strip whitespace characters from SEQRES entries

modules/base/src/string_ref.cc

@@ -113,4 +113,17 @@ std::vector<StringRef> StringRef::split(char p) const
   return result;
 }
 
+std::string StringRef::str_no_whitespace() const
+{
+  std::string whitespaceless_string;
+  whitespaceless_string.reserve(this->size());
+  for (const char* s=begin_; s!=end_; ++s) {
+    if (isspace(*s)) {
+      continue;
+    }
+    whitespaceless_string.push_back(*s);
+    
+  }
+  return whitespaceless_string;
+}
 }

modules/base/src/string_ref.hh

@@ -147,6 +147,10 @@ public:
 
   /// \brief split string into chunks delimited by \p p
   std::vector<StringRef> split(char p) const;
+  
+  /// \brief returns a new string with all whitespace removed from 
+  ///    this StringRef
+  std::string str_no_whitespace() const;
 private:
   const char* begin_;
   const char* end_;  

modules/io/src/mol/mmcif_reader.cc

@@ -518,22 +518,23 @@ void MMCifParser::ParseEntityPoly(const std::vector<StringRef>& columns)
                                              this->GetCurrentLinenum()));
   }
   if (read_seqres_) {
+    StringRef seqres;
     if (seqres_can_) {
       if (indices_[PDBX_SEQ_ONE_LETTER_CODE_CAN] != -1) {
-      edm_it->second.seqres =
-        columns[indices_[PDBX_SEQ_ONE_LETTER_CODE_CAN]].str();
+        seqres=columns[indices_[PDBX_SEQ_ONE_LETTER_CODE_CAN]];
       } else {
         throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
                    "'entity_poly.pdbx_seq_one_letter_code_can' not available.'",
                                                  this->GetCurrentLinenum()));
       }
     } else if (indices_[PDBX_SEQ_ONE_LETTER_CODE] != -1) {
-      edm_it->second.seqres = columns[indices_[PDBX_SEQ_ONE_LETTER_CODE]].str();
+      seqres=columns[indices_[PDBX_SEQ_ONE_LETTER_CODE]];
     } else {
       throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
                        "'entity_poly.pdbx_seq_one_letter_code' not available.'",
                                                this->GetCurrentLinenum()));
     }
+    edm_it->second.seqres = seqres.str_no_whitespace();
   }
 }