Index

A

accessible_mask (morfeus.geometry.Atom attribute) accessible_points (morfeus.geometry.Atom attribute) add_angle() (morfeus.geometry.InternalCoordinates method) add_bond() (morfeus.geometry.InternalCoordinates method) add_conformers() (morfeus.conformer.ConformerEnsemble method) add_dihedral() (morfeus.geometry.InternalCoordinates method) add_internal_coordinate() (morfeus.geometry.InternalCoordinates method) (morfeus.local_force.LocalForce method) (morfeus.LocalForce method) add_inverted() (morfeus.conformer.ConformerEnsemble method) align_conformers() (morfeus.conformer.ConformerEnsemble method) alpha (morfeus.Pyramidalization attribute) (morfeus.pyramidalization.Pyramidalization attribute) alphas (morfeus.Pyramidalization attribute) (morfeus.pyramidalization.Pyramidalization attribute) Angle (class in morfeus.geometry) angle (morfeus.bite_angle.BiteAngle attribute) (morfeus.BiteAngle attribute) (morfeus.geometry.Cone attribute) area (morfeus.Dispersion attribute) (morfeus.dispersion.Dispersion attribute) (morfeus.geometry.Atom attribute) (morfeus.geometry.Sphere attribute) (morfeus.SASA attribute) (morfeus.sasa.SASA attribute)

Atom (class in morfeus.geometry) atom_areas (morfeus.Dispersion attribute) (morfeus.dispersion.Dispersion attribute) (morfeus.SASA attribute) (morfeus.sasa.SASA attribute) atom_p_int (morfeus.Dispersion attribute) (morfeus.dispersion.Dispersion attribute) atom_p_max (morfeus.Dispersion attribute) (morfeus.dispersion.Dispersion attribute) atom_p_min (morfeus.Dispersion attribute) (morfeus.dispersion.Dispersion attribute) atom_volumes (morfeus.SASA attribute) (morfeus.sasa.SASA attribute) atomic_masses (in module morfeus.data) atomic_numbers (in module morfeus.data) atomic_symbols (in module morfeus.data) atoms (morfeus.geometry.Cone attribute)

B

B_1 (morfeus.Sterimol attribute) (morfeus.sterimol.Sterimol attribute) B_1_value (morfeus.Sterimol attribute) (morfeus.sterimol.Sterimol attribute) B_5 (morfeus.Sterimol attribute) (morfeus.sterimol.Sterimol attribute) B_5_value (morfeus.Sterimol attribute) (morfeus.sterimol.Sterimol attribute) BiteAngle (class in morfeus) (class in morfeus.bite_angle) boltzmann_average_dT() (in module morfeus.conformer) (morfeus.conformer.ConformerEnsemble method)

boltzmann_statistic() (in module morfeus.conformer) (morfeus.conformer.ConformerEnsemble method) boltzmann_weights() (in module morfeus.conformer) (morfeus.conformer.ConformerEnsemble method) Bond (class in morfeus.geometry) bond_length (morfeus.Sterimol attribute) (morfeus.sterimol.Sterimol attribute) buried_volume (morfeus.buried_volume.BuriedVolume attribute) (morfeus.BuriedVolume attribute) BuriedVolume (class in morfeus) (class in morfeus.buried_volume) bury() (morfeus.Sterimol method) (morfeus.sterimol.Sterimol method)

C

c6_coefficients (morfeus.io.D3Parser attribute) (morfeus.io.D4Parser attribute) c6_reference_data (in module morfeus.d3_data) c8_coefficients (morfeus.io.D3Parser attribute) (morfeus.io.D4Parser attribute) c_n_coefficients (morfeus.calculators.D3Calculator attribute) (morfeus.calculators.D4Grimme attribute) calculate() (morfeus.Sterimol method) (morfeus.sterimol.Sterimol method) center (morfeus.geometry.Sphere attribute) charge (morfeus.conformer.ConformerEnsemble attribute) charges (morfeus.calculators.D4Grimme attribute) check_distances() (in module morfeus.utils) cip_label (morfeus.conformer.Conformer attribute) circumference (morfeus.geometry.Sphere attribute) cli() (in module morfeus.bite_angle) (in module morfeus.buried_volume) (in module morfeus.cone_angle) (in module morfeus.conformer) (in module morfeus.dispersion) (in module morfeus.local_force) (in module morfeus.pyramidalization) (in module morfeus.sasa) (in module morfeus.solid_angle) (in module morfeus.sterimol) (in module morfeus.visible_volume) (in module morfeus.xtb) compute_coefficients() (morfeus.Dispersion method) (morfeus.dispersion.Dispersion method) compute_compliance() (morfeus.local_force.LocalForce method) (morfeus.LocalForce method) compute_distal_volume() (morfeus.buried_volume.BuriedVolume method) (morfeus.BuriedVolume method)

compute_frequencies() (morfeus.local_force.LocalForce method) (morfeus.LocalForce method) compute_local() (morfeus.local_force.LocalForce method) (morfeus.LocalForce method) compute_p_int() (morfeus.Dispersion method) (morfeus.dispersion.Dispersion method) condense_enantiomeric() (morfeus.conformer.ConformerEnsemble method) Cone (class in morfeus.geometry) cone (morfeus.geometry.Atom attribute) cone_angle (morfeus.cone_angle.ConeAngle attribute) (morfeus.ConeAngle attribute) (morfeus.solid_angle.SolidAngle attribute) (morfeus.SolidAngle attribute) ConeAngle (class in morfeus) (class in morfeus.cone_angle) Conformer (class in morfeus.conformer) conformer_coordinates (morfeus.io.CrestParser attribute) ConformerEnsemble (class in morfeus.conformer) conformers (morfeus.conformer.ConformerEnsemble attribute) conformers_from_ob_ff() (in module morfeus.conformer) conformers_from_ob_ga() (in module morfeus.conformer) conformers_from_rdkit() (in module morfeus.conformer) connectivity_matrix (morfeus.conformer.ConformerEnsemble attribute) convert_elements() (in module morfeus.utils) coordinates (morfeus.conformer.Conformer attribute) (morfeus.geometry.Atom attribute) coordination_number (morfeus.geometry.Atom attribute) coordination_numbers (morfeus.calculators.D3Calculator attribute) (morfeus.calculators.D4Grimme attribute) cov_radii_pyykko (in module morfeus.data) CrestParser (class in morfeus.io) CubeParser (class in morfeus.io)

D

D3Calculator (class in morfeus.calculators) D3Parser (class in morfeus.io) D4Grimme (class in morfeus.calculators) D4Parser (class in morfeus.io) degeneracies (morfeus.io.CrestParser attribute) degeneracy (morfeus.conformer.Conformer attribute) density (morfeus.geometry.Sphere attribute) detect_bonds() (morfeus.geometry.InternalCoordinates method) (morfeus.local_force.LocalForce method) (morfeus.LocalForce method) detect_enantiomers() (morfeus.conformer.ConformerEnsemble method) Dihedral (class in morfeus.geometry)

Dispersion (class in morfeus) (class in morfeus.dispersion) distal_area (morfeus.visible_volume.VisibleVolume attribute) (morfeus.VisibleVolume attribute) distal_visible_area (morfeus.visible_volume.VisibleVolume attribute) (morfeus.VisibleVolume attribute) distal_visible_volume (morfeus.visible_volume.VisibleVolume attribute) (morfeus.VisibleVolume attribute) distal_volume (morfeus.buried_volume.BuriedVolume attribute) (morfeus.BuriedVolume attribute) (morfeus.visible_volume.VisibleVolume attribute) (morfeus.VisibleVolume attribute)

E

element (morfeus.geometry.Atom attribute) elements (morfeus.conformer.Conformer attribute) (morfeus.conformer.ConformerEnsemble attribute) (morfeus.io.CrestParser attribute)

energies (morfeus.io.CrestParser attribute) energy (morfeus.conformer.Conformer attribute) extrapolate_c_n() (in module morfeus.calculators)

F

faces (morfeus.io.VertexParser attribute) formal_charges (morfeus.conformer.ConformerEnsemble attribute) fraction_buried_volume (morfeus.buried_volume.BuriedVolume attribute) (morfeus.BuriedVolume attribute) free_volume (morfeus.buried_volume.BuriedVolume attribute) (morfeus.BuriedVolume attribute)

from_crest() (morfeus.conformer.ConformerEnsemble class method) from_ob_ff() (morfeus.conformer.ConformerEnsemble class method) from_ob_ga() (morfeus.conformer.ConformerEnsemble class method) from_rdkit() (morfeus.conformer.ConformerEnsemble class method)

G

G (morfeus.solid_angle.SolidAngle attribute) (morfeus.SolidAngle attribute) generate_mol() (morfeus.conformer.ConformerEnsemble method) get_B_matrix() (morfeus.geometry.InternalCoordinates method) get_b_vector() (morfeus.geometry.Angle method) (morfeus.geometry.Bond method) (morfeus.geometry.Dihedral method) get_bond_order() (morfeus.XTB method) (morfeus.xtb.XTB method) get_bond_orders() (morfeus.XTB method) (morfeus.xtb.XTB method) get_charges() (morfeus.XTB method) (morfeus.xtb.XTB method) get_cip_labels() (morfeus.conformer.ConformerEnsemble method) get_cone() (morfeus.geometry.Atom method) get_connectivity_matrix() (in module morfeus.utils) get_coordinates() (morfeus.conformer.ConformerEnsemble method) get_degeneracies() (morfeus.conformer.ConformerEnsemble method) get_dipole() (morfeus.XTB method) (morfeus.xtb.XTB method) get_drawing_arrow() (in module morfeus.plotting) get_drawing_cone() (in module morfeus.plotting)

get_ea() (morfeus.XTB method) (morfeus.xtb.XTB method) get_energies() (morfeus.conformer.ConformerEnsemble method) get_excluded_from_connectivity() (in module morfeus.utils) get_fukui() (morfeus.XTB method) (morfeus.xtb.XTB method) get_global_descriptor() (morfeus.XTB method) (morfeus.xtb.XTB method) get_homo() (morfeus.XTB method) (morfeus.xtb.XTB method) get_ip() (morfeus.XTB method) (morfeus.xtb.XTB method) get_local_force_constant() (morfeus.local_force.LocalForce method) (morfeus.LocalForce method) get_local_frequency() (morfeus.local_force.LocalForce method) (morfeus.LocalForce method) get_lumo() (morfeus.XTB method) (morfeus.xtb.XTB method) get_properties() (morfeus.conformer.ConformerEnsemble method) get_radii() (in module morfeus.utils) get_relative_energies() (morfeus.conformer.ConformerEnsemble method) get_rmsd() (morfeus.conformer.ConformerEnsemble method) get_xyz_string() (in module morfeus.io)

I

i (morfeus.geometry.Angle attribute) (morfeus.geometry.Bond attribute) (morfeus.geometry.Dihedral attribute) Import (class in morfeus.utils) index (morfeus.geometry.Atom attribute) internal_coordinates (morfeus.geometry.InternalCoordinates attribute) (morfeus.local_force.LocalForce attribute) (morfeus.LocalForce attribute) InternalCoordinates (class in morfeus.geometry)

inverted (morfeus.bite_angle.BiteAngle attribute) (morfeus.BiteAngle attribute) invisible_area (morfeus.visible_volume.VisibleVolume attribute) (morfeus.VisibleVolume attribute) invisible_mask (morfeus.geometry.Atom attribute) invisible_volume (morfeus.visible_volume.VisibleVolume attribute) (morfeus.VisibleVolume attribute) is_inside() (morfeus.geometry.Cone method) is_inside_points() (morfeus.geometry.Cone method)

J

j (morfeus.geometry.Angle attribute) (morfeus.geometry.Bond attribute) (morfeus.geometry.Dihedral attribute)

jmol_colors (in module morfeus.data)

K

k (morfeus.geometry.Angle attribute) (morfeus.geometry.Dihedral attribute)

kabsch_rotation_matrix() (in module morfeus.geometry)

L

l (morfeus.geometry.Dihedral attribute) L (morfeus.Sterimol attribute) (morfeus.sterimol.Sterimol attribute) L_value (morfeus.Sterimol attribute) (morfeus.sterimol.Sterimol attribute) L_value_uncorrected (morfeus.Sterimol attribute) (morfeus.sterimol.Sterimol attribute) load_coefficients() (morfeus.Dispersion method) (morfeus.dispersion.Dispersion method)

load_file() (morfeus.local_force.LocalForce method) (morfeus.LocalForce method) local_force_constants (morfeus.local_force.LocalForce attribute) (morfeus.LocalForce attribute) local_frequencies (morfeus.local_force.LocalForce attribute) (morfeus.LocalForce attribute) LocalForce (class in morfeus) (class in morfeus.local_force)

M

min_x (morfeus.io.CubeParser attribute) min_y (morfeus.io.CubeParser attribute) min_z (morfeus.io.CubeParser attribute) module morfeus morfeus.bite_angle morfeus.buried_volume morfeus.calculators morfeus.cone_angle morfeus.conformer morfeus.d3_data morfeus.data morfeus.dispersion morfeus.geometry morfeus.io morfeus.local_force morfeus.plotting morfeus.pyramidalization morfeus.qc morfeus.sasa morfeus.solid_angle morfeus.sterimol morfeus.typing morfeus.utils morfeus.visible_volume morfeus.xtb mol (morfeus.conformer.ConformerEnsemble attribute) morfeus module morfeus.bite_angle module morfeus.buried_volume module morfeus.calculators module morfeus.cone_angle module

morfeus.conformer module morfeus.d3_data module morfeus.data module morfeus.dispersion module morfeus.geometry module morfeus.io module morfeus.local_force module morfeus.plotting module morfeus.pyramidalization module morfeus.qc module morfeus.sasa module morfeus.solid_angle module morfeus.sterimol module morfeus.typing module morfeus.utils module morfeus.visible_volume module morfeus.xtb module multiplicity (morfeus.conformer.ConformerEnsemble attribute)

N

n_conformers (morfeus.conformer.ConformerEnsemble property) n_imag (morfeus.local_force.LocalForce attribute) (morfeus.LocalForce attribute) n_points_x (morfeus.io.CubeParser attribute) n_points_y (morfeus.io.CubeParser attribute)

n_points_z (morfeus.io.CubeParser attribute) neighbor_indices (morfeus.Pyramidalization attribute) (morfeus.pyramidalization.Pyramidalization attribute) normal (morfeus.geometry.Cone attribute) normal_mode_analysis() (morfeus.local_force.LocalForce method) (morfeus.LocalForce method)

O

occluded_mask (morfeus.geometry.Atom attribute) occluded_points (morfeus.geometry.Atom attribute) octant_analysis() (morfeus.buried_volume.BuriedVolume method) (morfeus.BuriedVolume method)

OCTANT_SIGNS (in module morfeus.buried_volume) octants (morfeus.buried_volume.BuriedVolume attribute) (morfeus.BuriedVolume attribute) optimize_qc_engine() (morfeus.conformer.ConformerEnsemble method)

P

P (morfeus.Pyramidalization attribute) (morfeus.pyramidalization.Pyramidalization attribute) P_angle (morfeus.Pyramidalization attribute) (morfeus.pyramidalization.Pyramidalization attribute) p_int (morfeus.Dispersion attribute) (morfeus.dispersion.Dispersion attribute) p_max (morfeus.Dispersion attribute) (morfeus.dispersion.Dispersion attribute) p_min (morfeus.Dispersion attribute) (morfeus.dispersion.Dispersion attribute) p_values (morfeus.Dispersion attribute) (morfeus.dispersion.Dispersion attribute) (morfeus.geometry.Atom attribute) percent_buried_volume (morfeus.buried_volume.BuriedVolume property) (morfeus.BuriedVolume property) point (morfeus.geometry.Atom attribute) point_areas (morfeus.geometry.Atom attribute) point_volumes (morfeus.geometry.Atom attribute) points (morfeus.geometry.Sphere attribute) polarizabilities (morfeus.calculators.D4Grimme attribute) print_report() (morfeus.buried_volume.BuriedVolume method) (morfeus.BuriedVolume method) (morfeus.cone_angle.ConeAngle method) (morfeus.ConeAngle method) (morfeus.Dispersion method) (morfeus.dispersion.Dispersion method) (morfeus.local_force.LocalForce method) (morfeus.LocalForce method) (morfeus.Pyramidalization method) (morfeus.pyramidalization.Pyramidalization method) (morfeus.SASA method) (morfeus.sasa.SASA method) (morfeus.solid_angle.SolidAngle method) (morfeus.SolidAngle method) (morfeus.Sterimol method) (morfeus.sterimol.Sterimol method)

properties (morfeus.conformer.Conformer attribute) proximal_area (morfeus.visible_volume.VisibleVolume attribute) (morfeus.VisibleVolume attribute) proximal_mask (morfeus.geometry.Atom attribute) proximal_visible_area (morfeus.visible_volume.VisibleVolume attribute) (morfeus.VisibleVolume attribute) proximal_visible_volume (morfeus.visible_volume.VisibleVolume attribute) (morfeus.VisibleVolume attribute) proximal_volume (morfeus.visible_volume.VisibleVolume attribute) (morfeus.VisibleVolume attribute) prune_enantiomers() (morfeus.conformer.ConformerEnsemble method) prune_energy() (morfeus.conformer.ConformerEnsemble method) prune_rmsd() (morfeus.conformer.ConformerEnsemble method) Pyramidalization (class in morfeus) (class in morfeus.pyramidalization)

Q

QUADRANT_NAMES (in module morfeus.buried_volume) QUADRANT_OCTANT_MAP (in module morfeus.buried_volume)

QUADRANT_SIGNS (in module morfeus.buried_volume) quadrants (morfeus.buried_volume.BuriedVolume attribute) (morfeus.BuriedVolume attribute)

R

r2_r4 (in module morfeus.d3_data) radii_alvarez (in module morfeus.data) radii_bondi (in module morfeus.data) radii_crc (in module morfeus.data) radii_rahm (in module morfeus.data) radii_truhlar (in module morfeus.data) radius (morfeus.geometry.Atom attribute) (morfeus.geometry.Sphere attribute) read_geometry() (in module morfeus) (in module morfeus.io)

read_gjf() (in module morfeus) (in module morfeus.io) read_xyz() (in module morfeus) (in module morfeus.io) ref_cip_label (morfeus.conformer.ConformerEnsemble attribute) requires_dependency() (in module morfeus.utils) requires_executable() (in module morfeus.utils) reset_internal_coordinates() (morfeus.local_force.LocalForce method) (morfeus.LocalForce method) rotate_coordinates() (in module morfeus.geometry)

S

S (morfeus.io.CubeParser attribute) SASA (class in morfeus) (class in morfeus.sasa) save_vtk() (morfeus.Dispersion method) (morfeus.dispersion.Dispersion method) set_coordinates() (morfeus.conformer.ConformerEnsemble method) set_degeneracies() (morfeus.conformer.ConformerEnsemble method) set_energies() (morfeus.conformer.ConformerEnsemble method) set_multiplicity_from_mol() (morfeus.conformer.ConformerEnsemble method) set_points() (morfeus.Sterimol method) (morfeus.sterimol.Sterimol method) set_properties() (morfeus.conformer.ConformerEnsemble method) solid_angle (morfeus.solid_angle.SolidAngle attribute) (morfeus.SolidAngle attribute) SolidAngle (class in morfeus) (class in morfeus.solid_angle)

sort() (morfeus.conformer.ConformerEnsemble method) sp_qc_engine() (morfeus.conformer.ConformerEnsemble method) Sphere (class in morfeus.geometry) sphere_line_intersection() (in module morfeus.geometry) step_x (morfeus.io.CubeParser attribute) step_y (morfeus.io.CubeParser attribute) step_z (morfeus.io.CubeParser attribute) Sterimol (class in morfeus) (class in morfeus.sterimol) surface_from_cube() (morfeus.Dispersion method) (morfeus.dispersion.Dispersion method) surface_from_multiwfn() (morfeus.Dispersion method) (morfeus.dispersion.Dispersion method) surface_from_radii() (morfeus.Sterimol method) (morfeus.sterimol.Sterimol method)

T

tangent_atoms (morfeus.cone_angle.ConeAngle attribute) (morfeus.ConeAngle attribute) total_area (morfeus.visible_volume.VisibleVolume attribute) (morfeus.VisibleVolume attribute)

total_volume (morfeus.visible_volume.VisibleVolume attribute) (morfeus.VisibleVolume attribute)

U

update_mol() (morfeus.conformer.ConformerEnsemble method)

V

VertexParser (class in morfeus.io) vertices (morfeus.io.VertexParser attribute) visible_area (morfeus.visible_volume.VisibleVolume attribute) (morfeus.VisibleVolume attribute) visible_volume (morfeus.visible_volume.VisibleVolume attribute) (morfeus.VisibleVolume attribute) VisibleVolume (class in morfeus) (class in morfeus.visible_volume)

volume (morfeus.Dispersion attribute) (morfeus.dispersion.Dispersion attribute) (morfeus.geometry.Atom attribute) (morfeus.geometry.Sphere attribute) (morfeus.SASA attribute) (morfeus.sasa.SASA attribute)

W

write_xyz() (in module morfeus.io) (morfeus.conformer.ConformerEnsemble method)

X

X (morfeus.io.CubeParser attribute)

XTB (class in morfeus) (class in morfeus.xtb)

Y

Y (morfeus.io.CubeParser attribute)

Z

Z (morfeus.io.CubeParser attribute)