diff --git a/modules/io/src/mol/mmcif_writer.cc b/modules/io/src/mol/mmcif_writer.cc
index 4ca1e2a7893f2673e5c4ae0783f1e9dda45113e6..6965cc5dc5781b8802c758fef9ff51bdee9cd7b2 100644
--- a/modules/io/src/mol/mmcif_writer.cc
+++ b/modules/io/src/mol/mmcif_writer.cc
@@ -70,11 +70,158 @@ namespace {
std::vector<int> indices;
};
+ String GuessEntityPolyType(const ost::mol::ResidueHandleList& res_list) {
+
+ // guesses _entity_poly.type based on residue chem classes
+
+ // allowed values according to mmcif_pdbx_v50.dic:
+ // - cyclic-pseudo-peptide
+ // - other
+ // - peptide nucleic acid
+ // - polydeoxyribonucleotide
+ // - polydeoxyribonucleotide/polyribonucleotide hybrid
+ // - polypeptide(D)
+ // - polypeptide(L)
+ // - polyribonucleotide
+
+ // this function won't identify cyclic-pseudo-peptides
+
+ std::set<char> chem_classes;
+ for(auto res: res_list) {
+ chem_classes.insert(res.GetChemClass());
+ }
+
+ // check for polypeptide(L)
+ if(chem_classes.size() == 1 &&
+ chem_classes.find(ost::mol::ChemClass::L_PEPTIDE_LINKING) != chem_classes.end()) {
+ return "polypeptide(L)";
+ }
+
+ if(chem_classes.size() == 2 &&
+ chem_classes.find(ost::mol::ChemClass::L_PEPTIDE_LINKING) != chem_classes.end() &&
+ chem_classes.find(ost::mol::ChemClass::PEPTIDE_LINKING) != chem_classes.end()) {
+ return "polypeptide(L)";
+ }
+
+ // check for polypeptide(D)
+ if(chem_classes.size() == 1 &&
+ chem_classes.find(ost::mol::ChemClass::D_PEPTIDE_LINKING) != chem_classes.end()) {
+ return "polypeptide(D)";
+ }
+
+ if(chem_classes.size() == 2 &&
+ chem_classes.find(ost::mol::ChemClass::D_PEPTIDE_LINKING) != chem_classes.end() &&
+ chem_classes.find(ost::mol::ChemClass::PEPTIDE_LINKING) != chem_classes.end()) {
+ return "polypeptide(D)";
+ }
+
+ // check for polydeoxyribonucleotide
+ if(chem_classes.size() == 1 &&
+ chem_classes.find(ost::mol::ChemClass::DNA_LINKING) != chem_classes.end()) {
+ return "polydeoxyribonucleotide";
+ }
+
+ // check for polyribonucleotide
+ if(chem_classes.size() == 1 &&
+ chem_classes.find(ost::mol::ChemClass::RNA_LINKING) != chem_classes.end()) {
+ return "polyribonucleotide";
+ }
+
+ // check for polydeoxyribonucleotide/polyribonucleotide hybrid
+ if(chem_classes.size() == 2 &&
+ chem_classes.find(ost::mol::ChemClass::RNA_LINKING) != chem_classes.end() &&
+ chem_classes.find(ost::mol::ChemClass::DNA_LINKING) != chem_classes.end()) {
+ return "polydeoxyribonucleotide/polyribonucleotide hybrid";
+ }
+
+ // check for peptide nucleic acid
+ bool peptide_linking = chem_classes.find(ost::mol::ChemClass::L_PEPTIDE_LINKING) != chem_classes.end() ||
+ chem_classes.find(ost::mol::ChemClass::D_PEPTIDE_LINKING) != chem_classes.end() ||
+ chem_classes.find(ost::mol::ChemClass::PEPTIDE_LINKING) != chem_classes.end();
+ bool nucleotide_linking = chem_classes.find(ost::mol::ChemClass::DNA_LINKING) != chem_classes.end() ||
+ chem_classes.find(ost::mol::ChemClass::RNA_LINKING) != chem_classes.end();
+ std::set<char> pepnuc_set;
+ pepnuc_set.insert(ost::mol::ChemClass::L_PEPTIDE_LINKING);
+ pepnuc_set.insert(ost::mol::ChemClass::D_PEPTIDE_LINKING);
+ pepnuc_set.insert(ost::mol::ChemClass::PEPTIDE_LINKING);
+ pepnuc_set.insert(ost::mol::ChemClass::DNA_LINKING);
+ pepnuc_set.insert(ost::mol::ChemClass::RNA_LINKING);
+ pepnuc_set.insert(chem_classes.begin(), chem_classes.end());
+ if(peptide_linking && nucleotide_linking && pepnuc_set.size() == 5) {
+ return "peptide nucleic acid";
+ }
+
+ return "other";
+ }
+
+ String GuessEntityType(const ost::mol::ResidueHandleList& res_list) {
+
+ // guesses _entity.type based on residue chem classes
+
+ // allowed values according to mmcif_pdbx_v50.dic:
+ // - branched
+ // - macrolide
+ // - non-polymer
+ // - polymer
+ // - water
+
+ // this function won't identify macrolid
+
+ std::set<char> chem_classes;
+ for(auto res: res_list) {
+ chem_classes.insert(res.GetChemClass());
+ }
+
+ // check for water
+ if(chem_classes.size() == 1 &&
+ chem_classes.find(ost::mol::ChemClass::WATER) != chem_classes.end()) {
+ return "water";
+ }
+
+ // check for non-polymer
+ if(res_list.size() == 1) {
+ return "non-polymer";
+ }
+
+ // check for branched
+ std::set<char> sweet_set;
+ sweet_set.insert(ost::mol::ChemClass::L_SACCHARIDE);
+ sweet_set.insert(ost::mol::ChemClass::D_SACCHARIDE);
+ sweet_set.insert(ost::mol::ChemClass::SACCHARIDE);
+ // if the union of chem_classes and sweet_set has 3 elements, chem_classes
+ // only has sugars.
+ sweet_set.insert(chem_classes.begin(), chem_classes.end());
+ if(sweet_set.size() == 3) {
+ return "branched";
+ }
+
+ // DISCUSS THIS OVER A BEER...
+ // when arriving here, we excluded the possibility of branched and single
+ // residue chains.
+ // BUT: entities must have at least 3 residues to be considered polymers
+ // for now, we just set entities with 2 residues as non-polymer
+ if(res_list.size() == 2) {
+ return "non-polymer";
+ }
+
+ // If res_list represents a valid mmcif chain, chem_classes should only
+ // contain peptide- and nucleotide linking items
+ for(auto it: chem_classes) {
+ ost::mol::ChemClass chem_class(it);
+ if(!(chem_class.IsPeptideLinking() || chem_class.IsNucleotideLinking())) {
+ throw ost::io::IOException("Could not guess entity type");
+ }
+ }
+
+ return "polymer";
+ }
+
// 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) {
@@ -132,44 +279,6 @@ namespace {
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;
- }
-
inline String mon_id_to_olc(char chem_class,
const String& mon_id) {
@@ -291,9 +400,7 @@ namespace {
return "Y";
}
if(mon_id == "TPO") {
- return "(PTO)"; // This is stupid - PTO would be Pseudotropine in
- // the chem comp dictionary. But hey, thats what the
- // mmcif reference demands...
+ return "(TPO)";
}
break;
}
@@ -304,7 +411,6 @@ namespace {
break;
}
}
- return "(UNK)";
} else if(ost::mol::ChemClass(chem_class).IsNucleotideLinking()) {
switch(mon_id[0]) {
case 'A': {
@@ -353,15 +459,11 @@ namespace {
break;
}
}
-
- return "N";
-
} else {
throw ost::io::IOException("Can only get OLCs for peptides/nucleotides");
}
-
-
+ return "(" + mon_id + ")";
}
void Setup_chem_comp_(const ost::mol::ResidueHandleList& res_list,
@@ -386,129 +488,74 @@ namespace {
// 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 type; // relevant for _entity
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
+ bool is_poly; // in principle type == "polymer"
String seq; // _entity_poly.pdbx_seq_one_letter_code
String seq_can; // _entity_poly.pdbx_seq_one_letter_code_can
};
int Setup_entity_(const String& asym_chain_name,
- char chem_class,
const ost::mol::ResidueHandleList& res_list,
std::vector<EntityInfo>& entity_infos) {
-
- // deal with water
- if(chem_class == ost::mol::ChemClass::WATER) {
- for(size_t i = 0; i < entity_infos.size(); ++i) {
- if(entity_infos[i].chem_class == ost::mol::ChemClass::WATER) {
- entity_infos[i].asym_ids.push_back(asym_chain_name);
- return i;
- }
- }
- int entity_idx = entity_infos.size();
- entity_infos.push_back(EntityInfo());
- 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;
+ String type = GuessEntityType(res_list);
+ String poly_type = "";
+ bool is_poly = type == "polymer";
+ if(is_poly) {
+ poly_type = GuessEntityPolyType(res_list);
}
- // deal with NON_POLYMER
- if(chem_class == ost::mol::ChemClass::NON_POLYMER) {
- for(size_t i = 0; i < entity_infos.size(); ++i) {
- if(entity_infos[i].chem_class == ost::mol::ChemClass::NON_POLYMER &&
- res_list[0].GetName() == entity_infos[i].mon_ids[0]) {
- entity_infos[i].asym_ids.push_back(asym_chain_name);
- return i;
- }
- }
- int entity_idx = entity_infos.size();
- entity_infos.push_back(EntityInfo());
- 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;
- }
-
- // deal with UNKNOWN
- if(chem_class == ost::mol::ChemClass::UNKNOWN) {
- for(size_t i = 0; i < entity_infos.size(); ++i) {
- if(entity_infos[i].chem_class == ost::mol::ChemClass::UNKNOWN &&
- res_list[0].GetName() == entity_infos[i].mon_ids[0]) {
- entity_infos[i].asym_ids.push_back(asym_chain_name);
- return i;
- }
- }
- int entity_idx = entity_infos.size();
- entity_infos.push_back(EntityInfo());
- 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;
- }
-
- // with the current code, the following chem classes are considered
- // polymers: PEPTIDE_LINKING, D_PEPTIDE_LINKING, L_PEPTIDE_LINKING
- // RNA_LINKING, DNA_LINKING, L_SACCHARIDE, D_SACCHARIDE, SACCHARIDE
- // They're also considered polymers even if only one residue is there
- // Needs checking...
-
std::vector<String> mon_ids;
- for(auto res : res_list) {
- mon_ids.push_back(res.GetName());
+ if(type == "water") {
+ mon_ids.push_back("HOH");
+ } else {
+ for(auto res : res_list) {
+ mon_ids.push_back(res.GetName());
+ }
}
- // check whether we already have that entity
- // right now we're just looking for exact matches in chem_class and
- // mon_ids (i.e. sequence).
- int entity_idx = -1;
+ // check if entity is already there
for(size_t i = 0; i < entity_infos.size(); ++i) {
- if(entity_infos[i].chem_class == chem_class &&
- entity_infos[i].mon_ids == mon_ids) {
- entity_idx = i;
- break;
+ if(entity_infos[i].type == type &&
+ entity_infos[i].poly_type == poly_type &&
+ entity_infos[i].mon_ids == mon_ids) {
+ entity_infos[i].asym_ids.push_back(asym_chain_name);
+ return i;
}
}
- if(entity_idx != -1) {
- entity_infos[entity_idx].asym_ids.push_back(asym_chain_name);
- } else {
- entity_idx = entity_infos.size();
- entity_infos.push_back(EntityInfo());
- 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;
-
- // seqres basically follows a hardcoded table from the mmcif reference
- std::stringstream ss;
- for(auto mon_id: mon_ids) {
- ss << mon_id_to_olc(chem_class, mon_id);
- }
- entity_infos.back().seq = ss.str();
- ss.clear();
-
- // canonical seqres maps one letter codes of parent residues
- // OpenStructure does the same when setting up the entity in
- // the processor. There still might be '?' or similar which
- // should be treated separately... but hey, I'm in a rush for
- // now
+ // need to create new entity
+ int entity_idx = entity_infos.size();
+ entity_infos.push_back(EntityInfo());
+ entity_infos.back().type = type;
+ entity_infos.back().poly_type = poly_type;
+ entity_infos.back().asym_ids.push_back(asym_chain_name);
+ entity_infos.back().mon_ids = mon_ids;
+ entity_infos.back().is_poly = is_poly;
+ if(is_poly) {
+ std::stringstream seq;
+ std::stringstream seq_can;
for(auto res: res_list) {
- ss << res.GetOneLetterCode();
+ // seqres basically follows a hardcoded table from the mmcif reference
+ seq << mon_id_to_olc(res.GetChemClass(), res.GetName());
+ // canonical seqres maps one letter codes of parent residues
+ // OpenStructure does the same when setting up the entity in the
+ // processor. We just trust OpenStructure to do the right thing but set
+ // olc to 'X' in case of invalid olc outside [A-Z] (example is '?')
+ char olc = res.GetOneLetterCode();
+ if(olc < 'A' || olc > 'Z') {
+ seq_can << 'X';
+ } else {
+ seq_can << res.GetOneLetterCode();
+ }
}
- entity_infos.back().seq_can = ss.str();
+ entity_infos.back().seq = seq.str();
+ entity_infos.back().seq_can = seq_can.str();
}
+
return entity_idx;
}
@@ -723,25 +770,8 @@ namespace {
const std::vector<EntityInfo>& entity_info) {
for(size_t entity_idx = 0; entity_idx < entity_info.size(); ++entity_idx) {
std::vector<ost::io::StarLoopDataItemDO> ent_data;
- // id
ent_data.push_back(ost::io::StarLoopDataItemDO(entity_idx));
- // type
- ost::mol::ChemClass chem_class(entity_info[entity_idx].chem_class);
- if(chem_class.IsPeptideLinking() || chem_class.IsNucleotideLinking()) {
- ent_data.push_back(ost::io::StarLoopDataItemDO("polymer"));
- } else if(chem_class.IsWater()) {
- ent_data.push_back(ost::io::StarLoopDataItemDO("water"));
- } else if(chem_class == ost::mol::ChemClass::NON_POLYMER) {
- ent_data.push_back(ost::io::StarLoopDataItemDO("non-polymer"));
- } else if(chem_class.IsSaccharide()) {
- // NOT SURE WHETHER THIS MAKES ANY SENSE!
- ent_data.push_back(ost::io::StarLoopDataItemDO("branched"));
- } else if(chem_class == ost::mol::ChemClass::UNKNOWN) {
- // NOT SURE WHETHER THIS MAKES ANY SENSE!
- ent_data.push_back(ost::io::StarLoopDataItemDO("non-polymer"));
- } else {
- throw ost::io::IOException("Entity type issue");
- }
+ ent_data.push_back(ost::io::StarLoopDataItemDO(entity_info[entity_idx].type));
entity_ptr->AddData(ent_data);
}
}
@@ -894,11 +924,10 @@ void MMCifWriter::SetEntity(const ost::mol::EntityHandle& ent) {
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
- std::vector<std::vector<ost::mol::ResidueHandle> > X_chains; // L_SACCHARIDE
- std::vector<std::vector<ost::mol::ResidueHandle> > Y_chains; // D_SACCHARIDE
+ // 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::vector<ost::mol::ResidueHandle> U_chains; // UNKNOWN (1 res per chain)
std::map<String, CompInfo> comp_infos;
ost::mol::ChainHandleList chain_list = ent.GetChainList();
@@ -916,8 +945,7 @@ void MMCifWriter::SetEntity(const ost::mol::EntityHandle& ent) {
bool has_peptide_linking = false;
bool has_rna_linking = false;
bool has_dna_linking = false;
- bool has_l_saccharide = false;
- bool has_d_saccharide = false;
+ bool has_saccharide = false;
bool has_water = false;
for(auto res: res_list) {
@@ -950,11 +978,15 @@ void MMCifWriter::SetEntity(const ost::mol::EntityHandle& ent) {
}
if(res.GetChemClass() == ost::mol::ChemClass::L_SACCHARIDE) {
- has_l_saccharide = true;
+ has_saccharide = true;
}
if(res.GetChemClass() == ost::mol::ChemClass::D_SACCHARIDE) {
- has_d_saccharide = true;
+ has_saccharide = true;
+ }
+
+ if(res.GetChemClass() == ost::mol::ChemClass::SACCHARIDE) {
+ has_saccharide = true;
}
if(res.GetChemClass() == ost::mol::ChemClass::WATER) {
@@ -988,12 +1020,8 @@ void MMCifWriter::SetEntity(const ost::mol::EntityHandle& ent) {
S_chains.push_back(ost::mol::ResidueHandleList());
}
- if(has_l_saccharide) {
- X_chains.push_back(ost::mol::ResidueHandleList());
- }
-
- if(has_d_saccharide) {
- Y_chains.push_back(ost::mol::ResidueHandleList());
+ if(has_saccharide) {
+ Z_chains.push_back(ost::mol::ResidueHandleList());
}
if(has_water) {
@@ -1014,15 +1042,18 @@ void MMCifWriter::SetEntity(const ost::mol::EntityHandle& ent) {
} else if(res.GetChemClass() == ost::mol::ChemClass::DNA_LINKING) {
S_chains.back().push_back(res);
} else if(res.GetChemClass() == ost::mol::ChemClass::L_SACCHARIDE) {
- X_chains.back().push_back(res);
+ Z_chains.back().push_back(res);
} else if(res.GetChemClass() == ost::mol::ChemClass::D_SACCHARIDE) {
- Y_chains.back().push_back(res);
+ 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) {
- U_chains.push_back(res);
+ // 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...");
@@ -1037,7 +1068,6 @@ void MMCifWriter::SetEntity(const ost::mol::EntityHandle& ent) {
for(auto res_list: L_chains) {
String chain_name = chain_name_gen.Get();
int entity_id = Setup_entity_(chain_name,
- ost::mol::ChemClass::L_PEPTIDE_LINKING,
res_list,
entity_info);
Feed_atom_site_(atom_site_, chain_name, entity_id, res_list,
@@ -1052,7 +1082,6 @@ void MMCifWriter::SetEntity(const ost::mol::EntityHandle& ent) {
for(auto res_list: D_chains) {
String chain_name = chain_name_gen.Get();
int entity_id = Setup_entity_(chain_name,
- ost::mol::ChemClass::D_PEPTIDE_LINKING,
res_list,
entity_info);
Feed_atom_site_(atom_site_, chain_name, entity_id, res_list,
@@ -1067,7 +1096,6 @@ void MMCifWriter::SetEntity(const ost::mol::EntityHandle& ent) {
for(auto res_list: P_chains) {
String chain_name = chain_name_gen.Get();
int entity_id = Setup_entity_(chain_name,
- ost::mol::ChemClass::PEPTIDE_LINKING,
res_list,
entity_info);
Feed_atom_site_(atom_site_, chain_name, entity_id, res_list,
@@ -1082,7 +1110,6 @@ void MMCifWriter::SetEntity(const ost::mol::EntityHandle& ent) {
for(auto res_list: R_chains) {
String chain_name = chain_name_gen.Get();
int entity_id = Setup_entity_(chain_name,
- ost::mol::ChemClass::RNA_LINKING,
res_list,
entity_info);
Feed_atom_site_(atom_site_, chain_name, entity_id, res_list,
@@ -1097,7 +1124,6 @@ void MMCifWriter::SetEntity(const ost::mol::EntityHandle& ent) {
for(auto res_list: S_chains) {
String chain_name = chain_name_gen.Get();
int entity_id = Setup_entity_(chain_name,
- ost::mol::ChemClass::DNA_LINKING,
res_list,
entity_info);
Feed_atom_site_(atom_site_, chain_name, entity_id, res_list,
@@ -1108,26 +1134,10 @@ void MMCifWriter::SetEntity(const ost::mol::EntityHandle& ent) {
}
}
- // process L_SACHARIDE
- for(auto res_list: X_chains) {
+ // process SACHARIDE
+ for(auto res_list: Z_chains) {
String chain_name = chain_name_gen.Get();
int entity_id = Setup_entity_(chain_name,
- ost::mol::ChemClass::L_SACCHARIDE,
- 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_SACHARIDE
- for(auto res_list: Y_chains) {
- String chain_name = chain_name_gen.Get();
- int entity_id = Setup_entity_(chain_name,
- ost::mol::ChemClass::D_SACCHARIDE,
res_list,
entity_info);
Feed_atom_site_(atom_site_, chain_name, entity_id, res_list,
@@ -1142,7 +1152,6 @@ void MMCifWriter::SetEntity(const ost::mol::EntityHandle& ent) {
for(auto res_list: W_chains) {
String chain_name = chain_name_gen.Get();
int entity_id = Setup_entity_(chain_name,
- ost::mol::ChemClass::WATER,
res_list,
entity_info);
Feed_atom_site_(atom_site_, chain_name, entity_id, res_list,
@@ -1159,24 +1168,6 @@ void MMCifWriter::SetEntity(const ost::mol::EntityHandle& ent) {
res_list.push_back(res);
String chain_name = chain_name_gen.Get();
int entity_id = Setup_entity_(chain_name,
- ost::mol::ChemClass::NON_POLYMER,
- 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 UNKNOWN
- for(auto res: U_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,
- ost::mol::ChemClass::UNKNOWN,
res_list,
entity_info);
Feed_atom_site_(atom_site_, chain_name, entity_id, res_list,
diff --git a/modules/mol/base/src/chem_class.hh b/modules/mol/base/src/chem_class.hh
index aa4033e7f24d7a9c8a6ab04ad84432e234979159..14581ac5b0925f74e5fbc12a44f65a67eeff7416 100644
--- a/modules/mol/base/src/chem_class.hh
+++ b/modules/mol/base/src/chem_class.hh
@@ -26,30 +26,30 @@ namespace ost { namespace mol {
struct DLLEXPORT ChemClass {
- const static char PEPTIDE_LINKING ='P';
- const static char D_PEPTIDE_LINKING ='D';
- const static char L_PEPTIDE_LINKING ='L';
- const static char RNA_LINKING ='R';
- const static char DNA_LINKING ='S';
- const static char NON_POLYMER ='N';
- const static char L_SACCHARIDE ='X';
- const static char D_SACCHARIDE ='Y';
- const static char SACCHARIDE ='Z';
- const static char WATER ='W';
- const static char UNKNOWN ='U';
+ static constexpr char PEPTIDE_LINKING ='P';
+ static constexpr char D_PEPTIDE_LINKING ='D';
+ static constexpr char L_PEPTIDE_LINKING ='L';
+ static constexpr char RNA_LINKING ='R';
+ static constexpr char DNA_LINKING ='S';
+ static constexpr char NON_POLYMER ='N';
+ static constexpr char L_SACCHARIDE ='X';
+ static constexpr char D_SACCHARIDE ='Y';
+ static constexpr char SACCHARIDE ='Z';
+ static constexpr char WATER ='W';
+ static constexpr char UNKNOWN ='U';
// for backward compatibility to 1.1 and earlier
- const static char PeptideLinking =PEPTIDE_LINKING;
- const static char DPeptideLinking =D_PEPTIDE_LINKING;
- const static char LPeptideLinking =L_PEPTIDE_LINKING;
- const static char RNALinking =RNA_LINKING;
- const static char DNALinking =DNA_LINKING;
- const static char NonPolymer =NON_POLYMER;
- const static char LSaccharide =L_SACCHARIDE;
- const static char DSaccharide =D_SACCHARIDE;
- const static char Saccharide =SACCHARIDE;
- const static char Water =WATER;
- const static char Unknown =UNKNOWN;
+ static constexpr char PeptideLinking =PEPTIDE_LINKING;
+ static constexpr char DPeptideLinking =D_PEPTIDE_LINKING;
+ static constexpr char LPeptideLinking =L_PEPTIDE_LINKING;
+ static constexpr char RNALinking =RNA_LINKING;
+ static constexpr char DNALinking =DNA_LINKING;
+ static constexpr char NonPolymer =NON_POLYMER;
+ static constexpr char LSaccharide =L_SACCHARIDE;
+ static constexpr char DSaccharide =D_SACCHARIDE;
+ static constexpr char Saccharide =SACCHARIDE;
+ static constexpr char Water =WATER;
+ static constexpr char Unknown =UNKNOWN;
explicit ChemClass(char chem_class)
: chem_class_(chem_class) {
}