Fixed mmCIF parser, format clash

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;

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));

modules/io/src/mol/mmcif_info.hh

@@ -817,7 +817,7 @@ 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, 
+  MMCifInfoStructRefSeqDifPtr AddDif(int seq_num, const String& db_rnum, 
                                      const String& details);
   const std::vector<MMCifInfoStructRefSeqDifPtr>& GetDifs() const { return difs_; }
 private:
@@ -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_;
 };
 

modules/io/src/mol/mmcif_reader.cc

@@ -1543,12 +1543,9 @@ 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);
+  String db_rnum;
   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);
-	  
+    db_rnum=columns[indices_[SRSD_DB_RNUM]].str();
   }
   std::pair<bool,int> seq_rnum(true, -1);
   if (!is_undef(columns[indices_[SRSD_SEQ_RNUM]])) {
@@ -1557,7 +1554,7 @@ void MMCifReader::ParseStructRefSeqDif(const std::vector<StringRef>& columns)
                              profile_.fault_tolerant);
     
   }
-	if (!seq_rnum.first || !db_rnum.first) {
+  if (!seq_rnum.first) {
     return;
   }
   String details;
@@ -1568,7 +1565,7 @@ void MMCifReader::ParseStructRefSeqDif(const std::vector<StringRef>& columns)
   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;
  	 }