Index

A

af3code (NonProteinQuery.Type property) align() (MMseqs method) align_eval (MMseqsMonomerSearchParams attribute) alt_ali (MMseqsMonomerSearchParams attribute) apply() (Assembly method) aromatic (BondOrder attribute) Assembly (class in gmol.base.data.mmcif.assembly) assembly_gens (BioAssembly attribute) AssemblyAtom (class in gmol.base.data.mmcif.assembly) AssemblyConnection (class in gmol.base.data.mmcif.assembly) asym_id (Scheme attribute) asym_id_list (BioAssemblyGen attribute) atom_b_factors (NonPolymerLigand attribute) (PolymerChain attribute) atom_coords (NonPolymerLigand attribute) (PolymerChain attribute) atom_id (AssemblyAtom attribute) (BranchLinkPartner attribute) (BranchPartner attribute) (ChemCompAtom attribute) (ExtraBondPartner attribute)

atom_id_1 (ChemCompBond attribute) atom_id_2 (ChemCompBond attribute) atom_ids (NonPolymerLigand attribute) (RefLigandInput attribute) atom_idx (AssemblyAtom attribute) atom_idxs (Chain attribute) (Residue attribute) atom_site (Mmcif attribute) atoms (Assembly attribute) (ChemComp attribute) (MmcifRefLigand attribute) atoms_of_chain() (Assembly method) atoms_of_residue() (Assembly method) AtomSite (class in gmol.base.data.mmcif.parse) auth_asym_id (AtomSite attribute) (StructConnPartner attribute) auth_comp_id (AtomSite attribute) (StructConnPartner attribute) auth_seq_id (AtomSite attribute) (StructConnPartner attribute)

B

b_factor (AssemblyAtom attribute) b_iso_or_equiv (AtomSite attribute) backbone (PolymerConstants attribute) bb_dst_atom (PolymerConstants attribute) bb_dst_leaving (PolymerConstants attribute) bb_src_atom (PolymerConstants attribute) bb_src_leaving (PolymerConstants attribute) BioAssembly (class in gmol.base.data.mmcif.parse) BioAssemblyGen (class in gmol.base.data.mmcif.parse) bond_class (ExtraBond attribute) bond_order (ExtraBond attribute)

bond_stereo_EZ (ExtraBond attribute) BondClass (class in gmol.base.data.mmcif.input) BondOrder (class in gmol.base.data.mmcif.input) bonds (ChemComp attribute) (MmcifRefLigand attribute) Branch (class in gmol.base.data.mmcif.assembly) branches (Chain attribute) BranchLink (class in gmol.base.data.mmcif.parse) BranchLinkPartner (class in gmol.base.data.mmcif.parse) BranchPartner (class in gmol.base.data.mmcif.assembly) build_input() (in module gmol.base.data.mmcif.input) build_input_from_mmcif() (in module gmol.base.data.mmcif.input)

C

cartn (AtomSite attribute) CCD (NonProteinQuery.Type attribute) Chain (class in gmol.base.data.mmcif.assembly) chain_id (AssemblyAtom property) (Chain attribute) (ExtraBondPartner attribute) (NonPolymerLigand attribute) (PolymerChain attribute) (ResidueId attribute) chains (Assembly attribute) chains_of_type() (Assembly method) charge (ChemCompAtom attribute) chem_comp (Residue attribute) chem_comp_raw (PolymerChain attribute) chem_comps (Assembly property) ChemComp (class in gmol.base.data.mmcif.parse) ChemCompAtom (class in gmol.base.data.mmcif.parse) ChemCompBond (class in gmol.base.data.mmcif.parse)

classify_molecules() (in module gmol.base.data.seq.colabfold_input) cluster_sequences_using_mmseqs2() (in module gmol.base.data.seq.mmseqs_cluster) comp_id (AssemblyAtom attribute) (BranchLinkPartner attribute) (BranchPartner attribute) (SequenceToResidue attribute) comp_ids (Assembly property) conn_type (AssemblyConnection attribute) conn_type_id (StructConn attribute) connections (Assembly attribute) convert_chem_comp() (in module gmol.base.data.mmcif.smiles) convertalis() (MMseqs method) coords (Assembly attribute) copies (NonProteinQuery attribute) count_polymer_chains() (Assembly method) covalent (BondClass attribute) createdb() (MMseqs method) criteria (StructConnType attribute)

D

db_load_mode (MMseqsCommonSearchParams attribute) definition (NonProteinQuery attribute) details (BioAssembly attribute) diff (MMseqsMonomerSearchParams attribute) disulfide (BondClass attribute)

DNA (MolType attribute) (NonProteinQuery.Type attribute) double (BondOrder attribute) dst (ExtraBond attribute) dst_idx (AssemblyConnection attribute)

E

entities (Assembly attribute) Entity (class in gmol.base.data.mmcif.parse) entity (Mmcif attribute) entity_branch_list_num (BranchLinkPartner attribute) entity_id (Chain attribute) (NonPolymerLigand attribute) (PolymerChain attribute) (Scheme attribute) entry_id (Mmcif attribute) (PdbMetadata attribute)

expand_eval (MMseqsMonomerSearchParams attribute) expand_ops() (in module gmol.base.data.mmcif.assembly) expand_param (MMseqsMonomerSearchParams property) (MMseqsPairSearchParams property) expandaln() (MMseqs method) exptl_method (Mmcif attribute) (PdbMetadata attribute) extra_bonds (Input attribute) ExtraBond (class in gmol.base.data.mmcif.input) ExtraBondPartner (class in gmol.base.data.mmcif.input)

F

filter() (Assembly method) filter_chains() (Assembly method) filter_mmcif() (in module gmol.base.data.mmcif.filter) filter_param (MMseqsMonomerSearchParams property) filter_structure() (in module gmol.base.data.mmcif.filter) filterresult() (MMseqs method) find_all_bonds_with_atom_idx() (in module gmol.base.wrapper.rdkit) formula (ChemComp attribute) formula_weight (ChemComp attribute)

from_branch_scheme() (BranchPartner class method) from_mmcif_conn_type() (BondClass class method) from_mmcif_value_order() (BondOrder class method) from_msa_query() (MMseqsQuery class method) from_rdkit_bond_type() (BondOrder class method) from_scheme() (ResidueId class method) (SequenceToResidue class method) from_sequence() (MsaQuery class method) from_symop() (Transformation class method)

G

generate_conformer() (in module gmol.base.wrapper.rdkit) get_all_bonds() (in module gmol.base.wrapper.rdkit) get_queries() (in module gmol.base.data.seq.colabfold_input) gmol.base module gmol.base.const module gmol.base.const.af2 module gmol.base.const.af3 module gmol.base.const.seoklab module gmol.base.data module gmol.base.data.mmcif module gmol.base.data.mmcif.assembly module gmol.base.data.mmcif.filter module gmol.base.data.mmcif.input module gmol.base.data.mmcif.parse module

gmol.base.data.mmcif.smiles module gmol.base.data.mmcif.write module gmol.base.data.seq module gmol.base.data.seq.colabfold_input module gmol.base.data.seq.hhsearch_template module gmol.base.data.seq.mmseqs_cluster module gmol.base.data.seq.mmseqs_search module gmol.base.path module gmol.base.types module gmol.base.wrapper module gmol.base.wrapper.rdkit module gpu (MMseqsCommonSearchParams attribute) group_PDB (AtomSite attribute)

H

has_chain_type() (Assembly method) heteromer (MMseqsQuery property)

HHSearch (class in gmol.base.data.seq.hhsearch_template) hydrogen (BondClass attribute)

I

id (AtomSite attribute) (BioAssembly attribute) (ChemComp attribute) (Entity attribute) (MMseqsQuery attribute) (MsaQuery attribute) (StructConn attribute) ident (Transformation attribute)

ignore_index (MMseqsCommonSearchParams attribute) Input (class in gmol.base.data.mmcif.input) input_format (HHSearch attribute) input_from_reference() (in module gmol.base.data.mmcif.smiles) ins_code (ResidueId attribute) is_complex (MsaQuery property) is_distillation (Input attribute) is_hydrogen (AtomSite property) is_polymer (MolType property)

J

join() (Assembly class method)

L

label_alt_id (AtomSite attribute) label_asym_id (AtomSite attribute) (StructConnPartner attribute) label_atom_id (AtomSite attribute) (StructConnPartner attribute) label_comp_id (AtomSite attribute) (StructConnPartner attribute) label_seq_id (AtomSite attribute) (StructConnPartner attribute) leaving_atom_count (AssemblyConnection attribute) leaving_atom_id (BranchLinkPartner attribute) (BranchPartner attribute)

leaving_atoms (ExtraBondPartner attribute) Ligand (MolType attribute) ligand_atom_mask() (in module gmol.base.data.mmcif.filter) ligands (Input attribute) limit (MMseqsMonomerSearchParams attribute) lndb() (MMseqs method) load_ccd_dict_json() (in module gmol.base.data.mmcif.input) load_components() (in module gmol.base.data.mmcif.parse) load_mmcif_single() (in module gmol.base.data.mmcif.parse) LooseModel (class in gmol.base.types)

M

matrix (SymOp attribute) max_accept (MMseqsMonomerSearchParams attribute) max_res_atoms (PolymerConstants attribute) mdb1 (MMseqsMonomerSearchParams property) mdb2 (MMseqsMonomerSearchParams property) mergedbs() (MMseqs method) metadata (Assembly attribute) metadata() (Mmcif method) metagenomic_db (MMseqsMonomerSearchParams attribute) metal_coordinate (BondClass attribute) Mmcif (class in gmol.base.data.mmcif.parse) mmcif_assemblies() (in module gmol.base.data.mmcif.assembly) mmcif_bond_order() (in module gmol.base.data.mmcif.write) mmcif_bool() (in module gmol.base.data.mmcif.write) mmcif_chain_types() (in module gmol.base.data.mmcif.assembly) mmcif_write_block() (in module gmol.base.data.mmcif.write) MmcifRefLigand (class in gmol.base.data.mmcif.smiles) MMseqs (class in gmol.base.data.seq.mmseqs_search) mmseqs_search_monomer() (in module gmol.base.data.seq.mmseqs_search) mmseqs_search_pair() (in module gmol.base.data.seq.mmseqs_search) MMseqsCommonSearchParams (class in gmol.base.data.seq.mmseqs_search) MMseqsMonomerSearchParams (class in gmol.base.data.seq.mmseqs_search) MMseqsPairSearchParams (class in gmol.base.data.seq.mmseqs_search) MMseqsQuery (class in gmol.base.data.seq.mmseqs_search) modres_backbone_3 (PolymerConstants attribute) module gmol.base gmol.base.const gmol.base.const.af2 gmol.base.const.af3 gmol.base.const.seoklab gmol.base.data gmol.base.data.mmcif gmol.base.data.mmcif.assembly gmol.base.data.mmcif.filter gmol.base.data.mmcif.input gmol.base.data.mmcif.parse gmol.base.data.mmcif.smiles gmol.base.data.mmcif.write gmol.base.data.seq gmol.base.data.seq.colabfold_input gmol.base.data.seq.hhsearch_template gmol.base.data.seq.mmseqs_cluster gmol.base.data.seq.mmseqs_search gmol.base.path gmol.base.types gmol.base.wrapper gmol.base.wrapper.rdkit

mol2smi() (in module gmol.base.wrapper.rdkit) mol_from_chem_comp() (in module gmol.base.data.mmcif.smiles) mol_type (PolymerChain attribute) MolType (class in gmol.base.data.mmcif.assembly) moltype (NonProteinQuery attribute) mon_id (Scheme attribute) mon_nstd_flag (ChemComp attribute) msa_to_str() (in module gmol.base.data.seq.colabfold_input) MsaQuery (class in gmol.base.data.seq.colabfold_input) mvdb() (MMseqs method)

N

name (ChemComp attribute) (SymOp attribute) new_atom() (AssemblyAtom method) new_atom_mask() (in module gmol.base.data.mmcif.filter) new_chain() (Chain method)

new_residue() (Residue method) non_proteins (MsaQuery attribute) NonPolymerLigand (class in gmol.base.data.mmcif.input) NonProteinQuery (class in gmol.base.data.seq.colabfold_input) NonProteinQuery.Type (class in gmol.base.data.seq.colabfold_input)

O

occupancy (AssemblyAtom attribute) (AtomSite attribute) oligomeric_count (BioAssembly attribute) oligomeric_details (BioAssembly attribute)

operations (BioAssemblyGen attribute) order (Branch attribute) other (BondOrder attribute) output_format (HHSearch attribute)

P

pad_sequences() (in module gmol.base.data.seq.colabfold_input) pair_msa() (in module gmol.base.data.seq.colabfold_input) pair_sequences() (in module gmol.base.data.seq.colabfold_input) pairaln() (MMseqs method) pairing_strategy (MMseqsPairSearchParams attribute) parse_fasta() (in module gmol.base.data.seq.colabfold_input) pdb_ins_code (Scheme attribute) pdb_seq_num (Scheme attribute) PdbMetadata (class in gmol.base.data.mmcif.parse) pdbx_aromatic_flag (ChemCompAtom attribute) (ChemCompBond attribute) pdbx_branch_scheme (Mmcif attribute) pdbx_description (Entity attribute) pdbx_dist_value (StructConn attribute) pdbx_entity_branch_link (Mmcif attribute) pdbx_keywords (Mmcif attribute) (PdbMetadata attribute) pdbx_leaving_atom_flag (ChemCompAtom attribute) (StructConn attribute) pdbx_nonpoly_scheme (Mmcif attribute) pdbx_PDB_ins_code (AtomSite attribute) (StructConnPartner attribute)

pdbx_PDB_model_num (AtomSite attribute) pdbx_poly_seq_scheme (Mmcif attribute) pdbx_stereo_config (ChemCompAtom attribute) (ChemCompBond attribute) pdbx_struct_assembly (Mmcif attribute) pdbx_struct_oper_list (Mmcif attribute) polymer_mol_type() (in module gmol.base.data.mmcif.assembly) PolymerChain (class in gmol.base.data.mmcif.input) PolymerConstants (class in gmol.base.data.mmcif.input) polymers (Input attribute) prefilter_mode (MMseqsCommonSearchParams attribute) prev_msa (MsaQuery attribute) process_connections() (in module gmol.base.data.mmcif.input) process_ligand_chain() (in module gmol.base.data.mmcif.input) process_polymer_chain() (in module gmol.base.data.mmcif.input) Protein (MolType attribute) ptnr1 (Branch attribute) (BranchLink attribute) (StructConn attribute) ptnr2 (Branch attribute) (BranchLink attribute) (StructConn attribute)

Q

qsc (MMseqsMonomerSearchParams attribute)

quadruple (BondOrder attribute) query() (HHSearch method)

R

read_mols() (in module gmol.base.wrapper.rdkit) reference (StructConnType attribute) reference_from_mmcif() (in module gmol.base.data.mmcif.smiles) RefLigandInput (class in gmol.base.data.mmcif.smiles) release_date (Input attribute) remap() (AssemblyConnection method) remove_all_unknown_chains() (in module gmol.base.data.mmcif.filter) remove_clashing_chains() (in module gmol.base.data.mmcif.filter) remove_crystallization_aids() (in module gmol.base.data.mmcif.filter) remove_excluded_ligands() (in module gmol.base.data.mmcif.filter) remove_ions() (in module gmol.base.data.mmcif.filter) remove_large_ca_distance() (in module gmol.base.data.mmcif.filter) remove_leaving_atoms() (in module gmol.base.data.mmcif.filter) remove_min_resolved_chains() (in module gmol.base.data.mmcif.filter) remove_non_ccd_atoms() (in module gmol.base.data.mmcif.filter) remove_waters() (in module gmol.base.data.mmcif.filter) res_id (BranchPartner attribute) (SequenceToResidue attribute) res_idx (ExtraBondPartner attribute) Residue (class in gmol.base.data.mmcif.assembly) residue_atom_idxs (PolymerConstants attribute) residue_id (AssemblyAtom attribute) (Residue attribute)

residue_ids (Chain attribute) (PolymerChain attribute) residue_mol_type() (in module gmol.base.data.mmcif.assembly) ResidueId (class in gmol.base.data.mmcif.assembly) residues (Assembly attribute) residues_of_chain() (Assembly method) resolution (Input attribute) (Mmcif attribute) (PdbMetadata attribute) resseq (Chain property) restype (PolymerChain attribute) restype_3_to_1 (PolymerConstants attribute) restype_modres_backbone (PolymerConstants attribute) restype_order_with_x (PolymerConstants attribute) restype_x (PolymerConstants attribute) result2msa() (MMseqs method) revision_date (Mmcif attribute) (PdbMetadata attribute) rmdb() (MMseqs method) RNA (MolType attribute) (NonProteinQuery.Type attribute) run_search_from_path() (in module gmol.base.data.seq.mmseqs_search)

S

s (MMseqsCommonSearchParams attribute) safe_filename() (in module gmol.base.path) Scheme (class in gmol.base.data.mmcif.parse) search() (MMseqs method) search_db (MMseqsPairSearchParams attribute) search_param (MMseqsCommonSearchParams property) seq_counts (MMseqsQuery attribute) seq_id (BranchPartner attribute) (ResidueId attribute) (Scheme attribute) (SequenceToResidue attribute) seqres (Chain attribute) seqs (MsaQuery attribute) SequenceToResidue (class in gmol.base.data.mmcif.assembly) single (BondOrder attribute) smi2mol() (in module gmol.base.wrapper.rdkit) smiles (NonPolymerLigand attribute) SMILES (NonProteinQuery.Type attribute)

smiles (RefLigandInput attribute) src (ExtraBond attribute) src_idx (AssemblyConnection attribute) stereo_from_mmcif() (ExtraBond static method) struct_asym (Mmcif attribute) struct_conn (Mmcif attribute) struct_conn_type (Mmcif attribute) StructConn (class in gmol.base.data.mmcif.parse) StructConnPartner (class in gmol.base.data.mmcif.parse) StructConnType (class in gmol.base.data.mmcif.parse) suffix1 (MMseqsMonomerSearchParams attribute) (MMseqsPairSearchParams attribute) suffix2 (MMseqsMonomerSearchParams attribute) (MMseqsPairSearchParams attribute) suffix3 (MMseqsMonomerSearchParams attribute) symmetry (StructConnPartner attribute) symmetry_operation (SymOp attribute) SymOp (class in gmol.base.data.mmcif.parse) sync_mappings() (Chain method)

T

tdb (MMseqsMonomerSearchParams property) template_db (MMseqsMonomerSearchParams attribute) template_s (MMseqsMonomerSearchParams attribute) template_search_param (MMseqsMonomerSearchParams property) to_fasta() (Assembly method) to_mmcif() (Assembly method) to_mmcif_chain() (Assembly method) to_pdb() (Assembly method) to_rdkit_bond_type() (BondOrder method) to_scheme() (BranchPartner method)

transform() (Assembly method) Transformation (class in gmol.base.data.mmcif.assembly) triple (BondOrder attribute) type (Chain attribute) (ChemComp attribute) (Entity attribute) (SymOp attribute) type_symbol (AssemblyAtom attribute) (AtomSite attribute) (ChemCompAtom attribute)

U

udb1 (MMseqsMonomerSearchParams property) (MMseqsPairSearchParams property) udb2 (MMseqsMonomerSearchParams property) (MMseqsPairSearchParams property) unique_atom_id() (in module gmol.base.data.mmcif.smiles)

unique_seqs (MMseqsQuery attribute) uniref_db (MMseqsMonomerSearchParams attribute) unknown (BondClass attribute) unpackdb() (MMseqs method) upperclass (NonProteinQuery.Type property)

V

value_order (BranchLink attribute) (ChemCompBond attribute)

vector (SymOp attribute)

W

with_chain_suffix() (Branch method) (BranchPartner method) (ResidueId method) (SequenceToResidue method)

with_updates() (AssemblyAtom method) (Chain method) (Residue method) write_mols() (in module gmol.base.wrapper.rdkit)