Fixed a glitch in the PDBizer: if more than one set of tranfsormations &...

Fixed a glitch in the PDBizer: if more than one set of tranfsormations & chains exist, lingand/ water chains in the entity already exist, but are re-initialsied in a call to PDBizer.Add and added again to the entity... which does not work, of course.

modules/io/tests/test_io_mmcif.py

@@ -213,6 +213,36 @@ class TestMMCifInfo(unittest.TestCase):
                                            0,0,0,1),
                                  epsilon=0.01), True)
 
+  def test_mmcifinfo_biounit_pdbize_multi_transformations(self):
+    # in case we have more than one set of chains & transformations,
+    # ligand/ water chains may mess up
+    ent, seqres, info = io.LoadMMCIF("testfiles/mmcif/2ast.cif.gz",
+                                     seqres=True,
+                                     info=True)
+    pdb_ent = info.GetBioUnits()[2].PDBize(ent, seqres=seqres)
+    # chains
+    self.assertEquals(str(pdb_ent.GetChainList()[0]), 'A')
+    self.assertEquals(str(pdb_ent.GetChainList()[1]), 'B')
+    self.assertEquals(str(pdb_ent.GetChainList()[2]), '_')
+    self.assertEquals(str(pdb_ent.GetChainList()[3]), '-')
+    self.assertEquals(str(pdb_ent.GetChainList()[4]), 'C')
+    self.assertEquals(str(pdb_ent.GetChainList()[5]), 'D')
+    self.assertEquals(str(pdb_ent.GetChainList()[6]), 'E')
+    self.assertEquals(str(pdb_ent.GetChainList()[7]), 'F')
+    self.assertEquals(str(pdb_ent.GetChainList()[8]), 'G')
+    self.assertEquals(str(pdb_ent.GetChainList()[9]), 'H')
+    # size of chains
+    self.assertEquals(len(pdb_ent.GetChainList()[0].GetResidueList()),  142)
+    self.assertEquals(len(pdb_ent.GetChainList()[1].GetResidueList()),  325)
+    self.assertEquals(len(pdb_ent.GetChainList()[2].GetResidueList()),    4)
+    self.assertEquals(len(pdb_ent.GetChainList()[3].GetResidueList()),  530)
+    self.assertEquals(len(pdb_ent.GetChainList()[4].GetResidueList()),  142)
+    self.assertEquals(len(pdb_ent.GetChainList()[5].GetResidueList()),  325)
+    self.assertEquals(len(pdb_ent.GetChainList()[6].GetResidueList()),   69)
+    self.assertEquals(len(pdb_ent.GetChainList()[7].GetResidueList()),   10)
+    self.assertEquals(len(pdb_ent.GetChainList()[8].GetResidueList()),   69)
+    self.assertEquals(len(pdb_ent.GetChainList()[9].GetResidueList()),   10)
+
   def test_mmcifinfo_structdetails(self):
     d = io.MMCifInfoStructDetails()
 

modules/mol/alg/src/pdbize.cc

@@ -70,8 +70,6 @@ void PDBize::Add(EntityView asu, const geom::Mat4List& transforms,
 {
   XCSEditor edi = ent_.EditXCS(BUFFERED_EDIT);
 
-  ChainHandle ligand_chain;
-  ChainHandle water_chain;
   int last_rnum = 0;
   for (geom::Mat4List::const_iterator i = transforms.begin(), 
        e = transforms.end(); i != e; ++i) {
@@ -108,14 +106,14 @@ void PDBize::Add(EntityView asu, const geom::Mat4List& transforms,
         continue;
       }
       if (chain.GetType() == CHAINTYPE_WATER) {
-        if (!water_chain) {
-          water_chain = edi.InsertChain(WATER_CHAIN_NAME);
-          edi.SetChainDescription(water_chain, chain.GetDescription());
-          edi.SetChainType(water_chain, chain.GetType());
+        if (!water_chain_) {
+          water_chain_ = edi.InsertChain(WATER_CHAIN_NAME);
+          edi.SetChainDescription(water_chain_, chain.GetDescription());
+          edi.SetChainType(water_chain_, chain.GetType());
         }
         for (ResidueViewList::const_iterator k = chain.GetResidueList().begin(),
              e3 = chain.GetResidueList().end(); k != e3; ++k) {
-          ResidueHandle new_res = edi.AppendResidue(water_chain, k->GetName());
+          ResidueHandle new_res = edi.AppendResidue(water_chain_, k->GetName());
           transfer_residue_properties(*k, new_res);
           new_res.SetStringProp("type", StringFromChainType(chain.GetType()));
           new_res.SetStringProp("description", chain.GetDescription());
@@ -125,15 +123,15 @@ void PDBize::Add(EntityView asu, const geom::Mat4List& transforms,
         continue;
       }
       // deal with ligands...
-      if (!ligand_chain) {
-        ligand_chain = edi.InsertChain(LIGAND_CHAIN_NAME);
+      if (!ligand_chain_) {
+        ligand_chain_ = edi.InsertChain(LIGAND_CHAIN_NAME);
         last_rnum = 0;
       }
       char ins_code = chain.GetResidueCount()>1 ? 'A' : '\0';
      
       for (ResidueViewList::const_iterator k = chain.GetResidueList().begin(),
            e3 = chain.GetResidueList().end(); k != e3; ++k) {
-        ResidueHandle new_res = edi.AppendResidue(ligand_chain, k->GetName(),
+        ResidueHandle new_res = edi.AppendResidue(ligand_chain_, k->GetName(),
                                                   ResNum(last_rnum+1, ins_code));
         transfer_residue_properties(*k, new_res);
         new_res.SetStringProp("type", StringFromChainType(chain.GetType()));

modules/mol/alg/src/pdbize.hh

@@ -46,6 +46,8 @@ public:
 private:
   int                                   min_polymer_size_;
   EntityHandle                          ent_;
+  ChainHandle                           ligand_chain_;
+  ChainHandle                           water_chain_;
   const char*                           curr_chain_name_;
   bool                                  needs_adjustment_;
   std::map<ResidueHandle,ResidueHandle> dst_to_src_map_;