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) as_dict() (cosmolkit.BatchError method) assign_chiral_tags_from_structure_() (cosmolkit.Molecule method) Atom (class in cosmolkit) atoms() (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 Bond (class in cosmolkit) BondDirection (class in cosmolkit) BondOrder (class in cosmolkit) bonds() (cosmolkit.Molecule method) BondStereo (class in cosmolkit) C calc_crippen_descriptors() (in module cosmolkit) calc_exact_mol_wt() (in module cosmolkit) calc_fraction_csp3() (in module cosmolkit) calc_mol_formula() (in module cosmolkit) calc_mol_wt() (in module cosmolkit) calc_num_aromatic_rings() (in module cosmolkit) calc_num_hba() (in module cosmolkit) calc_num_hbd() (in module cosmolkit) calc_num_rotatable_bonds() (in module cosmolkit) calc_qed() (in module cosmolkit) calc_tpsa() (in module cosmolkit) chains() (cosmolkit.Protein method) ChiralTag (class in cosmolkit) clear_3d_conformers_() (cosmolkit.Molecule method) code() (cosmolkit.ProteinResidue method) (cosmolkit.ResidueInfo method) commit() (cosmolkit.MoleculeEdit method) compute_2d_coordinates_() (cosmolkit.Molecule method) coordinates_2d() (cosmolkit.Molecule method) coordinates_3d() (cosmolkit.Molecule method) cosmolkit module cosmolkit.Chem.MolFromInchi() (in module cosmolkit) cosmolkit.Chem.MolToInchi() (in module cosmolkit) cosmolkit.Chem.MolToInchiKey() (in module cosmolkit) cosmolkit.InchiToInchiKey() (in module cosmolkit) D dg_bounds_matrix() (cosmolkit.Molecule method) dg_bounds_matrix_list() (cosmolkit.MoleculeBatch method) E edit() (cosmolkit.Molecule method) element() (cosmolkit.ProteinAtom method) 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) 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_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_mmcif() (cosmolkit.Protein class method) from_mmcif_block() (cosmolkit.Molecule class method) from_mmcif_str() (cosmolkit.Protein class method) from_pdb() (cosmolkit.Protein class method) from_pdb_block() (cosmolkit.Molecule class method) from_pdb_str() (cosmolkit.Protein class method) from_rdkit() (cosmolkit.Molecule class method) from_smiles() (cosmolkit.Molecule class method) from_smiles_list() (cosmolkit.MoleculeBatch class method) from_xyz_block() (cosmolkit.Molecule class method) G 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 InchiAllocationError InchiDiagnosticWarning InchiError InchiToInchiKey() (in module cosmolkit) InchiUnsupportedStateError index() (cosmolkit.BatchError method) (cosmolkit.ProteinAtom method) (cosmolkit.ProteinChain method) (cosmolkit.ProteinResidue method) info() (cosmolkit.ProteinResidue method) invalid_count() (cosmolkit.MoleculeBatch method) invalid_mask() (cosmolkit.MoleculeBatch 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) mmff_has_all_molecule_params() (in module cosmolkit) mmff_optimize_molecule() (in module cosmolkit) mmff_optimize_molecule_confs() (in module cosmolkit) 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.ProteinAtom method) (cosmolkit.ProteinResidue method) (cosmolkit.ResidueInfo method) net_scaffold() (cosmolkit.Molecule method) num_atoms() (cosmolkit.Molecule method) (cosmolkit.Protein method) num_bonds() (cosmolkit.Molecule method) num_chains() (cosmolkit.Protein method) num_conformers() (cosmolkit.Molecule method) num_models() (cosmolkit.Protein method) num_residues() (cosmolkit.Protein method) O one_letter_code() (cosmolkit.ProteinResidue method) operation() (cosmolkit.BatchError method) P parallel_jobs() (cosmolkit.MoleculeBatch method) parse_smarts() (in module cosmolkit) perceive_stereochemistry() (cosmolkit.Molecule method) position() (cosmolkit.ProteinAtom method) progress_bar() (cosmolkit.MoleculeBatch method) Protein (class in cosmolkit) 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.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) 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_images() (cosmolkit.MoleculeBatch method) to_list() (cosmolkit.MoleculeBatch method) to_pdb_block() (cosmolkit.Molecule method) to_png() (cosmolkit.Molecule method) to_sdf() (cosmolkit.MoleculeBatch method) to_sdf_files() (cosmolkit.MoleculeBatch 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) 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_chiral_tags_from_structure() (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_png() (cosmolkit.Molecule method) write_sdf() (cosmolkit.Molecule method) write_sdf_to_directory() (cosmolkit.Molecule method) write_svg() (cosmolkit.Molecule method)