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Commit 1e3203f7 authored by David Rohr's avatar David Rohr
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convert indent spaces to tabs, unify indentation

parent 87ad9163
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Showing with 859 additions and 787 deletions
bioem.cpp
View file @ 1e3203f7
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bioem_algorithm.h
View file @ 1e3203f7
......@@ -61,8 +61,8 @@ __device__ static inline myfloat_t calc_logpro(const bioem_param_device& param,
const myfloat_t ForLogProb = (sumsquare * param.Ntotpi - sum * sum);
// Products of different cross-correlations (first element in formula)
const myfloat_t firstele = param.Ntotpi * (sumsquareref * sumsquare-crossproMapConv * crossproMapConv) +
2 * sumref * sum * crossproMapConv - sumsquareref * sum * sum - sumref * sumref * sumsquare;
const myfloat_t firstele = param.Ntotpi * (sumsquareref * sumsquare - crossproMapConv * crossproMapConv) +
2 * sumref * sum * crossproMapConv - sumsquareref * sum * sum - sumref * sumref * sumsquare;
//******* Calculating log of Prob*********/
// As in fortran code: logpro=(3-Ntotpi)*0.5*log(firstele/pConvMap[iOrient].ForLogProbfromConv[iConv])+(Ntotpi*0.5-2)*log(Ntotpi-2)-0.5*log(pConvMap[iOrient].ForLogProbfromConv[iConv])+0.5*log(PI)+(1-Ntotpi*0.5)*(log(2*PI)+1);
......@@ -70,7 +70,7 @@ __device__ static inline myfloat_t calc_logpro(const bioem_param_device& param,
return(logpro);
}
__device__ static inline void calProb(int iRefMap,int iOrient, int iConv,myfloat_t sumC,myfloat_t sumsquareC, float value, int disx, int disy, bioem_Probability* pProb, const bioem_param_device& param, const bioem_RefMap& RefMap)
__device__ static inline void calProb(int iRefMap, int iOrient, int iConv, myfloat_t sumC, myfloat_t sumsquareC, float value, int disx, int disy, bioem_Probability* pProb, const bioem_param_device& param, const bioem_RefMap& RefMap)
{
/********************************************************/
/*********** Calculates the BioEM probability ***********/
......@@ -80,8 +80,8 @@ __device__ static inline void calProb(int iRefMap,int iOrient, int iConv,myfloat
//update_prob<-1>(logpro, iRefMap, iOrient, iConv, disx, disy, pProb);
//GCC is too stupid to inline properly, so the code is copied here
if(pProb[iRefMap].Constoadd < logpro)
{
if(pProb[iRefMap].Constoadd < logpro)
{
pProb[iRefMap].Total = pProb[iRefMap].Total * exp(-logpro + pProb[iRefMap].Constoadd);
pProb[iRefMap].Constoadd = logpro;
}
......@@ -106,33 +106,33 @@ __device__ static inline void calProb(int iRefMap,int iOrient, int iConv,myfloat
__device__ static inline void doRefMapFFT(const int iRefMap, const int iOrient, const int iConv, const myfloat_t* lCC, const myfloat_t sumC, const myfloat_t sumsquareC, bioem_Probability* pProb, const bioem_param_device& param, const bioem_RefMap& RefMap)
{
for (int cent_x = 0; cent_x <= param.maxDisplaceCenter; cent_x=cent_x+param.GridSpaceCenter)
for (int cent_x = 0; cent_x <= param.maxDisplaceCenter; cent_x = cent_x + param.GridSpaceCenter)
{
for (int cent_y = 0; cent_y <= param.maxDisplaceCenter; cent_y=cent_y+param.GridSpaceCenter)
for (int cent_y = 0; cent_y <= param.maxDisplaceCenter; cent_y = cent_y + param.GridSpaceCenter)
{
calProb(iRefMap, iOrient, iConv, sumC, sumsquareC, (myfloat_t) lCC[cent_x*param.NumberPixels+cent_y]/ (myfloat_t) (param.NumberPixels * param.NumberPixels), cent_x, cent_y, pProb, param, RefMap);
calProb(iRefMap, iOrient, iConv, sumC, sumsquareC, (myfloat_t) lCC[cent_x * param.NumberPixels + cent_y] / (myfloat_t) (param.NumberPixels * param.NumberPixels), cent_x, cent_y, pProb, param, RefMap);
}
for (int cent_y = param.NumberPixels-param.maxDisplaceCenter; cent_y < param.NumberPixels; cent_y=cent_y+param.GridSpaceCenter)
for (int cent_y = param.NumberPixels - param.maxDisplaceCenter; cent_y < param.NumberPixels; cent_y = cent_y + param.GridSpaceCenter)
{
calProb(iRefMap, iOrient, iConv, sumC, sumsquareC, (myfloat_t) lCC[cent_x*param.NumberPixels+cent_y]/ (myfloat_t) (param.NumberPixels*param.NumberPixels), cent_x, cent_y - param.NumberPixels, pProb, param, RefMap);
calProb(iRefMap, iOrient, iConv, sumC, sumsquareC, (myfloat_t) lCC[cent_x * param.NumberPixels + cent_y] / (myfloat_t) (param.NumberPixels * param.NumberPixels), cent_x, cent_y - param.NumberPixels, pProb, param, RefMap);
}
}
for (int cent_x = param.NumberPixels-param.maxDisplaceCenter; cent_x < param.NumberPixels; cent_x=cent_x+param.GridSpaceCenter)
for (int cent_x = param.NumberPixels - param.maxDisplaceCenter; cent_x < param.NumberPixels; cent_x = cent_x + param.GridSpaceCenter)
{
for (int cent_y = 0; cent_y < param.maxDisplaceCenter; cent_y=cent_y+param.GridSpaceCenter)
for (int cent_y = 0; cent_y < param.maxDisplaceCenter; cent_y = cent_y + param.GridSpaceCenter)
{
calProb(iRefMap, iOrient, iConv, sumC, sumsquareC, (myfloat_t) lCC[cent_x*param.NumberPixels+cent_y]/ (myfloat_t) (param.NumberPixels*param.NumberPixels), cent_x - param.NumberPixels, cent_y, pProb, param, RefMap);
calProb(iRefMap, iOrient, iConv, sumC, sumsquareC, (myfloat_t) lCC[cent_x * param.NumberPixels + cent_y] / (myfloat_t) (param.NumberPixels * param.NumberPixels), cent_x - param.NumberPixels, cent_y, pProb, param, RefMap);
}
for (int cent_y = param.NumberPixels-param.maxDisplaceCenter; cent_y <= param.NumberPixels; cent_y=cent_y+param.GridSpaceCenter)
for (int cent_y = param.NumberPixels - param.maxDisplaceCenter; cent_y <= param.NumberPixels; cent_y = cent_y + param.GridSpaceCenter)
{
calProb(iRefMap, iOrient, iConv, sumC, sumsquareC, (myfloat_t) lCC[cent_x*param.NumberPixels+cent_y]/ (myfloat_t) (param.NumberPixels*param.NumberPixels), cent_x - param.NumberPixels, cent_y - param.NumberPixels, pProb, param, RefMap);
calProb(iRefMap, iOrient, iConv, sumC, sumsquareC, (myfloat_t) lCC[cent_x * param.NumberPixels + cent_y] / (myfloat_t) (param.NumberPixels * param.NumberPixels), cent_x - param.NumberPixels, cent_y - param.NumberPixels, pProb, param, RefMap);
}
}
}
template <int GPUAlgo, class RefT>
__device__ static inline void compareRefMap(const int iRefMap, const int iOrient, const int iConv, const bioem_map& Mapconv, bioem_Probability* pProb, const bioem_param_device& param, const RefT& RefMap,
const int cent_x, const int cent_y, const int myShift = 0, const int nShifts2 = 0, const int myRef = 0, const bool threadActive = true)
const int cent_x, const int cent_y, const int myShift = 0, const int nShifts2 = 0, const int myRef = 0, const bool threadActive = true)
{
/**************************************************************************************/
/********************** Calculating BioEM Probability ********************************/
......@@ -145,9 +145,9 @@ __device__ static inline void compareRefMap(const int iRefMap, const int iOrient
myfloat_t sum, sumsquare, crossproMapConv;
__m128 sum_v = _mm_setzero_ps(), sumsquare_v = _mm_setzero_ps(), cross_v = _mm_setzero_ps(), d1, d2;
#else
myfloat_t sum=0.0;
myfloat_t sumsquare=0.0;
myfloat_t crossproMapConv=0.0;
myfloat_t sum = 0.0;
myfloat_t sumsquare = 0.0;
myfloat_t crossproMapConv = 0.0;
#endif
/****** Loop over Pixels to calculate dot product and cross-correlations of displaced Ref Conv. Map***/
myfloat_t logpro;
......@@ -182,7 +182,7 @@ __device__ static inline void compareRefMap(const int iRefMap, const int iOrient
const float* ptr2 = RefMap.getp(iRefMap, i, jStart);
int j;
const int count = jEnd - jStart;
for (j = 0;j <= count - 4;j += 4)
for (j = 0; j <= count - 4; j += 4)
{
d1 = _mm_loadu_ps(ptr1);
d2 = _mm_loadu_ps(ptr2);
......@@ -201,7 +201,7 @@ __device__ static inline void compareRefMap(const int iRefMap, const int iOrient
// Crosscorrelation of calculated displaced map
sum += pointMap;
// Calculate Sum of pixels squared
sumsquare += pointMap*pointMap;
sumsquare += pointMap * pointMap;
}
#endif
}
......@@ -380,18 +380,18 @@ __device__ static inline void compareRefMap(const int iRefMap, const int iOrient
else
#endif
/***** Summing & Storing total/Orientation Probabilites for each map ************/
/***** Summing & Storing total/Orientation Probabilites for each map ************/
{
update_prob<-1>(logpro, iRefMap, iOrient, iConv, cent_x, cent_y, pProb);
update_prob < -1 > (logpro, iRefMap, iOrient, iConv, cent_x, cent_y, pProb);
}
}
template <int GPUAlgo, class RefT>
__device__ static inline void compareRefMapShifted(const int iRefMap, const int iOrient, const int iConv, const bioem_map& Mapconv, bioem_Probability* pProb, const bioem_param_device& param, const RefT& RefMap)
{
for (int cent_x = -param.maxDisplaceCenter; cent_x <= param.maxDisplaceCenter; cent_x=cent_x+param.GridSpaceCenter)
for (int cent_x = -param.maxDisplaceCenter; cent_x <= param.maxDisplaceCenter; cent_x = cent_x + param.GridSpaceCenter)
{
for (int cent_y = -param.maxDisplaceCenter; cent_y <= param.maxDisplaceCenter; cent_y=cent_y+param.GridSpaceCenter)
for (int cent_y = -param.maxDisplaceCenter; cent_y <= param.maxDisplaceCenter; cent_y = cent_y + param.GridSpaceCenter)
{
compareRefMap<GPUAlgo>(iRefMap, iOrient, iConv, Mapconv, pProb, param, RefMap, cent_x, cent_y);
}
......
bioem_cuda.cu
View file @ 1e3203f7
......@@ -39,7 +39,7 @@ __global__ void compareRefMap_kernel(const int iOrient, const int iConv, const b
const int iRefMap = myBlockIdxX * myBlockDimX + myThreadIdxX;
if (iRefMap < maxRef)
{
compareRefMap<0>(iRefMap,iOrient,iConv,*pMap, pProb, param, *RefMap, cent_x, cent_y);
compareRefMap<0>(iRefMap, iOrient, iConv, *pMap, pProb, param, *RefMap, cent_x, cent_y);
}
}
......@@ -48,7 +48,7 @@ __global__ void compareRefMapShifted_kernel(const int iOrient, const int iConv,
const int iRefMap = myBlockIdxX * myBlockDimX + myThreadIdxX;
if (iRefMap < maxRef)
{
compareRefMapShifted<1>(iRefMap,iOrient,iConv,*pMap, pProb, param, *RefMap);
compareRefMapShifted<1>(iRefMap, iOrient, iConv, *pMap, pProb, param, *RefMap);
}
}
......@@ -58,7 +58,7 @@ __global__ void cudaZeroMem(void* ptr, size_t size)
int mysize = size / sizeof(int);
int myid = myBlockDimX * myBlockIdxX + myThreadIdxX;
int mygrid = myBlockDimX * myGridDimX;
for (int i = myid;i < mysize;i += mygrid) myptr[i] = 0;
for (int i = myid; i < mysize; i += mygrid) myptr[i] = 0;
}
__global__ void compareRefMapLoopShifts_kernel(const int iOrient, const int iConv, const bioem_map* pMap, bioem_Probability* pProb, const bioem_param_device param, const bioem_RefMap* RefMap, const int blockoffset, const int nShifts, const int nShiftBits, const int maxRef)
......@@ -74,7 +74,7 @@ __global__ void compareRefMapLoopShifts_kernel(const int iOrient, const int iCon
const bool threadActive = myShiftIdx < nShifts && myShiftIdy < nShifts && iRefMap < maxRef;
compareRefMap<2>(iRefMap,iOrient,iConv,*pMap, pProb, param, *RefMap, cent_x, cent_y, myShift, nShifts * nShifts, myRef, threadActive);
compareRefMap<2>(iRefMap, iOrient, iConv, *pMap, pProb, param, *RefMap, cent_x, cent_y, myShift, nShifts * nShifts, myRef, threadActive);
}
__global__ void multComplexMap(const mycomplex_t* convmap, const mycomplex_t* refmap, mycuComplex_t* out, const int NumberPixelsTotal, const int MapSize, const int NumberMaps, const int Offset)
......@@ -82,7 +82,7 @@ __global__ void multComplexMap(const mycomplex_t* convmap, const mycomplex_t* re
if (myBlockIdxX >= NumberMaps) return;
const mycomplex_t* myin = &refmap[myBlockIdxX * MapSize + Offset];
mycuComplex_t* myout = &out[(myBlockIdxX * MapSize)];
for(int i = myThreadIdxX;i < NumberPixelsTotal;i += myBlockDimX)
for(int i = myThreadIdxX; i < NumberPixelsTotal; i += myBlockDimX)
{
myout[i].x = convmap[i][0] * myin[i][0] + convmap[i][1] * myin[i][1];
myout[i].y = convmap[i][1] * myin[i][0] - convmap[i][0] * myin[i][1];
......@@ -126,7 +126,7 @@ int bioem_cuda::compareRefMaps(int iProjectionOut, int iConv, const bioem_map& c
if (FFTAlgo)
{
checkCudaErrors(cudaMemcpyAsync(&pConvMapFFT[(iConv & 1) * param.RefMapSize], localmultFFT, param.RefMapSize * sizeof(mycomplex_t), cudaMemcpyHostToDevice, cudaStream));
for (int i = 0;i < maxRef;i += CUDA_FFTS_AT_ONCE)
for (int i = 0; i < maxRef; i += CUDA_FFTS_AT_ONCE)
{
const int num = min(CUDA_FFTS_AT_ONCE, maxRef - i);
multComplexMap<<<num, CUDA_THREAD_COUNT, 0, cudaStream>>>(&pConvMapFFT[(iConv & 1) * param.RefMapSize], pRefMapsFFT, pFFTtmp2, param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D, param.RefMapSize, num, i);
......@@ -164,24 +164,24 @@ int bioem_cuda::compareRefMaps(int iProjectionOut, int iConv, const bioem_map& c
const int nShiftBits = ilog2(nShifts);
size_t totalBlocks = divup((size_t) maxRef * (size_t) nShifts * (size_t) nShifts, (size_t) CUDA_THREAD_COUNT);
size_t nBlocks = CUDA_BLOCK_COUNT;
for (size_t i = 0;i < totalBlocks;i += nBlocks)
for (size_t i = 0; i < totalBlocks; i += nBlocks)
{
compareRefMapLoopShifts_kernel <<<min(nBlocks, totalBlocks - i), CUDA_THREAD_COUNT, (CUDA_THREAD_COUNT * 2 + CUDA_THREAD_COUNT / (nShifts * nShifts) * 4) * sizeof(myfloat_t), cudaStream>>> (iProjectionOut, iConv, pConvMap_device[iConv & 1], pProb_device, param.param_device, pRefMap_device, i, nShifts, nShiftBits, maxRef);
compareRefMapLoopShifts_kernel<<<min(nBlocks, totalBlocks - i), CUDA_THREAD_COUNT, (CUDA_THREAD_COUNT * 2 + CUDA_THREAD_COUNT / (nShifts * nShifts) * 4) * sizeof(myfloat_t), cudaStream >>> (iProjectionOut, iConv, pConvMap_device[iConv & 1], pProb_device, param.param_device, pRefMap_device, i, nShifts, nShiftBits, maxRef);
}
}
else if (GPUAlgo == 1) //Split shifts in multiple kernels
{
for (int cent_x = -param.param_device.maxDisplaceCenter; cent_x <= param.param_device.maxDisplaceCenter; cent_x=cent_x+param.param_device.GridSpaceCenter)
for (int cent_x = -param.param_device.maxDisplaceCenter; cent_x <= param.param_device.maxDisplaceCenter; cent_x = cent_x + param.param_device.GridSpaceCenter)
{
for (int cent_y = -param.param_device.maxDisplaceCenter; cent_y <= param.param_device.maxDisplaceCenter; cent_y=cent_y+param.param_device.GridSpaceCenter)
for (int cent_y = -param.param_device.maxDisplaceCenter; cent_y <= param.param_device.maxDisplaceCenter; cent_y = cent_y + param.param_device.GridSpaceCenter)
{
compareRefMap_kernel <<<divup(maxRef, CUDA_THREAD_COUNT), CUDA_THREAD_COUNT, 0, cudaStream>>> (iProjectionOut, iConv, pConvMap_device[iConv & 1], pProb_device, param.param_device, pRefMap_device_Mod, cent_x, cent_y, maxRef);
compareRefMap_kernel<<<divup(maxRef, CUDA_THREAD_COUNT), CUDA_THREAD_COUNT, 0, cudaStream>>> (iProjectionOut, iConv, pConvMap_device[iConv & 1], pProb_device, param.param_device, pRefMap_device_Mod, cent_x, cent_y, maxRef);
}
}
}
else if (GPUAlgo == 0) //All shifts in one kernel
{
compareRefMapShifted_kernel <<<divup(maxRef, CUDA_THREAD_COUNT), CUDA_THREAD_COUNT, 0, cudaStream>>> (iProjectionOut, iConv, pConvMap_device[iConv & 1], pProb_device, param.param_device, pRefMap_device_Mod, maxRef);
compareRefMapShifted_kernel<<<divup(maxRef, CUDA_THREAD_COUNT), CUDA_THREAD_COUNT, 0, cudaStream>>> (iProjectionOut, iConv, pConvMap_device[iConv & 1], pProb_device, param.param_device, pRefMap_device_Mod, maxRef);
}
else
{
......@@ -215,7 +215,7 @@ int bioem_cuda::deviceInit()
checkCudaErrors(cudaMalloc(&pRefMap_device, sizeof(bioem_RefMap)));
cout << "\tSize Probability\t" << sizeof(bioem_Probability) * RefMap.ntotRefMap << "\n";
checkCudaErrors(cudaMalloc(&pProb_device, sizeof(bioem_Probability) * RefMap.ntotRefMap));
for (int i = 0;i < 2;i++)
for (int i = 0; i < 2; i++)
{
checkCudaErrors(cudaEventCreate(&cudaEvent[i]));
checkCudaErrors(cudaMalloc(&pConvMap_device[i], sizeof(bioem_map)));
......@@ -256,7 +256,7 @@ int bioem_cuda::deviceExit()
cudaStreamDestroy(cudaStream);
cudaFree(pRefMap_device);
cudaFree(pProb_device);
for (int i = 0;i < 2;i++)
for (int i = 0; i < 2; i++)
{
cudaEventDestroy(cudaEvent[i]);
cudaFree(pConvMap_device);
......@@ -282,7 +282,7 @@ int bioem_cuda::deviceStartRun()
if (FFTAlgo)
{
for (int i = 0;i < 2;i++)
for (int i = 0; i < 2; i++)
{
int n[2] = {param.param_device.NumberPixels, param.param_device.NumberPixels};
if (cufftPlanMany(&plan[i], 2, n, NULL, 1, 0, NULL, 1, 0, CUFFT_C2R, i ? (maxRef % CUDA_FFTS_AT_ONCE) : CUDA_FFTS_AT_ONCE) != CUFFT_SUCCESS)
......@@ -312,7 +312,7 @@ int bioem_cuda::deviceFinishRun()
if (FFTAlgo)
{
for (int i = 0;i < 2;i++) cufftDestroy(plan[i]);
for (int i = 0; i < 2; i++) cufftDestroy(plan[i]);
}
return(0);
......
include/bioem.h
View file @ 1e3203f7
......@@ -21,13 +21,13 @@ public:
int dopreCalCrossCorrelation(int iRefMap, int iRefMapLocal);
int run();
int doProjections(int iMap);
int createConvolutedProjectionMap(int iOreint,int iMap, mycomplex_t* lproj,bioem_map& Mapconv,mycomplex_t* localmultFFT,myfloat_t& sumC,myfloat_t& sumsquareC);
int createConvolutedProjectionMap(int iOreint, int iMap, mycomplex_t* lproj, bioem_map& Mapconv, mycomplex_t* localmultFFT, myfloat_t& sumC, myfloat_t& sumsquareC);
virtual int compareRefMaps(int iProjectionOut, int iConv, const bioem_map& conv_map, mycomplex_t* localmultFFT, myfloat_t sumC, myfloat_t sumsquareC, const int startMap = 0);
int createProjection(int iMap, mycomplex_t* map);
int calcross_cor(bioem_map& localmap,myfloat_t& sum,myfloat_t& sumsquare);
void calculateCCFFT(int iMap, int iOrient, int iConv, myfloat_t sumC, myfloat_t sumsquareC, mycomplex_t* localConvFFT,mycomplex_t* localCCT,myfloat_t* lCC);
int calcross_cor(bioem_map& localmap, myfloat_t& sum, myfloat_t& sumsquare);
void calculateCCFFT(int iMap, int iOrient, int iConv, myfloat_t sumC, myfloat_t sumsquareC, mycomplex_t* localConvFFT, mycomplex_t* localCCT, myfloat_t* lCC);
bioem_Probability* pProb;
......
include/map.h
View file @ 1e3203f7
......@@ -22,13 +22,13 @@ public:
}
int readRefMaps(bioem_param& param);
int PreCalculateMapsFFT(bioem_param& param);
int read_int(int *currlong, FILE *fin, int swap);
int read_float(float *currfloat, FILE *fin, int swap);
int read_float_empty (FILE *fin);
int read_char_float (float *currfloat, FILE *fin) ;
int test_mrc (const char *vol_file, int swap);
int read_MRC(const char* filename,bioem_param& param);
int read_int(int *currlong, FILE *fin, int swap);
int read_float(float *currfloat, FILE *fin, int swap);
int read_float_empty (FILE *fin);
int read_char_float (float *currfloat, FILE *fin) ;
int test_mrc (const char *vol_file, int swap);
int read_MRC(const char* filename, bioem_param& param);
mycomplex_t* RefMapsFFT;
const char* filemap;
......@@ -38,7 +38,7 @@ public:
myfloat_t sumsquare_RefMap[BIOEM_MAX_MAPS];
myfloat_t ForLogProbfromRef[BIOEM_MAX_MAPS];
bool dumpMap, loadMap, readMRC,readMultMRC;
bool dumpMap, loadMap, readMRC, readMultMRC;
__host__ __device__ inline myfloat_t get(int map, int x, int y) const {return(Ref[map].points[x][y]);}
__host__ __device__ inline const myfloat_t* getp(int map, int x, int y) const {return(&Ref[map].points[x][y]);}
......@@ -65,12 +65,12 @@ public:
memcpy(sum_RefMap, map.sum_RefMap, sizeof(sum_RefMap));
memcpy(sumsquare_RefMap, map.sumsquare_RefMap, sizeof(sumsquare_RefMap));
memcpy(ForLogProbfromRef, map.ForLogProbfromRef, sizeof(ForLogProbfromRef));
#pragma omp parallel for
for (int i = 0;i < ntotRefMap;i++)
#pragma omp parallel for
for (int i = 0; i < ntotRefMap; i++)
{
for (int j = 0;j < BIOEM_MAP_SIZE_X;j++)
for (int j = 0; j < BIOEM_MAP_SIZE_X; j++)
{
for (int k = 0;k < BIOEM_MAP_SIZE_Y;k++)
for (int k = 0; k < BIOEM_MAP_SIZE_Y; k++)
{
Ref[j][k][i] = map.get(i, j, k);
}
......
include/model.h
View file @ 1e3203f7
......@@ -15,7 +15,7 @@ public:
myfloat_t getAminoAcidRad(char *name);
myfloat_t getAminoAcidDensity(char *name);
myfloat_t NormDen;
myfloat_t NormDen;
const char* filemodel;
......
main.cpp
View file @ 1e3203f7
......@@ -26,7 +26,7 @@ int main(int argc, char* argv[])
//*************************************************************************************
#ifdef _MM_SET_DENORMALS_ZERO_MODE
#pragma omp parallel
#pragma omp parallel
{
_MM_SET_DENORMALS_ZERO_MODE(_MM_DENORMALS_ZERO_ON); //Flush denormals to zero in all OpenMP threads
}
......@@ -47,7 +47,7 @@ int main(int argc, char* argv[])
//************ Configuration and Pre-calculating necessary objects *********************
printf("Configuring\n");
bio->configure(argc,argv);
bio->configure(argc, argv);
//******************************* Run BioEM routine ************************************
printf("Running\n");
......
map.cpp
View file @ 1e3203f7
This diff is collapsed.
model.cpp
View file @ 1e3203f7
......@@ -30,19 +30,19 @@ int bioem_model::readModel()
char line[512] = {' '};
char tmpLine[512] = {' '};
int numres=0;
NormDen=0.0;
int numres = 0;
NormDen = 0.0;
// cout << " HERE " << filemodel ;
// for eachline in the file
while (!input.eof())
{
input.getline(line,512);
input.getline(line, 512);
strncpy(tmpLine,line,strlen(line));
char *token = strtok(tmpLine," ");
strncpy(tmpLine, line, strlen(line));
char *token = strtok(tmpLine, " ");
if (strcmp(token,"ATOM")==0) // Optional,Mandatory if standard residues exist
if (strcmp(token, "ATOM") == 0) // Optional,Mandatory if standard residues exist
{
/*
1-6 "ATOM "
......@@ -66,26 +66,26 @@ int bioem_model::readModel()
char tmp[6] = {' '};
// parse name
strncpy(tmp,line+12,4);
sscanf (tmp,"%s",name);
strncpy(tmp, line + 12, 4);
sscanf (tmp, "%s", name);
// parse resName
strncpy(tmp,line+17,3);
sscanf (tmp,"%s",resName);
strncpy(tmp, line + 17, 3);
sscanf (tmp, "%s", resName);
// parse x, y, z
char tmpVals[36] = {' '};
strncpy (tmpVals,line+30,8);
sscanf (tmpVals,"%f",&x);
strncpy (tmpVals, line + 30, 8);
sscanf (tmpVals, "%f", &x);
strncpy (tmpVals,line+38,8);
sscanf (tmpVals,"%f",&y);
strncpy (tmpVals, line + 38, 8);
sscanf (tmpVals, "%f", &y);
strncpy (tmpVals,line+46,8);
sscanf (tmpVals,"%f",&z);
strncpy (tmpVals, line + 46, 8);
sscanf (tmpVals, "%f", &z);
if (strcmp(name,"CA") == 0)
if (strcmp(name, "CA") == 0)
{
if (numres >= BIOEM_MODEL_SIZE)
{
......@@ -93,30 +93,30 @@ int bioem_model::readModel()
exit(1);
}
//Getting residue Radius and electron density
radiusPointsModel[numres]=getAminoAcidRad(resName);
densityPointsModel[numres]=getAminoAcidDensity(resName);
NormDen+=densityPointsModel[numres];
radiusPointsModel[numres] = getAminoAcidRad(resName);
densityPointsModel[numres] = getAminoAcidDensity(resName);
NormDen += densityPointsModel[numres];
//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";
exampleReadCoor << "RESIDUE " << numres << " " << PointsModel[numres].pos[0] << " " << PointsModel[numres].pos[1] << " " << PointsModel[numres].pos[2] << " " << densityPointsModel[numres] << "\n";
numres++;
}
}
}
nPointsModel=numres;
nPointsModel = numres;
cout << "Protein structure read from PDB\nTotal Number of Residues " << nPointsModel;
}
else //Reading model from FILE FORMAT x,y,z,rad,density
{
char line[128];
int numres=0;
NormDen=0.0;
int numres = 0;
NormDen = 0.0;
FILE *file = fopen ( filemodel , "r" );
if ( file != NULL )
{
......@@ -135,13 +135,13 @@ int bioem_model::readModel()
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];
exampleReadCoor << "RESIDUE " << numres << " " << PointsModel[numres].pos[0] << " " << PointsModel[numres].pos[1] << " " << PointsModel[numres].pos[2] << " " << densityPointsModel[numres] << "\n";
NormDen += densityPointsModel[numres];
numres++;
}
nPointsModel=numres;
nPointsModel = numres;
cout << "Protein structure read from Standard File \nTotal Number of Voxels " << nPointsModel ;
}
}
exampleReadCoor.close();
......@@ -149,22 +149,22 @@ int bioem_model::readModel()
//Moving to Model to its center of mass:
myfloat3_t r_cm;
for(int n=0; n < 3; n++)r_cm.pos[n] = 0.0;
for(int n = 0; n < 3; n++)r_cm.pos[n] = 0.0;
for(int n=0; n < nPointsModel; n++)
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]=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++)
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];
PointsModel[n].pos[0] -= r_cm.pos[0];
PointsModel[n].pos[1] -= r_cm.pos[1];
PointsModel[n].pos[2] -= r_cm.pos[2];
}
......@@ -174,28 +174,28 @@ int bioem_model::readModel()
myfloat_t bioem_model::getAminoAcidRad(char *name)
{
//************** Function that gets the radius for each amino acid ****************
myfloat_t iaa=0;
if(std::strcmp(name,"CYS")==0)iaa=2.75;
if(std::strcmp(name,"PHE")==0)iaa=3.2;
if(std::strcmp(name,"LEU")==0)iaa=3.1;
if(std::strcmp(name,"TRP")==0)iaa=3.4;
if(std::strcmp(name,"VAL")==0)iaa=2.95;
if(std::strcmp(name,"ILE")==0)iaa=3.1;
if(std::strcmp(name,"MET")==0)iaa=3.1;
if(std::strcmp(name,"HIS")==0)iaa=3.05;
if(std::strcmp(name,"TYR")==0)iaa=3.25;
if(std::strcmp(name,"ALA")==0)iaa=2.5;
if(std::strcmp(name,"GLY")==0)iaa=2.25;
if(std::strcmp(name,"PRO")==0)iaa=2.8;
if(std::strcmp(name,"ASN")==0)iaa=2.85;
if(std::strcmp(name,"THR")==0)iaa=2.8;
if(std::strcmp(name,"SER")==0)iaa=2.6;
if(std::strcmp(name,"ARG")==0)iaa=3.3;
if(std::strcmp(name,"GLN")==0)iaa=3.0;
if(std::strcmp(name,"ASP")==0)iaa=2.8;
if(std::strcmp(name,"LYS")==0)iaa=3.2;
if(std::strcmp(name,"GLU")==0)iaa=2.95;
myfloat_t iaa = 0;
if(std::strcmp(name, "CYS") == 0)iaa = 2.75;
if(std::strcmp(name, "PHE") == 0)iaa = 3.2;
if(std::strcmp(name, "LEU") == 0)iaa = 3.1;
if(std::strcmp(name, "TRP") == 0)iaa = 3.4;
if(std::strcmp(name, "VAL") == 0)iaa = 2.95;
if(std::strcmp(name, "ILE") == 0)iaa = 3.1;
if(std::strcmp(name, "MET") == 0)iaa = 3.1;
if(std::strcmp(name, "HIS") == 0)iaa = 3.05;
if(std::strcmp(name, "TYR") == 0)iaa = 3.25;
if(std::strcmp(name, "ALA") == 0)iaa = 2.5;
if(std::strcmp(name, "GLY") == 0)iaa = 2.25;
if(std::strcmp(name, "PRO") == 0)iaa = 2.8;
if(std::strcmp(name, "ASN") == 0)iaa = 2.85;
if(std::strcmp(name, "THR") == 0)iaa = 2.8;
if(std::strcmp(name, "SER") == 0)iaa = 2.6;
if(std::strcmp(name, "ARG") == 0)iaa = 3.3;
if(std::strcmp(name, "GLN") == 0)iaa = 3.0;
if(std::strcmp(name, "ASP") == 0)iaa = 2.8;
if(std::strcmp(name, "LYS") == 0)iaa = 3.2;
if(std::strcmp(name, "GLU") == 0)iaa = 2.95;
if(iaa == 0)
{
......@@ -209,28 +209,28 @@ 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 ****************
myfloat_t iaa=0.0;
if(std::strcmp(name,"CYS")==0)iaa=64.0;
if(std::strcmp(name,"PHE")==0)iaa=88.0;
if(std::strcmp(name,"LEU")==0)iaa=72.0;
if(std::strcmp(name,"TRP")==0)iaa=108.0;
if(std::strcmp(name,"VAL")==0)iaa=64.0;
if(std::strcmp(name,"ILE")==0)iaa=72.0;
if(std::strcmp(name,"MET")==0)iaa=80.0;
if(std::strcmp(name,"HIS")==0)iaa=82.0;
if(std::strcmp(name,"TYR")==0)iaa=96.0;
if(std::strcmp(name,"ALA")==0)iaa=48.0;
if(std::strcmp(name,"GLY")==0)iaa=40.0;
if(std::strcmp(name,"PRO")==0)iaa=62.0;
if(std::strcmp(name,"ASN")==0)iaa=66.0;
if(std::strcmp(name,"THR")==0)iaa=64.0;
if(std::strcmp(name,"SER")==0)iaa=56.0;
if(std::strcmp(name,"ARG")==0)iaa=93.0;
if(std::strcmp(name,"GLN")==0)iaa=78.0;
if(std::strcmp(name,"ASP")==0)iaa=59.0;
if(std::strcmp(name,"LYS")==0)iaa=79.0;
if(std::strcmp(name,"GLU")==0)iaa=53.0;
myfloat_t iaa = 0.0;