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libcifpp
Commit d4972542 by Maarten L. Hekkelman
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re-added group to Compound. Seems to be important

parent b7330c07
Showing with 420 additions and 61 deletions
include/cif++/Compound.hpp
...@@ -104,6 +104,7 @@ class Compound ...@@ -104,6 +104,7 @@ class Compound
std::string id() const { return mID; } std::string id() const { return mID; }
std::string name() const { return mName; } std::string name() const { return mName; }
std::string type() const { return mType; } std::string type() const { return mType; }
std::string group() const { return mGroup; }
std::string formula() const { return mFormula; } std::string formula() const { return mFormula; }
float formulaWeight() const { return mFormulaWeight; } float formulaWeight() const { return mFormulaWeight; }
int formalCharge() const { return mFormalCharge; } int formalCharge() const { return mFormalCharge; }
...@@ -130,11 +131,12 @@ class Compound ...@@ -130,11 +131,12 @@ class Compound
friend class CCP4CompoundFactoryImpl; friend class CCP4CompoundFactoryImpl;
Compound(cif::Datablock &db); Compound(cif::Datablock &db);
Compound(cif::Datablock &db, const std::string &id, const std::string &name, const std::string &type); Compound(cif::Datablock &db, const std::string &id, const std::string &name, const std::string &type, const std::string &group);
std::string mID; std::string mID;
std::string mName; std::string mName;
std::string mType; std::string mType;
std::string mGroup;
std::string mFormula; std::string mFormula;
float mFormulaWeight = 0; float mFormulaWeight = 0;
int mFormalCharge = 0; int mFormalCharge = 0;
......
src/Compound.cpp
...@@ -127,6 +127,8 @@ Compound::Compound(cif::Datablock &db) ...@@ -127,6 +127,8 @@ Compound::Compound(cif::Datablock &db)
ba::replace_all(mName, "\n", ""); ba::replace_all(mName, "\n", "");
mGroup = "non-polymer";
auto &chemCompAtom = db["chem_comp_atom"]; auto &chemCompAtom = db["chem_comp_atom"];
for (auto row : chemCompAtom) for (auto row : chemCompAtom)
{ {
...@@ -150,10 +152,11 @@ Compound::Compound(cif::Datablock &db) ...@@ -150,10 +152,11 @@ Compound::Compound(cif::Datablock &db)
} }
} }
Compound::Compound(cif::Datablock &db, const std::string &id, const std::string &name, const std::string &type) Compound::Compound(cif::Datablock &db, const std::string &id, const std::string &name, const std::string &type, const std::string &group)
: mID(id) : mID(id)
, mName(name) , mName(name)
, mType(type) , mType(type)
, mGroup(group)
{ {
auto &chemCompAtom = db["chem_comp_atom"]; auto &chemCompAtom = db["chem_comp_atom"];
for (auto row : chemCompAtom) for (auto row : chemCompAtom)
...@@ -410,7 +413,7 @@ CompoundFactoryImpl::CompoundFactoryImpl(const std::filesystem::path &file, std: ...@@ -410,7 +413,7 @@ CompoundFactoryImpl::CompoundFactoryImpl(const std::filesystem::path &file, std:
auto &db = cifFile["comp_" + id]; auto &db = cifFile["comp_" + id];
mCompounds.push_back(new Compound(db, id, name, type)); mCompounds.push_back(new Compound(db, id, name, type, group));
} }
} }
else else
...@@ -616,7 +619,7 @@ Compound *CCP4CompoundFactoryImpl::create(const std::string &id) ...@@ -616,7 +619,7 @@ Compound *CCP4CompoundFactoryImpl::create(const std::string &id)
else else
type = "non-polymer"; type = "non-polymer";
mCompounds.push_back(new Compound(db, id, name, type)); mCompounds.push_back(new Compound(db, id, name, type, group));
result = mCompounds.back(); result = mCompounds.back();
} }
} }
......
src/PDB2Cif.cpp
...@@ -1540,7 +1540,8 @@ void PDBFileParser::ParseTitle() ...@@ -1540,7 +1540,8 @@ void PDBFileParser::ParseTitle()
while (mRec->is("CAVEAT")) // 1 - 6 Record name "CAVEAT" while (mRec->is("CAVEAT")) // 1 - 6 Record name "CAVEAT"
{ {
getCategory("database_PDB_caveat")->emplace({ getCategory("database_PDB_caveat")->emplace({
{"id", caveatID++}, {"text", std::string{mRec->vS(20)}} // 20 - 79 String comment Free text giving the reason for the CAVEAT. {"id", caveatID++},
{"text", std::string{mRec->vS(20)}} // 20 - 79 String comment Free text giving the reason for the CAVEAT.
}); });
GetNextRecord(); GetNextRecord();
...@@ -1674,7 +1675,9 @@ void PDBFileParser::ParseTitle() ...@@ -1674,7 +1675,9 @@ void PDBFileParser::ParseTitle()
if (not(keywords.empty() and pdbxKeywords.empty())) if (not(keywords.empty() and pdbxKeywords.empty()))
{ {
getCategory("struct_keywords")->emplace({{"entry_id", mStructureID}, {"pdbx_keywords", keywords}, {"text", pdbxKeywords}}); getCategory("struct_keywords")->emplace({{"entry_id", mStructureID},
{"pdbx_keywords", keywords},
{"text", pdbxKeywords}});
} }
// EXPDTA // EXPDTA
...@@ -1794,13 +1797,18 @@ void PDBFileParser::ParseTitle() ...@@ -1794,13 +1797,18 @@ void PDBFileParser::ParseTitle()
sort(revdats.begin(), revdats.end()); sort(revdats.begin(), revdats.end());
for (auto &revdat : revdats) for (auto &revdat : revdats)
{ {
getCategory("database_PDB_rev")->emplace({{"num", revdat.revNum}, {"date", revdat.date}, {"date_original", revdat.dateOriginal}, {"replaces", revdat.replaces}, {"mod_type", revdat.modType}}); getCategory("database_PDB_rev")->emplace({{"num", revdat.revNum},
{"date", revdat.date},
{"date_original", revdat.dateOriginal},
{"replaces", revdat.replaces},
{"mod_type", revdat.modType}});
for (auto &type : revdat.types) for (auto &type : revdat.types)
{ {
if (type.empty()) if (type.empty())
continue; continue;
getCategory("database_PDB_rev_record")->emplace({{"rev_num", revdat.revNum}, {"type", type}}); getCategory("database_PDB_rev_record")->emplace({{"rev_num", revdat.revNum},
{"type", type}});
} }
} }
//*/ //*/
...@@ -2036,7 +2044,10 @@ void PDBFileParser::ParseRemarks() ...@@ -2036,7 +2044,10 @@ void PDBFileParser::ParseRemarks()
if (desc == "NULL") if (desc == "NULL")
desc.clear(); desc.clear();
getCategory("exptl_crystal")->emplace({{"id", 1}, {"density_Matthews", iequals(density_Matthews, "NULL") ? "" : density_Matthews}, {"density_percent_sol", iequals(densityPercentSol, "NULL") ? "" : densityPercentSol}, {"description", desc}}); getCategory("exptl_crystal")->emplace({{"id", 1},
{"density_Matthews", iequals(density_Matthews, "NULL") ? "" : density_Matthews},
{"density_percent_sol", iequals(densityPercentSol, "NULL") ? "" : densityPercentSol},
{"description", desc}});
// now try to parse the conditions // now try to parse the conditions
const std::regex rx3(R"(TEMPERATURE +(\d+)K)"), rx4(R"(PH *(?:: *)?(\d+(?:\.\d+)?))") /*, rx5(R"(\b(\d+)C\b)")*/; const std::regex rx3(R"(TEMPERATURE +(\d+)K)"), rx4(R"(PH *(?:: *)?(\d+(?:\.\d+)?))") /*, rx5(R"(\b(\d+)C\b)")*/;
...@@ -2065,7 +2076,11 @@ void PDBFileParser::ParseRemarks() ...@@ -2065,7 +2076,11 @@ void PDBFileParser::ParseRemarks()
if (not(method.empty() and temp.empty() and ph.empty() and (conditions.empty() or conditions == "NULL"))) if (not(method.empty() and temp.empty() and ph.empty() and (conditions.empty() or conditions == "NULL")))
{ {
getCategory("exptl_crystal_grow")->emplace({{"crystal_id", 1}, {"method", method}, {"temp", temp}, {"pH", ph}, {"pdbx_details", conditions}}); getCategory("exptl_crystal_grow")->emplace({{"crystal_id", 1},
{"method", method},
{"temp", temp},
{"pH", ph},
{"pdbx_details", conditions}});
} }
break; break;
...@@ -2283,7 +2298,21 @@ void PDBFileParser::ParseRemarks() ...@@ -2283,7 +2298,21 @@ void PDBFileParser::ParseRemarks()
std::string distance = vF(63, 71); std::string distance = vF(63, 71);
getCategory("pdbx_validate_close_contact")->emplace({{"id", std::to_string(++id)}, {"PDB_model_num", 1}, {"auth_atom_id_1", atom1}, {"auth_asym_id_1", std::string{chain1}}, {"auth_comp_id_1", res1}, {"auth_seq_id_1", seq1}, {"PDB_ins_code_1", iCode1}, {"label_alt_id_1", alt1}, {"auth_atom_id_2", atom2}, {"auth_asym_id_2", std::string{chain2}}, {"auth_comp_id_2", res2}, {"auth_seq_id_2", seq2}, {"PDB_ins_code_2", iCode2}, {"label_alt_id_2", alt2}, {"dist", distance}}); getCategory("pdbx_validate_close_contact")->emplace({{"id", std::to_string(++id)},
{"PDB_model_num", 1},
{"auth_atom_id_1", atom1},
{"auth_asym_id_1", std::string{chain1}},
{"auth_comp_id_1", res1},
{"auth_seq_id_1", seq1},
{"PDB_ins_code_1", iCode1},
{"label_alt_id_1", alt1},
{"auth_atom_id_2", atom2},
{"auth_asym_id_2", std::string{chain2}},
{"auth_comp_id_2", res2},
{"auth_seq_id_2", seq2},
{"PDB_ins_code_2", iCode2},
{"label_alt_id_2", alt2},
{"dist", distance}});
} }
break; break;
} }
...@@ -2320,7 +2349,12 @@ void PDBFileParser::ParseRemarks() ...@@ -2320,7 +2349,12 @@ void PDBFileParser::ParseRemarks()
std::string distance = vF(63, 71); std::string distance = vF(63, 71);
getCategory("pdbx_validate_symm_contact")->emplace({{"id", std::to_string(++id)}, {"PDB_model_num", 1}, {"auth_atom_id_1", atom1}, {"auth_asym_id_1", std::string{chain1}}, {"auth_comp_id_1", res1}, {"auth_seq_id_1", seq1}, getCategory("pdbx_validate_symm_contact")->emplace({{"id", std::to_string(++id)},
{"PDB_model_num", 1},
{"auth_atom_id_1", atom1},
{"auth_asym_id_1", std::string{chain1}},
{"auth_comp_id_1", res1},
{"auth_seq_id_1", seq1},
// { "PDB_ins_code_1", "" }, // { "PDB_ins_code_1", "" },
// { "label_alt_id_1", "" }, // { "label_alt_id_1", "" },
{"site_symmetry_1", "1_555"}, {"site_symmetry_1", "1_555"},
...@@ -2371,7 +2405,21 @@ void PDBFileParser::ParseRemarks() ...@@ -2371,7 +2405,21 @@ void PDBFileParser::ParseRemarks()
if (iCode2 == " ") if (iCode2 == " ")
iCode2.clear(); iCode2.clear();
getCategory("pdbx_validate_rmsd_bond")->emplace({{"id", std::to_string(++id)}, {"PDB_model_num", model ? model : 1}, {"auth_atom_id_1", atm1}, {"auth_asym_id_1", chainID1}, {"auth_comp_id_1", resNam1}, {"auth_seq_id_1", seqNum1}, {"PDB_ins_code_1", iCode1}, {"label_alt_id_1", alt1}, {"auth_atom_id_2", atm2}, {"auth_asym_id_2", chainID2}, {"auth_comp_id_2", resNam2}, {"auth_seq_id_2", seqNum2}, {"PDB_ins_code_2", iCode2}, {"label_alt_id_2", alt2}, {"bond_deviation", deviation}}); getCategory("pdbx_validate_rmsd_bond")->emplace({{"id", std::to_string(++id)},
{"PDB_model_num", model ? model : 1},
{"auth_atom_id_1", atm1},
{"auth_asym_id_1", chainID1},
{"auth_comp_id_1", resNam1},
{"auth_seq_id_1", seqNum1},
{"PDB_ins_code_1", iCode1},
{"label_alt_id_1", alt1},
{"auth_atom_id_2", atm2},
{"auth_asym_id_2", chainID2},
{"auth_comp_id_2", resNam2},
{"auth_seq_id_2", seqNum2},
{"PDB_ins_code_2", iCode2},
{"label_alt_id_2", alt2},
{"bond_deviation", deviation}});
} }
break; break;
...@@ -2403,7 +2451,24 @@ void PDBFileParser::ParseRemarks() ...@@ -2403,7 +2451,24 @@ void PDBFileParser::ParseRemarks()
if (deviation == "*****") if (deviation == "*****")
deviation.clear(); deviation.clear();
getCategory("pdbx_validate_rmsd_angle")->emplace({{"id", std::to_string(++id)}, {"PDB_model_num", model ? model : 1}, {"auth_atom_id_1", atoms[0]}, {"auth_asym_id_1", chainID}, {"auth_comp_id_1", resNam}, {"auth_seq_id_1", seqNum}, {"PDB_ins_code_1", iCode}, {"auth_atom_id_2", atoms[1]}, {"auth_asym_id_2", chainID}, {"auth_comp_id_2", resNam}, {"auth_seq_id_2", seqNum}, {"PDB_ins_code_2", iCode}, {"auth_atom_id_3", atoms[2]}, {"auth_asym_id_3", chainID}, {"auth_comp_id_3", resNam}, {"auth_seq_id_3", seqNum}, {"PDB_ins_code_3", iCode}, {"angle_deviation", deviation}}); getCategory("pdbx_validate_rmsd_angle")->emplace({{"id", std::to_string(++id)},
{"PDB_model_num", model ? model : 1},
{"auth_atom_id_1", atoms[0]},
{"auth_asym_id_1", chainID},
{"auth_comp_id_1", resNam},
{"auth_seq_id_1", seqNum},
{"PDB_ins_code_1", iCode},
{"auth_atom_id_2", atoms[1]},
{"auth_asym_id_2", chainID},
{"auth_comp_id_2", resNam},
{"auth_seq_id_2", seqNum},
{"PDB_ins_code_2", iCode},
{"auth_atom_id_3", atoms[2]},
{"auth_asym_id_3", chainID},
{"auth_comp_id_3", resNam},
{"auth_seq_id_3", seqNum},
{"PDB_ins_code_3", iCode},
{"angle_deviation", deviation}});
} }
break; break;
...@@ -2432,7 +2497,14 @@ void PDBFileParser::ParseRemarks() ...@@ -2432,7 +2497,14 @@ void PDBFileParser::ParseRemarks()
std::string psi = vF(27, 35); std::string psi = vF(27, 35);
std::string phi = vF(37, 45); std::string phi = vF(37, 45);
getCategory("pdbx_validate_torsion")->emplace({{"id", std::to_string(++id)}, {"PDB_model_num", model ? model : 1}, {"auth_comp_id", resNam}, {"auth_asym_id", chainID}, {"auth_seq_id", seqNum}, {"PDB_ins_code", iCode}, {"phi", phi}, {"psi", psi}}); getCategory("pdbx_validate_torsion")->emplace({{"id", std::to_string(++id)},
{"PDB_model_num", model ? model : 1},
{"auth_comp_id", resNam},
{"auth_asym_id", chainID},
{"auth_seq_id", seqNum},
{"PDB_ins_code", iCode},
{"phi", phi},
{"psi", psi}});
} }
break; break;
...@@ -2463,7 +2535,17 @@ void PDBFileParser::ParseRemarks() ...@@ -2463,7 +2535,17 @@ void PDBFileParser::ParseRemarks()
std::string omega = vF(54, 60); std::string omega = vF(54, 60);
getCategory("pdbx_validate_peptide_omega")->emplace({{"id", std::to_string(++id)}, {"PDB_model_num", model ? model : 1}, {"auth_comp_id_1", resNam1}, {"auth_asym_id_1", chainID1}, {"auth_seq_id_1", seqNum1}, {"PDB_ins_code_1", iCode1}, {"auth_comp_id_2", resNam2}, {"auth_asym_id_2", chainID2}, {"auth_seq_id_2", seqNum2}, {"PDB_ins_code_2", iCode2}, {"omega", omega}}); getCategory("pdbx_validate_peptide_omega")->emplace({{"id", std::to_string(++id)},
{"PDB_model_num", model ? model : 1},
{"auth_comp_id_1", resNam1},
{"auth_asym_id_1", chainID1},
{"auth_seq_id_1", seqNum1},
{"PDB_ins_code_1", iCode1},
{"auth_comp_id_2", resNam2},
{"auth_asym_id_2", chainID2},
{"auth_seq_id_2", seqNum2},
{"PDB_ins_code_2", iCode2},
{"omega", omega}});
} }
break; break;
...@@ -2486,7 +2568,14 @@ void PDBFileParser::ParseRemarks() ...@@ -2486,7 +2568,14 @@ void PDBFileParser::ParseRemarks()
std::string rmsd = vF(32, 36); std::string rmsd = vF(32, 36);
std::string type = vS(41); std::string type = vS(41);
getCategory("pdbx_validate_planes")->emplace({{"id", std::to_string(++id)}, {"PDB_model_num", model ? model : 1}, {"auth_comp_id", resNam}, {"auth_asym_id", chainID}, {"auth_seq_id", seqNum}, {"PDB_ins_code", iCode}, {"rmsd", rmsd}, {"type", type}}); getCategory("pdbx_validate_planes")->emplace({{"id", std::to_string(++id)},
{"PDB_model_num", model ? model : 1},
{"auth_comp_id", resNam},
{"auth_asym_id", chainID},
{"auth_seq_id", seqNum},
{"PDB_ins_code", iCode},
{"rmsd", rmsd},
{"type", type}});
} }
break; break;
...@@ -2566,7 +2655,13 @@ void PDBFileParser::ParseRemarks() ...@@ -2566,7 +2655,13 @@ void PDBFileParser::ParseRemarks()
throw std::runtime_error("Invalid REMARK 800, no SITE record for id " + id); throw std::runtime_error("Invalid REMARK 800, no SITE record for id " + id);
// next record, store what we have // next record, store what we have
getCategory("struct_site")->emplace({{"id", id}, {"details", desc}, {"pdbx_auth_asym_id", pdbxAuthAsymID}, {"pdbx_auth_comp_id", pdbxAuthCompID}, {"pdbx_auth_seq_id", pdbxAuthSeqID}, {"pdbx_num_residues", site->vI(16, 17)}, {"pdbx_evidence_code", evidence}}); getCategory("struct_site")->emplace({{"id", id},
{"details", desc},
{"pdbx_auth_asym_id", pdbxAuthAsymID},
{"pdbx_auth_comp_id", pdbxAuthCompID},
{"pdbx_auth_seq_id", pdbxAuthSeqID},
{"pdbx_num_residues", site->vI(16, 17)},
{"pdbx_evidence_code", evidence}});
}; };
for (; mRec->is("REMARK 800"); GetNextRecord()) for (; mRec->is("REMARK 800"); GetNextRecord())
...@@ -2680,7 +2775,8 @@ void PDBFileParser::ParseRemarks() ...@@ -2680,7 +2775,8 @@ void PDBFileParser::ParseRemarks()
GetNextRecord(); GetNextRecord();
} }
getCategory("pdbx_database_remark")->emplace({{"id", remarkNr}, {"text", s.str()}}); getCategory("pdbx_database_remark")->emplace({{"id", remarkNr},
{"text", s.str()}});
break; break;
} }
...@@ -2694,7 +2790,10 @@ void PDBFileParser::ParseRemarks() ...@@ -2694,7 +2790,10 @@ void PDBFileParser::ParseRemarks()
if (not(compoundDetails.empty() and sequenceDetails.empty() and sourceDetails.empty())) if (not(compoundDetails.empty() and sequenceDetails.empty() and sourceDetails.empty()))
{ {
getCategory("pdbx_entry_details")->emplace({{"entry_id", mStructureID}, {"compound_details", compoundDetails}, {"sequence_details", sequenceDetails}, {"source_details", sourceDetails}}); getCategory("pdbx_entry_details")->emplace({{"entry_id", mStructureID},
{"compound_details", compoundDetails},
{"sequence_details", sequenceDetails},
{"source_details", sourceDetails}});
} }
// store remark 200 info (special case) // store remark 200 info (special case)
...@@ -2774,7 +2873,10 @@ void PDBFileParser::ParseRemark200() ...@@ -2774,7 +2873,10 @@ void PDBFileParser::ParseRemark200()
if (mRemark200[sw.b].empty()) if (mRemark200[sw.b].empty())
continue; continue;
getCategory("software")->emplace({{"name", mRemark200[sw.b]}, {"classification", sw.a}, {"version", "."}, {"pdbx_ordinal", mNextSoftwareOrd++}}); getCategory("software")->emplace({{"name", mRemark200[sw.b]},
{"classification", sw.a},
{"version", "."},
{"pdbx_ordinal", mNextSoftwareOrd++}});
} }
std::string scatteringType; std::string scatteringType;
...@@ -2812,10 +2914,19 @@ void PDBFileParser::ParseRemark200() ...@@ -2812,10 +2914,19 @@ void PDBFileParser::ParseRemark200()
collectionDate.clear(); collectionDate.clear();
} }
getCategory("diffrn_detector")->emplace({{"diffrn_id", diffrnNr}, {"detector", rm200("DETECTOR TYPE", diffrnNr)}, {"type", rm200("DETECTOR MANUFACTURER", diffrnNr)}, {"pdbx_collection_date", collectionDate}, {"details", rm200("OPTICS", diffrnNr)}}); getCategory("diffrn_detector")->emplace({{"diffrn_id", diffrnNr},
{"detector", rm200("DETECTOR TYPE", diffrnNr)},
{"type", rm200("DETECTOR MANUFACTURER", diffrnNr)},
{"pdbx_collection_date", collectionDate},
{"details", rm200("OPTICS", diffrnNr)}});
if (inRM200({"MONOCHROMATIC OR LAUE (M/L)", "MONOCHROMATOR", "DIFFRACTION PROTOCOL"}) or not scatteringType.empty()) if (inRM200({"MONOCHROMATIC OR LAUE (M/L)", "MONOCHROMATOR", "DIFFRACTION PROTOCOL"}) or not scatteringType.empty())
getCategory("diffrn_radiation")->emplace({{"diffrn_id", diffrnNr}, {"wavelength_id", 1}, {"pdbx_monochromatic_or_laue_m_l", rm200("MONOCHROMATIC OR LAUE (M/L)", diffrnNr)}, {"monochromator", rm200("MONOCHROMATOR", diffrnNr)}, {"pdbx_diffrn_protocol", rm200("DIFFRACTION PROTOCOL", diffrnNr)}, {"pdbx_scattering_type", scatteringType}}); getCategory("diffrn_radiation")->emplace({{"diffrn_id", diffrnNr},
{"wavelength_id", 1},
{"pdbx_monochromatic_or_laue_m_l", rm200("MONOCHROMATIC OR LAUE (M/L)", diffrnNr)},
{"monochromator", rm200("MONOCHROMATOR", diffrnNr)},
{"pdbx_diffrn_protocol", rm200("DIFFRACTION PROTOCOL", diffrnNr)},
{"pdbx_scattering_type", scatteringType}});
std::vector<std::string> wavelengths; std::vector<std::string> wavelengths;
std::string wl = rm200("WAVELENGTH OR RANGE (A)", diffrnNr); std::string wl = rm200("WAVELENGTH OR RANGE (A)", diffrnNr);
...@@ -2856,7 +2967,9 @@ void PDBFileParser::ParseRemark200() ...@@ -2856,7 +2967,9 @@ void PDBFileParser::ParseRemark200()
if (ba::ends_with(wl, "A")) if (ba::ends_with(wl, "A"))
wl.erase(wl.length() - 1, 1); wl.erase(wl.length() - 1, 1);
getCategory("diffrn_radiation_wavelength")->emplace({{"id", wavelengthNr++}, {"wavelength", wl.empty() ? "." : wl}, {"wt", "1.0"}}); getCategory("diffrn_radiation_wavelength")->emplace({{"id", wavelengthNr++},
{"wavelength", wl.empty() ? "." : wl},
{"wt", "1.0"}});
} }
if (inRM200({"METHOD USED TO DETERMINE THE STRUCTURE", "STARTING MODEL"})) if (inRM200({"METHOD USED TO DETERMINE THE STRUCTURE", "STARTING MODEL"}))
...@@ -2899,7 +3012,15 @@ void PDBFileParser::ParseRemark200() ...@@ -2899,7 +3012,15 @@ void PDBFileParser::ParseRemark200()
if (inRM200({"HIGHEST RESOLUTION SHELL, RANGE HIGH (A)"})) // that one field is mandatory... if (inRM200({"HIGHEST RESOLUTION SHELL, RANGE HIGH (A)"})) // that one field is mandatory...
{ {
getCategory("reflns_shell")->emplace({{"d_res_high", mRemark200["HIGHEST RESOLUTION SHELL, RANGE HIGH (A)"]}, {"d_res_low", mRemark200["HIGHEST RESOLUTION SHELL, RANGE LOW (A)"]}, {"percent_possible_all", mRemark200["COMPLETENESS FOR SHELL (%)"]}, {"Rmerge_I_obs", mRemark200["R MERGE FOR SHELL (I)"]}, {"pdbx_Rsym_value", mRemark200["R SYM FOR SHELL (I)"]}, {"meanI_over_sigI_obs", mRemark200["<I/SIGMA(I)> FOR SHELL"]}, {"pdbx_redundancy", mRemark200["DATA REDUNDANCY IN SHELL"]}, {"pdbx_ordinal", 1}, {"pdbx_diffrn_id", 1}}); getCategory("reflns_shell")->emplace({{"d_res_high", mRemark200["HIGHEST RESOLUTION SHELL, RANGE HIGH (A)"]},
{"d_res_low", mRemark200["HIGHEST RESOLUTION SHELL, RANGE LOW (A)"]},
{"percent_possible_all", mRemark200["COMPLETENESS FOR SHELL (%)"]},
{"Rmerge_I_obs", mRemark200["R MERGE FOR SHELL (I)"]},
{"pdbx_Rsym_value", mRemark200["R SYM FOR SHELL (I)"]},
{"meanI_over_sigI_obs", mRemark200["<I/SIGMA(I)> FOR SHELL"]},
{"pdbx_redundancy", mRemark200["DATA REDUNDANCY IN SHELL"]},
{"pdbx_ordinal", 1},
{"pdbx_diffrn_id", 1}});
} }
else if (inRM200({"HIGHEST RESOLUTION SHELL, RANGE LOW (A)", "COMPLETENESS FOR SHELL (%)", else if (inRM200({"HIGHEST RESOLUTION SHELL, RANGE LOW (A)", "COMPLETENESS FOR SHELL (%)",
"R MERGE FOR SHELL (I)", "R SYM FOR SHELL (I)", "<I/SIGMA(I)> FOR SHELL", "DATA REDUNDANCY IN SHELL"})) "R MERGE FOR SHELL (I)", "R SYM FOR SHELL (I)", "<I/SIGMA(I)> FOR SHELL", "DATA REDUNDANCY IN SHELL"}))
...@@ -3091,7 +3212,11 @@ void PDBFileParser::ParseRemark350() ...@@ -3091,7 +3212,11 @@ void PDBFileParser::ParseRemark350()
else else
details = "author_and_software_defined_assembly"; details = "author_and_software_defined_assembly";
getCategory("pdbx_struct_assembly")->emplace({{"id", biomolecule}, {"details", details}, {"method_details", values["SOFTWARE USED"]}, {"oligomeric_details", oligomer}, {"oligomeric_count", count > 0 ? std::to_string(count) : ""}}); getCategory("pdbx_struct_assembly")->emplace({{"id", biomolecule},
{"details", details},
{"method_details", values["SOFTWARE USED"]},
{"oligomeric_details", oligomer},
{"oligomeric_count", count > 0 ? std::to_string(count) : ""}});
auto cat = getCategory("pdbx_struct_assembly_prop"); auto cat = getCategory("pdbx_struct_assembly_prop");
...@@ -3115,7 +3240,9 @@ void PDBFileParser::ParseRemark350() ...@@ -3115,7 +3240,9 @@ void PDBFileParser::ParseRemark350()
boost::format fmt("%12.10f"); boost::format fmt("%12.10f");
getCategory("pdbx_struct_oper_list")->emplace({{"id", operID}, {"type", mat == std::vector<double>{1, 0, 0, 0, 1, 0, 0, 0, 1} and vec == std::vector<double>{0, 0, 0} ? "identity operation" : "crystal symmetry operation"}, getCategory("pdbx_struct_oper_list")->emplace({
{"id", operID},
{"type", mat == std::vector<double>{1, 0, 0, 0, 1, 0, 0, 0, 1} and vec == std::vector<double>{0, 0, 0} ? "identity operation" : "crystal symmetry operation"},
// { "name", "" }, // { "name", "" },
// { "symmetryOperation", "" }, // { "symmetryOperation", "" },
{"matrix[1][1]", (fmt % mat[0]).str()}, {"matrix[1][1]", (fmt % mat[0]).str()},
...@@ -3140,7 +3267,9 @@ void PDBFileParser::ParseRemark350() ...@@ -3140,7 +3267,9 @@ void PDBFileParser::ParseRemark350()
if (not(vec.empty() and mat.empty())) if (not(vec.empty() and mat.empty()))
throw std::runtime_error("Invalid REMARK 350"); throw std::runtime_error("Invalid REMARK 350");
getCategory("pdbx_struct_assembly_gen")->emplace({{"assembly_id", biomolecule}, {"oper_expression", ba::join(operExpression, ",")}, {"asym_id_list", ba::join(asymIdList, ",")}}); getCategory("pdbx_struct_assembly_gen")->emplace({{"assembly_id", biomolecule},
{"oper_expression", ba::join(operExpression, ",")},
{"asym_id_list", ba::join(asymIdList, ",")}});
biomolecule = stoi(m[1].str()); biomolecule = stoi(m[1].str());
asymIdList.clear(); asymIdList.clear();
...@@ -3154,7 +3283,9 @@ void PDBFileParser::ParseRemark350() ...@@ -3154,7 +3283,9 @@ void PDBFileParser::ParseRemark350()
if (not operExpression.empty()) if (not operExpression.empty())
{ {
getCategory("pdbx_struct_assembly_gen")->emplace({{"assembly_id", biomolecule}, {"oper_expression", ba::join(operExpression, ",")}, {"asym_id_list", ba::join(asymIdList, ",")}}); getCategory("pdbx_struct_assembly_gen")->emplace({{"assembly_id", biomolecule},
{"oper_expression", ba::join(operExpression, ",")},
{"asym_id_list", ba::join(asymIdList, ",")}});
} }
mRec = saved; mRec = saved;
...@@ -3641,7 +3772,8 @@ void PDBFileParser::ConstructEntities() ...@@ -3641,7 +3772,8 @@ void PDBFileParser::ConstructEntities()
mAsymID2EntityID[asymID] = entityID; mAsymID2EntityID[asymID] = entityID;
getCategory("struct_asym")->emplace({ getCategory("struct_asym")->emplace({
{"id", asymID}, {"pdbx_blank_PDB_chainid_flag", chain.mDbref.chainID == ' ' ? "Y" : "N"}, {"id", asymID},
{"pdbx_blank_PDB_chainid_flag", chain.mDbref.chainID == ' ' ? "Y" : "N"},
// pdbx_modified // pdbx_modified
{"entity_id", entityID}, {"entity_id", entityID},
// details // details
...@@ -3708,7 +3840,32 @@ void PDBFileParser::ConstructEntities() ...@@ -3708,7 +3840,32 @@ void PDBFileParser::ConstructEntities()
{ {
srcMethod = "man"; srcMethod = "man";
getCategory("entity_src_gen")->emplace({{"entity_id", mMolID2EntityID[cmp.mMolID]}, {"pdbx_src_id", structRefID}, {"gene_src_common_name", cmp.mSource["ORGANISM_COMMON"]}, {"pdbx_gene_src_gene", cmp.mSource["GENE"]}, {"gene_src_strain", cmp.mSource["STRAIN"]}, {"gene_src_tissue", cmp.mSource["TISSUE"]}, {"gene_src_tissue_fraction", cmp.mSource["TISSUE_FRACTION"]}, {"pdbx_gene_src_cell_line", cmp.mSource["CELL_LINE"]}, {"pdbx_gene_src_organelle", cmp.mSource["ORGANELLE"]}, {"pdbx_gene_src_cell", cmp.mSource["CELL"]}, {"pdbx_gene_src_cellular_location", cmp.mSource["CELLULAR_LOCATION"]}, {"host_org_common_name", cmp.mSource["EXPRESSION_SYSTEM_COMMON"]}, {"pdbx_gene_src_scientific_name", cmp.mSource["ORGANISM_SCIENTIFIC"]}, {"pdbx_gene_src_ncbi_taxonomy_id", cmp.mSource["ORGANISM_TAXID"]}, {"pdbx_host_org_scientific_name", cmp.mSource["EXPRESSION_SYSTEM"]}, {"pdbx_host_org_ncbi_taxonomy_id", cmp.mSource["EXPRESSION_SYSTEM_TAXID"]}, {"pdbx_host_org_strain", cmp.mSource["EXPRESSION_SYSTEM_STRAIN"]}, {"pdbx_host_org_variant", cmp.mSource["EXPRESSION_SYSTEM_VARIANT"]}, {"pdbx_host_org_cell_line", cmp.mSource["EXPRESSION_SYSTEM_CELL_LINE"]}, {"pdbx_host_org_cellular_location", cmp.mSource["EXPRESSION_SYSTEM_CELLULAR_LOCATION"]}, {"pdbx_host_org_vector_type", cmp.mSource["EXPRESSION_SYSTEM_VECTOR_TYPE"]}, {"pdbx_host_org_vector", cmp.mSource["EXPRESSION_SYSTEM_VECTOR"]}, {"pdbx_host_org_gene", cmp.mSource["EXPRESSION_SYSTEM_GENE"]}, {"plasmid_name", cmp.mSource["EXPRESSION_SYSTEM_PLASMID"]}, {"pdbx_description", cmp.mSource["OTHER_DETAILS"]}}); getCategory("entity_src_gen")->emplace({
{"entity_id", mMolID2EntityID[cmp.mMolID]},
{"pdbx_src_id", structRefID},
{"gene_src_common_name", cmp.mSource["ORGANISM_COMMON"]},
{"pdbx_gene_src_gene", cmp.mSource["GENE"]},
{"gene_src_strain", cmp.mSource["STRAIN"]},
{"gene_src_tissue", cmp.mSource["TISSUE"]},
{"gene_src_tissue_fraction", cmp.mSource["TISSUE_FRACTION"]},
{"pdbx_gene_src_cell_line", cmp.mSource["CELL_LINE"]},
{"pdbx_gene_src_organelle", cmp.mSource["ORGANELLE"]},
{"pdbx_gene_src_cell", cmp.mSource["CELL"]},
{"pdbx_gene_src_cellular_location", cmp.mSource["CELLULAR_LOCATION"]},
{"host_org_common_name", cmp.mSource["EXPRESSION_SYSTEM_COMMON"]},
{"pdbx_gene_src_scientific_name", cmp.mSource["ORGANISM_SCIENTIFIC"]},
{"pdbx_gene_src_ncbi_taxonomy_id", cmp.mSource["ORGANISM_TAXID"]},
{"pdbx_host_org_scientific_name", cmp.mSource["EXPRESSION_SYSTEM"]},
{"pdbx_host_org_ncbi_taxonomy_id", cmp.mSource["EXPRESSION_SYSTEM_TAXID"]},
{"pdbx_host_org_strain", cmp.mSource["EXPRESSION_SYSTEM_STRAIN"]},
{"pdbx_host_org_variant", cmp.mSource["EXPRESSION_SYSTEM_VARIANT"]},
{"pdbx_host_org_cell_line", cmp.mSource["EXPRESSION_SYSTEM_CELL_LINE"]},
{"pdbx_host_org_cellular_location", cmp.mSource["EXPRESSION_SYSTEM_CELLULAR_LOCATION"]},
{"pdbx_host_org_vector_type", cmp.mSource["EXPRESSION_SYSTEM_VECTOR_TYPE"]},
{"pdbx_host_org_vector", cmp.mSource["EXPRESSION_SYSTEM_VECTOR"]},
{"pdbx_host_org_gene", cmp.mSource["EXPRESSION_SYSTEM_GENE"]},
{"plasmid_name", cmp.mSource["EXPRESSION_SYSTEM_PLASMID"]},
{"pdbx_description", cmp.mSource["OTHER_DETAILS"]}});
} }
else if (not cmp.mSource["ORGANISM_SCIENTIFIC"].empty()) else if (not cmp.mSource["ORGANISM_SCIENTIFIC"].empty())
{ {
...@@ -3741,7 +3898,10 @@ void PDBFileParser::ConstructEntities() ...@@ -3741,7 +3898,10 @@ void PDBFileParser::ConstructEntities()
if (not cmp.mInfo["SYNONYM"].empty()) if (not cmp.mInfo["SYNONYM"].empty())
{ {
getCategory("entity_name_com")->emplace({{"entity_id", mMolID2EntityID[cmp.mMolID]}, {"name", cmp.mInfo["SYNONYM"]}}); getCategory("entity_name_com")->emplace({
{"entity_id", mMolID2EntityID[cmp.mMolID]},
{"name", cmp.mInfo["SYNONYM"]}
});
} }
std::string desc = cmp.mInfo["MOLECULE"]; std::string desc = cmp.mInfo["MOLECULE"];
...@@ -3761,7 +3921,11 @@ void PDBFileParser::ConstructEntities() ...@@ -3761,7 +3921,11 @@ void PDBFileParser::ConstructEntities()
if (ci != mChains.end() and not ci->mDbref.dbIdCode.empty()) if (ci != mChains.end() and not ci->mDbref.dbIdCode.empty())
{ {
getCategory("struct_ref")->emplace({ getCategory("struct_ref")->emplace({
{"id", structRefID}, {"entity_id", mMolID2EntityID[cmp.mMolID]}, {"db_name", ci->mDbref.database}, {"db_code", ci->mDbref.dbIdCode}, {"pdbx_db_accession", ci->mDbref.dbAccession}, {"id", structRefID},
{"entity_id", mMolID2EntityID[cmp.mMolID]},
{"db_name", ci->mDbref.database},
{"db_code", ci->mDbref.dbIdCode},
{"pdbx_db_accession", ci->mDbref.dbAccession},
// { "pdbx_align_begin", ci->mDbref.dbSeqBegin } // { "pdbx_align_begin", ci->mDbref.dbSeqBegin }
}); });
} }
...@@ -3810,7 +3974,23 @@ void PDBFileParser::ConstructEntities() ...@@ -3810,7 +3974,23 @@ void PDBFileParser::ConstructEntities()
{ {
} }
getCategory("struct_ref_seq")->emplace({{"align_id", structRefSeqAlignID}, {"ref_id", structRefID}, {"pdbx_PDB_id_code", dbref.PDBIDCode}, {"pdbx_strand_id", std::string{chain.mDbref.chainID}}, {"seq_align_beg", seqAlignBeg}, {"pdbx_seq_align_beg_ins_code", insToStr(dbref.insertBegin)}, {"seq_align_end", seqAlignEnd}, {"pdbx_seq_align_end_ins_code", insToStr(dbref.insertEnd)}, {"pdbx_db_accession", dbref.dbAccession}, {"db_align_beg", dbref.dbSeqBegin}, {"pdbx_db_align_beg_ins_code", insToStr(dbref.dbinsBeg)}, {"db_align_end", dbref.dbSeqEnd}, {"pdbx_db_align_end_ins_code", insToStr(dbref.dbinsEnd)}, {"pdbx_auth_seq_align_beg", dbref.seqBegin}, {"pdbx_auth_seq_align_end", dbref.seqEnd}}); getCategory("struct_ref_seq")->emplace({
{"align_id", structRefSeqAlignID},
{"ref_id", structRefID},
{"pdbx_PDB_id_code", dbref.PDBIDCode},
{"pdbx_strand_id", std::string{chain.mDbref.chainID}},
{"seq_align_beg", seqAlignBeg},
{"pdbx_seq_align_beg_ins_code", insToStr(dbref.insertBegin)},
{"seq_align_end", seqAlignEnd},
{"pdbx_seq_align_end_ins_code", insToStr(dbref.insertEnd)},
{"pdbx_db_accession", dbref.dbAccession},
{"db_align_beg", dbref.dbSeqBegin},
{"pdbx_db_align_beg_ins_code", insToStr(dbref.dbinsBeg)},
{"db_align_end", dbref.dbSeqEnd},
{"pdbx_db_align_end_ins_code", insToStr(dbref.dbinsEnd)},
{"pdbx_auth_seq_align_beg", dbref.seqBegin},
{"pdbx_auth_seq_align_end", dbref.seqEnd}
});
// write the struct_ref_seq_dif // write the struct_ref_seq_dif
for (auto &seqadv : mSeqadvs) for (auto &seqadv : mSeqadvs)
...@@ -3832,7 +4012,21 @@ void PDBFileParser::ConstructEntities() ...@@ -3832,7 +4012,21 @@ void PDBFileParser::ConstructEntities()
seqNum = std::to_string(labelSeq); seqNum = std::to_string(labelSeq);
getCategory("struct_ref_seq_dif")->emplace({{"align_id", structRefSeqAlignID}, {"pdbx_PDB_id_code", dbref.PDBIDCode}, {"mon_id", seqadv.resName}, {"pdbx_pdb_strand_id", seqadv.chainID}, {"seq_num", seqNum}, {"pdbx_pdb_ins_code", seqadv.iCode == ' ' ? std::string{} : std::string{seqadv.iCode}}, {"pdbx_seq_db_name", seqadv.database}, {"pdbx_seq_db_accession_code", seqadv.dbAccession}, {"db_mon_id", seqadv.dbRes}, {"pdbx_seq_db_seq_num", seqadv.dbSeq}, {"details", seqadv.conflict}, {"pdbx_auth_seq_num", seqadv.seqNum}, {"pdbx_ordinal", ++mPdbxDifOrdinal}}); getCategory("struct_ref_seq_dif")->emplace({
{"align_id", structRefSeqAlignID},
{"pdbx_PDB_id_code", dbref.PDBIDCode},
{"mon_id", seqadv.resName},
{"pdbx_pdb_strand_id", seqadv.chainID},
{"seq_num", seqNum},
{"pdbx_pdb_ins_code", seqadv.iCode == ' ' ? std::string{} : std::string{seqadv.iCode}},
{"pdbx_seq_db_name", seqadv.database},
{"pdbx_seq_db_accession_code", seqadv.dbAccession},
{"db_mon_id", seqadv.dbRes},
{"pdbx_seq_db_seq_num", seqadv.dbSeq},
{"details", seqadv.conflict},
{"pdbx_auth_seq_num", seqadv.seqNum},
{"pdbx_ordinal", ++mPdbxDifOrdinal}
});
} }
} }
...@@ -3932,15 +4126,23 @@ void PDBFileParser::ConstructEntities() ...@@ -3932,15 +4126,23 @@ void PDBFileParser::ConstructEntities()
else if (mightBeDNA and not mightBePolyPeptide) else if (mightBeDNA and not mightBePolyPeptide)
type = "polyribonucleotide"; type = "polyribonucleotide";
getCategory("entity_poly")->emplace({{"entity_id", mMolID2EntityID[cmp.mMolID]}, {"pdbx_seq_one_letter_code", seq}, {"pdbx_seq_one_letter_code_can", seqCan}, {"nstd_monomer", (nstdMonomer ? "yes" : "no")}, {"pdbx_strand_id", ba::join(chains, ",")}, {"nstd_linkage", nonstandardLinkage ? "yes" : "no"}, {"type", type}}); getCategory("entity_poly")->emplace({{"entity_id", mMolID2EntityID[cmp.mMolID]},
{"pdbx_seq_one_letter_code", seq},
{"pdbx_seq_one_letter_code_can", seqCan},
{"nstd_monomer", (nstdMonomer ? "yes" : "no")},
{"pdbx_strand_id", ba::join(chains, ",")},
{"nstd_linkage", nonstandardLinkage ? "yes" : "no"},
{"type", type}});
} }
if (not(structTitle.empty() and structDescription.empty())) if (not(structTitle.empty() and structDescription.empty()))
{ {
getCategory("struct")->emplace({{"entry_id", mStructureID}, getCategory("struct")->emplace({
{"entry_id", mStructureID},
{"title", ba::join(structTitle, ", ")}, {"title", ba::join(structTitle, ", ")},
{"pdbx_descriptor", ba::join(structDescription, ", ")}, {"pdbx_descriptor", ba::join(structDescription, ", ")},
{"pdbx_model_type_details", mModelTypeDetails}}); {"pdbx_model_type_details", mModelTypeDetails}
});
} }
// build sugar trees first // build sugar trees first
...@@ -4026,7 +4228,9 @@ void PDBFileParser::ConstructEntities() ...@@ -4026,7 +4228,9 @@ void PDBFileParser::ConstructEntities()
std::string name = mHetnams[hetID]; std::string name = mHetnams[hetID];
if (name.empty() and hetID == mWaterHetID) if (name.empty() and hetID == mWaterHetID)
name = "water"; name = "water";
getCategory("pdbx_entity_nonpoly")->emplace({{"entity_id", entityID}, {"name", name}, {"comp_id", hetID}}); getCategory("pdbx_entity_nonpoly")->emplace({{"entity_id", entityID},
{"name", name},
{"comp_id", hetID}});
} }
// create an asym for this het/chain combo, if needed // create an asym for this het/chain combo, if needed
...@@ -4063,7 +4267,8 @@ void PDBFileParser::ConstructEntities() ...@@ -4063,7 +4267,8 @@ void PDBFileParser::ConstructEntities()
{ {
writtenAsyms.insert(asymID); writtenAsyms.insert(asymID);
getCategory("struct_asym")->emplace({ getCategory("struct_asym")->emplace({
{"id", asymID}, {"pdbx_blank_PDB_chainid_flag", het.chainID == ' ' ? "Y" : "N"}, {"id", asymID},
{"pdbx_blank_PDB_chainid_flag", het.chainID == ' ' ? "Y" : "N"},
// pdbx_modified // pdbx_modified
{"entity_id", mHet2EntityID[hetID]}, {"entity_id", mHet2EntityID[hetID]},
// details // details
...@@ -4078,12 +4283,18 @@ void PDBFileParser::ConstructEntities() ...@@ -4078,12 +4283,18 @@ void PDBFileParser::ConstructEntities()
if (iCode.empty()) if (iCode.empty())
iCode = {'.'}; iCode = {'.'};
getCategory("pdbx_nonpoly_scheme")->emplace({{"asym_id", asymID}, {"entity_id", mHet2EntityID[hetID]}, {"mon_id", hetID}, {"ndb_seq_num", seqNr}, {"pdb_seq_num", het.seqNum}, getCategory("pdbx_nonpoly_scheme")->emplace({
{"asym_id", asymID},
{"entity_id", mHet2EntityID[hetID]},
{"mon_id", hetID},
{"ndb_seq_num", seqNr},
{"pdb_seq_num", het.seqNum},
// { "auth_seq_num", het.seqNum }, // ???? // { "auth_seq_num", het.seqNum }, // ????
{"pdb_mon_id", hetID}, {"pdb_mon_id", hetID},
// { "auth_mon_id", hetID }, // { "auth_mon_id", hetID },
{"pdb_strand_id", std::string{het.chainID}}, {"pdb_strand_id", std::string{het.chainID}},
{"pdb_ins_code", iCode}}); {"pdb_ins_code", iCode}
});
// mapping needed? // mapping needed?
mChainSeq2AsymSeq[std::make_tuple(het.chainID, het.seqNum, het.iCode)] = std::make_tuple(asymID, seqNr, false); mChainSeq2AsymSeq[std::make_tuple(het.chainID, het.seqNum, het.iCode)] = std::make_tuple(asymID, seqNr, false);
...@@ -4113,7 +4324,18 @@ void PDBFileParser::ConstructEntities() ...@@ -4113,7 +4324,18 @@ void PDBFileParser::ConstructEntities()
continue; continue;
} }
getCategory("pdbx_struct_mod_residue")->emplace({{"id", modResID++}, {"label_asym_id", asymID}, {"label_seq_id", seq}, {"label_comp_id", resName}, {"auth_asym_id", std::string(1, chainID)}, {"auth_seq_id", seqNum}, {"auth_comp_id", resName}, {"PDB_ins_code", iCode == ' ' ? "" : std::string{iCode}}, {"parent_comp_id", stdRes}, {"details", comment}}); getCategory("pdbx_struct_mod_residue")->emplace({
{"id", modResID++},
{"label_asym_id", asymID},
{"label_seq_id", seq},
{"label_comp_id", resName},
{"auth_asym_id", std::string(1, chainID)},
{"auth_seq_id", seqNum},
{"auth_comp_id", resName},
{"PDB_ins_code", iCode == ' ' ? "" : std::string{iCode}},
{"parent_comp_id", stdRes},
{"details", comment}
});
modResSet.insert(resName); modResSet.insert(resName);
} }
...@@ -4162,7 +4384,12 @@ void PDBFileParser::ConstructEntities() ...@@ -4162,7 +4384,12 @@ void PDBFileParser::ConstructEntities()
if (modResSet.count(cc)) if (modResSet.count(cc))
nstd = "n"; nstd = "n";
getCategory("chem_comp")->emplace({{"id", cc}, {"name", name}, {"formula", formula}, {"formula_weight", formulaWeight}, {"mon_nstd_flag", nstd}, {"type", type}}); getCategory("chem_comp")->emplace({{"id", cc},
{"name", name},
{"formula", formula},
{"formula_weight", formulaWeight},
{"mon_nstd_flag", nstd},
{"type", type}});
} }
getCategory("chem_comp")->reorderByIndex(); getCategory("chem_comp")->reorderByIndex();
...@@ -4195,16 +4422,39 @@ void PDBFileParser::ConstructEntities() ...@@ -4195,16 +4422,39 @@ void PDBFileParser::ConstructEntities()
if (unobs.atoms.empty()) if (unobs.atoms.empty())
{ {
getCategory("pdbx_unobs_or_zero_occ_residues")->emplace({{"id", std::to_string(++idRes)}, {"polymer_flag", isPolymer ? "Y" : "N"}, {"occupancy_flag", 1}, {"PDB_model_num", unobs.modelNr ? unobs.modelNr : 1}, {"auth_asym_id", std::string{unobs.chain}}, {"auth_comp_id", unobs.res}, {"auth_seq_id", unobs.seq}, {"PDB_ins_code", unobs.iCode == ' ' ? "" : std::string{unobs.iCode}}, {"label_asym_id", asymID}, {"label_comp_id", compID}, // TODO: change to correct comp_id getCategory("pdbx_unobs_or_zero_occ_residues")->emplace({
{"label_seq_id", seqNr > 0 ? std::to_string(seqNr) : ""}}); {"id", std::to_string(++idRes)},
{"polymer_flag", isPolymer ? "Y" : "N"},
{"occupancy_flag", 1},
{"PDB_model_num", unobs.modelNr ? unobs.modelNr : 1},
{"auth_asym_id", std::string{unobs.chain}},
{"auth_comp_id", unobs.res},
{"auth_seq_id", unobs.seq},
{"PDB_ins_code", unobs.iCode == ' ' ? "" : std::string{unobs.iCode}},
{"label_asym_id", asymID},
{"label_comp_id", compID}, // TODO: change to correct comp_id
{"label_seq_id", seqNr > 0 ? std::to_string(seqNr) : ""}
});
} }
else else
{ {
for (auto &atom : unobs.atoms) for (auto &atom : unobs.atoms)
{ {
getCategory("pdbx_unobs_or_zero_occ_atoms")->emplace({{"id", std::to_string(++idAtom)}, {"polymer_flag", isPolymer ? "Y" : "N"}, {"occupancy_flag", 1}, {"PDB_model_num", unobs.modelNr ? unobs.modelNr : 1}, {"auth_asym_id", std::string{unobs.chain}}, {"auth_comp_id", unobs.res}, {"auth_seq_id", unobs.seq}, {"PDB_ins_code", unobs.iCode == ' ' ? "" : std::string{unobs.iCode}}, {"auth_atom_id", atom}, {"label_asym_id", asymID}, {"label_comp_id", compID}, // TODO: change to correct comp_id getCategory("pdbx_unobs_or_zero_occ_atoms")->emplace({
{"id", std::to_string(++idAtom)},
{"polymer_flag", isPolymer ? "Y" : "N"},
{"occupancy_flag", 1},
{"PDB_model_num", unobs.modelNr ? unobs.modelNr : 1},
{"auth_asym_id", std::string{unobs.chain}},
{"auth_comp_id", unobs.res},
{"auth_seq_id", unobs.seq},
{"PDB_ins_code", unobs.iCode == ' ' ? "" : std::string{unobs.iCode}},
{"auth_atom_id", atom},
{"label_asym_id", asymID},
{"label_comp_id", compID}, // TODO: change to correct comp_id
{"label_seq_id", seqNr > 0 ? std::to_string(seqNr) : ""}, {"label_seq_id", seqNr > 0 ? std::to_string(seqNr) : ""},
{"label_atom_id", atom}}); {"label_atom_id", atom}
});
} }
} }
} }
...@@ -4288,14 +4538,18 @@ void PDBFileParser::ConstructSugarTrees(int &asymNr) ...@@ -4288,14 +4538,18 @@ void PDBFileParser::ConstructSugarTrees(int &asymNr)
{"src_method", "man"}, {"src_method", "man"},
{"pdbx_description", branchName}}); {"pdbx_description", branchName}});
getCategory("pdbx_entity_branch")->emplace({{"entity_id", entityID}, {"type", "oligosaccharide"}}); getCategory("pdbx_entity_branch")->emplace({{"entity_id", entityID},
{"type", "oligosaccharide"}});
int num = 0; int num = 0;
std::map<ATOM_REF, int> branch_list; std::map<ATOM_REF, int> branch_list;
for (auto &s : sugarTree) for (auto &s : sugarTree)
{ {
getCategory("pdbx_entity_branch_list")->emplace({{"entity_id", entityID}, {"comp_id", s.c1.resName}, {"num", ++num}, {"hetero", ci.size() == 1 ? "n" : "y"}}); getCategory("pdbx_entity_branch_list")->emplace({{"entity_id", entityID},
{"comp_id", s.c1.resName},
{"num", ++num},
{"hetero", ci.size() == 1 ? "n" : "y"}});
branch_list[s.c1] = num; branch_list[s.c1] = num;
} }
...@@ -4327,7 +4581,10 @@ void PDBFileParser::ConstructSugarTrees(int &asymNr) ...@@ -4327,7 +4581,10 @@ void PDBFileParser::ConstructSugarTrees(int &asymNr)
std::string asymID = cif::cifIdForNumber(asymNr++); std::string asymID = cif::cifIdForNumber(asymNr++);
getCategory("struct_asym")->emplace({{"id", asymID}, {"pdbx_blank_PDB_chainid_flag", si->chainID == ' ' ? "Y" : "N"}, {"pdbx_modified", "N"}, {"entity_id", entityID}}); getCategory("struct_asym")->emplace({{"id", asymID},
{"pdbx_blank_PDB_chainid_flag", si->chainID == ' ' ? "Y" : "N"},
{"pdbx_modified", "N"},
{"entity_id", entityID}});
std::string iCode{si->iCode}; std::string iCode{si->iCode};
ba::trim(iCode); ba::trim(iCode);
...@@ -4337,7 +4594,19 @@ void PDBFileParser::ConstructSugarTrees(int &asymNr) ...@@ -4337,7 +4594,19 @@ void PDBFileParser::ConstructSugarTrees(int &asymNr)
int num = 0; int num = 0;
for (auto s : sugarTree) for (auto s : sugarTree)
{ {
getCategory("pdbx_branch_scheme")->emplace({{"asym_id", asymID}, {"entity_id", entityID}, {"mon_id", s.c1.resName}, {"num", ++num}, {"pdb_asym_id", asymID}, {"pdb_mon_id", s.c1.resName}, {"pdb_seq_num", num}, {"auth_asym_id", std::string{s.c1.chainID}}, {"auth_mon_id", s.next.resName}, {"auth_seq_num", s.c1.resSeq}, {"hetero", ci.size() == 1 ? "n" : "y"}}); getCategory("pdbx_branch_scheme")->emplace({
{"asym_id", asymID},
{"entity_id", entityID},
{"mon_id", s.c1.resName},
{"num", ++num},
{"pdb_asym_id", asymID},
{"pdb_mon_id", s.c1.resName},
{"pdb_seq_num", num},
{"auth_asym_id", std::string{s.c1.chainID}},
{"auth_mon_id", s.next.resName},
{"auth_seq_num", s.c1.resSeq},
{"hetero", ci.size() == 1 ? "n" : "y"}
});
auto k = std::make_tuple(s.c1.chainID, s.c1.resSeq, s.c1.iCode); auto k = std::make_tuple(s.c1.chainID, s.c1.resSeq, s.c1.iCode);
assert(mChainSeq2AsymSeq.count(k) == 0); assert(mChainSeq2AsymSeq.count(k) == 0);
...@@ -4506,7 +4775,10 @@ void PDBFileParser::ParseSecondaryStructure() ...@@ -4506,7 +4775,10 @@ void PDBFileParser::ParseSecondaryStructure()
if (sense != 0) if (sense != 0)
{ {
getCategory("struct_sheet_order")->emplace({{"sheet_id", sheetID}, {"range_id_1", rangeID}, {"range_id_2", rangeID + 1}, {"sense", sense == -1 ? "anti-parallel" : "parallel"}}); getCategory("struct_sheet_order")->emplace({{"sheet_id", sheetID},
{"range_id_1", rangeID},
{"range_id_2", rangeID + 1},
{"sense", sense == -1 ? "anti-parallel" : "parallel"}});
} }
std::string begAsymID, endAsymID; std::string begAsymID, endAsymID;
...@@ -4559,7 +4831,19 @@ void PDBFileParser::ParseSecondaryStructure() ...@@ -4559,7 +4831,19 @@ void PDBFileParser::ParseSecondaryStructure()
std::cerr << "skipping unmatched pdbx_struct_sheet_hbond record" << std::endl; std::cerr << "skipping unmatched pdbx_struct_sheet_hbond record" << std::endl;
} }
else else
getCategory("pdbx_struct_sheet_hbond")->emplace({{"sheet_id", sheetID}, {"range_id_1", rangeID}, {"range_id_2", rangeID + 1}, {"range_1_label_atom_id", vS(57, 60)}, {"range_1_label_comp_id", vS(61, 63)}, {"range_1_label_asym_id", r1AsymID}, {"range_1_label_seq_id", r1Seq}, {"range_1_PDB_ins_code", vS(70, 70)}, {"range_1_auth_atom_id", vS(57, 60)}, {"range_1_auth_comp_id", vS(61, 63)}, {"range_1_auth_asym_id", vS(65, 65)}, {"range_1_auth_seq_id", vI(66, 69)}, getCategory("pdbx_struct_sheet_hbond")->emplace({
{"sheet_id", sheetID},
{"range_id_1", rangeID},
{"range_id_2", rangeID + 1},
{"range_1_label_atom_id", vS(57, 60)},
{"range_1_label_comp_id", vS(61, 63)},
{"range_1_label_asym_id", r1AsymID},
{"range_1_label_seq_id", r1Seq},
{"range_1_PDB_ins_code", vS(70, 70)},
{"range_1_auth_atom_id", vS(57, 60)},
{"range_1_auth_comp_id", vS(61, 63)},
{"range_1_auth_asym_id", vS(65, 65)},
{"range_1_auth_seq_id", vI(66, 69)},
{"range_2_label_atom_id", vS(42, 45)}, {"range_2_label_atom_id", vS(42, 45)},
{"range_2_label_comp_id", vS(46, 48)}, {"range_2_label_comp_id", vS(46, 48)},
...@@ -4569,7 +4853,8 @@ void PDBFileParser::ParseSecondaryStructure() ...@@ -4569,7 +4853,8 @@ void PDBFileParser::ParseSecondaryStructure()
{"range_2_auth_atom_id", vS(42, 45)}, {"range_2_auth_atom_id", vS(42, 45)},
{"range_2_auth_comp_id", vS(46, 48)}, {"range_2_auth_comp_id", vS(46, 48)},
{"range_2_auth_asym_id", vS(50, 50)}, {"range_2_auth_asym_id", vS(50, 50)},
{"range_2_auth_seq_id", vI(51, 54)}}); {"range_2_auth_seq_id", vI(51, 54)}
});
} }
if (sense != 0) if (sense != 0)
...@@ -4798,7 +5083,8 @@ void PDBFileParser::ParseConnectivtyAnnotation() ...@@ -4798,7 +5083,8 @@ void PDBFileParser::ParseConnectivtyAnnotation()
continue; continue;
} }
getCategory("struct_conn")->emplace({{"id", type + std::to_string(linkNr)}, {"conn_type_id", type}, getCategory("struct_conn")->emplace({{"id", type + std::to_string(linkNr)},
{"conn_type_id", type},
// { "ccp4_link_id", ccp4LinkID }, // { "ccp4_link_id", ccp4LinkID },
...@@ -4871,7 +5157,24 @@ void PDBFileParser::ParseConnectivtyAnnotation() ...@@ -4871,7 +5157,24 @@ void PDBFileParser::ParseConnectivtyAnnotation()
std::string iCode1str = iCode1 == ' ' ? std::string() : std::string{iCode1}; std::string iCode1str = iCode1 == ' ' ? std::string() : std::string{iCode1};
std::string iCode2str = iCode2 == ' ' ? std::string() : std::string{iCode2}; std::string iCode2str = iCode2 == ' ' ? std::string() : std::string{iCode2};
getCategory("struct_mon_prot_cis")->emplace({{"pdbx_id", serNum}, {"label_comp_id", pep1}, {"label_seq_id", lResSeq1}, {"label_asym_id", lAsym1}, {"label_alt_id", "."}, {"pdbx_PDB_ins_code", iCode1str}, {"auth_comp_id", pep1}, {"auth_seq_id", seqNum1}, {"auth_asym_id", std::string{chainID1}}, {"pdbx_label_comp_id_2", pep2}, {"pdbx_label_seq_id_2", lResSeq2}, {"pdbx_label_asym_id_2", lAsym2}, {"pdbx_PDB_ins_code_2", iCode2str}, {"pdbx_auth_comp_id_2", pep2}, {"pdbx_auth_seq_id_2", seqNum2}, {"pdbx_auth_asym_id_2", std::string{chainID2}}, {"pdbx_PDB_model_num", modNum}, {"pdbx_omega_angle", measure}}); getCategory("struct_mon_prot_cis")->emplace({{"pdbx_id", serNum},
{"label_comp_id", pep1},
{"label_seq_id", lResSeq1},
{"label_asym_id", lAsym1},
{"label_alt_id", "."},
{"pdbx_PDB_ins_code", iCode1str},
{"auth_comp_id", pep1},
{"auth_seq_id", seqNum1},
{"auth_asym_id", std::string{chainID1}},
{"pdbx_label_comp_id_2", pep2},
{"pdbx_label_seq_id_2", lResSeq2},
{"pdbx_label_asym_id_2", lAsym2},
{"pdbx_PDB_ins_code_2", iCode2str},
{"pdbx_auth_comp_id_2", pep2},
{"pdbx_auth_seq_id_2", seqNum2},
{"pdbx_auth_asym_id_2", std::string{chainID2}},
{"pdbx_PDB_model_num", modNum},
{"pdbx_omega_angle", measure}});
continue; continue;
} }
...@@ -4964,7 +5267,9 @@ void PDBFileParser::ParseCrystallographic() ...@@ -4964,7 +5267,9 @@ void PDBFileParser::ParseCrystallographic()
{ {
} }
getCategory("symmetry")->emplace({{"entry_id", mStructureID}, {"space_group_name_H-M", spaceGroup}, {"Int_Tables_number", intTablesNr}}); getCategory("symmetry")->emplace({{"entry_id", mStructureID},
{"space_group_name_H-M", spaceGroup},
{"Int_Tables_number", intTablesNr}});
GetNextRecord(); GetNextRecord();
} }
...@@ -5056,7 +5361,20 @@ void PDBFileParser::ParseCoordinateTransformation() ...@@ -5056,7 +5361,20 @@ void PDBFileParser::ParseCoordinateTransformation()
GetNextRecord(); // transformations of the molecule are GetNextRecord(); // transformations of the molecule are
} // contained in the datablock. Otherwise, blank. } // contained in the datablock. Otherwise, blank.
getCategory("struct_ncs_oper")->emplace({{"id", serial}, {"matrix[1][1]", m[0][0]}, {"matrix[1][2]", m[0][1]}, {"matrix[1][3]", m[0][2]}, {"matrix[2][1]", m[1][0]}, {"matrix[2][2]", m[1][1]}, {"matrix[2][3]", m[1][2]}, {"matrix[3][1]", m[2][0]}, {"matrix[3][2]", m[2][1]}, {"matrix[3][3]", m[2][2]}, {"vector[1]", v[0]}, {"vector[2]", v[1]}, {"vector[3]", v[2]}, {"code", igiven ? "given" : ""}}); getCategory("struct_ncs_oper")->emplace({{"id", serial},
{"matrix[1][1]", m[0][0]},
{"matrix[1][2]", m[0][1]},
{"matrix[1][3]", m[0][2]},
{"matrix[2][1]", m[1][0]},
{"matrix[2][2]", m[1][1]},
{"matrix[2][3]", m[1][2]},
{"matrix[3][1]", m[2][0]},
{"matrix[3][2]", m[2][1]},
{"matrix[3][3]", m[2][2]},
{"vector[1]", v[0]},
{"vector[2]", v[1]},
{"vector[3]", v[2]},
{"code", igiven ? "given" : ""}});
} }
} }
...@@ -5215,7 +5533,27 @@ void PDBFileParser::ParseCoordinate(int modelNr) ...@@ -5215,7 +5533,27 @@ void PDBFileParser::ParseCoordinate(int modelNr)
} }
} }
getCategory("atom_site")->emplace({{"group_PDB", groupPDB}, {"id", mAtomID}, {"type_symbol", element}, {"label_atom_id", name}, {"label_alt_id", altLoc != ' ' ? std::string{altLoc} : "."}, {"label_comp_id", resName}, {"label_asym_id", asymID}, {"label_entity_id", entityID}, {"label_seq_id", (isResseq and seqID > 0) ? std::to_string(seqID) : "."}, {"pdbx_PDB_ins_code", iCode == ' ' ? "" : std::string{iCode}}, {"Cartn_x", x}, {"Cartn_y", y}, {"Cartn_z", z}, {"occupancy", occupancy}, {"B_iso_or_equiv", tempFactor}, {"pdbx_formal_charge", charge}, {"auth_seq_id", resSeq}, {"auth_comp_id", resName}, {"auth_asym_id", std::string{chainID}}, {"auth_atom_id", name}, {"pdbx_PDB_model_num", modelNr}}); getCategory("atom_site")->emplace({{"group_PDB", groupPDB},
{"id", mAtomID},
{"type_symbol", element},
{"label_atom_id", name},
{"label_alt_id", altLoc != ' ' ? std::string{altLoc} : "."},
{"label_comp_id", resName},
{"label_asym_id", asymID},
{"label_entity_id", entityID},
{"label_seq_id", (isResseq and seqID > 0) ? std::to_string(seqID) : "."},
{"pdbx_PDB_ins_code", iCode == ' ' ? "" : std::string{iCode}},
{"Cartn_x", x},
{"Cartn_y", y},
{"Cartn_z", z},
{"occupancy", occupancy},
{"B_iso_or_equiv", tempFactor},
{"pdbx_formal_charge", charge},
{"auth_seq_id", resSeq},
{"auth_comp_id", resName},
{"auth_asym_id", std::string{chainID}},
{"auth_atom_id", name},
{"pdbx_PDB_model_num", modelNr}});
InsertAtomType(element); InsertAtomType(element);
...@@ -5237,7 +5575,23 @@ void PDBFileParser::ParseCoordinate(int modelNr) ...@@ -5237,7 +5575,23 @@ void PDBFileParser::ParseCoordinate(int modelNr)
auto f = [](float f) -> std::string auto f = [](float f) -> std::string
{ return (boost::format("%6.4f") % f).str(); }; { return (boost::format("%6.4f") % f).str(); };
getCategory("atom_site_anisotrop")->emplace({{"id", mAtomID}, {"type_symbol", element}, {"pdbx_label_atom_id", name}, {"pdbx_label_alt_id", altLoc != ' ' ? std::string{altLoc} : "."}, {"pdbx_label_comp_id", resName}, {"pdbx_label_asym_id", asymID}, {"pdbx_label_seq_id", (isResseq and seqID > 0) ? std::to_string(seqID) : "."}, {"U[1][1]", f(u11 / 10000.f)}, {"U[2][2]", f(u22 / 10000.f)}, {"U[3][3]", f(u33 / 10000.f)}, {"U[1][2]", f(u12 / 10000.f)}, {"U[1][3]", f(u13 / 10000.f)}, {"U[2][3]", f(u23 / 10000.f)}, {"pdbx_auth_seq_id", resSeq}, {"pdbx_auth_comp_id", resName}, {"pdbx_auth_asym_id", std::string{chainID}}, {"pdbx_auth_atom_id", name}}); getCategory("atom_site_anisotrop")->emplace({{"id", mAtomID},
{"type_symbol", element},
{"pdbx_label_atom_id", name},
{"pdbx_label_alt_id", altLoc != ' ' ? std::string{altLoc} : "."},
{"pdbx_label_comp_id", resName},
{"pdbx_label_asym_id", asymID},
{"pdbx_label_seq_id", (isResseq and seqID > 0) ? std::to_string(seqID) : "."},
{"U[1][1]", f(u11 / 10000.f)},
{"U[2][2]", f(u22 / 10000.f)},
{"U[3][3]", f(u33 / 10000.f)},
{"U[1][2]", f(u12 / 10000.f)},
{"U[1][3]", f(u13 / 10000.f)},
{"U[2][3]", f(u23 / 10000.f)},
{"pdbx_auth_seq_id", resSeq},
{"pdbx_auth_comp_id", resName},
{"pdbx_auth_asym_id", std::string{chainID}},
{"pdbx_auth_atom_id", name}});
} }
} }
......
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