From b763d4259fe2af0ca9a7ec50ab57838e1f0d0ee5 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 8 Dec 2023 10:32:05 +0100
Subject: [PATCH] mmcif writing: make mmCIFify optional
There are two modes of mmCIF writing.
- Entities that are already mmCIF conform: Water/ligands are in
separate chains etc.
- Entities are a mess: Chains must be split and we need to
assign educated guesses of chain types.
The writer currently implements the second scenario. This commit introduces
a flag to choose between the two scenarios. In case of the first scenario
there is not much guessing but rather sanity checks whether the residues
of the respective chains are compatible with the chain types that are set.
The code itself is not working yet.
---
modules/io/pymod/export_mmcif_io.cc | 2 +-
modules/io/src/mol/mmcif_writer.cc | 575 +++++++++++++++-------------
modules/io/src/mol/mmcif_writer.hh | 2 +-
3 files changed, 319 insertions(+), 260 deletions(-)
diff --git a/modules/io/pymod/export_mmcif_io.cc b/modules/io/pymod/export_mmcif_io.cc
index 0d3759a43..59265e130 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 6965cc5dc..65c630917 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 619ff270d..0258242e6 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_;
--
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