diff --git a/modules/io/pymod/export_mmcif_io.cc b/modules/io/pymod/export_mmcif_io.cc index d3213357183cf73841d9d1386e612b6e0828ca40..824d70340208f61ac9959cddcff4902833f1bed4 100644 --- a/modules/io/pymod/export_mmcif_io.cc +++ b/modules/io/pymod/export_mmcif_io.cc @@ -171,7 +171,8 @@ void export_mmcif_io() .add_property("details", make_function(&MMCifInfoStructRefSeqDif::GetDetails, return_value_policy<copy_const_reference>())) .add_property("seq_rnum", &MMCifInfoStructRefSeqDif::GetSeqRNum) - .add_property("db_rnum", &MMCifInfoStructRefSeqDif::GetDBRNum) + .add_property("db_rnum", make_function(&MMCifInfoStructRefSeqDif::GetDBRNum, + return_value_policy<copy_const_reference>())) ; typedef std::pair<int, int> IntPair; diff --git a/modules/io/src/mol/mmcif_info.cc b/modules/io/src/mol/mmcif_info.cc index e7f391894cab4e8ace515de79fa14f6e047fd683..e7d47078cc5ae4c9f3c4dabee23dd55c72dd12e1 100644 --- a/modules/io/src/mol/mmcif_info.cc +++ b/modules/io/src/mol/mmcif_info.cc @@ -168,7 +168,7 @@ MMCifInfoStructRef::GetAlignedSeq(const String& aid) const } MMCifInfoStructRefSeqDifPtr -MMCifInfoStructRefSeq::AddDif(int seq_rnum, int db_rnum, const String& details) +MMCifInfoStructRefSeq::AddDif(int seq_rnum, const String& db_rnum, const String& details) { MMCifInfoStructRefSeqDifPtr d(new MMCifInfoStructRefSeqDif(seq_rnum, db_rnum, details)); diff --git a/modules/io/src/mol/mmcif_info.hh b/modules/io/src/mol/mmcif_info.hh index 593fed6f2b70e25c777454bd3e8d95db8554ef56..ca8da62036b5151ff38cbefe65645515be2b0851 100644 --- a/modules/io/src/mol/mmcif_info.hh +++ b/modules/io/src/mol/mmcif_info.hh @@ -817,8 +817,8 @@ public: int GetSeqEnd() const { return seq_end_; } int GetDBBegin() const { return db_begin_; } int GetDBEnd() const { return db_end_; } - MMCifInfoStructRefSeqDifPtr AddDif(int seq_num, int db_num, - const String& details); + MMCifInfoStructRefSeqDifPtr AddDif(int seq_num, const String& db_rnum, + const String& details); const std::vector<MMCifInfoStructRefSeqDifPtr>& GetDifs() const { return difs_; } private: String id_; @@ -832,14 +832,14 @@ private: class DLLEXPORT_OST_IO MMCifInfoStructRefSeqDif { public: - MMCifInfoStructRefSeqDif(int seq_rnum, int db_rnum, const String& details): + MMCifInfoStructRefSeqDif(int seq_rnum, const String& db_rnum, const String& details): seq_rnum_(seq_rnum), db_rnum_(db_rnum), details_(details) {} int GetSeqRNum() const { return seq_rnum_;} - int GetDBRNum() const { return db_rnum_; } + const String& GetDBRNum() const { return db_rnum_; } const String& GetDetails() const { return details_; } private: int seq_rnum_; - int db_rnum_; + String db_rnum_; String details_; }; diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc index b6d90fc756685626909edc2e6d6209ce07a557fd..93807f921e50c1457dc3cf7d0cc890375900183f 100644 --- a/modules/io/src/mol/mmcif_reader.cc +++ b/modules/io/src/mol/mmcif_reader.cc @@ -1542,33 +1542,30 @@ void MMCifReader::ParseStructRefSeq(const std::vector<StringRef>& columns) void MMCifReader::ParseStructRefSeqDif(const std::vector<StringRef>& columns) { - String aln_id=columns[indices_[SRSD_ALIGN_ID]].str(); - std::pair<bool,int> db_rnum(true, -1); - if (!is_undef(columns[indices_[SRSD_DB_RNUM]])) { - db_rnum=this->TryGetInt(columns[indices_[SRSD_DB_RNUM]], - "_struct_ref_seq_dif.pdbx_seq_db_seq_num", - profile_.fault_tolerant); - - } - std::pair<bool,int> seq_rnum(true, -1); - if (!is_undef(columns[indices_[SRSD_SEQ_RNUM]])) { - seq_rnum=this->TryGetInt(columns[indices_[SRSD_SEQ_RNUM]], - "_struct_ref_seq_dif.seq_num", - profile_.fault_tolerant); - - } - if (!seq_rnum.first || !db_rnum.first) { - return; - } + String aln_id=columns[indices_[SRSD_ALIGN_ID]].str(); + String db_rnum; + if (!is_undef(columns[indices_[SRSD_DB_RNUM]])) { + db_rnum=columns[indices_[SRSD_DB_RNUM]].str(); + } + std::pair<bool,int> seq_rnum(true, -1); + if (!is_undef(columns[indices_[SRSD_SEQ_RNUM]])) { + seq_rnum=this->TryGetInt(columns[indices_[SRSD_SEQ_RNUM]], + "_struct_ref_seq_dif.seq_num", + profile_.fault_tolerant); + + } + if (!seq_rnum.first) { + return; + } String details; if (indices_[SRSD_DETAILS]!=-1) { details=columns[indices_[SRSD_DETAILS]].str(); - } - bool found=false; + } + bool found=false; for (MMCifInfoStructRefs::iterator i=struct_refs_.begin(), e=struct_refs_.end(); i!=e; ++i) { if (MMCifInfoStructRefSeqPtr s=(*i)->GetAlignedSeq(aln_id)) { - s->AddDif(seq_rnum.second, db_rnum.second, details); + s->AddDif(seq_rnum.second, db_rnum, details); found=true; break; }