diff --git a/modules/io/pymod/export_mmcif_io.cc b/modules/io/pymod/export_mmcif_io.cc
index cb12690443525ac61625e1f93d50aaf3e76c1646..0d3759a4364726841a8555b86d8eb8577d47ad41 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("Process_atom_site", &MMCifWriter::Process_atom_site)
+ .def("SetEntity", &MMCifWriter::SetEntity)
.def("Write", &MMCifWriter::Write)
;
diff --git a/modules/io/src/mol/mmcif_writer.cc b/modules/io/src/mol/mmcif_writer.cc
index 65a65774aa23f1aa90787e5dc2a9b8e75fdfca78..8632bba6ff251aaa5579eef4b3b05a995cd09b18 100644
--- a/modules/io/src/mol/mmcif_writer.cc
+++ b/modules/io/src/mol/mmcif_writer.cc
@@ -70,12 +70,133 @@ namespace {
std::vector<int> indices;
};
+ // internal object with all info to fill chem_comp_ category
+ struct CompInfo {
+ String type;
+ };
+
+ inline String chem_class_to_chem_comp_type(char chem_class) {
+ String type = "";
+ switch(chem_class) {
+ case 'P': {
+ type = "peptide linking";
+ break;
+ }
+ case 'D': {
+ type = "D-peptide linking";
+ break;
+ }
+ case 'L': {
+ type = "L-peptide linking";
+ break;
+ }
+ case 'R': {
+ type = "RNA linking";
+ break;
+ }
+ case 'S': {
+ type = "DNA linking";
+ break;
+ }
+ case 'N': {
+ type = "non-polymer";
+ break;
+ }
+ case 'X': {
+ type = "L-saccharide";
+ break;
+ }
+ case 'Y': {
+ type = "D-saccharide";
+ break;
+ }
+ case 'Z': {
+ type = "saccharide";
+ break;
+ }
+ case 'W': {
+ type = "non-polymer";
+ break;
+ }
+ case 'U': {
+ type = "non-polymer";
+ break;
+ }
+ default: {
+ std::stringstream err;
+ err << "Invalid chem class: "<<chem_class;
+ throw ost::io::IOException(err.str());
+
+ }
+ }
+ return type;
+ }
+
+ inline String chem_class_to_entity_poly_type(char chem_class) {
+ String type = "";
+ switch(chem_class) {
+ case 'P': {
+ type = "polypeptide(L)";
+ break;
+ }
+ case 'D': {
+ type = "polypeptide(D)";
+ break;
+ }
+ case 'L': {
+ type = "polypeptide(L)";
+ break;
+ }
+ case 'R': {
+ type = "polyribonucleotide";
+ break;
+ }
+ case 'S': {
+ type = "polydeoxyribonucleotide";
+ break;
+ }
+ case 'X': {
+ type = "polysaccharide(L)";
+ break;
+ }
+ case 'Y': {
+ type = "polysaccharide(D)";
+ break;
+ }
+ default: {
+ type = "other";
+ }
+ }
+ return type;
+ }
+
+ void Setup_chem_comp_(const ost::mol::ResidueHandleList& res_list,
+ std::map<String, CompInfo>& comp_infos) {
+ for(auto res: res_list) {
+ String res_name = res.GetName();
+ String type = chem_class_to_chem_comp_type(res.GetChemClass());
+ auto it = comp_infos.find(res_name);
+ if(it != comp_infos.end()) {
+ // check whether type is consistent
+ if(it->second.type != type) {
+ throw ost::io::IOException("There can be only one");
+ }
+ } else {
+ CompInfo info;
+ info.type = type;
+ comp_infos[res_name] = info;
+ }
+ }
+ }
+
// internal object with all info to fill entity_, struct_asym_,
// entity_poly_seq_ categories
struct EntityInfo {
char chem_class; // all residues of this entity have this ChemClass
+ String poly_type; // relevant for _entity_poly
std::vector<String> asym_ids; // relevant for _struct_asym.id
std::vector<String> mon_ids; // relevant for _entity_poly_seq.mon_id
+ bool is_poly; // in principle mon_ids.size() > 1
};
int Setup_entity_(const String& asym_chain_name,
@@ -97,6 +218,8 @@ namespace {
entity_infos.back().chem_class = ost::mol::ChemClass::WATER;
entity_infos.back().asym_ids.push_back(asym_chain_name);
entity_infos.back().mon_ids.push_back("HOH");
+ entity_infos.back().poly_type = "";
+ entity_infos.back().is_poly = false;
return entity_idx;
}
@@ -114,6 +237,8 @@ namespace {
entity_infos.back().chem_class = ost::mol::ChemClass::NON_POLYMER;
entity_infos.back().asym_ids.push_back(asym_chain_name);
entity_infos.back().mon_ids.push_back(res_list[0].GetName());
+ entity_infos.back().poly_type = "";
+ entity_infos.back().is_poly = false;
return entity_idx;
}
@@ -131,6 +256,8 @@ namespace {
entity_infos.back().chem_class = ost::mol::ChemClass::UNKNOWN;
entity_infos.back().asym_ids.push_back(asym_chain_name);
entity_infos.back().mon_ids.push_back(res_list[0].GetName());
+ entity_infos.back().poly_type = "";
+ entity_infos.back().is_poly = false;
return entity_idx;
}
@@ -165,10 +292,20 @@ namespace {
entity_infos.back().chem_class = chem_class;
entity_infos.back().asym_ids.push_back(asym_chain_name);
entity_infos.back().mon_ids = mon_ids;
+ entity_infos.back().poly_type = chem_class_to_entity_poly_type(chem_class);
+ entity_infos.back().is_poly = entity_infos.back().mon_ids.size() > 1;
}
return entity_idx;
}
+ ost::io::StarLoop* Setup_atom_type_ptr() {
+ ost::io::StarLoopDesc desc;
+ desc.SetCategory("_atom_type");
+ desc.Add("symbol");
+ ost::io::StarLoop* sl = new ost::io::StarLoop(desc);
+ return sl;
+ }
+
ost::io::StarLoop* Setup_atom_site_ptr() {
ost::io::StarLoopDesc desc;
desc.SetCategory("_atom_site");
@@ -193,6 +330,20 @@ namespace {
return sl;
}
+ ost::io::StarLoop* Setup_pdbx_poly_seq_scheme_ptr() {
+ ost::io::StarLoopDesc desc;
+ desc.SetCategory("_pdbx_poly_seq_scheme");
+ desc.Add("asym_id");
+ desc.Add("entity_id");
+ desc.Add("mon_id");
+ desc.Add("seq_id");
+ desc.Add("pdb_strand_id");
+ desc.Add("pdb_seq_num");
+ desc.Add("pdb_ins_code");
+ ost::io::StarLoop* sl = new ost::io::StarLoop(desc);
+ return sl;
+ }
+
ost::io::StarLoop* Setup_entity_ptr() {
ost::io::StarLoopDesc desc;
desc.SetCategory("_entity");
@@ -211,6 +362,15 @@ namespace {
return sl;
}
+ ost::io::StarLoop* Setup_entity_poly_ptr() {
+ ost::io::StarLoopDesc desc;
+ desc.SetCategory("_entity_poly");
+ desc.Add("entity_id");
+ desc.Add("type");
+ ost::io::StarLoop* sl = new ost::io::StarLoop(desc);
+ return sl;
+ }
+
ost::io::StarLoop* Setup_entity_poly_seq_ptr() {
ost::io::StarLoopDesc desc;
desc.SetCategory("_entity_poly_seq");
@@ -221,10 +381,72 @@ namespace {
return sl;
}
+ ost::io::StarLoop* Setup_chem_comp_ptr() {
+ ost::io::StarLoopDesc desc;
+ desc.SetCategory("_chem_comp");
+ desc.Add("id");
+ desc.Add("type");
+ ost::io::StarLoop* sl = new ost::io::StarLoop(desc);
+ return sl;
+ }
+
+ void Feed_atom_type_(ost::io::StarLoop* atom_type_ptr,
+ ost::io::StarLoop* atom_site_ptr) {
+ // we're just extracting every type_symbol that we observed
+ // in atom_site (this is a bit of circular stupidity...)
+ std::set<String> symbols;
+ int desc_size = atom_site_ptr->GetDesc().GetSize();
+ int type_symbol_idx = atom_site_ptr->GetDesc().GetIndex("type_symbol");
+ int N = atom_site_ptr->GetN();
+ const std::vector<ost::io::StarLoopDataItemDO>& data = atom_site_ptr->GetData();
+ for(int i = 0; i < N; ++i) {
+ symbols.insert(data[i*desc_size + type_symbol_idx].GetValue());
+ }
+ std::vector<ost::io::StarLoopDataItemDO> atom_type_data;
+ atom_type_data.push_back(ost::io::StarLoopDataItemDO(""));
+ for(auto symbol: symbols) {
+ atom_type_data[0] = ost::io::StarLoopDataItemDO(symbol);
+ atom_type_ptr->AddData(atom_type_data);
+ }
+ }
+
+ void Feed_pdbx_poly_seq_scheme(ost::io::StarLoop* pdbx_poly_seq_scheme_ptr,
+ const String& label_asym_id,
+ int label_entity_id,
+ const ost::mol::ResidueHandleList& res_list) {
+
+ std::vector<ost::io::StarLoopDataItemDO> data;
+ data.push_back(ost::io::StarLoopDataItemDO(label_asym_id));
+ data.push_back(ost::io::StarLoopDataItemDO(label_entity_id));
+ data.push_back(ost::io::StarLoopDataItemDO(""));
+ data.push_back(ost::io::StarLoopDataItemDO(0));
+ data.push_back(ost::io::StarLoopDataItemDO(""));
+ data.push_back(ost::io::StarLoopDataItemDO(0));
+ data.push_back(ost::io::StarLoopDataItemDO(""));
+ int label_seq_id = 1;
+ for(auto res: res_list) {
+ data[2] = ost::io::StarLoopDataItemDO(res.GetName());
+ data[3] = ost::io::StarLoopDataItemDO(label_seq_id);
+ data[4] = ost::io::StarLoopDataItemDO(res.GetChain().GetName());
+ data[5] = ost::io::StarLoopDataItemDO(res.GetNumber().GetNum());
+ char ins_code = res.GetNumber().GetInsCode();
+ if(ins_code == '\0') {
+ data[6] = ost::io::StarLoopDataItemDO("");
+ } else {
+ String tmp = " ";
+ tmp[0] = ins_code;
+ data[6] = ost::io::StarLoopDataItemDO(tmp);
+ }
+ pdbx_poly_seq_scheme_ptr->AddData(data);
+ label_seq_id += 1;
+ }
+ }
+
void Feed_atom_site_(ost::io::StarLoop* atom_site_ptr,
const String& label_asym_id,
int label_entity_id,
- const ost::mol::ResidueHandleList& res_list) {
+ const ost::mol::ResidueHandleList& res_list,
+ bool is_poly) {
int label_seq_id = 1;
for(auto res: res_list) {
String comp_id = res.GetName();
@@ -250,7 +472,11 @@ namespace {
// label_entity_id
at_data.push_back(ost::io::StarLoopDataItemDO(label_entity_id));
// label_seq_id
- at_data.push_back(ost::io::StarLoopDataItemDO(label_seq_id));
+ if(is_poly) {
+ at_data.push_back(ost::io::StarLoopDataItemDO(label_seq_id));
+ } else {
+ at_data.push_back(ost::io::StarLoopDataItemDO("."));
+ }
// label_alt_id
at_data.push_back(ost::io::StarLoopDataItemDO("."));
// Cartn_x
@@ -319,22 +545,50 @@ namespace {
void Feed_entity_poly_seq_(ost::io::StarLoop* entity_poly_seq_ptr,
const std::vector<EntityInfo>& entity_info) {
// reuse data vector for efficiency
- std::vector<ost::io::StarLoopDataItemDO> mon_data;
- mon_data.push_back(ost::io::StarLoopDataItemDO(0));
- mon_data.push_back(ost::io::StarLoopDataItemDO("ALA"));
- mon_data.push_back(ost::io::StarLoopDataItemDO(1));
+ std::vector<ost::io::StarLoopDataItemDO> entity_poly_seq_data;
+ entity_poly_seq_data.push_back(ost::io::StarLoopDataItemDO(0));
+ entity_poly_seq_data.push_back(ost::io::StarLoopDataItemDO("ALA"));
+ entity_poly_seq_data.push_back(ost::io::StarLoopDataItemDO(1));
+
+ for(size_t entity_idx = 0; entity_idx < entity_info.size(); ++entity_idx) {
+ if(entity_info[entity_idx].is_poly) {
+ const std::vector<String>& mon_ids = entity_info[entity_idx].mon_ids;
+ for(size_t mon_idx = 0; mon_idx < mon_ids.size(); ++mon_idx) {
+ entity_poly_seq_data[0] = ost::io::StarLoopDataItemDO(entity_idx);
+ entity_poly_seq_data[1] = ost::io::StarLoopDataItemDO(mon_ids[mon_idx]);
+ entity_poly_seq_data[2] = ost::io::StarLoopDataItemDO(mon_idx+1);
+ entity_poly_seq_ptr->AddData(entity_poly_seq_data);
+ }
+ }
+ }
+ }
+ void Feed_entity_poly_(ost::io::StarLoop* entity_poly_ptr,
+ const std::vector<EntityInfo>& entity_info) {
+ // reuse data vector for efficiency
+ std::vector<ost::io::StarLoopDataItemDO> entity_poly_data;
+ entity_poly_data.push_back(ost::io::StarLoopDataItemDO(0));
+ entity_poly_data.push_back(ost::io::StarLoopDataItemDO("other"));
for(size_t entity_idx = 0; entity_idx < entity_info.size(); ++entity_idx) {
- const std::vector<String>& mon_ids = entity_info[entity_idx].mon_ids;
- for(size_t mon_idx = 0; mon_idx < mon_ids.size(); ++mon_idx) {
- mon_data[0] = ost::io::StarLoopDataItemDO(entity_idx);
- mon_data[1] = ost::io::StarLoopDataItemDO(mon_ids[mon_idx]);
- mon_data[2] = ost::io::StarLoopDataItemDO(mon_idx+1);
- entity_poly_seq_ptr->AddData(mon_data);
+ if(entity_info[entity_idx].is_poly) {
+ entity_poly_data[0] = ost::io::StarLoopDataItemDO(entity_idx);
+ entity_poly_data[1] = ost::io::StarLoopDataItemDO(entity_info[entity_idx].poly_type);
+ entity_poly_ptr->AddData(entity_poly_data);
}
}
}
+ void Feed_chem_comp_(ost::io::StarLoop* chem_comp_ptr,
+ const std::map<String, CompInfo>& comp_infos) {
+ std::vector<ost::io::StarLoopDataItemDO> comp_data;
+ comp_data.push_back(ost::io::StarLoopDataItemDO("ALA"));
+ comp_data.push_back(ost::io::StarLoopDataItemDO("L-peptide linking"));
+ for(auto it = comp_infos.begin(); it != comp_infos.end(); ++it) {
+ comp_data[0] = it->first;
+ comp_data[1] = it->second.type;
+ chem_comp_ptr->AddData(comp_data);
+ }
+ }
}
namespace ost { namespace io {
@@ -342,47 +596,78 @@ namespace ost { namespace io {
MMCifWriter::MMCifWriter(const String& filename, const IOProfile& profile):
StarWriter(filename),
profile_(profile),
+ atom_type_(NULL),
atom_site_(NULL),
+ pdbx_poly_seq_scheme_(NULL),
entity_(NULL),
struct_asym_(NULL),
- entity_poly_seq_(NULL) { }
+ entity_poly_(NULL),
+ entity_poly_seq_(NULL),
+ chem_comp_(NULL) { }
MMCifWriter::~MMCifWriter() {
+ if(atom_type_ != NULL) {
+ delete atom_type_;
+ }
if(atom_site_ != NULL) {
delete atom_site_;
}
+ if(pdbx_poly_seq_scheme_ != NULL) {
+ delete pdbx_poly_seq_scheme_;
+ }
if(entity_ != NULL) {
delete entity_;
}
if(struct_asym_ != NULL) {
delete struct_asym_;
}
+ if(entity_poly_ != NULL) {
+ delete entity_poly_;
+ }
if(entity_poly_seq_ != NULL) {
delete entity_poly_seq_;
}
+ if(chem_comp_ != NULL) {
+ delete chem_comp_;
+ }
}
-void MMCifWriter::Process_atom_site(const ost::mol::EntityHandle& ent) {
-
+void MMCifWriter::SetEntity(const ost::mol::EntityHandle& ent) {
// tabula rasa
+ if(atom_type_ != NULL) {
+ delete atom_type_;
+ }
if(atom_site_ != NULL) {
delete atom_site_;
}
+ if(pdbx_poly_seq_scheme_ != NULL) {
+ delete pdbx_poly_seq_scheme_;
+ }
if(entity_ != NULL) {
delete entity_;
}
if(struct_asym_ != NULL) {
delete struct_asym_;
}
+ if(entity_poly_ != NULL) {
+ delete entity_poly_;
+ }
if(entity_poly_seq_ != NULL) {
delete entity_poly_seq_;
- }
+ }
+ if(chem_comp_ != NULL) {
+ delete chem_comp_;
+ }
+ atom_type_ = Setup_atom_type_ptr();
atom_site_ = Setup_atom_site_ptr();
+ pdbx_poly_seq_scheme_ = Setup_pdbx_poly_seq_scheme_ptr();
entity_ = Setup_entity_ptr();
struct_asym_ = Setup_struct_asym_ptr();
+ entity_poly_ = Setup_entity_poly_ptr();
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
@@ -394,16 +679,18 @@ void MMCifWriter::Process_atom_site(const ost::mol::EntityHandle& ent) {
std::vector<std::vector<ost::mol::ResidueHandle> > W_chains; // WATER
std::vector<ost::mol::ResidueHandle> N_chains; // NON_POLYMER (1 res per chain)
std::vector<ost::mol::ResidueHandle> U_chains; // UNKNOWN (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;
@@ -533,7 +820,12 @@ void MMCifWriter::Process_atom_site(const ost::mol::EntityHandle& ent) {
ost::mol::ChemClass::L_PEPTIDE_LINKING,
res_list,
entity_info);
- Feed_atom_site_(atom_site_, chain_name, entity_id, res_list);
+ 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
@@ -543,7 +835,12 @@ void MMCifWriter::Process_atom_site(const ost::mol::EntityHandle& ent) {
ost::mol::ChemClass::D_PEPTIDE_LINKING,
res_list,
entity_info);
- Feed_atom_site_(atom_site_, chain_name, entity_id, res_list);
+ 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
@@ -553,7 +850,12 @@ void MMCifWriter::Process_atom_site(const ost::mol::EntityHandle& ent) {
ost::mol::ChemClass::PEPTIDE_LINKING,
res_list,
entity_info);
- Feed_atom_site_(atom_site_, chain_name, entity_id, res_list);
+ 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
@@ -563,7 +865,12 @@ void MMCifWriter::Process_atom_site(const ost::mol::EntityHandle& ent) {
ost::mol::ChemClass::RNA_LINKING,
res_list,
entity_info);
- Feed_atom_site_(atom_site_, chain_name, entity_id, res_list);
+ 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
@@ -573,7 +880,12 @@ void MMCifWriter::Process_atom_site(const ost::mol::EntityHandle& ent) {
ost::mol::ChemClass::DNA_LINKING,
res_list,
entity_info);
- Feed_atom_site_(atom_site_, chain_name, entity_id, res_list);
+ 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 L_SACHARIDE
@@ -583,7 +895,12 @@ void MMCifWriter::Process_atom_site(const ost::mol::EntityHandle& ent) {
ost::mol::ChemClass::L_SACCHARIDE,
res_list,
entity_info);
- Feed_atom_site_(atom_site_, chain_name, entity_id, res_list);
+ 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_SACHARIDE
@@ -593,7 +910,12 @@ void MMCifWriter::Process_atom_site(const ost::mol::EntityHandle& ent) {
ost::mol::ChemClass::D_SACCHARIDE,
res_list,
entity_info);
- Feed_atom_site_(atom_site_, chain_name, entity_id, res_list);
+ 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
@@ -603,7 +925,12 @@ void MMCifWriter::Process_atom_site(const ost::mol::EntityHandle& ent) {
ost::mol::ChemClass::WATER,
res_list,
entity_info);
- Feed_atom_site_(atom_site_, chain_name, entity_id, res_list);
+ 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
@@ -615,7 +942,12 @@ void MMCifWriter::Process_atom_site(const ost::mol::EntityHandle& ent) {
ost::mol::ChemClass::NON_POLYMER,
res_list,
entity_info);
- Feed_atom_site_(atom_site_, chain_name, entity_id, res_list);
+ 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 UNKNOWN
@@ -627,17 +959,29 @@ void MMCifWriter::Process_atom_site(const ost::mol::EntityHandle& ent) {
ost::mol::ChemClass::UNKNOWN,
res_list,
entity_info);
- Feed_atom_site_(atom_site_, chain_name, entity_id, res_list);
+ 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);
Feed_entity_poly_seq_(entity_poly_seq_, entity_info);
+ Feed_chem_comp_(chem_comp_, comp_infos);
+ Feed_atom_type_(atom_type_, atom_site_);
// finalize
+ this->Push(chem_comp_);
this->Push(entity_);
this->Push(struct_asym_);
+ this->Push(entity_poly_);
this->Push(entity_poly_seq_);
+ this->Push(pdbx_poly_seq_scheme_);
+ this->Push(atom_type_);
this->Push(atom_site_);
}
diff --git a/modules/io/src/mol/mmcif_writer.hh b/modules/io/src/mol/mmcif_writer.hh
index d5f1e01bd18e66052232fff379e2495f3e5f53eb..619ff270d4093b15f346968315019d020db88b24 100644
--- a/modules/io/src/mol/mmcif_writer.hh
+++ b/modules/io/src/mol/mmcif_writer.hh
@@ -36,23 +36,20 @@ public:
virtual ~MMCifWriter();
- // initializes
- // atom_site_
- // entity_
- // struct_asym_
- // entity_poly_seq_
- void Process_atom_site(const ost::mol::EntityHandle& ent);
+ void SetEntity(const ost::mol::EntityHandle& ent);
private:
-
IOProfile profile_;
+ StarLoop* atom_type_;
StarLoop* atom_site_;
+ StarLoop* pdbx_poly_seq_scheme_;
StarLoop* entity_;
StarLoop* struct_asym_;
+ StarLoop* entity_poly_;
StarLoop* entity_poly_seq_;
+ StarLoop* chem_comp_;
};
-
}} // ns
-#endif
\ No newline at end of file
+#endif
diff --git a/modules/io/src/mol/star_base.hh b/modules/io/src/mol/star_base.hh
index 2433a0af6bb9deed53657bc636f7a60982c73b11..1441d2db6672b71e72205ef2d9b0d787ad1f20e0 100644
--- a/modules/io/src/mol/star_base.hh
+++ b/modules/io/src/mol/star_base.hh
@@ -232,9 +232,21 @@ public:
// - special characters in strings (put in quotation marks)
// - long strings (semicolon based syntax)
// see https://mmcif.wwpdb.org/docs/tutorials/mechanics/pdbx-mmcif-syntax.html
+
+
+ bool has_space = false;
+ for(char c: value) {
+ if(isspace(c)) {
+ has_space = true;
+ break;
+ }
+ }
if(value == "") {
value_ = ".";
- } else {
+ } else if(has_space) {
+ value_ = "'" + value + "'";
+ }
+ else {
value_ = value;
}
}
@@ -272,6 +284,8 @@ public:
desc_ = desc;
}
+ const StarLoopDesc& GetDesc() { return desc_; }
+
void AddData(const std::vector<StarLoopDataItemDO>& data) {
if(data.size() != desc_.GetSize()) {
throw ost::io::IOException("Invalid data size when adding to StarLoop");
@@ -279,6 +293,8 @@ public:
data_.insert(data_.end(), data.begin(), data.end());
}
+ const std::vector<StarLoopDataItemDO>& GetData() { return data_; }
+
int GetN() {
return data_.size() / desc_.GetSize();
}