Added logging to the LDT code proper and moved format info to the beginning of the log

modules/mol/alg/src/filter_clashes.cc

@@ -147,8 +147,6 @@ void StereoChemicalParams::PrintAllParameters() const
 EntityView CheckStereoChemistry(const EntityView& ent, const StereoChemicalParams& bond_table, const StereoChemicalParams& angle_table, Real bond_tolerance, Real angle_tolerance, bool always_remove_bb)
 {
   LOG_INFO("Checking stereo-chemistry")
-  LOG_INFO("BOND INFO FORMAT:" << " " << "Chain" << " " << "Residue" << " " << "ResNum" << " " << "Bond" << " " << "Min" << " " << "Max" << " " << "Observed" << " " << "Z-score" << " " << "Status")
-  LOG_INFO("ANGLE INFO FORMAT:" << " " << "Chain" << " " << "Residue" << " " << "ResNum" << " " << "Angle" << " " << "Min" << " " << "Max" << " " << "Observed" << " " << "Z-score" << " " << "Status")
   EntityView filtered=ent.CreateEmptyView();
   ResidueViewList residues=ent.GetResidueList();
   for (ResidueViewList::iterator i=residues.begin(), e=residues.end(); i!=e; ++i) {
@@ -289,7 +287,6 @@ EntityView CheckStereoChemistry(const EntityHandle& ent, const StereoChemicalPar
 EntityView FilterClashes(const EntityView& ent, const ClashingDistances& min_distances, bool always_remove_bb)
 {
   LOG_INFO("Filtering non-bonded clashes")
-  LOG_INFO("CLASH INFO FORMAT:" << " " << "Chain1" << " " << "Residue1" << " " << "ResNum1" << " " << "Atom1" << " " << "Chain2" << " " << "Residue2" << " " << "ResNum2" << " " << "Atom2" << " " << "Min" << " " << "Observed" << " " << "Difference" << " " << "Status")
   EntityView filtered=ent.CreateEmptyView();
   ResidueViewList residues=ent.GetResidueList();
   for (ResidueViewList::iterator 

modules/mol/alg/src/ldt.cc

@@ -316,6 +316,11 @@ int main (int argc, char **argv)
     std::cout << "Tolerance in stddevs for bonds: " << bond_tolerance << std::endl;
     std::cout << "Tolerance in stddevs for angles: " << angle_tolerance << std::endl;
     std::cout << "Clashing distance for unknown atom types: " << min_default_distance << std::endl;
+    LOG_INFO("Log entries format:"); 
+    LOG_INFO("BOND INFO FORMAT:" << " " << "Chain" << " " << "Residue" << " " << "ResNum" << " " << "Bond" << " " << "Min" << " " << "Max" << " " << "Observed" << " " << "Z-score" << " " << "Status");
+    LOG_INFO("ANGLE INFO FORMAT:" << " " << "Chain" << " " << "Residue" << " " << "ResNum" << " " << "Angle" << " " << "Min" << " " << "Max" << " " << "Observed" << " " << "Z-score" << " " << "Status");
+    LOG_INFO("CLASH INFO FORMAT:" << " " << "Chain1" << " " << "Residue1" << " " << "ResNum1" << " " << "Atom1" << " " << "Chain2" << " " << "Residue2" << " " << "ResNum2" << " " << "Atom2" << " " << "Min" << " " << "Observed" << " " << "Difference" << " " << "Status");
+    LOG_INFO("LDT INFO FORMAT:" << " " << "Chain1" << " " << "Residue1" << " " << "ResNum1" << " " << "Atom1" << " " << "Chain2" << " " << "Residue2" << " " << "ResNum2" << " " << "Atom2" << " " << "Min" << " " << "ModelDist" << " " << "TargetDist" << " " << "Difference" <<  " " << "Tolerance" << " " << "Status");
   }    
   for (size_t i=0; i<files.size(); ++i) {
     EntityHandle model=load(files[i], profile);

modules/mol/alg/src/local_dist_test.cc

@@ -106,10 +106,17 @@ std::pair<Real, Real> calc_overlap1(ResidueView ref_res,
         Real mdl_dist=geom::Length(av1.GetPos()-av2.GetPos());
         Real ref_dist=geom::Length(ai->GetPos()-aj->GetPos());
         if (std::abs(mdl_dist-ref_dist)<tol) {
+          LOG_VERBOSE("CLASH:" << " " << av1.GetResidue().GetChain() << " " << av1.GetResidue().GetName() << " " << av1.GetResidue().GetNumber() << " " << av1.GetName() 
+             << " " << av2.GetResidue().GetChain() << " " << av2.GetResidue().GetNumber() << " " << av2.GetResidue().GetName() << " " << av2.GetName() << " " 
+             << mdl_dist << " " << ref_dist << " " << mdl_dist-ref_dist << " " << tol << " " << "PASS")
           overlap.first+=1;
           overlap_list[ref_res.GetIndex()].first+=1.0;
           overlap_list[aj->GetResidue().GetIndex()].first+=1.0;
-        }
+        } else {
+          LOG_INFO("CLASH:" << " " << av1.GetResidue().GetChain() << " " << av1.GetResidue().GetName() << " " << av1.GetResidue().GetNumber() << " " << av1.GetName() 
+             << " " << av2.GetResidue().GetChain() << " " << av2.GetResidue().GetNumber() << " " << av2.GetResidue().GetName() << " " << av2.GetName() << " " 
+             << mdl_dist << " " << ref_dist << " " << mdl_dist-ref_dist << " " << tol << " " << "FAIL")
+        } 
       }
     }      
   }