diff --git a/modules/io/src/mol/omf.cc b/modules/io/src/mol/omf.cc index a7daf239274417ed140da8593ca54efd615a31b3..2ddda6b9da73cc42cc2f3b795caffb008d750984 100644 --- a/modules/io/src/mol/omf.cc +++ b/modules/io/src/mol/omf.cc @@ -967,7 +967,7 @@ DefaultPepLib::DefaultPepLib() { /* hardcoded constructor created with: from ost import conop - def ProcessCompound(comp_name, lib, skip_oxt=True): + def ProcessCompound(comp_name, lib, skip_oxt=True, ca_only=False): c = lib.FindCompound(comp_name) anames = list() idx_mapper = dict() @@ -977,6 +977,8 @@ DefaultPepLib::DefaultPepLib() { continue if skip_oxt and a.name == "OXT": continue + if ca_only and a.name != "CA": + continue idx_mapper[a_idx] = a.name anames.append(a.name) element_mapper[a.name] = a.element @@ -1015,12 +1017,12 @@ DefaultPepLib::DefaultPepLib() { lib = conop.GetDefaultLib() anames = ["ALA", "ARG", "ASN", "ASP", "GLN", "GLU", "LYS", "SER", "CYS", "MET", "TRP", "TYR", "THR", "VAL", "ILE", "LEU", "GLY", "PRO", "HIS", "PHE"] - print(" ResidueDefinition res_def;"); + print(" ResidueDefinition res_def;") for aname in anames: ProcessCompound(aname, lib) ProcessCompound(aname, lib, skip_oxt = False) + ProcessCompound(aname, lib, ca_only=True) */ - ResidueDefinition res_def; res_def = ResidueDefinition(); res_def.name = "ALA"; @@ -1087,6 +1089,16 @@ DefaultPepLib::DefaultPepLib() { res_def.bond_orders.push_back(1); residue_definitions.push_back(res_def); + res_def = ResidueDefinition(); + res_def.name = "ALA"; + res_def.olc = 'A'; + res_def.chem_type = 'A'; + res_def.chem_class = 'L'; + res_def.anames.push_back("CA"); + res_def.elements.push_back("C"); + res_def.is_hetatm.assign(1, false); + residue_definitions.push_back(res_def); + res_def = ResidueDefinition(); res_def.name = "ARG"; res_def.olc = 'R'; @@ -1212,6 +1224,16 @@ DefaultPepLib::DefaultPepLib() { res_def.bond_orders.push_back(2); residue_definitions.push_back(res_def); + res_def = ResidueDefinition(); + res_def.name = "ARG"; + res_def.olc = 'R'; + res_def.chem_type = 'A'; + res_def.chem_class = 'L'; + res_def.anames.push_back("CA"); + res_def.elements.push_back("C"); + res_def.is_hetatm.assign(1, false); + residue_definitions.push_back(res_def); + res_def = ResidueDefinition(); res_def.name = "ASN"; res_def.olc = 'N'; @@ -1307,6 +1329,16 @@ DefaultPepLib::DefaultPepLib() { res_def.bond_orders.push_back(2); residue_definitions.push_back(res_def); + res_def = ResidueDefinition(); + res_def.name = "ASN"; + res_def.olc = 'N'; + res_def.chem_type = 'A'; + res_def.chem_class = 'L'; + res_def.anames.push_back("CA"); + res_def.elements.push_back("C"); + res_def.is_hetatm.assign(1, false); + residue_definitions.push_back(res_def); + res_def = ResidueDefinition(); res_def.name = "ASP"; res_def.olc = 'D'; @@ -1402,6 +1434,16 @@ DefaultPepLib::DefaultPepLib() { res_def.bond_orders.push_back(1); residue_definitions.push_back(res_def); + res_def = ResidueDefinition(); + res_def.name = "ASP"; + res_def.olc = 'D'; + res_def.chem_type = 'A'; + res_def.chem_class = 'L'; + res_def.anames.push_back("CA"); + res_def.elements.push_back("C"); + res_def.is_hetatm.assign(1, false); + residue_definitions.push_back(res_def); + res_def = ResidueDefinition(); res_def.name = "GLN"; res_def.olc = 'Q'; @@ -1507,6 +1549,16 @@ DefaultPepLib::DefaultPepLib() { res_def.bond_orders.push_back(2); residue_definitions.push_back(res_def); + res_def = ResidueDefinition(); + res_def.name = "GLN"; + res_def.olc = 'Q'; + res_def.chem_type = 'A'; + res_def.chem_class = 'L'; + res_def.anames.push_back("CA"); + res_def.elements.push_back("C"); + res_def.is_hetatm.assign(1, false); + residue_definitions.push_back(res_def); + res_def = ResidueDefinition(); res_def.name = "GLU"; res_def.olc = 'E'; @@ -1612,6 +1664,16 @@ DefaultPepLib::DefaultPepLib() { res_def.bond_orders.push_back(1); residue_definitions.push_back(res_def); + res_def = ResidueDefinition(); + res_def.name = "GLU"; + res_def.olc = 'E'; + res_def.chem_type = 'A'; + res_def.chem_class = 'L'; + res_def.anames.push_back("CA"); + res_def.elements.push_back("C"); + res_def.is_hetatm.assign(1, false); + residue_definitions.push_back(res_def); + res_def = ResidueDefinition(); res_def.name = "LYS"; res_def.olc = 'K'; @@ -1717,6 +1779,16 @@ DefaultPepLib::DefaultPepLib() { res_def.bond_orders.push_back(1); residue_definitions.push_back(res_def); + res_def = ResidueDefinition(); + res_def.name = "LYS"; + res_def.olc = 'K'; + res_def.chem_type = 'A'; + res_def.chem_class = 'L'; + res_def.anames.push_back("CA"); + res_def.elements.push_back("C"); + res_def.is_hetatm.assign(1, false); + residue_definitions.push_back(res_def); + res_def = ResidueDefinition(); res_def.name = "SER"; res_def.olc = 'S'; @@ -1792,6 +1864,16 @@ DefaultPepLib::DefaultPepLib() { res_def.bond_orders.push_back(1); residue_definitions.push_back(res_def); + res_def = ResidueDefinition(); + res_def.name = "SER"; + res_def.olc = 'S'; + res_def.chem_type = 'A'; + res_def.chem_class = 'L'; + res_def.anames.push_back("CA"); + res_def.elements.push_back("C"); + res_def.is_hetatm.assign(1, false); + residue_definitions.push_back(res_def); + res_def = ResidueDefinition(); res_def.name = "CYS"; res_def.olc = 'C'; @@ -1867,6 +1949,16 @@ DefaultPepLib::DefaultPepLib() { res_def.bond_orders.push_back(1); residue_definitions.push_back(res_def); + res_def = ResidueDefinition(); + res_def.name = "CYS"; + res_def.olc = 'C'; + res_def.chem_type = 'A'; + res_def.chem_class = 'L'; + res_def.anames.push_back("CA"); + res_def.elements.push_back("C"); + res_def.is_hetatm.assign(1, false); + residue_definitions.push_back(res_def); + res_def = ResidueDefinition(); res_def.name = "MET"; res_def.olc = 'M'; @@ -1962,6 +2054,16 @@ DefaultPepLib::DefaultPepLib() { res_def.bond_orders.push_back(1); residue_definitions.push_back(res_def); + res_def = ResidueDefinition(); + res_def.name = "MET"; + res_def.olc = 'M'; + res_def.chem_type = 'A'; + res_def.chem_class = 'L'; + res_def.anames.push_back("CA"); + res_def.elements.push_back("C"); + res_def.is_hetatm.assign(1, false); + residue_definitions.push_back(res_def); + res_def = ResidueDefinition(); res_def.name = "TRP"; res_def.olc = 'W'; @@ -2129,6 +2231,16 @@ DefaultPepLib::DefaultPepLib() { res_def.bond_orders.push_back(1); residue_definitions.push_back(res_def); + res_def = ResidueDefinition(); + res_def.name = "TRP"; + res_def.olc = 'W'; + res_def.chem_type = 'A'; + res_def.chem_class = 'L'; + res_def.anames.push_back("CA"); + res_def.elements.push_back("C"); + res_def.is_hetatm.assign(1, false); + residue_definitions.push_back(res_def); + res_def = ResidueDefinition(); res_def.name = "TYR"; res_def.olc = 'Y'; @@ -2270,6 +2382,16 @@ DefaultPepLib::DefaultPepLib() { res_def.bond_orders.push_back(1); residue_definitions.push_back(res_def); + res_def = ResidueDefinition(); + res_def.name = "TYR"; + res_def.olc = 'Y'; + res_def.chem_type = 'A'; + res_def.chem_class = 'L'; + res_def.anames.push_back("CA"); + res_def.elements.push_back("C"); + res_def.is_hetatm.assign(1, false); + residue_definitions.push_back(res_def); + res_def = ResidueDefinition(); res_def.name = "THR"; res_def.olc = 'T'; @@ -2355,6 +2477,16 @@ DefaultPepLib::DefaultPepLib() { res_def.bond_orders.push_back(1); residue_definitions.push_back(res_def); + res_def = ResidueDefinition(); + res_def.name = "THR"; + res_def.olc = 'T'; + res_def.chem_type = 'A'; + res_def.chem_class = 'L'; + res_def.anames.push_back("CA"); + res_def.elements.push_back("C"); + res_def.is_hetatm.assign(1, false); + residue_definitions.push_back(res_def); + res_def = ResidueDefinition(); res_def.name = "VAL"; res_def.olc = 'V'; @@ -2440,6 +2572,16 @@ DefaultPepLib::DefaultPepLib() { res_def.bond_orders.push_back(1); residue_definitions.push_back(res_def); + res_def = ResidueDefinition(); + res_def.name = "VAL"; + res_def.olc = 'V'; + res_def.chem_type = 'A'; + res_def.chem_class = 'L'; + res_def.anames.push_back("CA"); + res_def.elements.push_back("C"); + res_def.is_hetatm.assign(1, false); + residue_definitions.push_back(res_def); + res_def = ResidueDefinition(); res_def.name = "ILE"; res_def.olc = 'I'; @@ -2535,6 +2677,16 @@ DefaultPepLib::DefaultPepLib() { res_def.bond_orders.push_back(1); residue_definitions.push_back(res_def); + res_def = ResidueDefinition(); + res_def.name = "ILE"; + res_def.olc = 'I'; + res_def.chem_type = 'A'; + res_def.chem_class = 'L'; + res_def.anames.push_back("CA"); + res_def.elements.push_back("C"); + res_def.is_hetatm.assign(1, false); + residue_definitions.push_back(res_def); + res_def = ResidueDefinition(); res_def.name = "LEU"; res_def.olc = 'L'; @@ -2630,6 +2782,16 @@ DefaultPepLib::DefaultPepLib() { res_def.bond_orders.push_back(1); residue_definitions.push_back(res_def); + res_def = ResidueDefinition(); + res_def.name = "LEU"; + res_def.olc = 'L'; + res_def.chem_type = 'A'; + res_def.chem_class = 'L'; + res_def.anames.push_back("CA"); + res_def.elements.push_back("C"); + res_def.is_hetatm.assign(1, false); + residue_definitions.push_back(res_def); + res_def = ResidueDefinition(); res_def.name = "GLY"; res_def.olc = 'G'; @@ -2685,6 +2847,16 @@ DefaultPepLib::DefaultPepLib() { res_def.bond_orders.push_back(1); residue_definitions.push_back(res_def); + res_def = ResidueDefinition(); + res_def.name = "GLY"; + res_def.olc = 'G'; + res_def.chem_type = 'A'; + res_def.chem_class = 'P'; + res_def.anames.push_back("CA"); + res_def.elements.push_back("C"); + res_def.is_hetatm.assign(1, false); + residue_definitions.push_back(res_def); + res_def = ResidueDefinition(); res_def.name = "PRO"; res_def.olc = 'P'; @@ -2776,6 +2948,16 @@ DefaultPepLib::DefaultPepLib() { res_def.bond_orders.push_back(1); residue_definitions.push_back(res_def); + res_def = ResidueDefinition(); + res_def.name = "PRO"; + res_def.olc = 'P'; + res_def.chem_type = 'A'; + res_def.chem_class = 'L'; + res_def.anames.push_back("CA"); + res_def.elements.push_back("C"); + res_def.is_hetatm.assign(1, false); + residue_definitions.push_back(res_def); + res_def = ResidueDefinition(); res_def.name = "HIS"; res_def.olc = 'H'; @@ -2897,6 +3079,16 @@ DefaultPepLib::DefaultPepLib() { res_def.bond_orders.push_back(1); residue_definitions.push_back(res_def); + res_def = ResidueDefinition(); + res_def.name = "HIS"; + res_def.olc = 'H'; + res_def.chem_type = 'A'; + res_def.chem_class = 'L'; + res_def.anames.push_back("CA"); + res_def.elements.push_back("C"); + res_def.is_hetatm.assign(1, false); + residue_definitions.push_back(res_def); + res_def = ResidueDefinition(); res_def.name = "PHE"; res_def.olc = 'F'; @@ -3027,6 +3219,16 @@ DefaultPepLib::DefaultPepLib() { res_def.bond_orders.push_back(2); res_def.bond_orders.push_back(1); residue_definitions.push_back(res_def); + + res_def = ResidueDefinition(); + res_def.name = "PHE"; + res_def.olc = 'F'; + res_def.chem_type = 'A'; + res_def.chem_class = 'L'; + res_def.anames.push_back("CA"); + res_def.elements.push_back("C"); + res_def.is_hetatm.assign(1, false); + residue_definitions.push_back(res_def); } OMFPtr OMF::FromEntity(const ost::mol::EntityHandle& ent,