get rid of max number of model points constant

bioem.cpp

@@ -516,7 +516,7 @@ int bioem::createProjection(int iMap, mycomplex_t* mapFFT)
 		{
 			for(int j = 0; j < 3; j++)
 			{
-				RotatedPointsModel[n].pos[k] += rotmat[k][j] * Model.PointsModel[n].pos[j];
+				RotatedPointsModel[n].pos[k] += rotmat[k][j] * Model.points[n].point.pos[j];
 			}
 		}
 	}
@@ -536,7 +536,7 @@ int bioem::createProjection(int iMap, mycomplex_t* mapFFT)
 			continue;
 		}
 
-		localproj[i * param.param_device.NumberPixels + j] += Model.densityPointsModel[n] / Model.NormDen;
+		localproj[i * param.param_device.NumberPixels + j] += Model.points[n].density / Model.NormDen;
 	}
 
 	// **** Output Just to check****

include/defs.h

@@ -41,7 +41,6 @@ typedef double myfloat_t;
 typedef myfloat_t mycomplex_t[2];
 
 #define BIOEM_FLOAT_3_PHYSICAL_SIZE 3	//Possible set to 4 for GPU
-#define BIOEM_MODEL_SIZE 120000
 
 struct myfloat3_t
 {

include/model.h

@@ -2,12 +2,21 @@
 #define BIOEM_MODEL_H
 
 #include "defs.h"
+#include <boost/concept_check.hpp>
 
 class bioem_model
 {
 public:
-	//bioem_model();
-	//~bioem_model();
+	class bioem_model_point
+	{
+	public:
+		myfloat3_t point;
+		myfloat_t radius;
+		myfloat_t density;
+	};
+	
+	bioem_model();
+	~bioem_model();
 
 	int readModel(const char* filemodel);
 
@@ -18,9 +27,7 @@ public:
 	myfloat_t NormDen;
 
 	int nPointsModel;
-	myfloat3_t PointsModel[BIOEM_MODEL_SIZE];
-	myfloat_t radiusPointsModel[BIOEM_MODEL_SIZE];
-	myfloat_t densityPointsModel[BIOEM_MODEL_SIZE];
+	bioem_model_point* points;
 };
 
 #endif

model.cpp

@@ -17,6 +17,15 @@
 
 using namespace std;
 
+bioem_model::bioem_model()
+{
+	points = NULL;
+}
+
+bioem_model::~bioem_model()
+{
+	if (points) free(points);
+}
 
 int bioem_model::readModel(const char* filemodel)
 {
@@ -26,6 +35,8 @@ int bioem_model::readModel(const char* filemodel)
 
 	ofstream exampleReadCoor;
 	exampleReadCoor.open ("COORDREAD");
+	
+	int allocsize = 0;
 
 	std::ifstream input(filemodel);
 	if(readPDB)
@@ -96,21 +107,27 @@ int bioem_model::readModel(const char* filemodel)
 
 				if (strcmp(name, "CA") == 0)
 				{
-					if (numres >= BIOEM_MODEL_SIZE)
+					if (allocsize == 0)
 					{
-						cout << "BIOEM_MODEL_SIZE too small\n";
-						exit(1);
+						allocsize = 64;
+						points = (bioem_model_point*) mallocchk(sizeof(bioem_model_point) * allocsize);
 					}
+					else if (numres + 1 >= allocsize)
+					{
+						allocsize *= 2;
+						points = (bioem_model_point*) reallocchk(points, sizeof(bioem_model_point) * allocsize);
+					}
+					
 					//Getting residue Radius and electron density
-					radiusPointsModel[numres] = getAminoAcidRad(resName);
-					densityPointsModel[numres] = getAminoAcidDensity(resName);
-					NormDen += densityPointsModel[numres];
+					points[numres].radius = getAminoAcidRad(resName);
+					points[numres].density = getAminoAcidDensity(resName);
+					NormDen += points[numres].density;
 
 					//Getting the coordinates
-					PointsModel[numres].pos[0] = (myfloat_t) x;
-					PointsModel[numres].pos[1] = (myfloat_t) y;
-					PointsModel[numres].pos[2] = (myfloat_t) z;
-					exampleReadCoor << "RESIDUE " << numres << " " << PointsModel[numres].pos[0] << " " <<  PointsModel[numres].pos[1] << " " << PointsModel[numres].pos[2] << " " << densityPointsModel[numres]  << "\n";
+					points[numres].point.pos[0] = (myfloat_t) x;
+					points[numres].point.pos[1] = (myfloat_t) y;
+					points[numres].point.pos[2] = (myfloat_t) z;
+					exampleReadCoor << "RESIDUE " << numres << " " << points[numres].point.pos[0] << " " <<  points[numres].point.pos[1] << " " << points[numres].point.pos[2] << " " << points[numres].density  << "\n";
 					numres++;
 				}
 			}
@@ -133,27 +150,34 @@ int bioem_model::readModel(const char* filemodel)
 		}
 		while ( fgets ( line, sizeof line, file ) != NULL )
 		{
-			if (numres >= BIOEM_MODEL_SIZE)
+			if (allocsize == 0)
+			{
+				allocsize = 64;
+				points = (bioem_model_point*) mallocchk(sizeof(bioem_model_point) * allocsize);
+			}
+			else if (numres + 1 >= allocsize)
 			{
-				cout << "BIOEM_MODEL_SIZE too small\n";
-				exit(1);
+				allocsize *= 2;
+				points = (bioem_model_point*) reallocchk(points, sizeof(bioem_model_point) * allocsize);
 			}
+					
 			float tmpval[5];
 			sscanf(line, "%f %f %f %f %f", &tmpval[0], &tmpval[1], &tmpval[2], &tmpval[3], &tmpval[4]);
-			PointsModel[numres].pos[0] = (myfloat_t) tmpval[0];
-			PointsModel[numres].pos[1] = (myfloat_t) tmpval[1];
-			PointsModel[numres].pos[2] = (myfloat_t) tmpval[2];
-			radiusPointsModel[numres] = (myfloat_t) tmpval[3];
-			densityPointsModel[numres] = (myfloat_t) tmpval[4];
-
-			exampleReadCoor << "RESIDUE " << numres << " " << PointsModel[numres].pos[0] << " " <<  PointsModel[numres].pos[1] << " " << PointsModel[numres].pos[2] << " " << densityPointsModel[numres] << "\n";
-			NormDen += densityPointsModel[numres];
+			points[numres].point.pos[0] = (myfloat_t) tmpval[0];
+			points[numres].point.pos[1] = (myfloat_t) tmpval[1];
+			points[numres].point.pos[2] = (myfloat_t) tmpval[2];
+			points[numres].radius = (myfloat_t) tmpval[3];
+			points[numres].density = (myfloat_t) tmpval[4];
+
+			exampleReadCoor << "RESIDUE " << numres << " " << points[numres].point.pos[0] << " " <<  points[numres].point.pos[1] << " " << points[numres].point.pos[2] << " " << points[numres].density << "\n";
+			NormDen += points[numres].density;
 			numres++;
 		}
 		fclose(file);
 		nPointsModel = numres;
 		cout << "Protein structure read from Standard File\n";
 	}
+	points = (bioem_model_point*) reallocchk(points, sizeof(bioem_model_point) * nPointsModel);
 	cout << "Total Number of Voxels " << nPointsModel ;
 	cout << "\n+++++++++++++++++++++++++++++++++++++++++ \n";
 	exampleReadCoor.close();
@@ -165,18 +189,18 @@ int bioem_model::readModel(const char* filemodel)
 
 	for(int n = 0; n < nPointsModel; n++)
 	{
-		r_cm.pos[0] += PointsModel[n].pos[0];
-		r_cm.pos[1] += PointsModel[n].pos[1];
-		r_cm.pos[2] += PointsModel[n].pos[2];
+		r_cm.pos[0] += points[n].point.pos[0];
+		r_cm.pos[1] += points[n].point.pos[1];
+		r_cm.pos[2] += points[n].point.pos[2];
 	}
 	r_cm.pos[0] = r_cm.pos[0] / (myfloat_t) nPointsModel;
 	r_cm.pos[1] = r_cm.pos[1] / (myfloat_t) nPointsModel;
 	r_cm.pos[2] = r_cm.pos[2] / (myfloat_t) nPointsModel;
 	for(int n = 0; n < nPointsModel; n++)
 	{
-		PointsModel[n].pos[0] -= r_cm.pos[0];
-		PointsModel[n].pos[1] -= r_cm.pos[1];
-		PointsModel[n].pos[2] -= r_cm.pos[2];
+		points[n].point.pos[0] -= r_cm.pos[0];
+		points[n].point.pos[1] -= r_cm.pos[1];
+		points[n].point.pos[2] -= r_cm.pos[2];
 
 	}