Index

_

_abc_impl (isicle.adducts.CRESTIonizationWrapper attribute) (isicle.adducts.ExplicitIonizationWrapper attribute) (isicle.conformers.ConformationalEnsemble attribute) (isicle.geometry.Geometry attribute) (isicle.interfaces.FileParserInterface attribute) (isicle.interfaces.GeometryInterface attribute) (isicle.interfaces.WrapperInterface attribute) (isicle.interfaces.XYZGeometryInterface attribute) (isicle.md.RDKitWrapper attribute) (isicle.md.XTBWrapper attribute) (isicle.mobility.MobcalWrapper attribute) (isicle.parse.ImpactParser attribute) (isicle.parse.MobcalParser attribute) (isicle.parse.NWChemParser attribute) (isicle.parse.ORCAParser attribute) (isicle.parse.XTBParser attribute) (isicle.qm.NWChemWrapper attribute) (isicle.qm.ORCAWrapper attribute) (isicle.utils.TypedList attribute) _add_ion() (isicle.adducts.ExplicitIonizationWrapper method) _apply_add_ion() (isicle.adducts.ExplicitIonizationWrapper method) _apply_function() (isicle.conformers.ConformationalEnsemble method) _apply_method() (isicle.conformers.ConformationalEnsemble method) _apply_remove_ion() (isicle.adducts.ExplicitIonizationWrapper method) _backend_selector() (in module isicle.md) (in module isicle.qm) _check_atom_group() (in module isicle.adducts) _check_attributes() (isicle.conformers.ConformationalEnsemble method) _check_mol() (in module isicle.io) _check_mol_obj() (in module isicle.io) _check_valid() (isicle.adducts.CRESTIonizationWrapper method) (isicle.adducts.ExplicitIonizationWrapper method) _configure_basis() (isicle.qm.NWChemWrapper method) _configure_cosmo() (isicle.qm.NWChemWrapper method) _configure_crest() (isicle.md.XTBWrapper method) _configure_dft() (isicle.qm.NWChemWrapper method) _configure_distance_geometry() (isicle.md.RDKitWrapper method) _configure_driver() (isicle.qm.NWChemWrapper method) _configure_energy() (isicle.qm.NWChemWrapper method) _configure_etdg() (isicle.md.RDKitWrapper method) _configure_etkdg1() (isicle.md.RDKitWrapper method) _configure_etkdg2() (isicle.md.RDKitWrapper method) _configure_etkdg3() (isicle.md.RDKitWrapper method) _configure_etkdg3_variant() (isicle.md.RDKitWrapper method) _configure_frequency() (isicle.qm.NWChemWrapper method) _configure_header() (isicle.qm.NWChemWrapper method) _configure_lennard_jones() (isicle.mobility.MobcalWrapper method) _configure_load() (isicle.qm.NWChemWrapper method) _configure_mobcal() (isicle.mobility.MobcalWrapper method) _configure_optimize() (isicle.qm.NWChemWrapper method) _configure_shielding() (isicle.qm.NWChemWrapper method) _configure_spin() (isicle.qm.NWChemWrapper method) _configure_xtb() (isicle.md.XTBWrapper method) _crest_energy() (isicle.parse.XTBParser method) _crest_timing() (isicle.parse.XTBParser method) _default_value (isicle.adducts.CRESTIonizationWrapper attribute) (isicle.adducts.ExplicitIonizationWrapper attribute) (isicle.geometry.Geometry attribute) (isicle.md.RDKitWrapper attribute) (isicle.md.XTBWrapper attribute) (isicle.mobility.MobcalWrapper attribute) (isicle.qm.NWChemWrapper attribute) (isicle.qm.ORCAWrapper attribute) _defaults (isicle.adducts.CRESTIonizationWrapper attribute) (isicle.adducts.ExplicitIonizationWrapper attribute) (isicle.geometry.Geometry attribute) (isicle.md.RDKitWrapper attribute) (isicle.md.XTBWrapper attribute) (isicle.mobility.MobcalWrapper attribute) (isicle.qm.NWChemWrapper attribute) (isicle.qm.ORCAWrapper attribute)

_energy_based() (in module isicle.conformers) _filter_by_substructure_match() (in module isicle.adducts) _filter_supported_by_xtb() (isicle.adducts.CRESTIonizationWrapper method) _find_output_by_header() (isicle.parse.ORCAParser method) _forcefield_selector() (isicle.adducts.ExplicitIonizationWrapper method) _function_selector() (in module isicle.conformers) _is_embedded() (isicle.geometry.Geometry method) _isomer_energy() (isicle.parse.XTBParser method) _isomer_timing() (isicle.parse.XTBParser method) _load_line_notation() (in module isicle.io) _load_mol_from_file() (in module isicle.io) _load_text() (in module isicle.io) _mobcal_selector() (in module isicle.mobility) _modify_atom_dict() (isicle.adducts.ExplicitIonizationWrapper method) _negative_mode() (isicle.adducts.CRESTIonizationWrapper method) (isicle.adducts.ExplicitIonizationWrapper method) _opt_energy() (isicle.parse.XTBParser method) _opt_timing() (isicle.parse.XTBParser method) _parse_charge() (isicle.parse.NWChemParser method) (isicle.parse.ORCAParser method) _parse_connectivity() (isicle.parse.NWChemParser method) (isicle.parse.ORCAParser method) _parse_energy() (isicle.parse.NWChemParser method) (isicle.parse.ORCAParser method) _parse_file_ions() (in module isicle.adducts) _parse_frequency() (isicle.parse.NWChemParser method) (isicle.parse.ORCAParser method) _parse_geometry() (isicle.parse.NWChemParser method) (isicle.parse.ORCAParser method) (isicle.parse.XTBParser method) _parse_ion_charge() (isicle.adducts.CRESTIonizationWrapper method) _parse_ions() (in module isicle.adducts) _parse_list_ions() (in module isicle.adducts) _parse_molden() (isicle.parse.NWChemParser method) (isicle.parse.ORCAParser method) _parse_orbital_energies() (isicle.parse.ORCAParser method) (isicle.parse.XTBParser method) _parse_protocol() (isicle.parse.NWChemParser method) (isicle.parse.ORCAParser method) (isicle.parse.XTBParser method) _parse_shielding() (isicle.parse.NWChemParser method) (isicle.parse.ORCAParser method) _parse_shielding_summary() (isicle.parse.ORCAParser method) _parse_spin() (isicle.parse.NWChemParser method) (isicle.parse.ORCAParser method) _parse_thermo() (isicle.parse.ORCAParser method) _parse_timing() (isicle.parse.NWChemParser method) (isicle.parse.ORCAParser method) _positive_mode() (isicle.adducts.CRESTIonizationWrapper method) (isicle.adducts.ExplicitIonizationWrapper method) _remove_ion() (isicle.adducts.ExplicitIonizationWrapper method) _save_config() (isicle.qm.ORCAWrapper method) _save_geometry() (isicle.qm.NWChemWrapper method) (isicle.qm.ORCAWrapper method) _set_ions() (isicle.adducts.CRESTIonizationWrapper method) (isicle.adducts.ExplicitIonizationWrapper method) _subset_atom_dict() (isicle.adducts.ExplicitIonizationWrapper method) _update_geometry_charge() (isicle.adducts.CRESTIonizationWrapper method) (isicle.adducts.ExplicitIonizationWrapper method)

A

add___dict__() (isicle.geometry.Geometry method) addHs() (isicle.geometry.Geometry method)

AdductEnsemble (class in isicle.adducts) apply() (isicle.conformers.ConformationalEnsemble method) atomic_masses() (in module isicle.utils)

B

boltzmann() (in module isicle.conformers)

build_adduct_ensemble() (in module isicle.adducts) build_conformational_ensemble() (in module isicle.conformers)

C

calculate_ccs() (in module isicle.mobility) ccs (isicle.geometry.Geometry property) charge (isicle.geometry.Geometry property) check() (isicle.utils.TypedList method) clear() (isicle.adducts.AdductEnsemble method) config (isicle.qm.ORCAWrapper attribute) configure() (isicle.adducts.CRESTIonizationWrapper method) (isicle.adducts.ExplicitIonizationWrapper method) (isicle.interfaces.WrapperInterface method) (isicle.md.RDKitWrapper method) (isicle.md.XTBWrapper method) (isicle.mobility.MobcalWrapper method) (isicle.qm.NWChemWrapper method) (isicle.qm.ORCAWrapper method)

configure_from_template() (isicle.qm.NWChemWrapper method) ConformationalEnsemble (class in isicle.conformers) connectivity (isicle.geometry.Geometry property) copy() (isicle.adducts.AdductEnsemble method) CRESTIonizationWrapper (class in isicle.adducts)

D

desalt() (isicle.geometry.Geometry method) dft() (in module isicle.qm) (isicle.geometry.Geometry method) (isicle.interfaces.XYZGeometryInterface method)

E

energy (isicle.geometry.Geometry property)

energy_threshold() (in module isicle.conformers) ExplicitIonizationWrapper (class in isicle.adducts)

F

FileParserInterface (class in isicle.interfaces) finish() (isicle.adducts.CRESTIonizationWrapper method) (isicle.adducts.ExplicitIonizationWrapper method) (isicle.interfaces.WrapperInterface method) (isicle.md.RDKitWrapper method) (isicle.md.XTBWrapper method) (isicle.mobility.MobcalWrapper method) (isicle.qm.NWChemWrapper method) (isicle.qm.ORCAWrapper method)

formal_charge (isicle.geometry.Geometry property) frequency (isicle.geometry.Geometry property)

G

geom (isicle.md.RDKitWrapper attribute) (isicle.md.XTBWrapper attribute) (isicle.mobility.MobcalWrapper attribute) (isicle.qm.NWChemWrapper attribute) (isicle.qm.ORCAWrapper attribute) Geometry (class in isicle.geometry) GeometryInterface (class in isicle.interfaces) get___dict__() (isicle.geometry.Geometry method) (isicle.interfaces.XYZGeometryInterface method) get_adducts() (isicle.adducts.CRESTIonizationWrapper method) (isicle.adducts.ExplicitIonizationWrapper method) get_atom_indices() (isicle.geometry.Geometry method) (isicle.interfaces.XYZGeometryInterface method)

get_basename() (isicle.geometry.Geometry method) get_natoms() (isicle.geometry.Geometry method) (isicle.interfaces.XYZGeometryInterface method) get_nested_dict_values() (in module isicle.adducts) get_structures() (isicle.adducts.AdductEnsemble method) (isicle.adducts.CRESTIonizationWrapper method) (isicle.adducts.ExplicitIonizationWrapper method) (isicle.conformers.ConformationalEnsemble method) get_total_partial_charge() (isicle.geometry.Geometry method) (isicle.interfaces.GeometryInterface method) gettempdir() (in module isicle.utils)

H

has_key() (isicle.adducts.AdductEnsemble method)

I

ImpactParser (class in isicle.parse) initial_optimize() (isicle.geometry.Geometry method) insert() (isicle.utils.TypedList method) ionize() (in module isicle.adducts) (isicle.geometry.Geometry method) isicle module isicle.adducts module isicle.conformers module isicle.geometry module

isicle.interfaces module isicle.io module isicle.md module isicle.mobility module isicle.parse module isicle.qm module isicle.utils module

K

kekulize() (isicle.geometry.Geometry method)

keys() (isicle.adducts.AdductEnsemble method)

L

list (isicle.utils.TypedList attribute) load() (in module isicle) (in module isicle.io) (isicle.interfaces.FileParserInterface method) (isicle.parse.ImpactParser method) (isicle.parse.MobcalParser method) (isicle.parse.NWChemParser method) (isicle.parse.ORCAParser method) (isicle.parse.XTBParser method)

load_inchi() (in module isicle.io) load_joblib() (in module isicle.io) load_mol() (in module isicle.io) load_mol2() (in module isicle.io) load_mol_obj() (in module isicle.io) load_pdb() (in module isicle.io) load_pickle() (in module isicle.io) load_smiles() (in module isicle.io) load_xyz() (in module isicle.io) lowest_energy() (in module isicle.conformers)

M

md() (in module isicle.md) (isicle.geometry.Geometry method) (isicle.interfaces.XYZGeometryInterface method) method (isicle.md.RDKitWrapper attribute) mkdtemp() (in module isicle.utils) MobcalParser (class in isicle.parse) MobcalWrapper (class in isicle.mobility) module isicle isicle.adducts isicle.conformers isicle.geometry isicle.interfaces isicle.io isicle.md isicle.mobility isicle.parse isicle.qm isicle.utils

molden (isicle.geometry.Geometry property)

N

neutralize() (isicle.geometry.Geometry method) numConfs (isicle.md.RDKitWrapper attribute)

NWChemParser (class in isicle.parse) NWChemWrapper (class in isicle.qm)

O

oktypes (isicle.utils.TypedList attribute) orbital_energies (isicle.geometry.Geometry property)

ORCAParser (class in isicle.parse) ORCAWrapper (class in isicle.qm)

P

parse() (isicle.interfaces.FileParserInterface method) (isicle.md.RDKitWrapper method) (isicle.md.XTBWrapper method) (isicle.mobility.MobcalWrapper method) (isicle.parse.ImpactParser method) (isicle.parse.MobcalParser method) (isicle.parse.NWChemParser method) (isicle.parse.ORCAParser method) (isicle.parse.XTBParser method) (isicle.qm.NWChemWrapper method) (isicle.qm.ORCAWrapper method)

R

RDKitWrapper (class in isicle.md) reduce() (in module isicle.conformers) (isicle.conformers.ConformationalEnsemble method) result (isicle.md.RDKitWrapper attribute) (isicle.md.XTBWrapper attribute) (isicle.mobility.MobcalWrapper attribute) (isicle.qm.NWChemWrapper attribute) (isicle.qm.ORCAWrapper attribute)

rmdtemp() (in module isicle.utils) run() (isicle.adducts.CRESTIonizationWrapper method) (isicle.adducts.ExplicitIonizationWrapper method) (isicle.interfaces.WrapperInterface method) (isicle.md.RDKitWrapper method) (isicle.md.XTBWrapper method) (isicle.mobility.MobcalWrapper method) (isicle.qm.NWChemWrapper method) (isicle.qm.ORCAWrapper method)

S

safelist() (in module isicle.utils) save() (in module isicle) (in module isicle.io) (isicle.adducts.CRESTIonizationWrapper method) (isicle.adducts.ExplicitIonizationWrapper method) (isicle.qm.NWChemWrapper method) (isicle.qm.ORCAWrapper method) save_config() (isicle.qm.NWChemWrapper method) save_csv() (in module isicle.io) save_geometry() (isicle.md.XTBWrapper method) (isicle.mobility.MobcalWrapper method) save_inchi() (in module isicle.io) save_joblib() (in module isicle.io) save_mfj() (in module isicle.io) save_mol() (in module isicle.io) save_pdb() (in module isicle.io) save_pickle() (in module isicle.io) (isicle.adducts.CRESTIonizationWrapper method) (isicle.adducts.ExplicitIonizationWrapper method) save_smiles() (in module isicle.io)

save_xyz() (in module isicle.io) set_geometry() (isicle.adducts.CRESTIonizationWrapper method) (isicle.adducts.ExplicitIonizationWrapper method) (isicle.interfaces.WrapperInterface method) (isicle.md.RDKitWrapper method) (isicle.md.XTBWrapper method) (isicle.mobility.MobcalWrapper method) (isicle.qm.NWChemWrapper method) (isicle.qm.ORCAWrapper method) shielding (isicle.geometry.Geometry property) simple_average() (in module isicle.conformers) spin (isicle.geometry.Geometry property) submit() (isicle.adducts.CRESTIonizationWrapper method) (isicle.adducts.ExplicitIonizationWrapper method) (isicle.interfaces.WrapperInterface method) (isicle.md.RDKitWrapper method) (isicle.md.XTBWrapper method) (isicle.mobility.MobcalWrapper method) (isicle.qm.NWChemWrapper method) (isicle.qm.ORCAWrapper method)

T

tautomerize() (isicle.geometry.Geometry method) temp_dir (isicle.md.XTBWrapper attribute) (isicle.mobility.MobcalWrapper attribute) (isicle.qm.NWChemWrapper attribute) (isicle.qm.ORCAWrapper attribute) tinker_lookup() (in module isicle.utils) to_inchi() (isicle.geometry.Geometry method) (isicle.interfaces.GeometryInterface method) to_mol() (isicle.geometry.Geometry method) (isicle.interfaces.GeometryInterface method)

to_molblock() (isicle.geometry.Geometry method) to_pdbblock() (isicle.geometry.Geometry method) to_smarts() (isicle.geometry.Geometry method) (isicle.interfaces.GeometryInterface method) to_smiles() (isicle.geometry.Geometry method) (isicle.interfaces.GeometryInterface method) to_xyzblock() (isicle.geometry.Geometry method) (isicle.interfaces.XYZGeometryInterface method) transform() (in module isicle.conformers) TypedList (class in isicle.utils)

U

update() (isicle.adducts.AdductEnsemble method)

update_coordinates() (isicle.geometry.Geometry method)

V

values() (isicle.adducts.AdductEnsemble method)

view() (isicle.geometry.Geometry method)

W

WrapperInterface (class in isicle.interfaces)

write() (in module isicle.adducts)

X

XTBParser (class in isicle.parse)

XTBWrapper (class in isicle.md) XYZGeometryInterface (class in isicle.interfaces)