Fixed a problem with asking for a parameter file even without structural...

Fixed a problem with asking for a parameter file even without structural checks, set the default tolerance level to 8.0 stddev

modules/mol/alg/src/ldt.cc

@@ -210,8 +210,8 @@ int main (int argc, char **argv)
   
   Real min_default_distance = 1.5;
   Real min_distance_tolerance = 0.0;
-  Real bond_tolerance = 5.0;
-  Real angle_tolerance = 5.0;
+  Real bond_tolerance = 8.0;
+  Real angle_tolerance = 8.0;
   
   IOProfile profile;
   profile.bond_feasibility_check=false;
@@ -257,7 +257,7 @@ int main (int argc, char **argv)
   String parameter_filename;  
   if (vm.count("parameter-file")) {
     parameter_filename=vm["parameter-file"].as<String>();
-  } else {
+  } else if (structural_checks==true) {
     std::cout << "Please specify a stereo-chemical parameter file" << std::endl;
     exit(-1);
   }
@@ -284,19 +284,6 @@ int main (int argc, char **argv)
   if (vm.count("default_clash")) {
     min_default_distance=vm["default_clash"].as<Real>();
   }
-  boost::filesystem::path loc(parameter_filename);
-  boost::filesystem::ifstream infile(loc);
-  if (!infile) {
-    std::cout << "Couldn't find " << parameter_filename << std::endl;
-    exit(-1);
-  }
-  std::vector<String> stereo_chemical_props;
-  String line;
-  while (std::getline(infile, line))
-  {
-   std::stringstream line_stream(line);
-   stereo_chemical_props.push_back(line);
-  }
 
   String ref_file=files.back();
   EntityHandle ref=load(ref_file, profile);
@@ -335,6 +322,19 @@ int main (int argc, char **argv)
     ClashingDistances nonbonded_table(min_default_distance,min_distance_tolerance);    
     EntityView v=model.CreateFullView();
     if (structural_checks) {
+      boost::filesystem::path loc(parameter_filename);
+      boost::filesystem::ifstream infile(loc);
+      if (!infile) {
+        std::cout << "Couldn't find " << parameter_filename << std::endl;
+        exit(-1);
+      }
+      std::vector<String> stereo_chemical_props;
+      String line;
+      while (std::getline(infile, line))
+      {
+        std::stringstream line_stream(line);
+        stereo_chemical_props.push_back(line);
+      }
       try {
 	FillStereoChemicalParams("Bond",bond_table,stereo_chemical_props);
       }	
@@ -379,11 +379,13 @@ int main (int argc, char **argv)
     for (ResidueViewIter rit=v.ResiduesBegin();rit!=v.ResiduesEnd();++rit){
       ResidueView ritv = *rit;
       Real ldt_local_sum = 0;
-      for (int n=0; n<4; ++n) { 
-        ldt_local_sum+=ritv.GetFloatProp(labels[n]);
-      }      
-      ldt_local_sum/=4.0;
-      std::cout << ritv.GetChain() << "\t" << ritv.GetName() << "\t" << ritv.GetNumber() << '\t' << ldt_local_sum << std::endl;
+      if (ritv.HasProp("localldt0.5")) {
+        for (int n=0; n<4; ++n) {
+          ldt_local_sum+=ritv.GetFloatProp(labels[n]);
+        }     
+        ldt_local_sum/=4.0;
+        std::cout << ritv.GetChain() << "\t" << ritv.GetName() << "\t" << ritv.GetNumber() << '\t' << ldt_local_sum << std::endl;
+      }  
     }  
     std::cout << std::endl;
   }