Index

A

AC2BO() (in module rdmc.external.xyz2mol) AC2mol() (in module rdmc.external.xyz2mol) add_angle_constraint() (rdmc.forcefield.OpenBabelFF method) (rdmc.forcefield.RDKitFF method) add_distance_constraint() (rdmc.forcefield.OpenBabelFF method) (rdmc.forcefield.RDKitFF method) add_torsion_constraint() (rdmc.forcefield.OpenBabelFF method) (rdmc.forcefield.RDKitFF method)

AddNullConformer() (rdmc.mol.RDKitMol method) AddRedundantBonds() (rdmc.mol.RDKitMol method) AlignMol() (rdmc.mol.RDKitMol method) AssignStereochemistryFrom3D() (rdmc.mol.RDKitMol method) atom_maps (rdmc.conf.ConformerFilter property) available_force_field (rdmc.forcefield.OpenBabelFF attribute) (rdmc.forcefield.RDKitFF attribute) available_solver (rdmc.forcefield.OpenBabelFF attribute)

B

BO2mol() (in module rdmc.external.xyz2mol)

BO_is_OK() (in module rdmc.external.xyz2mol)

C

CalcRMSD() (rdmc.mol.RDKitMol method) charge_is_OK() (in module rdmc.external.xyz2mol) check_dihed_angle_diff() (rdmc.conf.ConformerFilter method) check_isomorphic_molecules() (in module rdmc.external.rmg) chiral_stereo_check() (in module rdmc.external.xyz2mol)

clean_charges() (in module rdmc.external.xyz2mol) CombineMol() (rdmc.mol.RDKitMol method) conformer_viewer() (in module rdmc.view) ConformerCluster (class in rdmc.conf) ConformerFilter (class in rdmc.conf) Copy() (rdmc.mol.RDKitMol method)

D

determine_smallest_atom_index_in_torsion() (in module rdmc.utils)

E

edit_conf_by_add_bonds() (in module rdmc.conf) EmbedConformer() (rdmc.mol.RDKitMol method)

EmbedMultipleConfs() (rdmc.mol.RDKitMol method) EmbedMultipleNullConfs() (rdmc.mol.RDKitMol method) EmbedNullConformer() (rdmc.mol.RDKitMol method)

F

filter_by_dihed_angles() (rdmc.conf.ConformerFilter method) filter_by_iter_hcluster() (rdmc.conf.ConformerFilter method) find_internal_torsions() (in module rdmc.utils) find_reaction_family() (in module rdmc.external.rmg) find_ring_torsions() (in module rdmc.utils) fix_atom() (rdmc.forcefield.OpenBabelFF method) (rdmc.forcefield.RDKitFF method) fix_CO_openbabel() (in module rdmc.utils) freq_viewer() (in module rdmc.view) from_rdkit_mol() (in module rdmc.external.rmg) FromConformer() (rdmc.conf.RDKitConf class method)

FromFile() (rdmc.mol.RDKitMol class method) FromInchi() (rdmc.mol.RDKitMol class method) FromMol() (rdmc.conf.RDKitConf class method) (rdmc.mol.RDKitMol class method) FromOBMol() (rdmc.mol.RDKitMol class method) FromRDKitMol() (rdmc.conf.RDKitConf class method) FromRMGMol() (rdmc.mol.RDKitMol class method) FromSDF() (rdmc.mol.RDKitMol class method) FromSmarts() (rdmc.mol.RDKitMol class method) FromSmiles() (rdmc.mol.RDKitMol class method) FromXYZ() (rdmc.mol.RDKitMol class method)

G

generate_radical_resonance_structures() (in module rdmc.mol) generate_reaction_complex() (in module rdmc.external.rmg) generate_rmsds_of_cluster() (rdmc.conf.ConformerFilter method) generate_vdw_mat() (in module rdmc.mol) get_AC() (in module rdmc.external.xyz2mol) get_atom_masses() (in module rdmc.utils) get_atomic_charge() (in module rdmc.external.xyz2mol) get_BO() (in module rdmc.external.xyz2mol) get_bonds() (in module rdmc.external.xyz2mol) get_conformer_energies() (rdmc.forcefield.RDKitFF method) get_element_symbols() (in module rdmc.utils) get_energy() (rdmc.forcefield.RDKitFF method) get_internal_coords() (in module rdmc.utils) get_obmol_coords() (in module rdmc.utils) get_optimized_mol() (rdmc.forcefield.OpenBabelFF method) (rdmc.forcefield.RDKitFF method) get_proto_mol() (in module rdmc.external.xyz2mol) get_roo_radical_atoms() (in module rdmc.forcefield) get_tor_matrix() (rdmc.conf.ConformerFilter method) get_torsional_angles() (rdmc.conf.ConformerFilter method) get_UA() (in module rdmc.external.xyz2mol) get_UA_pairs() (in module rdmc.external.xyz2mol) get_unique_mols() (in module rdmc.mol) GetAdjacencyMatrix() (rdmc.mol.RDKitMol method) GetAllConformers() (rdmc.mol.RDKitMol method) GetAllTorsionsDeg() (rdmc.conf.RDKitConf method) GetAngleDeg() (rdmc.conf.RDKitConf method)

GetAngleRad() (rdmc.conf.RDKitConf method) GetAtomicNumbers() (rdmc.mol.RDKitMol method) GetAtomMapNumbers() (rdmc.mol.RDKitMol method) GetAtomMasses() (rdmc.mol.RDKitMol method) GetBestAlign() (rdmc.mol.RDKitMol method) GetBondLength() (rdmc.conf.RDKitConf method) GetBondsAsTuples() (rdmc.mol.RDKitMol method) GetConformer() (rdmc.mol.RDKitMol method) GetConformers() (rdmc.mol.RDKitMol method) GetDistanceMatrix() (rdmc.conf.RDKitConf method) (rdmc.mol.RDKitMol method) GetElementSymbols() (rdmc.mol.RDKitMol method) GetFormalCharge() (rdmc.mol.RDKitMol method) GetInternalCoordinates() (rdmc.mol.RDKitMol method) GetMolFrags() (rdmc.mol.RDKitMol method) GetOwningMol() (rdmc.conf.RDKitConf method) GetPositions() (rdmc.mol.RDKitMol method) GetSpinMultiplicity() (rdmc.mol.RDKitMol method) GetSubstructMatch() (rdmc.mol.RDKitMol method) GetSubstructMatches() (rdmc.mol.RDKitMol method) GetSymmSSSR() (rdmc.mol.RDKitMol method) GetTorsionalModes() (rdmc.conf.RDKitConf method) (rdmc.mol.RDKitMol method) GetTorsionDeg() (rdmc.conf.RDKitConf method) GetTorsionTops() (rdmc.mol.RDKitMol method) GetVdwMatrix() (rdmc.conf.RDKitConf method) (rdmc.mol.RDKitMol method) grid_viewer() (in module rdmc.view)

H

has_matched_mol() (in module rdmc.mol) HasCollidingAtoms() (rdmc.conf.RDKitConf method) (rdmc.mol.RDKitMol method)

HasOwningMol() (rdmc.conf.RDKitConf method) HasSameConnectivity() (rdmc.mol.RDKitMol method) hierarchy_cluster() (rdmc.conf.ConformerFilter method)

I

int_atom() (in module rdmc.external.xyz2mol) interactive_conformer_viewer() (in module rdmc.view)

is_optimizable() (rdmc.forcefield.OpenBabelFF method) (rdmc.forcefield.RDKitFF method)

K

Kekulize() (rdmc.mol.RDKitMol method)

L

load_rmg_database() (in module rdmc.external.rmg)

load_rxn_family_database() (in module rdmc.external.rmg)

M

main() (in module rdmc.external.xyz2mol) make_optimizable() (rdmc.forcefield.RDKitFF method) merge() (rdmc.conf.ConformerCluster method) module rdmc rdmc.conf rdmc.external rdmc.external.rmg rdmc.external.xyz2mol rdmc.forcefield rdmc.mol rdmc.utils rdmc.view

mol (rdmc.forcefield.OpenBabelFF property) (rdmc.forcefield.RDKitFF property) mol_animation() (in module rdmc.view) mol_viewer() (in module rdmc.view)

O

openbabel_mol_to_rdkit_mol() (in module rdmc.utils) OpenBabelFF (class in rdmc.forcefield) optimize() (rdmc.forcefield.OpenBabelFF method) (rdmc.forcefield.RDKitFF method)

optimize_confs() (rdmc.forcefield.RDKitFF method) optimize_mol() (in module rdmc.forcefield)

P

pairwise_rmsd() (rdmc.conf.ConformerFilter method) parse_xyz_by_jensen() (in module rdmc.external.xyz2mol) (in module rdmc.utils)

parse_xyz_by_openbabel() (in module rdmc.utils) parse_xyz_or_smiles_list() (in module rdmc.mol) PrepareOutputMol() (rdmc.mol.RDKitMol method)

R

rdkit_mol_to_openbabel_mol() (in module rdmc.utils) rdkit_mol_to_openbabel_mol_manual() (in module rdmc.utils) RDKitConf (class in rdmc.conf) RDKitFF (class in rdmc.forcefield) RDKitMol (class in rdmc.mol) rdmc module rdmc.conf module rdmc.external module rdmc.external.rmg module rdmc.external.xyz2mol module

rdmc.forcefield module rdmc.mol module rdmc.utils module rdmc.view module read_xyz_file() (in module rdmc.external.xyz2mol) recover_mol() (rdmc.forcefield.RDKitFF method) Reflect() (rdmc.mol.RDKitMol method) RemoveHs() (rdmc.mol.RDKitMol method) RenumberAtoms() (rdmc.mol.RDKitMol method) reset_atom_maps() (rdmc.conf.ConformerFilter method) reverse_map() (in module rdmc.utils) rmg_mol_to_rdkit_mol() (in module rdmc.utils)

S

Sanitize() (rdmc.mol.RDKitMol method) SaturateBiradicalSites12() (rdmc.mol.RDKitMol method) SaturateBiradicalSitesCDB() (rdmc.mol.RDKitMol method) SaturateCarbene() (rdmc.mol.RDKitMol method) SaturateMol() (rdmc.mol.RDKitMol method) set_atomic_charges() (in module rdmc.external.xyz2mol) set_atomic_radicals() (in module rdmc.external.xyz2mol) set_obmol_coords() (in module rdmc.utils) set_rdconf_coordinates() (in module rdmc.utils) set_solver() (rdmc.forcefield.OpenBabelFF method) SetAllTorsionsDeg() (rdmc.conf.RDKitConf method) SetAngleDeg() (rdmc.conf.RDKitConf method)

SetAngleRad() (rdmc.conf.RDKitConf method) SetAtomMapNumbers() (rdmc.mol.RDKitMol method) SetBondLength() (rdmc.conf.RDKitConf method) SetOwningMol() (rdmc.conf.RDKitConf method) SetPositions() (rdmc.conf.RDKitConf method) (rdmc.mol.RDKitMol method) SetTorsionalModes() (rdmc.conf.RDKitConf method) SetTorsionDeg() (rdmc.conf.RDKitConf method) setup() (rdmc.forcefield.OpenBabelFF method) (rdmc.forcefield.RDKitFF method) SetVdwMatrix() (rdmc.mol.RDKitMol method) split_by_energies() (rdmc.conf.ConformerCluster method) str_atom() (in module rdmc.external.xyz2mol)

T

ToAtoms() (rdmc.mol.RDKitMol method) ToConformer() (rdmc.conf.RDKitConf method) ToGraph() (rdmc.mol.RDKitMol method) ToInchi() (rdmc.mol.RDKitMol method) ToMol() (rdmc.conf.RDKitConf method) ToMolBlock() (rdmc.mol.RDKitMol method) ToOBMol() (rdmc.mol.RDKitMol method)

torsional_scan_1d() (rdmc.forcefield.RDKitFF method) ToRWMol() (rdmc.mol.RDKitMol method) ToSDFFile() (rdmc.mol.RDKitMol method) ToSmiles() (rdmc.mol.RDKitMol method) ToXYZ() (rdmc.mol.RDKitMol method) ts_viewer() (in module rdmc.view) type (rdmc.forcefield.OpenBabelFF property) (rdmc.forcefield.RDKitFF property)

U

update_atom_idx() (rdmc.forcefield.OpenBabelFF method) (rdmc.forcefield.RDKitFF method)

V

valences_not_too_large() (in module rdmc.external.xyz2mol)

X

xyz2AC() (in module rdmc.external.xyz2mol) xyz2AC_huckel() (in module rdmc.external.xyz2mol)

xyz2AC_vdW() (in module rdmc.external.xyz2mol) xyz2mol() (in module rdmc.external.xyz2mol)