diff --git a/modules/io/src/mol/mmcif_writer.cc b/modules/io/src/mol/mmcif_writer.cc
index a246fc297ef97e90b022b13f417346d2eb62c9b8..9c0b8ce4d7c0d162ad726ffbe79004e4e0e3a471 100644
--- a/modules/io/src/mol/mmcif_writer.cc
+++ b/modules/io/src/mol/mmcif_writer.cc
@@ -522,9 +522,7 @@ namespace {
break;
}
}
- } else {
- throw ost::io::IOException("Can only get OLCs for peptides/nucleotides");
- }
+ }
return "(" + mon_id + ")";
}
@@ -551,69 +549,244 @@ namespace {
// internal object with all info to fill entity_, struct_asym_,
// entity_poly_seq_ categories
struct EntityInfo {
+
+ int GetAsymIdx(const String& asym_id) const {
+ for(size_t i = 0; i < asym_ids.size(); ++i) {
+ if(asym_ids[i] == asym_id) {
+ return i;
+ }
+ }
+ throw "asdf";
+ }
+
String type; // relevant for _entity
String poly_type; // relevant for _entity_poly
+ bool is_poly; // in principle type == "polymer"
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 type == "polymer"
- String seq; // _entity_poly.pdbx_seq_one_letter_code
- String seq_can; // _entity_poly.pdbx_seq_one_letter_code_can
+ std::vector<String> seq_olcs; // relevant for pdbx_seq_one_letter_code
+ std::vector<String> seq_can_olcs; // relevant for pdbx_seq_one_letter_code_can
+ std::vector<std::vector<String> > asym_alns; // one alignment to mon_ids for
+ // each element in asym_ids.
+ // relevant for label_seq_id
+ // contains "-" for residues
+ // that are missing in ATOMSEQ.
+ // in theory that would only be
+ // necessary for polymers but
+ // here we add everything...
};
+ bool Match_entity_resnum(const ost::mol::ResidueHandleList& res_list,
+ const EntityInfo& info,
+ Real beyond_frac = 0.05) {
+ // Checks if res_list matches SEQRES given in info.mon_ids
+ // It may be that res_list defines residues beyond this SEQRES or
+ // has residues that are not yet defined, i.e. the respective mon_id is "-".
+ // This function returns True if the number of such occurences is below
+ // the specified fraction of actual matches (default: 5%).
+ int n_beyond = 0;
+ int n_matches = 0;
+ int num_mon_ids = info.mon_ids.size();
+ for(auto res: res_list) {
+ int num = res.GetNumber().GetNum();
+ if(num < 1) {
+ std::stringstream ss;
+ ss << "Cannot perform resnum based alignment with invalid resnum in ";
+ ss << "residue " << res;
+ throw ost::io::IOException(ss.str());
+ } else if (num > num_mon_ids) {
+ ++n_beyond;
+ } else {
+ if(info.mon_ids[num-1] == "-") {
+ ++n_beyond; // we're basically filling an unknown gap...
+ } else if(info.mon_ids[num-1] == res.GetName()) {
+ ++n_matches;
+ } else {
+ return false;
+ }
+ }
+ }
+ if(n_matches == 0) {
+ return false;
+ } else {
+ return n_beyond / n_matches <= beyond_frac;
+ }
+ }
+
+ bool Match_entity(const ost::mol::ResidueHandleList& res_list,
+ const EntityInfo& info) {
+ // checks if the residue names in res_list are an exact match
+ // with mon_ids in info
+ std::vector<String> mon_ids;
+ for(auto res : res_list) {
+ mon_ids.push_back(res.GetName());
+ }
+ return mon_ids == info.mon_ids;
+ }
+
+ void Add_asym(const String& asym_chain_name,
+ EntityInfo& info) {
+ // adds asym_chain_name to info under the assumption that mon_ids
+ // exactly match => just add a copy of mon_ids to asym_alns
+ info.asym_ids.push_back(asym_chain_name);
+ info.asym_alns.push_back(info.mon_ids);
+ }
+
+ void Add_asym_resnum(const String& asym_chain_name,
+ const ost::mol::ResidueHandleList& res_list,
+ EntityInfo& info) {
+
+ if(!info.is_poly) {
+ // no need for SEQRES alignment vodoo
+ Add_asym(asym_chain_name, info);
+ return;
+ }
+
+ int max_resnum = info.mon_ids.size();
+ std::vector<String> mon_ids;
+ std::vector<int> resnums;
+
+ for(auto res: res_list) {
+ int num = res.GetNumber().GetNum();
+ // assumes that Match_entity_resnum has already been run to check for
+ // resnum < 1
+ mon_ids.push_back(res.GetName());
+ resnums.push_back(num);
+ max_resnum = std::max(max_resnum, num);
+ }
+
+ std::vector<String> aln_mon_ids(max_resnum, "-");
+ for(size_t i = 0; i < mon_ids.size(); ++i) {
+ aln_mon_ids[resnums[i]-1] = mon_ids[i];
+ }
+
+ if(max_resnum > static_cast<int>(info.mon_ids.size())) {
+ // This chain covers more residues towards C-terminus than any chain that
+ // is associated with this entity - expand to enforce equal size
+ int N = max_resnum - info.mon_ids.size();
+ info.mon_ids.insert(info.mon_ids.end(), N, "-");
+ info.seq_olcs.insert(info.seq_olcs.end(), N, "-");
+ info.seq_can_olcs.insert(info.seq_can_olcs.end(), N, "-");
+ for(size_t asym_idx = 0; asym_idx < info.asym_alns.size(); ++asym_idx) {
+ info.asym_alns[asym_idx].insert(info.asym_alns[asym_idx].end(), N, "-");
+ }
+ }
+
+ // Fill SEQRES infos newly covered by this asym chain
+ for(size_t i = 0; i < resnums.size(); ++i) {
+ if(info.mon_ids[resnums[i]-1] == "-") {
+ info.mon_ids[resnums[i]-1] = mon_ids[i];
+ const ost::mol::ResidueHandle& res = res_list[i];
+ info.seq_olcs[resnums[i]-1] = mon_id_to_olc(res.GetChemClass(),
+ mon_ids[i]);
+ char olc = res.GetOneLetterCode();
+ if(olc < 'A' || olc > 'Z') {
+ info.seq_can_olcs[resnums[i]-1] = "X";
+ } else {
+ info.seq_can_olcs[resnums[i]-1] = String(1, olc);
+ }
+ }
+ }
+
+ // finalize
+ info.asym_ids.push_back(asym_chain_name);
+ info.asym_alns.push_back(aln_mon_ids);
+ }
+
int Setup_entity(const String& asym_chain_name,
const String& type,
const String& poly_type,
const ost::mol::ResidueHandleList& res_list,
+ bool resnum_alignment,
std::vector<EntityInfo>& entity_infos) {
bool is_poly = type == "polymer";
- std::vector<String> mon_ids;
- if(type == "water") {
- mon_ids.push_back("HOH");
- } else {
- for(auto res : res_list) {
- mon_ids.push_back(res.GetName());
- }
+ if(!is_poly && res_list.size() != 1 && type != "water") {
+ std::stringstream ss;
+ ss << "Cannot setup entity with " << res_list.size() << " residues ";
+ ss << "but is of type: " << type;
+ throw ost::io::IOException(ss.str());
}
// check if entity is already there
for(size_t i = 0; i < entity_infos.size(); ++i) {
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;
+ entity_infos[i].poly_type == poly_type) {
+ if(is_poly && resnum_alignment) {
+ if(Match_entity_resnum(res_list, entity_infos[i])) {
+ Add_asym_resnum(asym_chain_name, res_list, entity_infos[i]);
+ return i;
+ }
+ } else {
+ if(Match_entity(res_list, entity_infos[i])) {
+ Add_asym(asym_chain_name, entity_infos[i]);
+ return i;
+ }
+ }
}
}
// 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;
+ std::vector<String> mon_ids;
+ std::vector<String> seq;
+ std::vector<String> seq_can;
+
+ if(is_poly && resnum_alignment) {
+ int max_resnum = res_list.size();
+ std::vector<String> res_mon_ids;
+ std::vector<int> resnums;
+ for(auto res: res_list) {
+ int num = res.GetNumber().GetNum();
+ if(num < 1) {
+ throw "asdf";
+ }
+ res_mon_ids.push_back(res.GetName());
+ resnums.push_back(num);
+ max_resnum = std::max(max_resnum, num);
+ }
+ mon_ids.assign(max_resnum, "-");
+ seq.assign(max_resnum, "-");
+ seq_can.assign(max_resnum, "-");
+ for(size_t i = 0; i < res_mon_ids.size(); ++i) {
+ mon_ids[resnums[i]-1] = res_mon_ids[i];
+ const ost::mol::ResidueHandle& res = res_list[i];
+ seq[resnums[i]-1] = mon_id_to_olc(res.GetChemClass(),
+ mon_ids[resnums[i]-1]);
+ char olc = res.GetOneLetterCode();
+ if(olc < 'A' || olc > 'Z') {
+ seq_can[resnums[i]-1] = "X";
+ } else {
+ seq_can[resnums[i]-1] = String(1, olc);
+ }
+ }
+ } else {
for(auto res: res_list) {
- // 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 '?')
+ mon_ids.push_back(res.GetName());
+ seq.push_back(mon_id_to_olc(res.GetChemClass(), res.GetName()));
char olc = res.GetOneLetterCode();
if(olc < 'A' || olc > 'Z') {
- seq_can << 'X';
+ seq_can.push_back("X");
} else {
- seq_can << res.GetOneLetterCode();
+ seq_can.push_back(String(1, olc));
}
}
- entity_infos.back().seq = seq.str();
- entity_infos.back().seq_can = seq_can.str();
+ }
+
+
+ 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().mon_ids = mon_ids;
+ entity_infos.back().seq_olcs = seq;
+ entity_infos.back().seq_can_olcs = seq_can;
+ entity_infos.back().is_poly = is_poly;
+
+ if(is_poly && resnum_alignment) {
+ Add_asym_resnum(asym_chain_name, res_list, entity_infos.back());
+ } else {
+ Add_asym(asym_chain_name, entity_infos.back());
}
return entity_idx;
@@ -621,6 +794,7 @@ namespace {
int Setup_entity_(const String& asym_chain_name,
const ost::mol::ResidueHandleList& res_list,
+ bool resnum_alignment,
std::vector<EntityInfo>& entity_infos) {
String type = GuessEntityType(res_list);
@@ -630,12 +804,13 @@ namespace {
poly_type = GuessEntityPolyType(res_list);
}
return Setup_entity(asym_chain_name, type, poly_type, res_list,
- entity_infos);
+ resnum_alignment, entity_infos);
}
int Setup_entity_(const String& asym_chain_name,
ost::mol::ChainType chain_type,
const ost::mol::ResidueHandleList& res_list,
+ bool resnum_alignment,
std::vector<EntityInfo>& entity_infos) {
// use chain_type info attached to chain to determine
// _entity.type and _entity_poly.type
@@ -657,7 +832,7 @@ namespace {
}
}
return Setup_entity(asym_chain_name, type, poly_type, res_list,
- entity_infos);
+ resnum_alignment, entity_infos);
}
ost::io::StarLoop* Setup_atom_type_ptr() {
@@ -777,7 +952,9 @@ namespace {
void Feed_pdbx_poly_seq_scheme(ost::io::StarLoop* pdbx_poly_seq_scheme_ptr,
const String& label_asym_id,
int label_entity_id,
+ EntityInfo& entity_info,
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));
@@ -786,20 +963,52 @@ namespace {
data.push_back(ost::io::StarLoopDataItemDO(""));
data.push_back(ost::io::StarLoopDataItemDO(0));
data.push_back(ost::io::StarLoopDataItemDO(""));
- int label_seq_id = 1;
+
+ int asym_idx = entity_info.GetAsymIdx(label_asym_id);
+ const std::vector<String>& aln = entity_info.asym_alns[asym_idx];
+ int label_seq_id = 0; // 0-based index
+
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("");
+ String res_name = res.GetName();
+ while(aln[label_seq_id] == "-") {
+ ++label_seq_id;
+ }
+
+ if(res_name != aln[label_seq_id]) {
+ throw "ksajdhfgjkaljshdfsfgd";
+ }
+
+ data[2] = ost::io::StarLoopDataItemDO(res_name);
+ data[3] = ost::io::StarLoopDataItemDO(label_seq_id + 1);
+
+ // the remaining data items honor String properties if set:
+ // pdb_auth_chain_name, pdb_auth_resnum and pdb_auth_ins_code
+
+ if(res.GetChain().HasProp("pdb_auth_chain_name")) {
+ data[4] =
+ ost::io::StarLoopDataItemDO(res.GetChain().GetStringProp("pdb_auth_chain_name"));
} else {
- String tmp = " ";
- tmp[0] = ins_code;
- data[6] = ost::io::StarLoopDataItemDO(tmp);
- }
+ data[4] = ost::io::StarLoopDataItemDO(res.GetChain().GetName());
+ }
+
+ if(res.HasProp("pdb_auth_resnum")) {
+ data[5] = ost::io::StarLoopDataItemDO(res.GetStringProp("pdb_auth_resnum"));
+ } else {
+ data[5] = ost::io::StarLoopDataItemDO(res.GetNumber().GetNum());
+ }
+
+ if(res.HasProp("pdb_auth_ins_code")) {
+ data[6] = ost::io::StarLoopDataItemDO(res.GetStringProp("pdb_auth_ins_code"));
+ } else {
+ 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;
}
@@ -808,14 +1017,41 @@ namespace {
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,
- bool is_poly) {
- int label_seq_id = 1;
+ const EntityInfo& entity_info,
+ const ost::mol::ResidueHandleList& res_list) {
+
+ int asym_idx = entity_info.GetAsymIdx(label_asym_id);
+ const std::vector<String>& aln = entity_info.asym_alns[asym_idx];
+ int label_seq_id = 0; // 0-based index
+
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")) {
+ auth_asym_id = res.GetStringProp("pdb_auth_chain_name");
+ }
String auth_seq_id = res.GetNumber().AsString();
+ if(res.HasProp("pdb_auth_resnum")) {
+ std::stringstream ss;
+ ss << res.GetStringProp("pdb_auth_resnum");
+ if(res.HasProp("pdb_auth_ins_code")) {
+ String ins_code = res.GetStringProp("pdb_auth_ins_code");
+ if(ins_code != "?") {
+ ss << ins_code;
+ }
+ }
+ auth_seq_id = ss.str();
+ }
for(auto at: at_list) {
std::vector<ost::io::StarLoopDataItemDO> at_data;
// group_PDB
@@ -835,8 +1071,8 @@ namespace {
// label_entity_id
at_data.push_back(ost::io::StarLoopDataItemDO(label_entity_id));
// label_seq_id
- if(is_poly) {
- at_data.push_back(ost::io::StarLoopDataItemDO(label_seq_id));
+ if(entity_info.is_poly) {
+ at_data.push_back(ost::io::StarLoopDataItemDO(label_seq_id+1));
} else {
at_data.push_back(ost::io::StarLoopDataItemDO("."));
}
@@ -859,7 +1095,7 @@ namespace {
// id
at_data.push_back(ost::io::StarLoopDataItemDO(atom_site_ptr->GetN()));
// pdbx_PDB_ins_code
- at_data.push_back(ost::io::StarLoopDataItemDO(""));
+ at_data.push_back(ost::io::StarLoopDataItemDO("")); // CHECK THIS, ADD STUFF FROM AUTH_SEQ_ID?
atom_site_ptr->AddData(at_data);
}
++label_seq_id;
@@ -921,8 +1157,24 @@ namespace {
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_data[2] = ost::io::StarLoopDataItemDO(entity_info[entity_idx].seq);
- entity_poly_data[3] = ost::io::StarLoopDataItemDO(entity_info[entity_idx].seq_can);
+ std::stringstream seq;
+ std::stringstream seq_can;
+ for(size_t idx = 0; idx < entity_info[entity_idx].mon_ids.size(); ++idx) {
+ if(entity_info[entity_idx].seq_olcs[idx] == "-") {
+ // X IS PROBABLY NOT THE RIGHT THING FOR
+ // pdbx_seq_one_letter_code
+ seq << "X";
+ } else {
+ seq << entity_info[entity_idx].seq_olcs[idx];
+ }
+ if(entity_info[entity_idx].seq_can_olcs[idx] == "-") {
+ seq_can << "X";
+ } else {
+ seq_can << entity_info[entity_idx].seq_can_olcs[idx];
+ }
+ }
+ entity_poly_data[2] = seq.str();
+ entity_poly_data[3] = seq_can.str();
entity_poly_ptr->AddData(entity_poly_data);
}
}
@@ -955,12 +1207,13 @@ namespace {
int entity_id = Setup_entity_(chain_name,
ch.GetType(),
res_list,
+ true,
entity_info);
- Feed_atom_site_(atom_site, chain_name, entity_id, res_list,
- entity_info[entity_id].is_poly);
+ 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, res_list);
+ entity_id, entity_info[entity_id], res_list);
}
}
}
@@ -1119,12 +1372,13 @@ namespace {
String chain_name = chain_name_gen.Get();
int entity_id = Setup_entity_(chain_name,
res_list,
+ false,
entity_info);
- Feed_atom_site_(atom_site, chain_name, entity_id, res_list,
- entity_info[entity_id].is_poly);
+ 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, res_list);
+ entity_id, entity_info[entity_id], res_list);
}
}
@@ -1133,12 +1387,13 @@ namespace {
String chain_name = chain_name_gen.Get();
int entity_id = Setup_entity_(chain_name,
res_list,
+ false,
entity_info);
- Feed_atom_site_(atom_site, chain_name, entity_id, res_list,
- entity_info[entity_id].is_poly);
+ 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, res_list);
+ entity_id, entity_info[entity_id], res_list);
}
}
@@ -1147,12 +1402,13 @@ namespace {
String chain_name = chain_name_gen.Get();
int entity_id = Setup_entity_(chain_name,
res_list,
+ false,
entity_info);
- Feed_atom_site_(atom_site, chain_name, entity_id, res_list,
- entity_info[entity_id].is_poly);
+ 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, res_list);
+ entity_id, entity_info[entity_id], res_list);
}
}
@@ -1161,12 +1417,13 @@ namespace {
String chain_name = chain_name_gen.Get();
int entity_id = Setup_entity_(chain_name,
res_list,
+ false,
entity_info);
- Feed_atom_site_(atom_site, chain_name, entity_id, res_list,
- entity_info[entity_id].is_poly);
+ 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, res_list);
+ entity_id, entity_info[entity_id], res_list);
}
}
@@ -1175,12 +1432,13 @@ namespace {
String chain_name = chain_name_gen.Get();
int entity_id = Setup_entity_(chain_name,
res_list,
+ false,
entity_info);
- Feed_atom_site_(atom_site, chain_name, entity_id, res_list,
- entity_info[entity_id].is_poly);
+ 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, res_list);
+ entity_id, entity_info[entity_id], res_list);
}
}
@@ -1189,12 +1447,13 @@ namespace {
String chain_name = chain_name_gen.Get();
int entity_id = Setup_entity_(chain_name,
res_list,
+ false,
entity_info);
- Feed_atom_site_(atom_site, chain_name, entity_id, res_list,
- entity_info[entity_id].is_poly);
+ 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, res_list);
+ entity_id, entity_info[entity_id], res_list);
}
}
@@ -1203,12 +1462,13 @@ namespace {
String chain_name = chain_name_gen.Get();
int entity_id = Setup_entity_(chain_name,
res_list,
+ false,
entity_info);
- Feed_atom_site_(atom_site, chain_name, entity_id, res_list,
- entity_info[entity_id].is_poly);
+ 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, res_list);
+ entity_id, entity_info[entity_id], res_list);
}
}
@@ -1219,12 +1479,13 @@ namespace {
String chain_name = chain_name_gen.Get();
int entity_id = Setup_entity_(chain_name,
res_list,
+ false,
entity_info);
- Feed_atom_site_(atom_site, chain_name, entity_id, res_list,
- entity_info[entity_id].is_poly);
+ 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, res_list);
+ entity_id, entity_info[entity_id], res_list);
}
}
}