diff --git a/modules/io/pymod/export_mmcif_io.cc b/modules/io/pymod/export_mmcif_io.cc
index 0d3759a4364726841a8555b86d8eb8577d47ad41..59265e130d228185dde4bdb2deef752cb410ebd7 100644
--- a/modules/io/pymod/export_mmcif_io.cc
+++ b/modules/io/pymod/export_mmcif_io.cc
@@ -77,7 +77,7 @@ void export_mmcif_io()
;
class_<MMCifWriter, boost::noncopyable>("MMCifWriter", init<const String&, const IOProfile&>())
- .def("SetEntity", &MMCifWriter::SetEntity)
+ .def("SetEntity", &MMCifWriter::SetEntity, (arg("ent"), arg("mmcif_conform")=true))
.def("Write", &MMCifWriter::Write)
;
diff --git a/modules/io/src/mol/mmcif_writer.cc b/modules/io/src/mol/mmcif_writer.cc
index 6965cc5dc5781b8802c758fef9ff51bdee9cd7b2..65c630917ed3473c4240b396f954c941082863cf 100644
--- a/modules/io/src/mol/mmcif_writer.cc
+++ b/modules/io/src/mol/mmcif_writer.cc
@@ -221,7 +221,6 @@ namespace {
String type;
};
-
inline String chem_class_to_chem_comp_type(char chem_class) {
String type = "";
switch(chem_class) {
@@ -273,7 +272,6 @@ namespace {
std::stringstream err;
err << "Invalid chem class: "<<chem_class;
throw ost::io::IOException(err.str());
-
}
}
return type;
@@ -559,6 +557,16 @@ namespace {
return entity_idx;
}
+ int Setup_entity_(const String& asym_chain_name,
+ ost::mol::ChainType chain_type,
+ const ost::mol::ResidueHandleList& res_list,
+ std::vector<EntityInfo>& entity_infos) {
+ // instead of infering a chain type, we're just checking whether the
+ // residues in res_list are allowed to be present in given chain type.
+ int entity_idx = 0;
+ return entity_idx;
+ }
+
ost::io::StarLoop* Setup_atom_type_ptr() {
ost::io::StarLoopDesc desc;
desc.SetCategory("_atom_type");
@@ -839,6 +847,295 @@ namespace {
chem_comp_ptr->AddData(comp_data);
}
}
+
+ void SetEntity_(const ost::mol::EntityHandle& ent,
+ std::map<String, CompInfo>& comp_infos,
+ std::vector<EntityInfo>& entity_info,
+ ost::io::StarLoop* atom_site,
+ ost::io::StarLoop* pdbx_poly_seq_scheme) {
+ ost::mol::ChainHandleList chain_list = ent.GetChainList();
+ for(auto ch: chain_list) {
+
+ ost::mol::ResidueHandleList res_list = ch.GetResidueList();
+
+ Setup_chem_comp_(res_list, comp_infos);
+ String chain_name = ch.GetName();
+ int entity_id = Setup_entity_(chain_name,
+ ch.GetType(),
+ res_list,
+ entity_info);
+ Feed_atom_site_(atom_site, chain_name, entity_id, res_list,
+ entity_info[entity_id].is_poly);
+ if(entity_info[entity_id].is_poly) {
+ Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme, chain_name,
+ entity_id, res_list);
+ }
+ }
+ }
+
+ void SetEntitymmCIFify_(const ost::mol::EntityHandle& ent,
+ std::map<String, CompInfo>& comp_infos,
+ std::vector<EntityInfo>& entity_info,
+ ost::io::StarLoop* atom_site,
+ ost::io::StarLoop* 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)
+
+ ost::mol::ChainHandleList chain_list = ent.GetChainList();
+ for(auto ch: chain_list) {
+
+ ost::mol::ResidueHandleList res_list = ch.GetResidueList();
+
+ Setup_chem_comp_(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...
+ 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 "
+ "contains D- and L-peptides");
+ }
+ has_d_peptide_linking = true;
+ }
+ if(res.GetChemClass() == ost::mol::ChemClass::L_PEPTIDE_LINKING) {
+ if(has_d_peptide_linking) {
+ throw ost::io::IOException("Cannot write mmCIF when same chain "
+ "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);
+ } else if(has_d_peptide_linking) {
+ D_chains.back().push_back(res);
+ } else {
+ P_chains.back().push_back(res);
+ }
+ } else if(res.GetChemClass() == ost::mol::ChemClass::RNA_LINKING) {
+ R_chains.back().push_back(res);
+ } else if(res.GetChemClass() == ost::mol::ChemClass::DNA_LINKING) {
+ S_chains.back().push_back(res);
+ } else if(res.GetChemClass() == ost::mol::ChemClass::L_SACCHARIDE) {
+ Z_chains.back().push_back(res);
+ } else if(res.GetChemClass() == ost::mol::ChemClass::D_SACCHARIDE) {
+ Z_chains.back().push_back(res);
+ } else if(res.GetChemClass() == ost::mol::ChemClass::SACCHARIDE) {
+ Z_chains.back().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);
+ } 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 = Setup_entity_(chain_name,
+ res_list,
+ entity_info);
+ Feed_atom_site_(atom_site, chain_name, entity_id, res_list,
+ entity_info[entity_id].is_poly);
+ if(entity_info[entity_id].is_poly) {
+ Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme, chain_name,
+ entity_id, res_list);
+ }
+ }
+
+ // process D_PEPTIDE_LINKING
+ for(auto res_list: D_chains) {
+ String chain_name = chain_name_gen.Get();
+ int entity_id = Setup_entity_(chain_name,
+ res_list,
+ entity_info);
+ Feed_atom_site_(atom_site, chain_name, entity_id, res_list,
+ entity_info[entity_id].is_poly);
+ if(entity_info[entity_id].is_poly) {
+ Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme, chain_name,
+ entity_id, res_list);
+ }
+ }
+
+ // process PEPTIDE_LINKING
+ for(auto res_list: P_chains) {
+ String chain_name = chain_name_gen.Get();
+ int entity_id = Setup_entity_(chain_name,
+ res_list,
+ entity_info);
+ Feed_atom_site_(atom_site, chain_name, entity_id, res_list,
+ entity_info[entity_id].is_poly);
+ if(entity_info[entity_id].is_poly) {
+ Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme, chain_name,
+ entity_id, res_list);
+ }
+ }
+
+ // process RNA_LINKING
+ for(auto res_list: R_chains) {
+ String chain_name = chain_name_gen.Get();
+ int entity_id = Setup_entity_(chain_name,
+ res_list,
+ entity_info);
+ Feed_atom_site_(atom_site, chain_name, entity_id, res_list,
+ entity_info[entity_id].is_poly);
+ if(entity_info[entity_id].is_poly) {
+ Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme, chain_name,
+ entity_id, res_list);
+ }
+ }
+
+ // process DNA_LINKING
+ for(auto res_list: S_chains) {
+ String chain_name = chain_name_gen.Get();
+ int entity_id = Setup_entity_(chain_name,
+ res_list,
+ entity_info);
+ Feed_atom_site_(atom_site, chain_name, entity_id, res_list,
+ entity_info[entity_id].is_poly);
+ if(entity_info[entity_id].is_poly) {
+ Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme, chain_name,
+ entity_id, res_list);
+ }
+ }
+
+ // process SACHARIDE
+ for(auto res_list: Z_chains) {
+ String chain_name = chain_name_gen.Get();
+ int entity_id = Setup_entity_(chain_name,
+ res_list,
+ entity_info);
+ Feed_atom_site_(atom_site, chain_name, entity_id, res_list,
+ entity_info[entity_id].is_poly);
+ if(entity_info[entity_id].is_poly) {
+ Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme, chain_name,
+ entity_id, res_list);
+ }
+ }
+
+ // process WATER
+ for(auto res_list: W_chains) {
+ String chain_name = chain_name_gen.Get();
+ int entity_id = Setup_entity_(chain_name,
+ res_list,
+ entity_info);
+ Feed_atom_site_(atom_site, chain_name, entity_id, res_list,
+ entity_info[entity_id].is_poly);
+ if(entity_info[entity_id].is_poly) {
+ Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme, chain_name,
+ 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 = Setup_entity_(chain_name,
+ res_list,
+ entity_info);
+ Feed_atom_site_(atom_site, chain_name, entity_id, res_list,
+ entity_info[entity_id].is_poly);
+ if(entity_info[entity_id].is_poly) {
+ Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme, chain_name,
+ entity_id, res_list);
+ }
+ }
+ }
}
namespace ost { namespace io {
@@ -882,7 +1179,8 @@ MMCifWriter::~MMCifWriter() {
}
}
-void MMCifWriter::SetEntity(const ost::mol::EntityHandle& ent) {
+void MMCifWriter::SetEntity(const ost::mol::EntityHandle& ent,
+ bool mmcif_conform) {
// tabula rasa
if(atom_type_ != NULL) {
@@ -919,265 +1217,26 @@ void MMCifWriter::SetEntity(const ost::mol::EntityHandle& ent) {
entity_poly_seq_ = Setup_entity_poly_seq_ptr();
chem_comp_ = Setup_chem_comp_ptr();
- 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)
std::map<String, CompInfo> comp_infos;
-
- ost::mol::ChainHandleList chain_list = ent.GetChainList();
- for(auto ch: chain_list) {
-
- ost::mol::ResidueHandleList res_list = ch.GetResidueList();
-
- Setup_chem_comp_(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...
- 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 "
- "contains D- and L-peptides");
- }
- has_d_peptide_linking = true;
- }
- if(res.GetChemClass() == ost::mol::ChemClass::L_PEPTIDE_LINKING) {
- if(has_d_peptide_linking) {
- throw ost::io::IOException("Cannot write mmCIF when same chain "
- "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);
- } else if(has_d_peptide_linking) {
- D_chains.back().push_back(res);
- } else {
- P_chains.back().push_back(res);
- }
- } else if(res.GetChemClass() == ost::mol::ChemClass::RNA_LINKING) {
- R_chains.back().push_back(res);
- } else if(res.GetChemClass() == ost::mol::ChemClass::DNA_LINKING) {
- S_chains.back().push_back(res);
- } else if(res.GetChemClass() == ost::mol::ChemClass::L_SACCHARIDE) {
- Z_chains.back().push_back(res);
- } else if(res.GetChemClass() == ost::mol::ChemClass::D_SACCHARIDE) {
- Z_chains.back().push_back(res);
- } else if(res.GetChemClass() == ost::mol::ChemClass::SACCHARIDE) {
- Z_chains.back().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);
- } else {
- // TODO: make error message more insightful...
- throw ost::io::IOException("Unsupported chem class...");
- }
- }
- }
-
- ChainNameGenerator chain_name_gen;
std::vector<EntityInfo> entity_info;
- // process L_PEPTIDE_LINKING
- for(auto res_list: L_chains) {
- String chain_name = chain_name_gen.Get();
- int entity_id = Setup_entity_(chain_name,
- res_list,
- entity_info);
- Feed_atom_site_(atom_site_, chain_name, entity_id, res_list,
- entity_info[entity_id].is_poly);
- if(entity_info[entity_id].is_poly) {
- Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme_, chain_name,
- entity_id, res_list);
- }
- }
-
- // process D_PEPTIDE_LINKING
- for(auto res_list: D_chains) {
- String chain_name = chain_name_gen.Get();
- int entity_id = Setup_entity_(chain_name,
- res_list,
- entity_info);
- Feed_atom_site_(atom_site_, chain_name, entity_id, res_list,
- entity_info[entity_id].is_poly);
- if(entity_info[entity_id].is_poly) {
- Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme_, chain_name,
- entity_id, res_list);
- }
+ // The SetEntity functions fill CompInfo and EntityInfo, i.e. gather info on
+ // all unique compounds and entities observed in ent and relate the entities
+ // with asym chain names that are directly written to
+ // atom_site_/pdbx_poly_seq_scheme_.
+ if(mmcif_conform) {
+ // chains are assumed to be mmCIF conform - that means water in separate
+ // chains, ligands in separate chains etc. Chain types are inferred from
+ // chain type property set to the chains in ent. If any of the residues in
+ // the respective chains is incompatible with the set chain type, an error
+ // is thrown.
+ SetEntity_(ent, comp_infos, entity_info,
+ atom_site_, pdbx_poly_seq_scheme_);
+ } else {
+ // rule based splitting of chains into mmCIF conform chains
+ SetEntitymmCIFify_(ent, comp_infos, entity_info,
+ atom_site_, pdbx_poly_seq_scheme_);
}
-
- // process PEPTIDE_LINKING
- for(auto res_list: P_chains) {
- String chain_name = chain_name_gen.Get();
- int entity_id = Setup_entity_(chain_name,
- res_list,
- entity_info);
- Feed_atom_site_(atom_site_, chain_name, entity_id, res_list,
- entity_info[entity_id].is_poly);
- if(entity_info[entity_id].is_poly) {
- Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme_, chain_name,
- entity_id, res_list);
- }
- }
-
- // process RNA_LINKING
- for(auto res_list: R_chains) {
- String chain_name = chain_name_gen.Get();
- int entity_id = Setup_entity_(chain_name,
- res_list,
- entity_info);
- Feed_atom_site_(atom_site_, chain_name, entity_id, res_list,
- entity_info[entity_id].is_poly);
- if(entity_info[entity_id].is_poly) {
- Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme_, chain_name,
- entity_id, res_list);
- }
- }
-
- // process DNA_LINKING
- for(auto res_list: S_chains) {
- String chain_name = chain_name_gen.Get();
- int entity_id = Setup_entity_(chain_name,
- res_list,
- entity_info);
- Feed_atom_site_(atom_site_, chain_name, entity_id, res_list,
- entity_info[entity_id].is_poly);
- if(entity_info[entity_id].is_poly) {
- Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme_, chain_name,
- entity_id, res_list);
- }
- }
-
- // process SACHARIDE
- for(auto res_list: Z_chains) {
- String chain_name = chain_name_gen.Get();
- int entity_id = Setup_entity_(chain_name,
- res_list,
- entity_info);
- Feed_atom_site_(atom_site_, chain_name, entity_id, res_list,
- entity_info[entity_id].is_poly);
- if(entity_info[entity_id].is_poly) {
- Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme_, chain_name,
- entity_id, res_list);
- }
- }
-
- // process WATER
- for(auto res_list: W_chains) {
- String chain_name = chain_name_gen.Get();
- int entity_id = Setup_entity_(chain_name,
- res_list,
- entity_info);
- Feed_atom_site_(atom_site_, chain_name, entity_id, res_list,
- entity_info[entity_id].is_poly);
- if(entity_info[entity_id].is_poly) {
- Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme_, chain_name,
- 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 = Setup_entity_(chain_name,
- res_list,
- entity_info);
- Feed_atom_site_(atom_site_, chain_name, entity_id, res_list,
- entity_info[entity_id].is_poly);
- if(entity_info[entity_id].is_poly) {
- Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme_, chain_name,
- entity_id, res_list);
- }
- }
-
Feed_entity_(entity_, entity_info);
Feed_struct_asym_(struct_asym_, entity_info);
Feed_entity_poly_(entity_poly_, entity_info);
diff --git a/modules/io/src/mol/mmcif_writer.hh b/modules/io/src/mol/mmcif_writer.hh
index 619ff270d4093b15f346968315019d020db88b24..0258242e63737058b684a74b7e0d360ed6a05f17 100644
--- a/modules/io/src/mol/mmcif_writer.hh
+++ b/modules/io/src/mol/mmcif_writer.hh
@@ -36,7 +36,7 @@ public:
virtual ~MMCifWriter();
- void SetEntity(const ost::mol::EntityHandle& ent);
+ void SetEntity(const ost::mol::EntityHandle& ent, bool mmcif_conform=true);
private:
IOProfile profile_;