diff --git a/modules/io/src/mol/mmcif_writer.cc b/modules/io/src/mol/mmcif_writer.cc
index 8632bba6ff251aaa5579eef4b3b05a995cd09b18..4ca1e2a7893f2673e5c4ae0783f1e9dda45113e6 100644
--- a/modules/io/src/mol/mmcif_writer.cc
+++ b/modules/io/src/mol/mmcif_writer.cc
@@ -170,6 +170,200 @@ namespace {
return type;
}
+ inline String mon_id_to_olc(char chem_class,
+ const String& mon_id) {
+
+ // hardcoded table according
+ // https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_entity_poly.pdbx_seq_one_letter_code.html
+
+ if(ost::mol::ChemClass(chem_class).IsPeptideLinking()) {
+ switch(mon_id[0]) {
+ case 'A': {
+ if(mon_id == "ALA") {
+ return "A";
+ }
+ if(mon_id == "ACE") {
+ return "(ACE)";
+ }
+ if(mon_id == "ASP") {
+ return "D";
+ }
+ if(mon_id == "ASN") {
+ return "N";
+ }
+ if(mon_id == "ARG") {
+ return "R";
+ }
+ break;
+ }
+ case 'C': {
+ if(mon_id == "CYS") {
+ return "C";
+ }
+ break;
+ }
+ case 'G': {
+ if(mon_id == "GLU") {
+ return "E";
+ }
+ if(mon_id == "GLY") {
+ return "G";
+ }
+ if(mon_id == "GLN") {
+ return "Q";
+ }
+ break;
+ }
+ case 'H': {
+ if(mon_id == "HIS") {
+ return "H";
+ }
+ break;
+ }
+ case 'I': {
+ if(mon_id == "ILE") {
+ return "I";
+ }
+ break;
+ }
+ case 'L': {
+ if(mon_id == "LEU") {
+ return "L";
+ }
+ if(mon_id == "LYS") {
+ return "K";
+ }
+ break;
+ }
+ case 'M': {
+ if(mon_id == "MET") {
+ return "M";
+ }
+ if(mon_id == "MSE") {
+ return "(MSE)";
+ }
+ break;
+ }
+ case 'N': {
+ if(mon_id == "NH2") {
+ return "(NH2)";
+ }
+ break;
+ }
+ case 'P': {
+ if(mon_id == "PHE") {
+ return "F";
+ }
+ if(mon_id == "PYL") {
+ return "O";
+ }
+ if(mon_id == "PRO") {
+ return "P";
+ }
+ if(mon_id == "PTR") {
+ return "(PTR)";
+ }
+ if(mon_id == "PCA") {
+ return "(PCA)";
+ }
+ break;
+ }
+ case 'S': {
+ if(mon_id == "SER") {
+ return "S";
+ }
+ if(mon_id == "SEC") {
+ return "U";
+ }
+ if(mon_id == "SEP") {
+ return "(SEP)";
+ }
+ break;
+ }
+ case 'T': {
+ if(mon_id == "THR") {
+ return "T";
+ }
+ if(mon_id == "TRP") {
+ return "W";
+ }
+ if(mon_id == "TYR") {
+ 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...
+ }
+ break;
+ }
+ case 'V': {
+ if(mon_id == "VAL") {
+ return "V";
+ }
+ break;
+ }
+ }
+ return "(UNK)";
+ } else if(ost::mol::ChemClass(chem_class).IsNucleotideLinking()) {
+ switch(mon_id[0]) {
+ case 'A': {
+ if(mon_id == "A") {
+ return "A";
+ }
+ break;
+ }
+ case 'C': {
+ if(mon_id == "C") {
+ return "C";
+ }
+ break;
+ }
+ case 'D': {
+ if(mon_id == "DA") {
+ return "(DA)";
+ }
+ if(mon_id == "DC") {
+ return "(DC)";
+ }
+ if(mon_id == "DG") {
+ return "(DG)";
+ }
+ if(mon_id == "DT") {
+ return "(DT)";
+ }
+ break;
+ }
+ case 'G': {
+ if(mon_id == "G") {
+ return "G";
+ }
+ break;
+ }
+ case 'I': {
+ if(mon_id == "I") {
+ return "I";
+ }
+ break;
+ }
+ case 'U': {
+ if(mon_id == "U") {
+ return "U";
+ }
+ break;
+ }
+ }
+
+ return "N";
+
+ } else {
+ throw ost::io::IOException("Can only get OLCs for peptides/nucleotides");
+ }
+
+
+
+ }
+
void Setup_chem_comp_(const ost::mol::ResidueHandleList& res_list,
std::map<String, CompInfo>& comp_infos) {
for(auto res: res_list) {
@@ -197,6 +391,8 @@ namespace {
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
+ 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,
@@ -294,6 +490,24 @@ namespace {
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
+ for(auto res: res_list) {
+ ss << res.GetOneLetterCode();
+ }
+ entity_infos.back().seq_can = ss.str();
}
return entity_idx;
}
@@ -367,6 +581,8 @@ namespace {
desc.SetCategory("_entity_poly");
desc.Add("entity_id");
desc.Add("type");
+ desc.Add("pdbx_seq_one_letter_code");
+ desc.Add("pdbx_seq_one_letter_code_can");
ost::io::StarLoop* sl = new ost::io::StarLoop(desc);
return sl;
}
@@ -569,10 +785,14 @@ namespace {
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"));
+ entity_poly_data.push_back(ost::io::StarLoopDataItemDO("A"));
+ entity_poly_data.push_back(ost::io::StarLoopDataItemDO("A"));
for(size_t entity_idx = 0; entity_idx < entity_info.size(); ++entity_idx) {
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);
entity_poly_ptr->AddData(entity_poly_data);
}
}