Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W A add_3d_conformer_() (cosmolkit.Molecule method) add_atom() (cosmolkit.MoleculeEdit method) add_bond() (cosmolkit.MoleculeEdit method) add_hydrogens_() (cosmolkit.Molecule method) align_conformers_() (cosmolkit.Molecule method) align_to_() (cosmolkit.Molecule method) alignment_transform_to() (cosmolkit.Molecule method) all_conformer_best_rmsds() (cosmolkit.Molecule method) analyze_potential_stereo() (cosmolkit.Molecule method) as_dict() (cosmolkit.BatchError method) assign_chiral_tags_from_structure_() (cosmolkit.Molecule method) assign_cip_labels_() (cosmolkit.Molecule method) Atom (class in cosmolkit) atomic_num() (cosmolkit.ProteinAtom method) atoms() (cosmolkit.BioStructure method) (cosmolkit.Molecule method) (cosmolkit.Protein method) (cosmolkit.ProteinChain method) (cosmolkit.ProteinResidue method) avalon_fingerprint() (cosmolkit.Molecule method) B BatchError (class in cosmolkit) BatchErrorMode (class in cosmolkit) BatchExportReport (class in cosmolkit) BatchValidationError best_alignment_to() (cosmolkit.Molecule method) best_rmsd_to() (cosmolkit.Molecule method) BioStructure (class in cosmolkit) Bond (class in cosmolkit) BondDirection (class in cosmolkit) BondOrder (class in cosmolkit) bonds() (cosmolkit.Molecule method) BondStereo (class in cosmolkit) C calc_chi_0() (in module cosmolkit) calc_chi_1() (in module cosmolkit) calc_chi_nn() (in module cosmolkit) calc_chi_nv() (in module cosmolkit) calc_crippen_descriptors() (in module cosmolkit) calc_exact_mol_wt() (in module cosmolkit) calc_fraction_csp3() (in module cosmolkit) calc_hall_kier_alpha() (in module cosmolkit) calc_hall_kier_alpha_with_contributions() (in module cosmolkit) calc_kappa_1() (in module cosmolkit) calc_kappa_2() (in module cosmolkit) calc_kappa_3() (in module cosmolkit) calc_labute_asa() (in module cosmolkit) calc_labute_asa_contributions() (in module cosmolkit) calc_lipinski_hba() (in module cosmolkit) calc_lipinski_hbd() (in module cosmolkit) calc_mol_formula() (in module cosmolkit) calc_mol_wt() (in module cosmolkit) calc_mqns() (in module cosmolkit) calc_num_aliphatic_carbocycles() (in module cosmolkit) calc_num_aliphatic_heterocycles() (in module cosmolkit) calc_num_aliphatic_rings() (in module cosmolkit) calc_num_amide_bonds() (in module cosmolkit) calc_num_aromatic_carbocycles() (in module cosmolkit) calc_num_aromatic_heterocycles() (in module cosmolkit) calc_num_aromatic_rings() (in module cosmolkit) calc_num_atom_stereo_centers() (in module cosmolkit) calc_num_atoms() (in module cosmolkit) calc_num_bridgehead_atoms() (in module cosmolkit) calc_num_hba() (in module cosmolkit) calc_num_hbd() (in module cosmolkit) calc_num_heavy_atoms() (in module cosmolkit) calc_num_heteroatoms() (in module cosmolkit) calc_num_heterocycles() (in module cosmolkit) calc_num_rings() (in module cosmolkit) calc_num_rotatable_bonds() (in module cosmolkit) calc_num_saturated_carbocycles() (in module cosmolkit) calc_num_saturated_heterocycles() (in module cosmolkit) calc_num_saturated_rings() (in module cosmolkit) calc_num_spiro_atoms() (in module cosmolkit) calc_num_unspecified_atom_stereo_centers() (in module cosmolkit) calc_phi() (in module cosmolkit) calc_qed() (in module cosmolkit) calc_slogp_vsa() (in module cosmolkit) calc_slogp_vsa_1() (in module cosmolkit) calc_slogp_vsa_10() (in module cosmolkit) calc_slogp_vsa_11() (in module cosmolkit) calc_slogp_vsa_12() (in module cosmolkit) calc_slogp_vsa_2() (in module cosmolkit) calc_slogp_vsa_3() (in module cosmolkit) calc_slogp_vsa_4() (in module cosmolkit) calc_slogp_vsa_5() (in module cosmolkit) calc_slogp_vsa_6() (in module cosmolkit) calc_slogp_vsa_7() (in module cosmolkit) calc_slogp_vsa_8() (in module cosmolkit) calc_slogp_vsa_9() (in module cosmolkit) calc_smr_vsa() (in module cosmolkit) calc_smr_vsa_1() (in module cosmolkit) calc_smr_vsa_10() (in module cosmolkit) calc_smr_vsa_2() (in module cosmolkit) calc_smr_vsa_3() (in module cosmolkit) calc_smr_vsa_4() (in module cosmolkit) calc_smr_vsa_5() (in module cosmolkit) calc_smr_vsa_6() (in module cosmolkit) calc_smr_vsa_7() (in module cosmolkit) calc_smr_vsa_8() (in module cosmolkit) calc_smr_vsa_9() (in module cosmolkit) calc_tpsa() (in module cosmolkit) canonical_one_letter_code() (cosmolkit.ProteinResidue method) chains() (cosmolkit.BioStructure method) (cosmolkit.Protein method) ChiralTag (class in cosmolkit) cip_computed() (cosmolkit.Molecule method) clear_3d_conformers_() (cosmolkit.Molecule method) code() (cosmolkit.ProteinResidue method) (cosmolkit.ResidueInfo method) commit() (cosmolkit.MoleculeEdit method) compute_2d_coordinates_() (cosmolkit.Molecule method) coordinate_rmsd_to() (cosmolkit.Molecule method) coordinates_2d() (cosmolkit.Molecule method) coordinates_3d() (cosmolkit.Molecule method) cosmolkit module cosmolkit.inchi_to_key() (in module cosmolkit) D dg_bounds_matrix() (cosmolkit.Molecule method) dg_bounds_matrix_list() (cosmolkit.MoleculeBatch method) E edit() (cosmolkit.Molecule method) Element (class in cosmolkit) element() (cosmolkit.ProteinAtom method) element_from_symbol() (in module cosmolkit) element_symbol() (cosmolkit.ProteinAtom method) ElementInfo (class in cosmolkit) embed_3d_conformer_() (cosmolkit.Molecule method) embed_3d_conformer_result_() (cosmolkit.Molecule method) embed_3d_conformers_() (cosmolkit.Molecule method) embed_3d_conformers_result_() (cosmolkit.Molecule method) entities() (cosmolkit.BioStructure method) errors() (cosmolkit.BatchExportReport method) (cosmolkit.MoleculeBatch method) expand_one_letter() (in module cosmolkit) expand_one_letter_sequence() (in module cosmolkit) expand_protein_one_letter() (in module cosmolkit) expand_protein_one_letter_string() (in module cosmolkit) F failed() (cosmolkit.BatchExportReport method) fasta_code() (cosmolkit.ProteinResidue method) filter_valid() (cosmolkit.MoleculeBatch method) find_chiral_centers() (cosmolkit.Molecule method) find_tabulated_residue() (in module cosmolkit) find_tabulated_residue_idx() (in module cosmolkit) fingerprint_atom_pair() (cosmolkit.Molecule method) fingerprint_atom_pair_count() (cosmolkit.Molecule method) fingerprint_atom_pair_list() (cosmolkit.MoleculeBatch method) fingerprint_atom_pair_sparse_bits() (cosmolkit.Molecule method) fingerprint_atom_pair_sparse_count() (cosmolkit.Molecule method) fingerprint_atom_pair_with_output() (cosmolkit.Molecule method) fingerprint_layered() (cosmolkit.Molecule method) fingerprint_layered_list() (cosmolkit.MoleculeBatch method) fingerprint_layered_with_output() (cosmolkit.Molecule method) fingerprint_layered_with_output_list() (cosmolkit.MoleculeBatch method) fingerprint_morgan() (cosmolkit.Molecule method) fingerprint_morgan_list() (cosmolkit.MoleculeBatch method) fingerprint_morgan_with_output() (cosmolkit.Molecule method) fingerprint_morgan_with_output_list() (cosmolkit.MoleculeBatch method) fragments() (cosmolkit.Molecule method) from_inchi() (cosmolkit.cosmolkit.Molecule class method) (cosmolkit.Molecule class method) from_mmcif() (cosmolkit.BioStructure class method) (cosmolkit.Protein class method) from_mmcif_block() (cosmolkit.Molecule class method) from_mmcif_str() (cosmolkit.BioStructure class method) (cosmolkit.Protein class method) from_pdb() (cosmolkit.BioStructure class method) (cosmolkit.Protein class method) from_pdb_block() (cosmolkit.Molecule class method) from_pdb_str() (cosmolkit.BioStructure class method) (cosmolkit.Protein class method) from_rdkit() (cosmolkit.Molecule class method) from_smiles() (cosmolkit.Molecule class method) from_smiles_list() (cosmolkit.MoleculeBatch class method) from_structure_str() (cosmolkit.BioStructure class method) from_xyz_block() (cosmolkit.Molecule class method) G get_element_info() (in module cosmolkit) get_residue_info() (in module cosmolkit) get_substruct_match() (in module cosmolkit) get_substruct_matches() (in module cosmolkit) get_substruct_matches_with_params() (in module cosmolkit) H has_2d_coordinates() (cosmolkit.Molecule method) has_mmff_params() (cosmolkit.Molecule method) has_substruct_match() (in module cosmolkit) has_uff_params() (cosmolkit.Molecule method) hash() (cosmolkit.Molecule method) hash_with_ranks() (cosmolkit.Molecule method) I inchi_to_key() (in module cosmolkit) InchiAllocationError InchiDiagnosticWarning InchiError InchiUnsupportedStateError index() (cosmolkit.BatchError method) (cosmolkit.ProteinAtom method) (cosmolkit.ProteinChain method) (cosmolkit.ProteinResidue method) info() (cosmolkit.ProteinResidue method) input_format() (cosmolkit.BioStructure method) invalid_count() (cosmolkit.MoleculeBatch method) invalid_mask() (cosmolkit.MoleculeBatch method) is_modified_amino_acid() (cosmolkit.ProteinResidue method) is_standard() (cosmolkit.ProteinResidue method) K kekulize_() (cosmolkit.Molecule method) kind() (cosmolkit.ProteinChain method) (cosmolkit.ProteinResidue method) (cosmolkit.ResidueInfo method) kind_name() (cosmolkit.ResidueInfo method) L largest_fragment() (cosmolkit.Molecule method) M maccs_fingerprint() (cosmolkit.Molecule method) message() (cosmolkit.BatchError method) MmcifOutputGroups (class in cosmolkit) MmcifWriteOptions (class in cosmolkit) mmff_has_all_molecule_params() (in module cosmolkit) mmff_optimize_molecule() (in module cosmolkit) mmff_optimize_molecule_confs() (in module cosmolkit) models() (cosmolkit.BioStructure method) module cosmolkit mol_from_binary() (cosmolkit.Molecule class method) (in module cosmolkit) mol_to_binary() (cosmolkit.Molecule method) (in module cosmolkit) Molecule (class in cosmolkit) MoleculeBatch (class in cosmolkit) MoleculeEdit (class in cosmolkit) murcko_scaffold() (cosmolkit.Molecule method) N name() (cosmolkit.BioStructure method) (cosmolkit.ProteinAtom method) (cosmolkit.ProteinResidue method) (cosmolkit.ResidueInfo method) net_scaffold() (cosmolkit.Molecule method) num_atoms() (cosmolkit.BioStructure method) (cosmolkit.Molecule method) (cosmolkit.Protein method) num_bonds() (cosmolkit.Molecule method) num_chains() (cosmolkit.BioStructure method) (cosmolkit.Protein method) num_conformers() (cosmolkit.Molecule method) num_entities() (cosmolkit.BioStructure method) num_models() (cosmolkit.BioStructure method) (cosmolkit.Protein method) num_residues() (cosmolkit.BioStructure method) (cosmolkit.Protein method) O one_letter_code() (cosmolkit.ProteinResidue method) operation() (cosmolkit.BatchError method) P parallel_jobs() (cosmolkit.MoleculeBatch method) parent_standard_code() (cosmolkit.ProteinResidue method) parse_smarts() (in module cosmolkit) pattern_fingerprint() (cosmolkit.Molecule method) pattern_fingerprint_list() (cosmolkit.MoleculeBatch method) perceive_stereochemistry() (cosmolkit.Molecule method) position() (cosmolkit.ProteinAtom method) progress_bar() (cosmolkit.MoleculeBatch method) Protein (class in cosmolkit) protein() (cosmolkit.BioStructure method) ProteinAtom (class in cosmolkit) ProteinChain (class in cosmolkit) ProteinResidue (class in cosmolkit) R read_mol() (cosmolkit.Molecule class method) read_mol2() (cosmolkit.Molecule class method) read_mol2_from_str() (cosmolkit.Molecule class method) read_mol_from_str() (cosmolkit.Molecule class method) read_sdf() (cosmolkit.Molecule class method) (cosmolkit.MoleculeBatch class method) read_sdf_from_str() (cosmolkit.Molecule class method) read_sdf_records_from_str() (cosmolkit.MoleculeBatch class method) remove_hydrogens_() (cosmolkit.Molecule method) residue_code_from_name() (in module cosmolkit) ResidueCode (class in cosmolkit) ResidueInfo (class in cosmolkit) ResidueInfoKind (class in cosmolkit) residues() (cosmolkit.BioStructure method) (cosmolkit.Protein method) (cosmolkit.ProteinChain method) S sanitize() (cosmolkit.MoleculeBatch method) SdfDataset (class in cosmolkit) SdfReader (class in cosmolkit) SdfRecord (class in cosmolkit) SdfRecordMetadata (class in cosmolkit) set_2d_coordinates_() (cosmolkit.Molecule method) set_3d_coordinates_() (cosmolkit.Molecule method) set_atom_charge() (cosmolkit.MoleculeEdit method) set_only_3d_conformer_() (cosmolkit.Molecule method) stereoisomer_count() (cosmolkit.Molecule method) stereoisomers() (cosmolkit.Molecule method) StructureAtom (class in cosmolkit) StructureChain (class in cosmolkit) StructureEntity (class in cosmolkit) StructureModel (class in cosmolkit) StructureResidue (class in cosmolkit) success() (cosmolkit.BatchExportReport method) T tetrahedral_stereo() (cosmolkit.Molecule method) to_2d_sdf_string() (cosmolkit.Molecule method) to_3d_sdf_string() (cosmolkit.Molecule method) to_cx_smarts() (cosmolkit.Molecule method) to_images() (cosmolkit.MoleculeBatch method) to_inchi() (cosmolkit.cosmolkit.Molecule method) (cosmolkit.Molecule method) to_inchi_key() (cosmolkit.cosmolkit.Molecule method) (cosmolkit.Molecule method) to_list() (cosmolkit.MoleculeBatch method) to_mmcif() (cosmolkit.BioStructure method) to_molecule() (cosmolkit.BioStructure method) to_pdb_block() (cosmolkit.Molecule method) to_png() (cosmolkit.Molecule method) to_sdf() (cosmolkit.MoleculeBatch method) to_sdf_files() (cosmolkit.MoleculeBatch method) to_smarts() (cosmolkit.Molecule method) to_smiles() (cosmolkit.Molecule method) to_smiles_list() (cosmolkit.MoleculeBatch method) to_svg() (cosmolkit.Molecule method) to_svg_list() (cosmolkit.MoleculeBatch method) topological_fingerprint() (cosmolkit.Molecule method) topological_fingerprint_with_output() (cosmolkit.Molecule method) total() (cosmolkit.BatchExportReport method) U uff_has_all_molecule_params() (in module cosmolkit) uff_optimize_molecule() (in module cosmolkit) uff_optimize_molecule_confs() (in module cosmolkit) V valid_count() (cosmolkit.MoleculeBatch method) valid_mask() (cosmolkit.MoleculeBatch method) W with_2d_coordinates() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) with_3d_conformer() (cosmolkit.Molecule method) with_3d_conformer_result() (cosmolkit.Molecule method) with_3d_conformers() (cosmolkit.Molecule method) with_3d_conformers_result() (cosmolkit.Molecule method) with_3d_coordinates() (cosmolkit.Molecule method) with_added_3d_conformer() (cosmolkit.Molecule method) with_aligned_conformers() (cosmolkit.Molecule method) with_alignment_to() (cosmolkit.Molecule method) with_chiral_tags_from_structure() (cosmolkit.Molecule method) with_cip_labels() (cosmolkit.Molecule method) with_cleared_3d_conformers() (cosmolkit.Molecule method) with_hydrogens() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) with_kekulized_bonds() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) with_mmff_optimized() (cosmolkit.Molecule method) with_mmff_optimized_confs() (cosmolkit.Molecule method) with_only_3d_conformer() (cosmolkit.Molecule method) with_parallel_jobs() (cosmolkit.MoleculeBatch method) with_progress_bar() (cosmolkit.MoleculeBatch method) with_uff_optimized() (cosmolkit.Molecule method) with_uff_optimized_confs() (cosmolkit.Molecule method) without_hydrogens() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) write_mmcif() (cosmolkit.BioStructure method) write_png() (cosmolkit.Molecule method) write_sdf() (cosmolkit.Molecule method) write_sdf_to_directory() (cosmolkit.Molecule method) write_svg() (cosmolkit.Molecule method)