Fix bug reported in OpenChemistry#1637 with mis-parsing selenium atoms

Signed-off-by: Geoff Hutchison <[email protected]>
ghutchis · Mar 2, 2024 · 863255f · 863255f
1 parent 12e5606
commit 863255f
Showing 1 changed file with 3 additions and 2 deletions.
diff --git a/avogadro/io/pdbformat.cpp b/avogadro/io/pdbformat.cpp
@@ -144,8 +144,6 @@ bool PdbFormat::read(std::istream& in, Core::Molecule& mol)
       if (buffer.size() >= 78) {
         element = buffer.substr(76, 2);
         element = trimmed(element);
-        if (element == "SE") // For Sulphur
-          element = 'S';
         if (element.length() == 2)
           element[1] = std::tolower(element[1]);
 
@@ -161,6 +159,9 @@ bool PdbFormat::read(std::istream& in, Core::Molecule& mol)
         while (element.size() && std::isdigit(element.back()))
           element.pop_back();
 
+        if (element == "SE") // For Sulphur
+          element = 'S';
+
         atomicNum = Elements::atomicNumberFromSymbol(element);
         if (atomicNum == 255) {
           appendError("Invalid element");