morfeus.xtb module#

xtb interface code.

class morfeus.xtb.XTB(elements, coordinates, version='2', charge=0, n_unpaired=None, solvent=None, electronic_temperature=None)[source]#

Bases: object

Calculates electronic properties with the xtb-python package.

Parameters:

elements (Iterable[int] | Iterable[str]) – Elements as atomic symbols or numbers
coordinates (ArrayLike2D) – Coordinates (Å)
version (str) – Version of xtb to use. Currently works with ‘1’ or ‘2’.
charge (int) – Molecular charge
n_unpaired (int | None) – Number of unpaired electrons
solvent (str | None) – Solvent. See xtb-python documentation
electronic_temperature (int | None) – Electronic temperature (K)

get_bond_order(i, j)[source]#

Returns bond order between two atoms.

Parameters:

i (int) – Index of atom 1 (1-indexed)
j (int) – Index of atom 2 (1-indexed)

Returns:

Bond order

Return type:

bond_order

get_bond_orders(charge_state=0)[source]#

Returns bond orders.

Parameters:: charge_state (int) – Charge state relative to original charge
Returns:: Bond orders
Return type:: bond_orders

get_charges(charge_state=0)[source]#

Returns atomic charges.

Parameters:: charge_state (int) – Charge state relative to original charge
Returns:: Atomic charges
Return type:: charges

get_dipole(charge_state=0)[source]#

Calculate dipole vector (a.u.).

Parameters:: charge_state (int) – Charge state relative to original charge
Returns:: Dipole vector
Return type:: dipole

get_ea(corrected=False)[source]#

Calculate electron affinity.

Parameters:: corrected (bool) – Whether to apply correction term
Returns:: Electron affinity (eV)
Return type:: ea

get_fukui(variety)[source]#

Calculate Fukui coefficients.

Parameters:: variety (str) – Type of Fukui coefficient: ‘nucleophilicity’, ‘electrophilicity’, ‘radical’, ‘dual’, ‘local_nucleophilicity’ or ‘local_electrophilicity’.
Returns:: Atomic Fukui coefficients
Return type:: fukui
Raises:: ValueError – When variety does not exist

get_global_descriptor(variety, corrected=False)[source]#

Calculate global reactivity descriptors.

Parameters:

corrected (bool) – Whether to apply correction term
variety (str) – Type of descriptor: ‘electrophilicity’, ‘nucleophilicity’, ‘electrofugality’ or ‘nucleofugality’

Returns:

Global reactivity descriptor (eV)

Return type:

descriptor

Raises:

ValueError – When variety does not exist

get_homo()[source]#

Calculate HOMO energy.

Returns:: HOMO energy (a.u.)
Return type:: homo_energy

get_ip(corrected=False)[source]#

Calculate ionization potential.

Parameters:: corrected (bool) – Whether to apply correction term
Returns:: Ionization potential (eV)
Return type:: ip

get_lumo()[source]#

Calculate LUMO energy.

Returns:: LUMO energy (a.u.)
Return type:: lumo_energy

morfeus.xtb.cli(file)[source]#

CLI for XTB.

Parameters:: file (str) – Geometry file
Returns:: Partially instantiated class
Return type:: Any