#ifndef IOTBX_PDB_COMMON_RESIDUE_NAMES_H #define IOTBX_PDB_COMMON_RESIDUE_NAMES_H #include #include #include #include #include #include namespace iotbx { namespace pdb { namespace common_residue_names { static const char* amino_acid[] = { "GLY", "ALA", "VAL", "LEU", "ILE", "MET", "MSE", "PRO", "PHE", "TRP", "SER", "THR", "ASN", "GLN", "TYR", "CYS", "LYS", "ARG", "HIS", "ASP", "GLU", 0 }; static const char* d_amino_acid[] = { "DAL", // ALA "DAR", // ARG "DAS", // ASP "DCY", // CYS "DGL", // GLU "DGN", // GLN "DHI", // HIS "DIL", // ILE "DLE", // LEU "DLY", // LYS "DPN", // PHE "DPR", // PRO "DSG", // ASN "DSN", // SER "DTH", // THR "DTR", // TRP "DTY", // TYR "DVA", // VAL "MED", // MET 0 }; static const char* rna_dna[] = { "A ", "C ", "G ", "T ", "U ", " A", " C", " G", " T", " U", " A ", " C ", " G ", " T ", " U ", "+A ", "+C ", "+G ", "+T ", "+U ", " +A", " +C", " +G", " +T", " +U", "DA ", // PDB-V3 "DC ", // PDB-V3 "DG ", // PDB-V3 "DT ", // PDB-V3 " DA", // PDB-V3 " DC", // PDB-V3 " DG", // PDB-V3 " DT", // PDB-V3 "ADE", // CNS dna-rna.top "CYT", // CNS dna-rna.top "GUA", // CNS dna-rna.top "THY", // CNS dna-rna.top "URI", // CNS dna-rna.top 0 }; static const char* ccp4_mon_lib_rna_dna[] = { "AD ", "AR ", "CD ", "CR ", "GD ", "GR ", "TD ", "UR ", " AD", " AR", " CD", " CR", " GD", " GR", " TD", " UR", "Ad ", "Ar ", "Cd ", "Cr ", "Gd ", "Gr ", "Td ", "Ur ", " Ad", " Ar", " Cd", " Cr", " Gd", " Gr", " Td", " Ur", 0 }; static const char* water[] = { "HOH", "H2O", "OH2", "DOD", "OD2", "WAT", 0 }; static const char* small_molecule[] = { "GOL", "PO4", "SO4", 0 }; static const char* common_saccharide[] = { "NAG", "NDG", "MAN", "BMA", "FUC", "FUL", "BGC", "GLC", 0 }; /* Survey of PDB as of 2006/05/25. The following element names appear as HETATM residue names, but do not correspond to isolated atoms or ions: Frequency Element HETNAM in PDB symbol 36 NO NITROGEN OXIDE 1 AS ADENOSINE-5'-THIO-MONOPHOSPHATE 1 NP 4-HYDROXY-3-NITROPHENYLACETYL-EPSILON-AMINOCAPROIC ACID 1 SC CYTIDINE-5'-THIO-MONOPHOSPHATE 1 PU PUROMYCIN-N-AMINOPHOSPHONIC ACID 1 Y 2'-DEOXY-N6-(S)STYRENE OXIDE ADENOSINE MONOPHOSPHATE The element names AS, CM, H, I, IN, N, O, P, S appear as residue names but not on HETATM records. The following element names appear exclusively as HETATM residue names for isolated atoms or ions (these are the only names included in the element_set below): Frequency Element in PDB symbol 2579 ZN 2577 CA 2376 MG 1581 CL 1188 NA 743 MN 501 K 386 FE 319 CU 312 CD 215 HG 214 NI 165 CO 62 BR 47 XE 41 SR 33 CS 31 PT 25 BA 23 TL 23 PB 19 SM 19 AU 15 RB 14 YB 13 LI 12 KR 10 MO 7 LU 7 CR 6 OS 6 GD 4 TB 4 LA 4 F 4 AR 4 AG 3 HO 3 GA 3 CE 2 W 2 SE 2 RU 2 RE 2 PR 2 IR 2 EU 2 AL 1 V 1 TE 1 SB 1 PD */ static const char* element[] = { "ZN ", " ZN", "CA ", " CA", "MG ", " MG", "CL ", " CL", "NA ", " NA", "MN ", " MN", "K ", " K ", " K", "FE ", " FE", "CU ", " CU", "CD ", " CD", "HG ", " HG", "NI ", " NI", "CO ", " CO", "BR ", " BR", "XE ", " XE", "SR ", " SR", "CS ", " CS", "PT ", " PT", "BA ", " BA", "TL ", " TL", "PB ", " PB", "SM ", " SM", "AU ", " AU", "RB ", " RB", "YB ", " YB", "LI ", " LI", "KR ", " KR", "MO ", " MO", "LU ", " LU", "CR ", " CR", "OS ", " OS", "GD ", " GD", "TB ", " TB", "LA ", " LA", "F ", " F ", " F", "AR ", " AR", "AG ", " AG", "HO ", " HO", "GA ", " GA", "CE ", " CE", "W ", " W ", " W", "SE ", " SE", "RU ", " RU", "RE ", " RE", "PR ", " PR", "IR ", " IR", "EU ", " EU", "AL ", " AL", "V ", " V ", " V", "TE ", " TE", "SB ", " SB", "PD ", " PD", 0 }; inline void initialize_set( std::set& name_set, const char** names) { if (name_set.size() != 0) return; for(const char** n=names; *n; n++) name_set.insert(str3(*n)); } inline str3 std_string_as_str3(std::string const& name) { if (name.size() > 3) { throw std::runtime_error( "residue name with more than 3 characters: \""+name+"\""); } return str3(name.data(), name.size(), /*i_begin*/ 0, /*pad_with*/ ' '); } inline void initialize_set( std::set& name_set, scitbx::af::const_ref const& names) { for(std::size_t i=0;i& amino_acid_set() { static std::set result; initialize_set(result, amino_acid); return result; } inline const std::set& d_amino_acid_set() { static std::set result; initialize_set(result, d_amino_acid); return result; } inline const std::set& modified_amino_acid_set() { static std::set result; initialize_set(result, modified_amino_acid); return result; } inline const std::set& rna_dna_set() { static std::set result; initialize_set(result, rna_dna); return result; } inline const std::set& modified_rna_dna_set() { static std::set result; initialize_set(result, modified_rna_dna); return result; } inline const std::set& ccp4_mon_lib_rna_dna_set() { static std::set result; initialize_set(result, ccp4_mon_lib_rna_dna); return result; } inline const std::set& water_set() { static std::set result; initialize_set(result, water); return result; } inline const std::set& small_molecule_set() { static std::set result; initialize_set(result, small_molecule); return result; } inline const std::set& saccharide_set() { static std::set result; initialize_set(result, common_saccharide); return result; } inline const std::set& element_set() { static std::set result; initialize_set(result, element); return result; } inline std::string const& get_class(str3 const& name, bool consider_ccp4_mon_lib_rna_dna=false) { static const std::set& aa_set = amino_acid_set(); static const std::set& d_aa_set = d_amino_acid_set(); static const std::set& modified_aa_set = modified_amino_acid_set(); static const std::set& na_set = rna_dna_set(); static const std::set& modified_na_set = modified_rna_dna_set(); static const std::set& ml_na_set = ccp4_mon_lib_rna_dna_set(); static const std::set& w_set = water_set(); static const std::set& sm_set = small_molecule_set(); static const std::set& s_set = saccharide_set(); static const std::set& e_set = element_set(); static const std::string common_amino_acid("common_amino_acid"); static const std::string d_amino_acid("d_amino_acid"); static const std::string modified_amino_acid("modified_amino_acid"); static const std::string common_rna_dna("common_rna_dna"); static const std::string modified_rna_dna("modified_rna_dna"); static const std::string ccp4_mon_lib_rna_dna("ccp4_mon_lib_rna_dna"); static const std::string common_water("common_water"); static const std::string common_small_molecule("common_small_molecule"); static const std::string common_saccharide("common_saccharide"); static const std::string common_element("common_element"); static const std::string other("other"); if (aa_set.find(name) != aa_set.end()) { return common_amino_acid; } if (d_aa_set.find(name) != d_aa_set.end()) { return d_amino_acid; } if (modified_aa_set.find(name) != modified_aa_set.end()) { return modified_amino_acid; } if (na_set.find(name) != na_set.end()) { return common_rna_dna; } if (modified_na_set.find(name) != modified_na_set.end()) { return modified_rna_dna; } if ( consider_ccp4_mon_lib_rna_dna && ml_na_set.find(name) != ml_na_set.end()) { return ccp4_mon_lib_rna_dna; } if (w_set.find(name) != w_set.end()) { return common_water; } if (sm_set.find(name) != sm_set.end()) { return common_small_molecule; } if (s_set.find(name) != s_set.end()) { return common_saccharide; } if (e_set.find(name) != e_set.end()) { return common_element; } return other; } inline std::string const& get_class(std::string const& name, bool consider_ccp4_mon_lib_rna_dna=false) { return get_class(std_string_as_str3(name), consider_ccp4_mon_lib_rna_dna); } }}} // namespace iotbx::pdb::common_residue_names #endif // IOTBX_PDB_COMMON_RESIDUE_NAMES_H