diff --git a/modules/io/src/mol/mmcif_writer.cc b/modules/io/src/mol/mmcif_writer.cc
index 8398f4c0ec26b5378b0f23ab89ded228cf138e52..1f8bbed2d3d600a54a52a158dfe98188082bb11b 100644
--- a/modules/io/src/mol/mmcif_writer.cc
+++ b/modules/io/src/mol/mmcif_writer.cc
@@ -679,6 +679,10 @@ namespace {
// check if entity is already there
for(size_t i = 0; i < entity_infos.size(); ++i) {
+ if(entity_infos[i].type == "water" && type == "water") {
+ AddAsym(asym_chain_name, entity_infos[i]);
+ return i;
+ }
if(entity_infos[i].type == type &&
entity_infos[i].poly_type == poly_type) {
if(is_poly && resnum_alignment) {
@@ -729,14 +733,20 @@ namespace {
}
}
} else {
- for(auto res: res_list) {
- mon_ids.push_back(res.GetName());
- seq.push_back(MonIDToOLC(res.GetChemClass(), res.GetName()));
- char olc = res.GetOneLetterCode();
- if(olc < 'A' || olc > 'Z') {
- seq_can.push_back("X");
- } else {
- seq_can.push_back(String(1, olc));
+ if(type == "water") {
+ mon_ids.push_back("HOH");
+ seq.push_back("X");
+ seq_can.push_back("X");
+ } else {
+ for(auto res: res_list) {
+ mon_ids.push_back(res.GetName());
+ seq.push_back(MonIDToOLC(res.GetChemClass(), res.GetName()));
+ char olc = res.GetOneLetterCode();
+ if(olc < 'A' || olc > 'Z') {
+ seq_can.push_back("X");
+ } else {
+ seq_can.push_back(String(1, olc));
+ }
}
}
}
@@ -994,14 +1004,6 @@ namespace {
for(auto res: res_list) {
String comp_id = res.GetName();
- while(aln[label_seq_id] == "-") {
- ++label_seq_id;
- }
-
- if(comp_id != aln[label_seq_id]) {
- throw "ksajdhfgjkaljshdfsfgd";
- }
-
ost::mol::AtomHandleList at_list = res.GetAtomList();
String auth_asym_id = res.GetChain().GetName();
if(res.HasProp("pdb_auth_chain_name")) {
@@ -1019,6 +1021,16 @@ namespace {
}
auth_seq_id = ss.str();
}
+
+ if(entity_info.is_poly) {
+ while(aln[label_seq_id] == "-") {
+ ++label_seq_id;
+ }
+ if(comp_id != aln[label_seq_id]) {
+ throw "ksajdhfgjkaljshdfsfgd";
+ }
+ }
+
for(auto at: at_list) {
std::vector<ost::io::StarWriterLoopDataItem> at_data;
// group_PDB
@@ -1065,6 +1077,7 @@ namespace {
at_data.push_back(ost::io::StarWriterLoopDataItem("")); // CHECK THIS, ADD STUFF FROM AUTH_SEQ_ID?
atom_site_ptr->AddData(at_data);
}
+
++label_seq_id;
}
}
@@ -1191,15 +1204,7 @@ namespace {
ost::io::StarWriterLoopPtr atom_site,
ost::io::StarWriterLoopPtr pdbx_poly_seq_scheme) {
- std::vector<std::vector<ost::mol::ResidueHandle> > L_chains; // L_PEPTIDE_LINKING
- std::vector<std::vector<ost::mol::ResidueHandle> > D_chains; // D_PEPTIDE_LINKING
- std::vector<std::vector<ost::mol::ResidueHandle> > P_chains; // PEPTIDE_LINKING
- std::vector<std::vector<ost::mol::ResidueHandle> > R_chains; // RNA_LINKING
- std::vector<std::vector<ost::mol::ResidueHandle> > S_chains; // DNA_LINKING
- // all Saccharides go into the same chain
- std::vector<std::vector<ost::mol::ResidueHandle> > Z_chains; // SACCHARIDE
- std::vector<std::vector<ost::mol::ResidueHandle> > W_chains; // WATER
- std::vector<ost::mol::ResidueHandle> N_chains; // NON_POLYMER (1 res per chain)
+ ChainNameGenerator chain_name_gen;
ost::mol::ChainHandleList chain_list = ent.GetChainList();
for(auto ch: chain_list) {
@@ -1208,19 +1213,21 @@ namespace {
SetupChemComp(res_list, comp_infos);
- // we don't just go for chain type here...
- // just think of PDB entries that have a polypeptide, water and a ligand
- // in the same chain...
+ std::vector<ost::mol::ResidueHandle> L_chain;
+ std::vector<ost::mol::ResidueHandle> D_chain;
+ std::vector<ost::mol::ResidueHandle> P_chain;
+ std::vector<ost::mol::ResidueHandle> R_chain;
+ std::vector<ost::mol::ResidueHandle> S_chain;
+ std::vector<ost::mol::ResidueHandle> Z_chain;
+ std::vector<ost::mol::ResidueHandle> W_chain;
+
+ // first scan only concerning peptides...
+ // Avoid mix of both in same chain: L-peptide linking, D-peptide linking
+ // But we still want to know that in advance as we assign non chiral
+ // peptides to either of those
bool has_l_peptide_linking = false;
bool has_d_peptide_linking = false;
- bool has_peptide_linking = false;
- bool has_rna_linking = false;
- bool has_dna_linking = false;
- bool has_saccharide = false;
- bool has_water = false;
for(auto res: res_list) {
-
- // Peptide chains must not mix L_PEPTIDE_LINKING AND D_PEPTIDE_LINKING
if(res.GetChemClass() == ost::mol::ChemClass::D_PEPTIDE_LINKING) {
if(has_l_peptide_linking) {
throw ost::io::IOException("Cannot write mmCIF when same chain "
@@ -1234,225 +1241,92 @@ namespace {
"contains D- and L-peptides");
}
has_l_peptide_linking = true;
- }
-
- if(res.GetChemClass() == ost::mol::ChemClass::PEPTIDE_LINKING) {
- has_peptide_linking = true;
- }
-
- if(res.GetChemClass() == ost::mol::ChemClass::RNA_LINKING) {
- has_rna_linking = true;
- }
-
- if(res.GetChemClass() == ost::mol::ChemClass::DNA_LINKING) {
- has_dna_linking = true;
- }
-
- if(res.GetChemClass() == ost::mol::ChemClass::L_SACCHARIDE) {
- has_saccharide = true;
- }
-
- if(res.GetChemClass() == ost::mol::ChemClass::D_SACCHARIDE) {
- has_saccharide = true;
- }
-
- if(res.GetChemClass() == ost::mol::ChemClass::SACCHARIDE) {
- has_saccharide = true;
- }
-
- if(res.GetChemClass() == ost::mol::ChemClass::WATER) {
- has_water = true;
- }
- }
-
- // if there is any L-peptide or D-peptide, all peptides without
- // chiral center get assigned to it. No need for specific chain.
- if(has_l_peptide_linking || has_d_peptide_linking) {
- has_peptide_linking = false;
- }
-
- if(has_l_peptide_linking) {
- L_chains.push_back(ost::mol::ResidueHandleList());
- }
-
- if(has_d_peptide_linking) {
- D_chains.push_back(ost::mol::ResidueHandleList());
- }
-
- if(has_peptide_linking) {
- P_chains.push_back(ost::mol::ResidueHandleList());
- }
-
- if(has_rna_linking) {
- R_chains.push_back(ost::mol::ResidueHandleList());
- }
-
- if(has_dna_linking) {
- S_chains.push_back(ost::mol::ResidueHandleList());
- }
-
- if(has_saccharide) {
- Z_chains.push_back(ost::mol::ResidueHandleList());
- }
-
- if(has_water) {
- W_chains.push_back(ost::mol::ResidueHandleList());
+ }
}
for(auto res: res_list) {
if(res.GetChemClass().IsPeptideLinking()) {
if(has_l_peptide_linking) {
- L_chains.back().push_back(res);
+ L_chain.push_back(res);
} else if(has_d_peptide_linking) {
- D_chains.back().push_back(res);
+ D_chain.push_back(res);
} else {
- P_chains.back().push_back(res);
+ P_chain.push_back(res);
}
} else if(res.GetChemClass() == ost::mol::ChemClass::RNA_LINKING) {
- R_chains.back().push_back(res);
+ R_chain.push_back(res);
} else if(res.GetChemClass() == ost::mol::ChemClass::DNA_LINKING) {
- S_chains.back().push_back(res);
+ S_chain.push_back(res);
} else if(res.GetChemClass() == ost::mol::ChemClass::L_SACCHARIDE) {
- Z_chains.back().push_back(res);
+ Z_chain.push_back(res);
} else if(res.GetChemClass() == ost::mol::ChemClass::D_SACCHARIDE) {
- Z_chains.back().push_back(res);
+ Z_chain.push_back(res);
} else if(res.GetChemClass() == ost::mol::ChemClass::SACCHARIDE) {
- Z_chains.back().push_back(res);
+ Z_chain.push_back(res);
} else if(res.GetChemClass() == ost::mol::ChemClass::WATER) {
- W_chains.back().push_back(res);
- } else if(res.GetChemClass() == ost::mol::ChemClass::NON_POLYMER) {
- N_chains.push_back(res);
- } else if(res.GetChemClass() == ost::mol::ChemClass::UNKNOWN) {
- // unknown is just treated as non-poly
- N_chains.push_back(res);
+ W_chain.push_back(res);
+ } else if(res.GetChemClass() == ost::mol::ChemClass::NON_POLYMER ||
+ res.GetChemClass() == ost::mol::ChemClass::UNKNOWN) {
+ // already process non-poly and unknown
+ ost::mol::ResidueHandleList tmp;
+ tmp.push_back(res);
+ String chain_name = chain_name_gen.Get();
+ int entity_id = SetupEntity(chain_name,
+ tmp,
+ false,
+ entity_info);
+ Feed_atom_site(atom_site, chain_name, entity_id, entity_info[entity_id],
+ tmp);
} else {
// TODO: make error message more insightful...
throw ost::io::IOException("Unsupported chem class...");
}
}
- }
-
- ChainNameGenerator chain_name_gen;
- // process L_PEPTIDE_LINKING
- for(auto res_list: L_chains) {
- String chain_name = chain_name_gen.Get();
- int entity_id = SetupEntity(chain_name,
- res_list,
- false,
- entity_info);
- Feed_atom_site(atom_site, chain_name, entity_id, entity_info[entity_id],
- res_list);
- if(entity_info[entity_id].is_poly) {
- Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme, chain_name,
- entity_id, entity_info[entity_id], res_list);
- }
- }
-
- // process D_PEPTIDE_LINKING
- for(auto res_list: D_chains) {
- String chain_name = chain_name_gen.Get();
- int entity_id = SetupEntity(chain_name,
- res_list,
- false,
- entity_info);
- Feed_atom_site(atom_site, chain_name, entity_id, entity_info[entity_id],
- res_list);
- if(entity_info[entity_id].is_poly) {
- Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme, chain_name,
- entity_id, entity_info[entity_id], res_list);
- }
- }
-
- // process PEPTIDE_LINKING
- for(auto res_list: P_chains) {
- String chain_name = chain_name_gen.Get();
- int entity_id = SetupEntity(chain_name,
- res_list,
- false,
- entity_info);
- Feed_atom_site(atom_site, chain_name, entity_id, entity_info[entity_id],
- res_list);
- if(entity_info[entity_id].is_poly) {
- Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme, chain_name,
- entity_id, entity_info[entity_id], res_list);
- }
- }
-
- // process RNA_LINKING
- for(auto res_list: R_chains) {
- String chain_name = chain_name_gen.Get();
- int entity_id = SetupEntity(chain_name,
- res_list,
- false,
- entity_info);
- Feed_atom_site(atom_site, chain_name, entity_id, entity_info[entity_id],
- res_list);
- if(entity_info[entity_id].is_poly) {
- Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme, chain_name,
- entity_id, entity_info[entity_id], res_list);
- }
- }
-
- // process DNA_LINKING
- for(auto res_list: S_chains) {
- String chain_name = chain_name_gen.Get();
- int entity_id = SetupEntity(chain_name,
- res_list,
- false,
- entity_info);
- Feed_atom_site(atom_site, chain_name, entity_id, entity_info[entity_id],
- res_list);
- if(entity_info[entity_id].is_poly) {
- Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme, chain_name,
- entity_id, entity_info[entity_id], res_list);
+ // process poly chains
+ std::vector<ost::mol::ResidueHandle>* poly_chains[5] = {&L_chain,
+ &D_chain,
+ &P_chain,
+ &R_chain,
+ &S_chain};
+ for(int i = 0; i < 5; ++i) {
+ if(!poly_chains[i]->empty()) {
+ String chain_name = chain_name_gen.Get();
+ int entity_id = SetupEntity(chain_name,
+ *poly_chains[i],
+ false,
+ entity_info);
+ Feed_atom_site(atom_site, chain_name, entity_id, entity_info[entity_id],
+ *poly_chains[i]);
+ // still check whether we're dealing with poly here, we could have a
+ // lonely amino acid that ends up as non-poly and doesn't need
+ // pdbx_poly_seq_scheme
+ if(entity_info[entity_id].is_poly) {
+ Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme, chain_name,
+ entity_id, entity_info[entity_id], *poly_chains[i]);
+ }
+ }
}
- }
- // process SACHARIDE
- for(auto res_list: Z_chains) {
- String chain_name = chain_name_gen.Get();
- int entity_id = SetupEntity(chain_name,
- res_list,
- false,
- entity_info);
- Feed_atom_site(atom_site, chain_name, entity_id, entity_info[entity_id],
- res_list);
- if(entity_info[entity_id].is_poly) {
- Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme, chain_name,
- entity_id, entity_info[entity_id], res_list);
+ // process water chain
+ if(!W_chain.empty()) {
+ String chain_name = chain_name_gen.Get();
+ int entity_id = SetupEntity(chain_name,
+ W_chain,
+ false,
+ entity_info);
+ Feed_atom_site(atom_site, chain_name, entity_id, entity_info[entity_id],
+ W_chain);
}
- }
-
- // process WATER
- for(auto res_list: W_chains) {
- String chain_name = chain_name_gen.Get();
- int entity_id = SetupEntity(chain_name,
- res_list,
- false,
- entity_info);
- Feed_atom_site(atom_site, chain_name, entity_id, entity_info[entity_id],
- res_list);
- if(entity_info[entity_id].is_poly) {
- Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme, chain_name,
- entity_id, entity_info[entity_id], res_list);
- }
- }
-
- // process NON_POLYMER
- for(auto res: N_chains) {
- ost::mol::ResidueHandleList res_list;
- res_list.push_back(res);
- String chain_name = chain_name_gen.Get();
- int entity_id = SetupEntity(chain_name,
- res_list,
- false,
- entity_info);
- Feed_atom_site(atom_site, chain_name, entity_id, entity_info[entity_id],
- res_list);
- if(entity_info[entity_id].is_poly) {
- Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme, chain_name,
- entity_id, entity_info[entity_id], res_list);
+ // process sugar chain
+ if(!Z_chain.empty()) {
+ String chain_name = chain_name_gen.Get();
+ int entity_id = SetupEntity(chain_name,
+ Z_chain,
+ false,
+ entity_info);
+ Feed_atom_site(atom_site, chain_name, entity_id, entity_info[entity_id],
+ Z_chain);
}
}
}