Included Input Checks

main.cpp

@@ -21,9 +21,9 @@
 
 int main(int argc, char* argv[])
 {
-	/**************************************************************************************/
-	/*********************************  Main BioEM code **********************************/
-	/************************************************************************************/
+	//*************************************************************************************
+	//*********************************  Main BioEM code **********************************
+	//*************************************************************************************
 
 #pragma omp parallel
 	{
@@ -43,17 +43,17 @@ int main(int argc, char* argv[])
 		bio = new bioem;
 	}
 
-	/************  Configuration and Pre-calculating necessary objects *****************/
+	//************  Configuration and Pre-calculating necessary objects *********************
 	printf("Configuring\n");
 	bio->configure(argc,argv);
 
-	/*******************************  Run BioEM routine ******************************/
+	//*******************************  Run BioEM routine ************************************
 	printf("Running\n");
 	timer.Start();
 	bio->run();
 	timer.Stop();
 
-	/************************************ End **********************************/
+	//************************************ End ***********************************************
 	printf ("The code ran for %f seconds.\n", timer.GetElapsedTime());
 	delete bio;
 

map.cpp

@@ -13,9 +13,9 @@ using namespace std;
 
 int bioem_RefMap::readRefMaps(bioem_param& param)
 {
-  /**************************************************************************************/
-  /***********************Reading reference Particle Maps************************/
-  /**************************************************************************************/
+  //**************************************************************************************
+  //***********************Reading reference Particle Maps************************
+  //**************************************************************************************
   if (loadMap)
     {
       FILE* fp = fopen("maps.dump", "rb");
@@ -34,7 +34,7 @@ int bioem_RefMap::readRefMaps(bioem_param& param)
       fclose(fp);
 
       cout << "Particle Maps read from Map Dump \nTotal Number of particles: " << ntotRefMap ;
-      cout << "\n+++++++++++++++++++++++++++++++++++++++++ \n";
+      cout << "\n+++++++++++++++++++++++++++++++++++++++ \n";
     }
   else
     {
@@ -79,11 +79,13 @@ int bioem_RefMap::readRefMaps(bioem_param& param)
 		for(int i=3;i<100;i++)mapname[i] = {0};	
 		
 	      }
+	      cout << "\n+++++++++++++++++++++++++++++++++++++++++++ \n";
 	      cout << "Particle Maps read from MULTIPLE MRC Files in: " << filemap << "\n" ;
 	      
 	      } else {
 	      
 		read_MRC(filemap,param);
+		cout << "\n++++++++++++++++++++++++++++++++++++++++++ \n";
 		cout << "Particle Maps read from ONE MRC File: " << filemap << "\n" ;
 		
 	      }
@@ -160,6 +162,7 @@ int bioem_RefMap::readRefMaps(bioem_param& param)
 	  }
 	cout << ".";
 	ntotRefMap=nummap+1;
+	cout << "\n++++++++++++++++++++++++++++++++++++++++++ \n";
 	cout << "Particle Maps read from Standard File\n" ;	
       }
         cout << "Total Number of particles: " << ntotRefMap ;
@@ -184,9 +187,9 @@ int bioem_RefMap::readRefMaps(bioem_param& param)
 
 int bioem_RefMap::PreCalculateMapsFFT(bioem_param& param)
 {
-  /**************************************************************************************/
-  /********** Routine that pre-calculates Kernels for Convolution **********************/
-  /************************************************************************************/
+  //**************************************************************************************
+  //********** Routine that pre-calculates Kernels for Convolution ***********************
+  //**************************************************************************************
 
   myfloat_t* localMap;
 
@@ -249,7 +252,7 @@ int bioem_RefMap::read_MRC(const char* filename,bioem_param& param)
 	 n_range_viol1 = test_mrc(filename,1);
 
 
-  if (n_range_viol0 < n_range_viol1) { /* guess endianism */
+  if (n_range_viol0 < n_range_viol1) { //* guess endianism 
     swap = 0;
     if (n_range_viol0 > 0) {
       printf(" Warning: %i header field range violations detected in file %s \n", n_range_viol0,filename);
@@ -260,7 +263,7 @@ int bioem_RefMap::read_MRC(const char* filename,bioem_param& param)
       printf("Warning: %i header field range violations detected in file %s \n", n_range_viol1,filename);
     }
   }
-       printf("++++++++++++++++++++++++++++++++++++++++++++++\n");
+       printf("\n+++++++++++++++++++++++++++++++++++++++++++\n");
 	printf("Reading Information from MRC: %s \n", filename);
 	header_ok *= read_int(&nc,fin,swap);
 	header_ok *= read_int(&nr,fin,swap);
@@ -291,8 +294,8 @@ int bioem_RefMap::read_MRC(const char* filename,bioem_param& param)
 	printf("Number Columns  = %8d \n",nc);
 	printf("Number Rows     = %8d \n",nr);
 	printf("Number Sections = %8d \n",ns);
-	printf("MODE = %8d  (only data type mode 2: 32-bit)\n",mode);
-       printf("NSYMBT = %8d  (# bytes symmetry operators)\n",nsymbt);
+	printf("MODE = %4d (only data type mode 2: 32-bit)\n",mode);
+       printf("NSYMBT = %4d (# bytes symmetry operators)\n",nsymbt);
 
 	/* printf("  NCSTART = %8d  (index of first column, counting from 0)\n",ncstart);
 	   printf(">  NRSTART = %8d  (index of first row, counting from 0)\n",nrstart);
@@ -444,7 +447,7 @@ int  bioem_RefMap::test_mrc (const char *vol_file, int swap) {
           exit(1);
   }
 
-  /* read header info */
+ //* read header info 
   header_ok *= read_int(&nc,fin,swap);
   header_ok *= read_int(&nr,fin,swap);
   header_ok *= read_int(&ns,fin,swap);

model.cpp

@@ -11,9 +11,9 @@ using namespace std;
 
 int bioem_model::readModel()
 {
-	/**************************************************************************************/
-	/***************Reading reference Models either PDB or x,y,z,r,d format****************/
-	/**************************************************************************************/
+	//**************************************************************************************
+	//***************Reading reference Models either PDB or x,y,z,r,d format****************
+	//**************************************************************************************
 
 	ofstream exampleReadCoor;
 	exampleReadCoor.open ("COORDREAD");
@@ -110,7 +110,7 @@ int bioem_model::readModel()
 		}
 		nPointsModel=numres;
 		cout << "Protein structure read from PDB\nTotal Number of Residues " << nPointsModel;
-		cout << "\n+++++++++++++++++++++++++++++++++++++++++ \n";
+		
 	}
 	else //Reading model from FILE FORMAT x,y,z,rad,density
 	{
@@ -140,8 +140,8 @@ int bioem_model::readModel()
 				numres++;
 			}
 			nPointsModel=numres;
-			cout << "Protein structure read from Standard File \nTotal Number of Residues " << nPointsModel ;
-			cout << "\n+++++++++++++++++++++++++++++++++++++++++ \n";
+			cout << "Protein structure read from Standard File \nTotal Number of Voxels " << nPointsModel ;
+			
 		}
 	}
 	exampleReadCoor.close();
@@ -173,7 +173,7 @@ int bioem_model::readModel()
 
 myfloat_t bioem_model::getAminoAcidRad(char *name)
 {
-	/*************** Function that gets the radius for each amino acid ****************/
+	//************** Function that gets the radius for each amino acid ****************
 	myfloat_t iaa=0;
 
 	if(std::strcmp(name,"CYS")==0)iaa=2.75;
@@ -208,7 +208,7 @@ myfloat_t bioem_model::getAminoAcidRad(char *name)
 
 myfloat_t bioem_model::getAminoAcidDensity(char *name)
 {
-	/*************** Function that gets the number of electrons for each amino acid ****************/
+	//************** Function that gets the number of electrons for each amino acid ****************
 	myfloat_t iaa=0.0;
 
 	if(std::strcmp(name,"CYS")==0)iaa=64.0;