make molck ready for the mmcif format

When loading the structure, molck checks now for the file endings
.mmcif and .cif and invokes the corresponding reader. Everything
else is still expected to be in pdb format.

tools/molck/main.cc

@@ -10,6 +10,7 @@
 #include <ost/conop/amino_acids.hh>
 #include <ost/io/mol/pdb_reader.hh>
 #include <ost/io/mol/pdb_writer.hh>
+#include <ost/io/mol/mmcif_reader.hh>
 #include <ost/io/io_exception.hh>
 #include <ost/conop/nonstandard.hh>
 #if defined(__APPLE__)
@@ -26,15 +27,25 @@ namespace fs=boost::filesystem;
 EntityHandle load_x(const String& file, const IOProfile& profile)
 {
   try {
-    PDBReader reader(file, profile);
-    if (reader.HasNext()) {
-      EntityHandle ent=CreateEntity();
-      reader.Import(ent);
+    EntityHandle ent = CreateEntity();
+    if(file.compare(file.length() - 6, 6, ".mmcif") == 0 ||
+       file.compare(file.length() - 4, 4, ".cif") == 0){
+      MMCifReader reader(file,ent,profile);
+      reader.Parse();
       return ent;
     }
-    std::cerr << "ERROR: '" << file << "' does not contain any ATOM records. "
+    //if its not mmcif, we assume the file to be in pdb format without even
+    //looking at the filename
+    else{
+      PDBReader reader(file, profile);
+      if (reader.HasNext()) {
+        reader.Import(ent);
+        return ent;
+      }
+      std::cerr << "ERROR: '" << file << "' does not contain any ATOM records. "
               << "Are you sure this is a PDB file?" << std::endl;
-    return EntityHandle();
+      return EntityHandle();
+    }
   } catch (std::exception& e) {
     std::cerr << "ERROR: " << e.what() << std::endl;
     return EntityHandle();