diff --git a/modules/io/src/mol/mmcif_writer.cc b/modules/io/src/mol/mmcif_writer.cc
index 9322195764a44290d6e60a3164c508599d47d204..496957c8514639bf036b6327252c7703413b5014 100644
--- a/modules/io/src/mol/mmcif_writer.cc
+++ b/modules/io/src/mol/mmcif_writer.cc
@@ -329,10 +329,13 @@ namespace {
}
void AddAsym(const String& asym_chain_name,
- ost::io::MMCifWriterEntity& info) {
+ ost::io::MMCifWriterEntity& info,
+ bool skip_asym_id=false) {
// 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);
+ if(!skip_asym_id) {
+ info.asym_ids.push_back(asym_chain_name);
+ }
info.asym_alns.push_back(info.mon_ids);
}
@@ -385,7 +388,7 @@ namespace {
if(n_matches == 0) {
return false;
} else {
- return n_beyond / n_matches <= beyond_frac;
+ return static_cast<Real>(n_beyond) / n_matches <= beyond_frac;
}
}
@@ -393,7 +396,8 @@ namespace {
template<class T>
void AddAsymResnum(const String& asym_chain_name,
const T& res_list,
- ost::io::MMCifWriterEntity& info) {
+ ost::io::MMCifWriterEntity& info,
+ bool skip_asym_id=false) {
if(!info.is_poly) {
// no need for SEQRES alignment vodoo
@@ -446,7 +450,9 @@ namespace {
}
// finalize
- info.asym_ids.push_back(asym_chain_name);
+ if(!skip_asym_id) {
+ info.asym_ids.push_back(asym_chain_name);
+ }
info.asym_alns.push_back(aln_mon_ids);
}
@@ -1181,6 +1187,130 @@ namespace {
atom_site, pdbx_poly_seq_scheme);
}
+ template <class T>
+ void ProcessEntmmCIF(const T& ent,
+ ost::conop::CompoundLibPtr compound_lib,
+ std::vector<ost::io::MMCifWriterEntity>& entity_info,
+ 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::stringstream ss;
+ ss << "Expected predefined chain \"" << ai << "\" to be of type \"";
+ ss << entity_info[ei_idx].type <<"\", got \"" << 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, entity_info[ei_idx], res_list);
+ Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme, ai, ei_idx,
+ 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 res_list = chain.GetResidueList();
+ if(!MatchEntity(res_list, entity_info[ei_idx])) {
+ std::stringstream ss;
+ ss << "Failed to match predefined chain \"" << ai;
+ ss << "\" to respective entity";
+ throw ost::io::IOException(ss.str());
+ }
+ AddAsym(ai, entity_info[ei_idx], true);
+ Feed_atom_site(atom_site, ai, ei_idx, 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, entity_info[ei_idx], res_list);
+ preprocessed_chains.insert(ai);
+ } else {
+ auto res_list = chain.GetResidueList();
+ if(!MatchEntity(res_list, entity_info[ei_idx])) {
+ std::stringstream ss;
+ ss << "Failed to match predefined chain \"" << ai;
+ ss << "\" to respective entity";
+ throw ost::io::IOException(ss.str());
+ }
+ AddAsym(ai, entity_info[ei_idx], true);
+ Feed_atom_site(atom_site, ai, ei_idx, 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, 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, entity_info[entity_id], res_list);
+ }
+ }
+ }
+
// template to allow ost::mol::EntityHandle and ost::mol::EntityView
template<class T>
void ProcessEnt(const T& ent,
@@ -1191,23 +1321,18 @@ namespace {
ost::io::StarWriterLoopPtr pdbx_poly_seq_scheme) {
if(mmcif_conform) {
- auto chain_list = ent.GetChainList();
- for(auto ch: chain_list) {
- 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);
+ 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");
}
}
- } else {
// delegate to more complex ProcessEntmmCIFify
ProcessEntmmCIFify(ent, compound_lib, entity_info, atom_site,
pdbx_poly_seq_scheme);