fix pdb output for alt atom locations

modules/io/src/mol/pdb_writer.cc

@@ -136,7 +136,8 @@ void write_atom(std::ostream& ostr, FormattedLine& line,
   } else {
     for (std::vector<String>::const_iterator
          i=names.begin(), e=names.end(); i!=e; ++i) {
-      p=atom.GetAltPos(*i);
+      geom::Mat4 tf=atom.GetEntity().GetTransformationMatrix();
+      p=geom::Vec3(tf*geom::Vec4(atom.GetAltPos(*i)));
       line(30, 50).Clear();
 
       if (i->size()>1) {

modules/io/tests/test_io_pdb.cc

@@ -364,6 +364,31 @@ BOOST_AUTO_TEST_CASE(write_conect)
                             "testfiles/pdb/conect-out.pdb"));
 }
 
+BOOST_AUTO_TEST_CASE(alt_loc_tf)
+{
+  String fname("testfiles/pdb/alt-loc.pdb");  
+  // this scope is required to force the writer stream to be closed before 
+  // opening the file again in compare_files. Avoids a race condition.
+  mol::EntityHandle ent=mol::CreateEntity();  
+  PDBReader reader(fname);
+  reader.Import(ent);
+  String out_name("testfiles/pdb/alt-loc-tf-out.pdb");
+  {
+    PDBWriter writer(out_name);
+    geom::Mat4 shift;
+    shift.PasteTranslation(geom::Vec3(10,20,30));
+    ent.RequestXCSEditor().ApplyTransform(shift);
+    writer.Write(ent);
+  }
+  PDBReader r2(out_name);
+  mol::EntityHandle ent2=mol::CreateEntity();
+  r2.Import(ent2);
+  mol::ResidueHandle res1=ent2.FindResidue("A", mol::ResNum(1));
+  mol::AtomHandle a1=res1.FindAtom("N");
+  BOOST_CHECK_EQUAL(res1.GetAltAtomPos(a1, "A"), geom::Vec3(26,84,30));
+  BOOST_CHECK_EQUAL(res1.GetAltAtomPos(a1, "B"), geom::Vec3(18,-108,30));  
+}
+
 BOOST_AUTO_TEST_CASE(res_name_too_long)
 {
   std::stringstream out;