Index

_

__init__() (MultiwfnInterface method)

A

amassdict (Electrostatics attribute) ANGSTROM_TO_M (in module pyef.constants) (in module pyef.utility)

ATOMIC_MASS_DICT (in module pyef.constants) (in module pyef.utility)

B

BOHR_TO_ANGSTROM (in module pyef.constants) (in module pyef.utility) BOHR_TO_M (in module pyef.constants) (in module pyef.utility) bondEfield() (Electrostatics method)

bondEfield_pointcharges() (Electrostatics method) build_core_map() (MoldenObject method) build_hybrid_core_map() (MoldenObject method) build_interaction_tensor() (Electrostatics method) build_multipole_vector() (Electrostatics method)

C

calc_bond_dipoles() (Electrostatics method) calc_firstTermE() (Electrostatics method) changeDielectric() (Electrostatics method) charge_atom() (Electrostatics method) charge_atoms() (Electrostatics method) CHARGE_SCHEMES (MultiwfnInterface attribute), [1], [2] check_index_overlap() (in module pyef.validation) check_path_exists() (in module pyef.validation) cli() (in module pyef.cli) compareESP() (Visualize method) compute_atomwise_contributions() (Electrostatics method)

compute_atomwise_dipole_contributions() (Electrostatics method) compute_dipole() (Electrostatics method) compute_esp() (Electrostatics method) compute_esp_from_qm() (Electrostatics method) config (Electrostatics attribute) (MultiwfnInterface attribute), [1], [2] COULOMB_CONSTANT (in module pyef.constants) (in module pyef.utility) count_atoms() (MultiwfnInterface static method), [1], [2] countBasis() (MoldenObject method), [1], [2] countCloseContacts() (Geometry method) createpdbfromcoords() (Geometry method)

D

dict_of_calcs (Electrostatics attribute) (MultiwfnInterface attribute), [1], [2]

dict_of_multipole (Electrostatics attribute) (MultiwfnInterface attribute), [1], [2] diff_pdbs() (Visualize method)

E

Electrostatics (class in pyef.analysis) ELEMENTARY_CHARGE (in module pyef.constants) (in module pyef.utility)

esp_atom_idx (Electrostatics attribute) esp_bydistance() (Electrostatics method) esp_coord_shell() (Electrostatics method)

F

filter_charge_types_for_monopole() (in module pyef.validation) filter_charge_types_for_multipole() (in module pyef.validation)

fix_allECPmolden() (Electrostatics method) fix_ECPmolden() (MoldenObject method)

G

Geometry (class in pyef.geometry) get_atom_count_from_xyz() (in module pyef.validation) get_monopole_commands() (MultiwfnInterface static method), [1] get_openbabel_charges() (in module pyef.utility) get_residueDipoles() (Electrostatics method) get_residues() (Electrostatics method) getAtomInfo() (Electrostatics method) getAtomsInfo() (Electrostatics method) getBondedAtoms() (Geometry method) getCentroidDistance() (Geometry method) getcharge_residues() (Electrostatics method) getCharges() (Electrostatics method)

getCloseHcontacts() (Geometry method) getdipole_residues() (Electrostatics method) getEfield() (Electrostatics method) getElectrostatic_stabilization() (Electrostatics method) getESP() (Electrostatics method) getGeomInfo() (Geometry method) getGeomInfovDW() (Geometry method) getmultipoles() (Electrostatics static method) (MultiwfnInterface static method), [1], [2] getpartialchgs() (Electrostatics method) getPdbCharges() (Electrostatics method) getPtChgs() (Electrostatics method) getSubstrateFramePosition() (Geometry method)

H

hbond_check() (Geometry method)

I

includePtChgs() (Electrostatics method)

initialize_excludeAtomsFromEfieldCalc() (Electrostatics method)

L

list_openbabel_charge_models() (in module pyef.utility)

M

main() (in module pyef.run) makePDB() (Visualize method) makePDBcontributionEfield() (Visualize method) makePDBcontributionESP() (Visualize method) makePDBpercentEfield() (Visualize method) mapcount() (Electrostatics static method) minDielecBonds() (Electrostatics method) module pyef pyef.analysis pyef.cli, [1], [2] pyef.constants, [1] pyef.geometry pyef.manage, [1] pyef.multiwfn_interface, [1], [2] pyef.resources pyef.run pyef.utility pyef.validation

molden_paths (Electrostatics attribute) MoldenObject (class in pyef.multiwfn_interface), [1] (class in pyef.utility) monopole_atomicEfield() (Electrostatics method) monopole_esp() (Electrostatics method) monopole_esp_df() (Electrostatics method) multipole_atomicEfield() (Electrostatics method) multipole_esp() (Electrostatics method) MULTIPOLE_SCHEMES (MultiwfnInterface attribute), [1], [2] MultiwfnInterface (class in pyef.multiwfn_interface), [1] (class in pyef.utility)

P

parse_job_batch_file() (in module pyef.cli), [1] (in module pyef.manage) parser (in module pyef.run) partitionCharge() (Electrostatics method) (MultiwfnInterface method), [1], [2] pdb_esp() (Visualize method) periodic_table (Electrostatics attribute) PERIODIC_TABLE (in module pyef.constants) (in module pyef.utility) pointcharge_atomicEfield() (Electrostatics method) prepData() (Electrostatics method) prepData_pdb() (Electrostatics method) ptchgdf (Electrostatics attribute) pyef module pyef.analysis module

pyef.cli module, [1], [2] pyef.constants module, [1] pyef.geometry module pyef.manage module, [1] pyef.multiwfn_interface module, [1], [2] pyef.resources module pyef.run module pyef.utility module pyef.validation module

R

read_config() (in module pyef.cli), [1] read_file_lines() (in module pyef.cli), [1] (in module pyef.run) rePrep() (Electrostatics method)

run() (in module pyef.cli) run_analysis() (in module pyef.cli), [1] run_multiwfn() (Electrostatics method) (MultiwfnInterface method), [1], [2] runlowmemory() (Electrostatics method)

S

set_dielec_scale() (Electrostatics method) set_molden_filename() (Electrostatics method)

set_xyzfilename() (Electrostatics method) setExcludeAtomFromCalc() (Electrostatics method)

U

updateCalcSettings() (Electrostatics method)

V

VALID_CHARGE_TYPES (in module pyef.validation) VALID_MULTIPOLE_CHARGE_TYPES (in module pyef.validation) validate_atom_indices() (in module pyef.validation) validate_charge_type() (in module pyef.validation) validate_numeric_range() (in module pyef.validation) VDW_RADII_DICT (in module pyef.constants) (in module pyef.utility)

Visualize (class in pyef.geometry) visualize_atomwise_contributions() (Electrostatics method) visualize_charges_pdb() (in module pyef.analysis) VM_TO_VA (in module pyef.constants) (in module pyef.utility)

W

weak_Hbond_check() (Geometry method)

welcome() (in module pyef.cli), [1]

X

xyz_paths (Electrostatics attribute)