Cleaning up code/doc/tests of consistency checks.

modules/mol/alg/doc/molalg.rst

@@ -1075,7 +1075,7 @@ The following function detects steric clashes in atomic structures. Two atoms ar
   The function requires a reference structure and a probe structure. The
   function checks that all the residues in the reference structure that appear
   in the probe structure (i.e., that have the same ResNum) are of the same
-  residue type. Chains are comapred by order, not by chain name (i.e.: the first
+  residue type. Chains are compared by order, not by chain name (i.e.: the first
   chain of the reference will be compared with the first chain of the probe
   structure, etc.)
 

modules/mol/alg/src/consistency_checks.cc

@@ -31,21 +31,29 @@ bool ResidueNamesMatch(const EntityView& probe, const EntityView& reference,
   ChainViewList ref_chains = reference.GetChainList();
   ChainViewList probe_chains = probe.GetChainList();
   for (unsigned int rci = 0; rci < ref_chains.size(); ++rci) {
-     ChainView ref_chain= ref_chains[rci];
-     if (rci<probe_chains.size()) {
+     ChainView ref_chain = ref_chains[rci];
+     if (rci < probe_chains.size()) {
       ChainView probe_chain = probe_chains[rci];     
       ResidueViewList ref_residues = ref_chain.GetResidueList();       
-      for (ResidueViewList::iterator rri=ref_residues.begin(), rre=ref_residues.end(); rri!=rre; ++rri) {
+      for (ResidueViewList::iterator rri = ref_residues.begin(),
+           rre = ref_residues.end(); rri != rre; ++rri) {
         ResidueView probe_residue = probe_chain.FindResidue(rri->GetNumber());
         if (probe_residue.IsValid()) {
           if (probe_residue.GetName()!=rri->GetName()) {
             return_value = false;
             if (log_as_error) {
-              LOG_ERROR("Name mismatch for residue " << probe_residue.GetNumber() << ": in the reference structure(s) is " << rri->GetName() << ", in the model " << probe_residue.GetName());
+              LOG_ERROR("Name mismatch for residue "
+                        << probe_residue.GetNumber()
+                        << ": in the reference structure(s) is "
+                        << rri->GetName() << ", in the model "
+                        << probe_residue.GetName());
             } else {
-              LOG_WARNING("Name mismatch for residue " << probe_residue.GetNumber() << ": in the reference structure(s) is " << rri->GetName() << ", in the model " << probe_residue.GetName());
+              LOG_WARNING("Name mismatch for residue "
+                          << probe_residue.GetNumber()
+                          << ": in the reference structure(s) is "
+                          << rri->GetName() << ", in the model "
+                          << probe_residue.GetName());
             }
-
           } 
         }            
       }

modules/mol/alg/tests/test_consistency_checks.cc

@@ -35,37 +35,40 @@ BOOST_AUTO_TEST_SUITE( mol_alg );
 BOOST_AUTO_TEST_CASE(consistency_check) 
 {
 
-  EntityHandle a=CreateEntity();
-  XCSEditor eda=a.EditXCS();
-  ChainHandle ca=eda.InsertChain("A");
-  ResidueHandle r1a = eda.AppendResidue(ca, "ALA",1);
-  ResidueHandle r2a = eda.AppendResidue(ca, "TYR",2);
-  ResidueHandle r3a = eda.AppendResidue(ca, "LEU",3);
-  ResidueHandle r4a = eda.AppendResidue(ca, "GLY",4);
-  ChainHandle ca2=eda.InsertChain("C");
-  ResidueHandle r1a2 = eda.AppendResidue(ca2, "PRO",1);
+  EntityHandle a = CreateEntity();
+  XCSEditor eda = a.EditXCS();
+  ChainHandle ca = eda.InsertChain("A");
+  ResidueHandle r1a = eda.AppendResidue(ca, "ALA", 1);
+  ResidueHandle r2a = eda.AppendResidue(ca, "TYR", 2);
+  ResidueHandle r3a = eda.AppendResidue(ca, "LEU", 3);
+  ResidueHandle r4a = eda.AppendResidue(ca, "GLY", 4);
+  ChainHandle ca2 = eda.InsertChain("C");
+  ResidueHandle r1a2 = eda.AppendResidue(ca2, "PRO", 1);
 
+  EntityHandle b = CreateEntity();
+  XCSEditor edb = b.EditXCS();
+  ChainHandle cb = edb.InsertChain("A");
+  ResidueHandle r1b = edb.AppendResidue(cb, "ALA", 1);
+  ResidueHandle r2b = edb.AppendResidue(cb, "TYR", 2);
+  ResidueHandle r3b = edb.AppendResidue(cb, "LEU", 3);
+  ResidueHandle r4b = edb.AppendResidue(cb, "GLY", 4);
+  ResidueHandle r5b = edb.AppendResidue(cb, "PRO", 5);
 
-  EntityHandle b=CreateEntity();
-  XCSEditor edb=b.EditXCS();
-  ChainHandle cb=edb.InsertChain("A");
-  ResidueHandle r1b = edb.AppendResidue(cb, "ALA",1);
-  ResidueHandle r2b = edb.AppendResidue(cb, "TYR",2);
-  ResidueHandle r3b = edb.AppendResidue(cb, "LEU",3);
-  ResidueHandle r4b = edb.AppendResidue(cb, "GLY",4);
-  ResidueHandle r5b = edb.AppendResidue(cb, "PRO",5);
-
-
-  EntityHandle c=CreateEntity();
-  XCSEditor edc=c.EditXCS();
-  ChainHandle cc=edc.InsertChain("A");
-  ResidueHandle r1c = edc.AppendResidue(cc, "ALA",1);
-  ResidueHandle r2c = edc.AppendResidue(cc, "PRO",2);
-  ResidueHandle r3c = edc.AppendResidue(cc, "LEU",3);
-  ResidueHandle r4c = edc.AppendResidue(cc, "GLY",4);
+  EntityHandle c = CreateEntity();
+  XCSEditor edc = c.EditXCS();
+  ChainHandle cc = edc.InsertChain("A");
+  ResidueHandle r1c = edc.AppendResidue(cc, "ALA", 1);
+  ResidueHandle r2c = edc.AppendResidue(cc, "PRO", 2);
+  ResidueHandle r3c = edc.AppendResidue(cc, "LEU", 3);
+  ResidueHandle r4c = edc.AppendResidue(cc, "GLY", 4);
    
-  BOOST_CHECK(ost::mol::alg::ResidueNamesMatch(a.CreateFullView(),b.CreateFullView())==true);   
-  BOOST_CHECK(ost::mol::alg::ResidueNamesMatch(c.CreateFullView(),b.CreateFullView())==false);    
+  const EntityView eva = a.CreateFullView();
+  const EntityView evb = b.CreateFullView();
+  const EntityView evc = c.CreateFullView();
+  BOOST_CHECK(ResidueNamesMatch(eva, evb) == true);
+  BOOST_CHECK(ResidueNamesMatch(evb, eva) == true);
+  BOOST_CHECK(ResidueNamesMatch(evc, evb) == false);
+  BOOST_CHECK(ResidueNamesMatch(evb, evc) == false);
 }
 
 BOOST_AUTO_TEST_SUITE_END();