrix, supply a 9-element list of lists. do_resort (bool or array-like, optional) – Whether to shuffle atoms (True) or leave 1st atom 1st, etc. (False). To specify shuffle, supply a nat-element list of indices. deflection (float, optional) – If do_rotate, how random a rotation: 0.0 is no change, 0.1 is small perturbation, 1.0 is completely random. do_mirror (bool, optional) – Whether to construct the mirror image structure by inverting y-axis. do_plot (bool, optional) – Pops up a mpl plot showing before, after, and ref geometries. run_to_completion (bool, optional) – By construction, scrambled systems are fully alignable (final RMSD=0). Even so, True turns off the mechanism to stop when RMSD reaches zero and instead proceed to worst possible time. run_resorting (bool, optional) – Even if atoms not shuffled, test the resorting machinery. verbose (int, optional) – Print level.
Returns:
Return type:	None

set_active_fragment(self: psi4.core.Molecule, arg0: int) → None¶: Sets the specified fragment arg0 to be Real

set_active_fragments(self: psi4.core.Molecule, arg0: List[int]) → None¶: Sets the specified list arg0 of fragments to be Real

set_basis_all_atoms(self: psi4.core.Molecule, arg0: str, arg1: str) → None¶: Sets basis set arg0 to all atoms

set_basis_by_label(self: psi4.core.Molecule, arg0: str, arg1: str, arg2: str) → None¶: Sets basis set arg1 to all atoms with label (e.g., H4) arg0

set_basis_by_symbol(self: psi4.core.Molecule, arg0: str, arg1: str, arg2: str) → None¶: Sets basis set arg1 to all atoms with symbol (e.g., H) arg0

set_comment(self: psi4.core.Molecule, arg0: str) → None¶: Sets molecule comment

set_connectivity(self: psi4.core.Molecule, arg0: List[Tuple[int, int, float]]) → None¶: Sets molecule connectivity

set_full_geometry(self: psi4.core.Molecule, arg0: psi4.core.Matrix) → None¶: Sets the geometry, given a (Natom X 3) matrix arg0 of coordinates (in Bohr) (including dummies

set_geometry(self: psi4.core.Molecule, arg0: psi4.core.Matrix) → None¶: Sets the geometry, given a (Natom X 3) matrix arg0 of coordinates [a0] (excluding dummies)

set_ghost_fragment(self: psi4.core.Molecule, arg0: int) → None¶: Sets the specified fragment arg0 to be Ghost

set_ghost_fragments(self: psi4.core.Molecule, arg0: List[int]) → None¶: Sets the specified list arg0 of fragments to be Ghost

set_input_units_to_au(self: psi4.core.Molecule, arg0: float) → None¶: Sets unit conversion to [a0] for geometry

set_mass(self: psi4.core.Molecule, atom: int, mass: float) → None¶: Sets mass of atom (0-indexed) to mass (good for isotopic substitutions)

set_molecular_charge(self: psi4.core.Molecule, arg0: int) → None¶: Change the overall molecular charge. Setting in initial molecule string or constructor preferred.

set_multiplicity(self: psi4.core.Molecule, arg0: int) → None¶: Change the multiplicity (defined as 2S + 1). Setting in initial molecule string or constructor preferred.

set_name(self: psi4.core.Molecule, arg0: str) → None¶: Sets molecule name

set_nuclear_charge(self: psi4.core.Molecule, arg0: int, arg1: float) → None¶: Set the nuclear charge of the given atom arg0 to the value arg1 (primarily for ECP).

set_point_group(self: psi4.core.Molecule, arg0: psi4.core.PointGroup) → None¶: Sets the molecular point group to the point group object arg0

set_provenance(self: psi4.core.Molecule, arg0: Dict[str, str]) → None¶: Sets molecule provenance

set_units(self: psi4.core.Molecule, arg0: psi4.core.GeometryUnits) → None¶: Sets units (Angstrom or Bohr) used to define the geometry. Imposes Psi4 physical constants conversion for input_units_to_au.

set_variable(self: psi4.core.Molecule, arg0: str, arg1: float) → None¶: Sets the value arg1 to the variable arg0 in the list of structure variables, then calls update_geometry()

symbol(self: psi4.core.Molecule, atom: int) → str¶: Gets the cleaned up label of atom (C2 => C, H4 = H) (0-indexed without dummies)

symmetrize(self: psi4.core.Molecule, arg0: float) → None¶: Finds the highest point Abelian point group within the specified tolerance, and forces the geometry to have that symmetry.

symmetry_from_input(self: psi4.core.Molecule) → str¶: Returns the symmetry specified in the input

to_arrays(dummy=False, ghost_as_dummy=False)[source]¶

Exports coordinate info into NumPy arrays.

Parameters:

dummy (bool, optional) – Whether or not to include dummy atoms in returned arrays.
ghost_as_dummy (bool, optional) – Whether or not to treat ghost atoms as dummies.

Returns:

geom, mass, elem, elez, uniq (ndarray, ndarray, ndarray, ndarray, ndarray) – (nat, 3) geometry [a0]. (nat,) mass [u]. (nat,) element symbol. (nat,) atomic number. (nat,) hash of element symbol and mass. Note that coordinate, orientation, and element information is preserved but fragmentation, chgmult, and dummy/ghost is lost.
Usage
—–
geom, mass, elem, elez, uniq = molinstance.to_arrays()

to_dict(force_c1=False, force_units=False, np_out=True)[source]¶: Serializes instance into Molecule dictionary.

to_schema(dtype, units='Bohr')[source]¶: Serializes instance into dictionary according to schema dtype.

to_string(dtype, units='Angstrom', atom_format=None, ghost_format=None, width=17, prec=12)[source]¶: Format a string representation of QM molecule.

translate(self: psi4.core.Molecule, arg0: psi4.core.Vector3) → None¶: Translates molecule by arg0

true_atomic_number(self: psi4.core.Molecule, atom: int) → int¶: Gets atomic number of atom from element (0-indexed without dummies)

units(self: psi4.core.Molecule) → str¶: Returns units used to define the geometry, i.e. ‘Angstrom’ or ‘Bohr’

update_geometry(self: psi4.core.Molecule) → None¶: Reevaluates the geometry with current variable values, orientation directives, etc. by clearing the atoms list and rebuilding it. Idempotent. Use liberally.Must be called after initial Molecule definition by string.

x(self: psi4.core.Molecule, arg0: int) → float¶: x position [Bohr] of atom arg0 (0-indexed without dummies)

xyz(self: psi4.core.Molecule, i: int) → psi4.core.Vector3¶: Return the Vector3 for atom i (0-indexed without dummies)

y(self: psi4.core.Molecule, arg0: int) → float¶: y position [Bohr] of atom arg0 (0-indexed without dummies)

z(self: psi4.core.Molecule, arg0: int) → float¶: z position [Bohr] of atom arg0 (0-indexed without dummies)

B787(ref_mol, do_plot=False, verbose=1, atoms_map=False, run_resorting=False, mols_align=False, run_to_completion=False, uno_cutoff=0.001, run_mirror=False)[source]

Finds shift, rotation, and atom reordering of concern_mol that best aligns with ref_mol.

Wraps qcdb.align.B787() for qcdb.Molecule or psi4.core.Molecule. Employs the Kabsch, Hungarian, and Uno algorithms to exhaustively locate the best alignment for non-oriented, non-ordered structures.

Parameters:	concern_mol (qcdb.Molecule or psi4.core.Molecule) – Molecule of concern, to be shifted, rotated, and reordered into best coincidence with ref_mol. ref_mol (qcdb.Molecule or psi4.core.Molecule) – Molecule to match. atoms_map (bool, optional) – Whether atom1 of ref_mol corresponds to atom1 of concern_mol, etc. If true, specifying True can save much time. mols_align (bool, optional) – Whether ref_mol and concern_mol have identical geometries by eye (barring orientation or atom mapping) and expected final RMSD = 0. If True, procedure is truncated when RMSD condition met, saving time. do_plot (bool, optional) – Pops up a mpl plot showing before, after, and ref geometries. run_to_completion (bool, optional) – Run reorderings to completion (past RMSD = 0) even if unnecessary because mols_align=True. Used to test worst-case timings. run_resorting (bool, optional) – Run the resorting machinery even if unnecessary because atoms_map=True. uno_cutoff (float, optional) – TODO run_mirror (bool, optional) – Run alternate geometries potentially allowing best match to ref_mol from mirror image of concern_mol. Only run if system confirmed to be nonsuperimposable upon mirror reflection.
Returns:	First item is RMSD [A] between ref_mol and the optimally aligned geometry computed. Second item is a AlignmentMill namedtuple with fields (shift, rotation, atommap, mirror) that prescribe the transformation from concern_mol and the optimally aligned geometry. Third item is a crude charge-, multiplicity-, fragment-less Molecule at optimally aligned (and atom-ordered) geometry. Return type determined by concern_mol type.
Return type:	float, tuple, qcdb.Molecule or psi4.core.Molecule

BFS(seed_atoms=None, bond_threshold=1.2, return_arrays=False, return_molecules=False, return_molecule=False)[source]

Detect fragments among real atoms through a breadth-first search (BFS) algorithm.

Parameters:

self (qcdb.Molecule or psi4.core.Molecule) –
seed_atoms (list, optional) – 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]]
bond_threshold (float, optional) – Factor beyond average of covalent radii to determine bond cutoff.
return_arrays (bool, optional) – If True, also return fragments as list of arrays.
return_molecules (bool, optional) – If True, also return fragments as list of Molecules.
return_molecule (bool, optional) – If True, also return one big Molecule with fragmentation encoded.

Returns:

bfs_map (list of lists) – Array of atom indices (0-indexed) of detected fragments.
bfs_arrays (tuple of lists of ndarray, optional) – geom, mass, elem info per-fragment. Only provided if return_arrays is True.
bfs_molecules (list of qcdb.Molecule or psi4.core.Molecule, optional) – List of molecules, each built from one fragment. Center and orientation of fragments is fixed so orientation info from self is not lost. Loses chgmult and ghost/dummy info from self and contains default chgmult. Only provided if return_molecules is True. Returned are of same type as self.
bfs_molecule (qcdb.Molecule or psi4.core.Molecule, optional) – Single molecule with same number of real atoms as self with atoms reordered into adjacent fragments and fragment markers inserted. Loses ghost/dummy info from self; keeps total charge but not total mult. Only provided if return_molecule is True. Returned is of same type as self.

Notes

Relies upon van der Waals radii and so faulty for close (especially: hydrogen-bonded) fragments. See seed_atoms.

Any existing fragmentation info/chgmult encoded in self is lost.

Original code from Michael S. Marshall, linear-scaling algorithm from Trent M. Parker, revamped by Lori A. Burns

Z(self: psi4.core.Molecule, arg0: int) → float: Nuclear charge of atom arg0 (0-indexed without dummies)

activate_all_fragments(self: psi4.core.Molecule) → None: Sets all fragments in the molecule to be active

add_atom(self: psi4.core.Molecule, Z: float, x: float, y: float, z: float, symbol: str, mass: float, charge: float, label: str, A: int) → None: Adds 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

atom_at_position(*args, **kwargs)

Overloaded function.

atom_at_position(self: psi4.core.Molecule, coord: float, tol: float) -> int

Tests to see if an atom is at the position coord with a given tolerance tol

atom_at_position(self: psi4.core.Molecule, coord: List[float[3]], tol: float) -> int

Tests to see if an atom is at the position coord with a given tolerance tol

basis_on_atom(self: psi4.core.Molecule, arg0: int) → str: Gets the label of the orbital basis set on a given atom arg0

center_of_mass(self: psi4.core.Molecule) → psi4.core.Vector3: Computes center of mass of molecule (does not translate molecule)

charge(self: psi4.core.Molecule, atom: int) → float: Gets charge of atom (0-indexed without dummies)

clone(self: psi4.core.Molecule) → psi4.core.Molecule: Returns a new Molecule identical to arg1

com_fixed(self: psi4.core.Molecule) → bool: Gets whether or not center of mass is fixed

comment(self: psi4.core.Molecule) → str: Gets molecule comment

connectivity(self: psi4.core.Molecule) → List[Tuple[int, int, float]]: Gets molecule connectivity

create_psi4_string_from_molecule(self: psi4.core.Molecule) → str: 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.

deactivate_all_fragments(self: psi4.core.Molecule) → None: Sets all fragments in the molecule to be inactive

distance_matrix(self: psi4.core.Molecule) → psi4.core.Matrix: Returns Matrix of interatom distances

extract_subsets(*args, **kwargs)

Overloaded function.

extract_subsets(self: psi4.core.Molecule, arg0: List[int], arg1: List[int]) -> psi4.core.Molecule

Returns copy of self with arg0 fragments Real and arg1 fragments Ghost

extract_subsets(self: psi4.core.Molecule, arg0: List[int], arg1: int) -> psi4.core.Molecule

Returns copy of self with arg0 fragments Real and arg1 fragment Ghost

extract_subsets(self: psi4.core.Molecule, arg0: int, arg1: List[int]) -> psi4.core.Molecule

Returns copy of self with arg0 fragment Real and arg1 fragments Ghost

extract_subsets(self: psi4.core.Molecule, arg0: int, arg1: int) -> psi4.core.Molecule

Returns copy of self with arg0 fragment Real and arg1 fragment Ghost

extract_subsets(self: psi4.core.Molecule, arg0: List[int]) -> psi4.core.Molecule

Returns copy of self with arg0 fragments Real

extract_subsets(self: psi4.core.Molecule, arg0: int) -> psi4.core.Molecule

Returns copy of self with arg0 fragment Real

fZ(self: psi4.core.Molecule, arg0: int) → float: Nuclear charge of atom arg1 (0-indexed including dummies)

fcharge(self: psi4.core.Molecule, atom: int) → float: Gets charge of atom (0-indexed including dummies)

find_highest_point_group(self: psi4.core.Molecule, tolerance: float=1e-08) → psi4.core.PointGroup: Finds highest possible computational molecular point group

find_point_group(self: psi4.core.Molecule, tolerance: float=1e-08) → psi4.core.PointGroup: Finds computational molecular point group, user can override this with the symmetry keyword

fix_com(self: psi4.core.Molecule, arg0: bool) → None: Sets whether to fix the Cartesian position, or to translate to the C.O.M.

fix_orientation(self: psi4.core.Molecule, arg0: bool) → None: Fix the orientation at its current frame

flabel(self: psi4.core.Molecule, atom: int) → str: Gets the original label of the atom arg0 as given in the input file (C2, H4)(0-indexed including dummies)

fmass(self: psi4.core.Molecule, atom: int) → float: Gets mass of atom (0-indexed including dummies)

form_symmetry_information(self: psi4.core.Molecule, arg0: float) → None: Uses the point group object obtain by calling point_group()

format_molecule_for_mol()

Returns a string of Molecule formatted for mol2.

Written by Trent M. Parker 9 Jun 2014

classmethod from_arrays(geom=None, elea=None, elez=None, elem=None, mass=None, real=None, elbl=None, name=None, units='Angstrom', input_units_to_au=None, fix_com=None, fix_orientation=None, fix_symmetry=None, fragment_separators=None, fragment_charges=None, fragment_multiplicities=None, molecular_charge=None, molecular_multiplicity=None, comment=None, provenance=None, connectivity=None, missing_enabled_return='error', tooclose=0.1, zero_ghost_fragments=False, nonphysical=False, mtol=0.001, verbose=1, return_dict=False)

Construct Molecule from unvalidated arrays and variables.

Light wrapper around from_arrays() that is a full-featured constructor to dictionary representa- tion of Molecule. This follows one step further to return Molecule instance.

:param See from_arrays().:

Returns:
Return type:	`psi4.core.Molecule`

from_dict(arg0: dict) → psi4.core.Molecule: Returns a new Molecule constructed from python dictionary. In progress: name and capabilities should not be relied upon

classmethod from_schema(molschema, return_dict=False, verbose=1)

Construct Molecule from non-Psi4 schema.

Light wrapper around from_arrays().

Parameters:

molschema (dict) – Dictionary form of Molecule following known schema.
return_dict (bool, optional) – Additionally return Molecule dictionary intermediate.
verbose (int, optional) – Amount of printing.

Returns:

mol (psi4.core.Molecule)
molrec (dict, optional) – Dictionary representation of instance. Only provided if return_dict is True.

classmethod from_string(molstr, dtype=None, name=None, fix_com=None, fix_orientation=None, fix_symmetry=None, return_dict=False, enable_qm=True, enable_efp=True, missing_enabled_return_qm='none', missing_enabled_return_efp='none', verbose=1)

fsymbol(self: psi4.core.Molecule, atom: int) → str: Gets the cleaned up label of atom (C2 => C, H4 = H) (0-indexed including dummies)

ftrue_atomic_number(self: psi4.core.Molecule, atom: int) → int: Gets atomic number of atom from element (0-indexed including dummies)

full_geometry(self: psi4.core.Molecule) → psi4.core.Matrix: Gets the geometry [Bohr] as a (Natom X 3) matrix of coordinates (including dummies)

full_pg_n(self: psi4.core.Molecule) → int: Gets n in Cnv, etc.; If there is no n (e.g. Td) it’s the highest-order rotation axis

fx(self: psi4.core.Molecule, arg0: int) → float: x position of atom arg0 (0-indexed including dummies in Bohr)

fy(self: psi4.core.Molecule, arg0: int) → float: y position of atom arg0 (0-indexed including dummies in Bohr)

fz(self: psi4.core.Molecule, arg0: int) → float: z position of atom arg0 (0-indexed including dummies in Bohr)

geometry(self: psi4.core.Molecule) → psi4.core.Matrix: Gets the geometry [Bohr] as a (Natom X 3) matrix of coordinates (excluding dummies)

get_fragment_charges(self: psi4.core.Molecule) → List[int]: Gets the charge of each fragment

get_fragment_multiplicities(self: psi4.core.Molecule) → List[int]: Gets the multiplicity of each fragment

get_fragment_types(self: psi4.core.Molecule) → List[str]: Returns a list describing how to handle each fragment {Real, Ghost, Absent}

get_fragments(self: psi4.core.Molecule) → List[Tuple[int, int]]: Returns list of pairs of atom ranges defining each fragment from parent molecule(fragments[frag_ind] = <Afirst,Alast+1>)

get_full_point_group(self: psi4.core.Molecule) → str: Gets point group name such as C3v or S8

get_full_point_group_with_n(self: psi4.core.Molecule) → str: Gets point group name such as Cnv or Sn

get_variable(self: psi4.core.Molecule, arg0: str) → float: Returns the value of variable arg0 in the structural variables list

inertia_tensor(self: psi4.core.Molecule) → psi4.core.Matrix: Returns intertial tensor

input_units_to_au(self: psi4.core.Molecule) → float: Returns unit conversion to [a0] for geometry

irrep_labels(self: psi4.core.Molecule) → List[str]: Returns Irreducible Representation symmetry labels

is_variable(self: psi4.core.Molecule, arg0: str) → bool: Checks if variable arg0 is in the structural variables list

label(self: psi4.core.Molecule, atom: int) → str: Gets the original label of the atom as given in the input file (C2, H4)(0-indexed without dummies)

mass(self: psi4.core.Molecule, atom: int) → float: Returns mass of atom (0-indexed)

mass_number(self: psi4.core.Molecule, arg0: int) → int: Mass number (A) of atom if known, else -1

molecular_charge(self: psi4.core.Molecule) → int: Gets the molecular charge

move_to_com(self: psi4.core.Molecule) → None: Moves molecule to center of mass

multiplicity(self: psi4.core.Molecule) → int: Gets the multiplicity (defined as 2Ms + 1)

nallatom(self: psi4.core.Molecule) → int: Number of real and dummy atoms

name(self: psi4.core.Molecule) → str: Gets molecule name

natom(self: psi4.core.Molecule) → int: Number of real atoms

nfragments(self: psi4.core.Molecule) → int: Gets the number of fragments in the molecule

nuclear_dipole(*args, **kwargs)

Overloaded function.

nuclear_dipole(self: psi4.core.Molecule, arg0: psi4.core.Vector3) -> psi4.core.Vector3

Gets the nuclear contribution to the dipole, with respect to a specified origin atg0

nuclear_dipole(self: psi4.core.Molecule) -> psi4.core.Vector3

Gets the nuclear contribution to the dipole, with respect to the origin

nuclear_repulsion_energy(self: psi4.core.Molecule, dipole_field: List[float[3]]=[0.0, 0.0, 0.0]) → float: Computes nuclear repulsion energy

nuclear_repulsion_energy_deriv1(self: psi4.core.Molecule, dipole_field: List[float[3]]=[0.0, 0.0, 0.0]) → psi4.core.Matrix: Returns first derivative of nuclear repulsion energy as a matrix (natom, 3)

nuclear_repulsion_energy_deriv2(self: psi4.core.Molecule) → psi4.core.Matrix: Returns second derivative of nuclear repulsion energy as a matrix (natom X 3, natom X 3)

orientation_fixed(self: psi4.core.Molecule) → bool: Get whether or not orientation is fixed

point_group(self: psi4.core.Molecule) → psi4.core.PointGroup: Returns the current point group object

print_bond_angles(self: psi4.core.Molecule) → None: Print the bond angle geometrical parameters

print_cluster(self: psi4.core.Molecule) → None: Prints the molecule in Cartesians in input units adding fragment separators

print_distances(self: psi4.core.Molecule) → None: Print the interatomic distance geometrical parameters

print_in_input_format(self: psi4.core.Molecule) → None: Prints the molecule as Cartesian or ZMatrix entries, just as inputted.

print_out(self: psi4.core.Molecule) → None: Prints the molecule in Cartesians in input units to output file

print_out_in_angstrom(self: psi4.core.Molecule) → None: Prints the molecule in Cartesians in Angstroms to output file

print_out_in_bohr(self: psi4.core.Molecule) → None: Prints the molecule in Cartesians in Bohr to output file

print_out_of_planes(self: psi4.core.Molecule) → None: Print the out-of-plane angle geometrical parameters to output file

print_rotational_constants(self: psi4.core.Molecule) → None: Print the rotational constants to output file

provenance(self: psi4.core.Molecule) → Dict[str, str]: Gets molecule provenance

reinterpret_coordentry(self: psi4.core.Molecule, arg0: bool) → None: Do reinterpret coordinate entries during update_geometry().

reset_point_group(self: psi4.core.Molecule, arg0: str) → None: Overrides symmetry from outside the molecule string

rotational_constants(self: psi4.core.Molecule) → psi4.core.Vector: Returns the rotational constants [cm^-1] of the molecule

rotational_symmetry_number(self: psi4.core.Molecule) → int: Returns number of unique orientations of the rigid molecule that only interchange identical atoms

rotor_type(self: psi4.core.Molecule) → str: Returns rotor type, e.g. ‘RT_ATOM’ or ‘RT_SYMMETRIC_TOP’

run_dftd3(func=None, dashlvl=None, dashparam=None, dertype=None, verbose=1)[source]

Compute dispersion correction via Grimme’s DFTD3 program.

Parameters:

func (str, optional) – Name of functional (func only, func & disp, or disp only) for which to compute dispersion (e.g., blyp, BLYP-D2, blyp-d3bj, blyp-d3(bj), hf+d). Any or all parameters initialized from dashcoeff[dashlvl][func] can be overwritten via dashparam.
dashlvl (str, optional) – Name of dispersion correction to be applied (e.g., d, D2, d3(bj), das2010). Must be key in dashcoeff or “alias” or “formal” to one.
dashparam (dict, optional) – Values for the same keys as dashcoeff[dashlvl][‘default’] used to override any or all values initialized by func. Extra parameters will error.
dertype (int or str, optional) – Maximum derivative level at which to run DFTD3. For large molecules, energy-only calculations can be significantly more efficient. Influences return values, see below.
verbose (int, optional) – Amount of printing.

Returns:

energy (float) – When dertype=0, energy [Eh].
gradient (ndarray) – When dertype=1, (nat, 3) gradient [Eh/a0].
(energy, gradient) (tuple of float and ndarray) – When dertype=None, both energy [Eh] and (nat, 3) gradient [Eh/a0].

run_gcp(func=None, dertype=None, verbose=False): Function to call Grimme’s GCP program https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/gcp/gcp to compute an a posteriori geometrical BSSE correction to self for several HF, generic DFT, and specific HF-3c and PBEh-3c method/basis combinations, func. Returns energy if dertype is 0, gradient if dertype is 1, else tuple of energy and gradient if dertype unspecified. The gcp executable must be independently compiled and found in PATH or PSIPATH. self may be either a qcdb.Molecule (sensibly) or a psi4.Molecule (works b/c psi4.Molecule has been extended by this method py-side and only public interface fns used) or a string that can be instantiated into a qcdb.Molecule.

save_string_xyz(self: psi4.core.Molecule) → str: Saves the string of an XYZ file to arg2

save_string_xyz_file(self: psi4.core.Molecule) → str: Saves an XYZ file to arg2

save_xyz_file(self: psi4.core.Molecule, arg0: str, arg1: bool) → None: Saves an XYZ file to arg0

schoenflies_symbol(self: psi4.core.Molecule) → str: Returns the Schoenflies symbol

scramble(do_shift=True, do_rotate=True, do_resort=True, deflection=1.0, do_mirror=False, do_plot=False, run_to_completion=False, run_resorting=False, verbose=1)[source]

Tester for B787 by shifting, rotating, and atom shuffling ref_mol and checking that the aligner returns the opposite transformation.

Parameters:	ref_mol (qcdb.Molecule or psi4.core.Molecule) – Molecule to perturb. do_shift (bool or array-like, optional) – Whether to generate a random atom shift on interval [-3, 3) in each dimension (True) or leave at current origin. To shift by a specified vector, supply a 3-element list. do_rotate (bool or array-like, optional) – Whether to generate a random 3D rotation according to algorithm of Arvo. To rotate by a specified matrix, supply a 9-element list of lists. do_resort (bool or array-like, optional) – Whether to shuffle atoms (True) or leave 1st atom 1st, etc. (False). To specify shuffle, supply a nat-element list of indices. deflection (float, optional) – If do_rotate, how random a rotation: 0.0 is no change, 0.1 is small perturbation, 1.0 is completely random. do_mirror (bool, optional) – Whether to construct the mirror image structure by inverting y-axis. do_plot (bool, optional) – Pops up a mpl plot showing before, after, and ref geometries. run_to_completion (bool, optional) – By construction, scrambled systems are fully alignable (final RMSD=0). Even so, True turns off the mechanism to stop when RMSD reaches zero and instead proceed to worst possible time. run_resorting (bool, optional) – Even if atoms not shuffled, test the resorting machinery. verbose (int, optional) – Print level.
Returns:
Return type:	None

set_active_fragment(self: psi4.core.Molecule, arg0: int) → None: Sets the specified fragment arg0 to be Real

set_active_fragments(self: psi4.core.Molecule, arg0: List[int]) → None: Sets the specified list arg0 of fragments to be Real

set_basis_all_atoms(self: psi4.core.Molecule, arg0: str, arg1: str) → None: Sets basis set arg0 to all atoms

set_basis_by_label(self: psi4.core.Molecule, arg0: str, arg1: str, arg2: str) → None: Sets basis set arg1 to all atoms with label (e.g., H4) arg0

set_basis_by_symbol(self: psi4.core.Molecule, arg0: str, arg1: str, arg2: str) → None: Sets basis set arg1 to all atoms with symbol (e.g., H) arg0

set_comment(self: psi4.core.Molecule, arg0: str) → None: Sets molecule comment

set_connectivity(self: psi4.core.Molecule, arg0: List[Tuple[int, int, float]]) → None: Sets molecule connectivity

set_full_geometry(self: psi4.core.Molecule, arg0: psi4.core.Matrix) → None: Sets the geometry, given a (Natom X 3) matrix arg0 of coordinates (in Bohr) (including dummies

set_geometry(self: psi4.core.Molecule, arg0: psi4.core.Matrix) → None: Sets the geometry, given a (Natom X 3) matrix arg0 of coordinates [a0] (excluding dummies)

set_ghost_fragment(self: psi4.core.Molecule, arg0: int) → None: Sets the specified fragment arg0 to be Ghost

set_ghost_fragments(self: psi4.core.Molecule, arg0: List[int]) → None: Sets the specified list arg0 of fragments to be Ghost

set_input_units_to_au(self: psi4.core.Molecule, arg0: float) → None: Sets unit conversion to [a0] for geometry

set_mass(self: psi4.core.Molecule, atom: int, mass: float) → None: Sets mass of atom (0-indexed) to mass (good for isotopic substitutions)

set_molecular_charge(self: psi4.core.Molecule, arg0: int) → None: Change the overall molecular charge. Setting in initial molecule string or constructor preferred.

set_multiplicity(self: psi4.core.Molecule, arg0: int) → None: Change the multiplicity (defined as 2S + 1). Setting in initial molecule string or constructor preferred.

set_name(self: psi4.core.Molecule, arg0: str) → None: Sets molecule name

set_nuclear_charge(self: psi4.core.Molecule, arg0: int, arg1: float) → None: Set the nuclear charge of the given atom arg0 to the value arg1 (primarily for ECP).

set_point_group(self: psi4.core.Molecule, arg0: psi4.core.PointGroup) → None: Sets the molecular point group to the point group object arg0

set_provenance(self: psi4.core.Molecule, arg0: Dict[str, str]) → None: Sets molecule provenance

set_units(self: psi4.core.Molecule, arg0: psi4.core.GeometryUnits) → None: Sets units (Angstrom or Bohr) used to define the geometry. Imposes Psi4 physical constants conversion for input_units_to_au.

set_variable(self: psi4.core.Molecule, arg0: str, arg1: float) → None: Sets the value arg1 to the variable arg0 in the list of structure variables, then calls update_geometry()

symbol(self: psi4.core.Molecule, atom: int) → str: Gets the cleaned up label of atom (C2 => C, H4 = H) (0-indexed without dummies)

symmetrize(self: psi4.core.Molecule, arg0: float) → None: Finds the highest point Abelian point group within the specified tolerance, and forces the geometry to have that symmetry.

symmetry_from_input(self: psi4.core.Molecule) → str: Returns the symmetry specified in the input

to_arrays(dummy=False, ghost_as_dummy=False)[source]

Exports coordinate info into NumPy arrays.

Parameters:

dummy (bool, optional) – Whether or not to include dummy atoms in returned arrays.
ghost_as_dummy (bool, optional) – Whether or not to treat ghost atoms as dummies.

Returns:

geom, mass, elem, elez, uniq (ndarray, ndarray, ndarray, ndarray, ndarray) – (nat, 3) geometry [a0]. (nat,) mass [u]. (nat,) element symbol. (nat,) atomic number. (nat,) hash of element symbol and mass. Note that coordinate, orientation, and element information is preserved but fragmentation, chgmult, and dummy/ghost is lost.
Usage
—–
geom, mass, elem, elez, uniq = molinstance.to_arrays()

to_dict(force_c1=False, force_units=False, np_out=True)[source]: Serializes instance into Molecule dictionary.

to_schema(dtype, units='Bohr')[source]: Serializes instance into dictionary according to schema dtype.

to_string(dtype, units='Angstrom', atom_format=None, ghost_format=None, width=17, prec=12)[source]: Format a string representation of QM molecule.

translate(self: psi4.core.Molecule, arg0: psi4.core.Vector3) → None: Translates molecule by arg0

true_atomic_number(self: psi4.core.Molecule, atom: int) → int: Gets atomic number of atom from element (0-indexed without dummies)

units(self: psi4.core.Molecule) → str: Returns units used to define the geometry, i.e. ‘Angstrom’ or ‘Bohr’

update_geometry(self: psi4.core.Molecule) → None: Reevaluates the geometry with current variable values, orientation directives, etc. by clearing the atoms list and rebuilding it. Idempotent. Use liberally.Must be called after initial Molecule definition by string.

x(self: psi4.core.Molecule, arg0: int) → float: x position [Bohr] of atom arg0 (0-indexed without dummies)

xyz(self: psi4.core.Molecule, i: int) → psi4.core.Vector3: Return the Vector3 for atom i (0-indexed without dummies)

y(self: psi4.core.Molecule, arg0: int) → float: y position [Bohr] of atom arg0 (0-indexed without dummies)

z(self: psi4.core.Molecule, arg0: int) → float: z position [Bohr] of atom arg0 (0-indexed without dummies)