diff --git a/modules/io/src/mol/mmcif_writer.cc b/modules/io/src/mol/mmcif_writer.cc
index 3020a68aaf5e02dd90e8e1624edb6bea27f21d26..c7cfffd4678c817d32b3149742f87158e31c2564 100644
--- a/modules/io/src/mol/mmcif_writer.cc
+++ b/modules/io/src/mol/mmcif_writer.cc
@@ -336,7 +336,7 @@ namespace {
if(!skip_asym_id) {
info.asym_ids.push_back(asym_chain_name);
}
- info.asym_alns.push_back(info.mon_ids);
+ info.asym_alns[asym_chain_name] = info.mon_ids;
}
// template to allow ost::mol::ResidueHandleList and ost::mol::ResidueViewList
@@ -430,8 +430,9 @@ namespace {
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, "-");
+ for(std::map<String, std::vector<String> >::iterator it = info.asym_alns.begin();
+ it != info.asym_alns.end(); ++it) {
+ it->second.insert(it->second.end(), N, "-");
}
}
@@ -453,7 +454,7 @@ namespace {
if(!skip_asym_id) {
info.asym_ids.push_back(asym_chain_name);
}
- info.asym_alns.push_back(aln_mon_ids);
+ info.asym_alns[asym_chain_name] = aln_mon_ids;
}
// template to allow ost::mol::ResidueHandleList and ost::mol::ResidueViewList
@@ -725,7 +726,7 @@ namespace {
void Feed_pdbx_poly_seq_scheme(ost::io::StarWriterLoopPtr pdbx_poly_seq_scheme_ptr,
const String& label_asym_id,
int label_entity_id,
- ost::io::MMCifWriterEntity& entity_info,
+ const ost::io::MMCifWriterEntity& entity_info,
const T& res_list) {
std::vector<ost::io::StarWriterValue> data(7);
@@ -733,8 +734,12 @@ namespace {
data[0] = ost::io::StarWriterValue::FromString(label_asym_id);
data[1] = ost::io::StarWriterValue::FromInt(label_entity_id);
- int asym_idx = entity_info.GetAsymIdx(label_asym_id);
- const std::vector<String>& aln = entity_info.asym_alns[asym_idx];
+ std::map<String, std::vector<String> >::const_iterator it =
+ entity_info.asym_alns.find(label_asym_id);
+ if(it == entity_info.asym_alns.end()) {
+ throw ost::io::IOException("This should never happen");
+ }
+ const std::vector<String>& aln = it->second;
int label_seq_id = 0; // 0-based index
for(auto res: res_list) {
@@ -786,8 +791,12 @@ namespace {
const ost::io::MMCifWriterEntity& entity_info,
const T& res_list) {
- int asym_idx = entity_info.GetAsymIdx(label_asym_id);
- const std::vector<String>& aln = entity_info.asym_alns[asym_idx];
+ std::map<String, std::vector<String> >::const_iterator it =
+ entity_info.asym_alns.find(label_asym_id);
+ if(it == entity_info.asym_alns.end()) {
+ throw ost::io::IOException("This should never happen");
+ }
+ const std::vector<String>& aln = it->second;
int label_seq_id = 0; // 0-based index
std::vector<ost::io::StarWriterValue> at_data(17);
@@ -977,6 +986,12 @@ namespace {
ost::io::StarWriterLoopPtr atom_site,
ost::io::StarWriterLoopPtr pdbx_poly_seq_scheme) {
+ // don't allow any predefined entity
+ if(!entity_info.empty()) {
+ throw ost::io::IOException("Cannot provide MMCifWriterEntities if ent "
+ "is not mmcif_conform");
+ }
+
ChainNameGenerator chain_name_gen;
std::set<String> unique_compounds;
@@ -1194,119 +1209,99 @@ namespace {
ost::io::StarWriterLoopPtr atom_site,
ost::io::StarWriterLoopPtr pdbx_poly_seq_scheme) {
- // deal with preset asym_ids in entity_info
- // need to properly setup alignments in these cases
- std::set<String> preprocessed_chains;
- for(size_t ei_idx = 0; ei_idx < entity_info.size(); ++ei_idx) {
- if(!entity_info[ei_idx].asym_ids.empty()) {
- // Assumption that the code below fills all alignments
- if(!entity_info[ei_idx].asym_alns.empty()) {
- std::stringstream ss;
- throw ost::io::IOException("Expect alignments to be empty in "
- "MMCifWriterEntity when predefining asym "
- "ids");
- }
- }
- for(auto ai: entity_info[ei_idx].asym_ids) {
- // Plenty of checks that chain really matches with specified
- // MMCifWriterEntity
- if(preprocessed_chains.find(ai) != preprocessed_chains.end()) {
- std::stringstream ss;
- ss << "Tried to predefine entity for chain \"" << ai;
- ss << "\" multiple times";
- throw ost::io::IOException(ss.str());
- }
- auto chain = ent.FindChain(ai);
- if(!chain.IsValid()) {
- std::stringstream ss;
- ss << "Tried to predefine entity for chain \"" << ai;
- ss << "\" but couldnt find that chain in provided entity";
- throw ost::io::IOException(ss.str());
- }
- String type = ost::mol::EntityTypeFromChainType(chain.GetType());
- if(type != entity_info[ei_idx].type) {
+ std::map<String, int> preassigned_polymer_chains;
+ if(!entity_info.empty()) {
+ // The following must be fulfilled
+ // - Only allow MMCifWriterEntity of type polymer
+ // - All chains in ent that are of type polymer must be assigned
+ // to exactly one of these entity_info objects and must match the SEQRES
+ // (MMCifWriterEntity::mon_ids)
+ // - All chain names that are assigned to entity_info must be valid chains
+ // in ent
+ for(auto ei: entity_info) {
+ if(ei.type != "polymer") {
std::stringstream ss;
- ss << "Expected predefined chain \"" << ai << "\" to be of type \"";
- ss << entity_info[ei_idx].type <<"\", got \"" << type << "\"";
+ ss << "All predefined MMCifWriterEntity objects must be of type ";
+ ss << "\"polymer\", got \"" << ei.type << "\"";
throw ost::io::IOException(ss.str());
}
- if(entity_info[ei_idx].type == "polymer") {
- String poly_type = ost::mol::EntityPolyTypeFromChainType(chain.GetType());
- if(poly_type != entity_info[ei_idx].poly_type) {
- std::stringstream ss;
- ss << "Expected predefined chain \"" << ai << "\" to be of ";
- ss << "poly_type \"" << entity_info[ei_idx].poly_type <<"\", got \"" << poly_type;
- ss << "\"";
- throw ost::io::IOException(ss.str());
- }
- auto res_list = chain.GetResidueList();
- if(!MatchEntityResnum(res_list, entity_info[ei_idx], 0.0)) {
- std::stringstream ss;
- ss << "Failed to match predefined chain \"" << ai;
- ss << "\" to respective entity";
- throw ost::io::IOException(ss.str());
- }
- AddAsymResnum(ai, res_list, entity_info[ei_idx], true);
- Feed_atom_site(atom_site, ai, ei_idx+1, entity_info[ei_idx], res_list);
- Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme, ai, ei_idx+1,
- entity_info[ei_idx], res_list);
- preprocessed_chains.insert(ai);
- } else if(entity_info[ei_idx].type == "branched") {
- String branch_type = ost::mol::BranchedTypeFromChainType(chain.GetType());
- if(branch_type != entity_info[ei_idx].branch_type) {
- std::stringstream ss;
- ss << "Expected predefined chain \"" << ai << "\" to be of ";
- ss << "branched_type \"" << entity_info[ei_idx].branch_type;
- ss << "\", got \"" << branch_type << "\"";
- throw ost::io::IOException(ss.str());
+ }
+ auto chain_list = ent.GetChainList();
+ for(auto ch: chain_list) {
+ if(ost::mol::EntityTypeFromChainType(ch.GetType()) == "polymer") {
+ String cname = ch.GetName();
+ int entity_idx = 0;
+ for(auto ei: entity_info) {
+ for(auto ai: ei.asym_ids) {
+ if(cname == ai) {
+ if(preassigned_polymer_chains.find(cname) !=
+ preassigned_polymer_chains.end()) {
+ // already assigned
+ std::stringstream ss;
+ ss << "Found multiple MMCifWriterEntity assignments for ";
+ ss << "chain \"" << cname << "\"";
+ throw ost::io::IOException(ss.str());
+ }
+ auto res_list = ch.GetResidueList();
+ if(!MatchEntityResnum(res_list, ei, 0.0)) {
+ std::stringstream ss;
+ ss << "Cannot match pre-assigned chain \"" << cname;
+ ss << "\" to respective entity";
+ throw ost::io::IOException(ss.str());
+ }
+ preassigned_polymer_chains[cname] = entity_idx;
+ }
+ }
+ ++entity_idx;
}
- auto res_list = chain.GetResidueList();
- if(!MatchEntity(res_list, entity_info[ei_idx])) {
+ if(preassigned_polymer_chains.find(cname) ==
+ preassigned_polymer_chains.end()) {
std::stringstream ss;
- ss << "Failed to match predefined chain \"" << ai;
- ss << "\" to respective entity";
+ ss << "If MMCifWriterEntity is provided, all polymer chains must ";
+ ss << "assigned. No assignment for chain \"" << cname << "\"";
throw ost::io::IOException(ss.str());
}
- AddAsym(ai, entity_info[ei_idx], true);
- Feed_atom_site(atom_site, ai, ei_idx+1, entity_info[ei_idx], res_list);
- preprocessed_chains.insert(ai);
- } else if (entity_info[ei_idx].type == "water") {
- auto res_list = chain.GetResidueList();
- AddAsym(ai, entity_info[ei_idx], true);
- Feed_atom_site(atom_site, ai, ei_idx+1, entity_info[ei_idx], res_list);
- preprocessed_chains.insert(ai);
- } else {
- auto res_list = chain.GetResidueList();
- if(!MatchEntity(res_list, entity_info[ei_idx])) {
+ }
+ }
+ for(auto ei: entity_info) {
+ for(auto ai: ei.asym_ids) {
+ auto chain = ent.FindChain(ai);
+ if(!chain.IsValid()) {
std::stringstream ss;
- ss << "Failed to match predefined chain \"" << ai;
- ss << "\" to respective entity";
+ ss << "Chain \"" << ai << "\" has been assigned to ";
+ ss << "MMCifWriterEntity. But provided OpenStrucure entity has ";
+ ss << "no such chain"<<std::endl;
throw ost::io::IOException(ss.str());
}
- AddAsym(ai, entity_info[ei_idx], true);
- Feed_atom_site(atom_site, ai, ei_idx+1, entity_info[ei_idx], res_list);
- preprocessed_chains.insert(ai);
}
}
}
auto chain_list = ent.GetChainList();
- for(auto ch: chain_list) {
- if(preprocessed_chains.find(ch.GetName()) != preprocessed_chains.end()) {
- continue; // already done
- }
- auto res_list = ch.GetResidueList();
- String chain_name = ch.GetName();
- int entity_id = SetupEntity(chain_name,
- ch.GetType(),
- res_list,
- true,
- entity_info);
- Feed_atom_site(atom_site, chain_name, entity_id+1, 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+1, entity_info[entity_id], res_list);
+ for(auto chain: chain_list) {
+ String cname = chain.GetName();
+ if(preassigned_polymer_chains.find(cname) !=
+ preassigned_polymer_chains.end()) {
+ auto res_list = chain.GetResidueList();
+ int entity_id = preassigned_polymer_chains[cname];
+ AddAsymResnum(cname, res_list, entity_info[entity_id], true);
+ Feed_atom_site(atom_site, cname, entity_id+1, entity_info[entity_id], res_list);
+ Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme, cname, entity_id+1,
+ entity_info[entity_id], res_list);
+ } else {
+ // do automated matching
+ auto res_list = chain.GetResidueList();
+ int entity_id = SetupEntity(cname,
+ chain.GetType(),
+ res_list,
+ true,
+ entity_info);
+ Feed_atom_site(atom_site, cname, entity_id+1, entity_info[entity_id],
+ res_list);
+ if(entity_info[entity_id].is_poly) {
+ Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme, cname,
+ entity_id+1, entity_info[entity_id], res_list);
+ }
}
}
}
@@ -1320,20 +1315,12 @@ namespace {
ost::io::StarWriterLoopPtr atom_site,
ost::io::StarWriterLoopPtr pdbx_poly_seq_scheme) {
+
+
if(mmcif_conform) {
ProcessEntmmCIF(ent, compound_lib, entity_info, atom_site,
pdbx_poly_seq_scheme);
} else {
- // cannot predefine asym_ids in entity_info when mmcif_conform is
- // False. You're welcome to implement it... But its a bit awkward...
- // I warned you...
- for(auto ei: entity_info) {
- if(!ei.asym_ids.empty()) {
- throw ost::io::IOException("Predefine chains to entities not "
- "supported when mmcif_conform is False");
- }
- }
- // delegate to more complex ProcessEntmmCIFify
ProcessEntmmCIFify(ent, compound_lib, entity_info, atom_site,
pdbx_poly_seq_scheme);
}
diff --git a/modules/io/src/mol/mmcif_writer.hh b/modules/io/src/mol/mmcif_writer.hh
index 50d7d8908522bb5f4e0ede39782e3adfbe6a12e4..5516360e1431ed3441f8b69896d7b79ec6238fb3 100644
--- a/modules/io/src/mol/mmcif_writer.hh
+++ b/modules/io/src/mol/mmcif_writer.hh
@@ -88,7 +88,7 @@ struct MMCifWriterEntity {
// alignment. Contains "-" for residues that are missing in ATOMSEQ.
// irrelevant if is_poly is false. The assumption is that aligned residues
// exactly match with the respective position in mon_ids.
- std::vector<std::vector<String> > asym_alns;
+ std::map<String, std::vector<String> > asym_alns;
};
class DLLEXPORT_OST_IO MMCifWriter : public StarWriter {