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Commit 9768552f authored by Pilar Cossio's avatar Pilar Cossio
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Correcting bug accessing ilegal memory in CC mat & tidying up

parent 19bc6d4d
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CMakeLists.txt
View file @ 9768552f
......@@ -6,7 +6,7 @@ option (INCLUDE_CUDA "Build BioEM with CUDA support" ON)
option (INCLUDE_OPENMP "Build BioEM with OpenMP support" ON)
option (INCLUDE_MPI "Build BioEM with MPI support" ON)
option (PRINT_CMAKE_VARIABLES "List all CMAKE Variables" OFF)
option (CUDA_FORCE_GCC "Force GCC as host compiler for CUDA part (If standard host compiler is incompatible with CUDA)" OFF)
option (CUDA_FORCE_GCC "Force GCC as host compiler for CUDA part (If standard host compiler is incompatible with CUDA)" ON)
###Set up general variables
set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/Modules/")
......@@ -18,9 +18,9 @@ set (BIOEM_ICC_FLAGS "-xHost -O3 -fno-alias -fno-fnalias -unroll -g0 -ipo")
set (BIOEM_GCC_FLAGS "-O3 -march=native -fweb -mfpmath=sse -frename-registers -minline-all-stringops -ftracer -funroll-loops -fpeel-loops -fprefetch-loop-arrays -ffast-math -ggdb")
if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${BIOEM_ICC_FLAGS}")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${BIOEM_ICC_FLAGS}")
else()
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${BIOEM_GCC_FLAGS}")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${BIOEM_GCC_FLAGS}")
endif()
set (BIOEM_SOURCE_FILES "bioem.cpp" "main.cpp" "map.cpp" "model.cpp" "param.cpp" "cmodules/timer.cpp")
......@@ -43,93 +43,94 @@ include_directories(${Boost_INCLUDE_DIRS})
###Find CUDA
set (BIOEM_CUDA_STATUS "Disabled")
if (INCLUDE_CUDA)
set (BIOEM_CUDA_STATUS "Not Found")
find_package(CUDA)
set (BIOEM_CUDA_STATUS "Not Found")
find_package(CUDA)
endif()
if (CUDA_FOUND)
if (CUDA_FORCE_GCC)
cmake_minimum_required(VERSION 2.8.10.1)
#Use GCC as host compiler for CUDA even though host compiler for other files is not GCC
set (CUDA_HOST_COMPILER gcc)
endif()
set(CUDA_NVCC_FLAGS "${CUDA_NVCC_FLAGS};--use_fast_math;-ftz=true;-O4;-Xptxas -O4")
list(APPEND CUDA_NVCC_FLAGS "-gencode=arch=compute_13,code=sm_13")
list(APPEND CUDA_NVCC_FLAGS "-gencode=arch=compute_20,code=sm_20")
list(APPEND CUDA_NVCC_FLAGS "-gencode=arch=compute_20,code=sm_21")
list(APPEND CUDA_NVCC_FLAGS "-gencode=arch=compute_30,code=sm_30")
list(APPEND CUDA_NVCC_FLAGS "-gencode=arch=compute_35,code=sm_35")
add_definitions(-DWITH_CUDA)
set (BIOEM_CUDA_STATUS "Found")
if (CUDA_FORCE_GCC)
cmake_minimum_required(VERSION 2.8.10.1)
#Use GCC as host compiler for CUDA even though host compiler for other files is not GCC
set (CUDA_HOST_COMPILER gcc)
endif()
set(CUDA_NVCC_FLAGS "${CUDA_NVCC_FLAGS};--use_fast_math;-ftz=true;-O4;-Xptxas -O4")
list(APPEND CUDA_NVCC_FLAGS "-gencode=arch=compute_13,code=sm_13")
list(APPEND CUDA_NVCC_FLAGS "-gencode=arch=compute_20,code=sm_20")
list(APPEND CUDA_NVCC_FLAGS "-gencode=arch=compute_20,code=sm_21")
list(APPEND CUDA_NVCC_FLAGS "-gencode=arch=compute_30,code=sm_30")
list(APPEND CUDA_NVCC_FLAGS "-gencode=arch=compute_35,code=sm_35")
list(APPEND CUDA_NVCC_FLAGS "-gencode=arch=compute_52,code=sm_52")
add_definitions(-DWITH_CUDA)
set (BIOEM_CUDA_STATUS "Found")
endif()
###Find OpenMP
set (BIOEM_OPENMP_STATUS "Disabled")
if (INCLUDE_OPENMP)
set (BIOEM_OPENMP_STATUS "Not Found")
find_package(OpenMP)
set (BIOEM_OPENMP_STATUS "Not Found")
find_package(OpenMP)
endif()
if(OPENMP_FOUND)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
add_definitions(-DWITH_OPENMP)
set (BIOEM_OPENMP_STATUS "Found")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
add_definitions(-DWITH_OPENMP)
set (BIOEM_OPENMP_STATUS "Found")
endif()
###Find MPI
set (BIOEM_MPI_STATUS "Disabled")
if (INCLUDE_MPI)
set (BIOEM_MPI_STATUS "Not Found")
find_package(MPI)
set (BIOEM_MPI_STATUS "Not Found")
find_package(MPI)
endif()
if (MPI_FOUND)
include_directories(${MPI_INCLUDE_PATH})
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${MPI_LINK_FLAGS}")
add_definitions(-DWITH_MPI)
set (BIOEM_MPI_STATUS "Found")
include_directories(${MPI_INCLUDE_PATH})
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${MPI_LINK_FLAGS}")
add_definitions(-DWITH_MPI)
set (BIOEM_MPI_STATUS "Found")
endif()
###Build Executable
if (CUDA_FOUND)
set(BIOEM_TMP_CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS})
if (CUDA_FORCE_GCC)
#Hack to use GCC flags for GCC host compiler during NVCC compilation, although host compiler is in fact not GCC for other files
set(CMAKE_CXX_FLAGS ${BIOEM_GCC_FLAGS})
endif()
cuda_add_executable(bioEM ${BIOEM_SOURCE_FILES} bioem_cuda.cu)
set(CMAKE_CXX_FLAGS ${BIOEM_TMP_CMAKE_CXX_FLAGS})
set(BIOEM_TMP_CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS})
if (CUDA_FORCE_GCC)
#Hack to use GCC flags for GCC host compiler during NVCC compilation, although host compiler is in fact not GCC for other files
set(CMAKE_CXX_FLAGS ${BIOEM_GCC_FLAGS})
endif()
cuda_add_executable(bioEM ${BIOEM_SOURCE_FILES} bioem_cuda.cu)
set(CMAKE_CXX_FLAGS ${BIOEM_TMP_CMAKE_CXX_FLAGS})
else()
add_executable(bioEM ${BIOEM_SOURCE_FILES})
add_executable(bioEM ${BIOEM_SOURCE_FILES})
endif()
#Additional CXX Flags not used by CUDA compiler
#Additional CXX Flags not used by CUDA compiler
if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -Wall -pedantic")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -Wall -pedantic")
else()
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -Wall -Wno-vla -Wno-unused-result -Wno-unused-local-typedefs -pedantic")
endif()
if (NOT OPENMP_FOUND)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-unknown-pragmas")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-vla -Wno-long-long -Wall -pedantic")
endif()
###Add Libraries
if (CUDA_FOUND)
cuda_add_cufft_to_target(bioEM)
target_link_libraries(bioEM ${CUDA_CUDA_LIBRARY})
cuda_add_cufft_to_target(bioEM)
#set(CUDA_LIBRARIES "/afs/ipp/.cs/cuda/6.5-gtx9/amd64_sles11/lib64/stubs/libcuda.so")
#cuda_add_library()
target_link_libraries(bioEM ${CUDA_CUDA_LIBRARY})
# target_link_libraries(bioEM ${CUDA_LIBRARIES})
endif()
if (FFTWF_LIBRARIES)
target_link_libraries(bioEM ${FFTWF_LIBRARIES})
target_link_libraries(bioEM ${FFTWF_LIBRARIES})
else()
target_link_libraries(bioEM -L${FFTW_LIBDIR} -lfftw3 -lfftw3f)
target_link_libraries(bioEM -L${FFTW_LIBDIR} -lfftw3 -lfftw3f)
endif()
target_link_libraries(bioEM -L${Boost_LIBRARY_DIRS} -lboost_program_options)
if (MPI_FOUND)
target_link_libraries(bioEM ${MPI_LIBRARIES})
target_link_libraries(bioEM ${MPI_LIBRARIES})
endif()
###Show Status
......@@ -137,14 +138,16 @@ message(STATUS "Build Status")
message(STATUS "FFTW library: ${FFTW_LIBDIR}")
message(STATUS "Boost directory: ${Boost_LIBRARY_DIRS}")
message(STATUS "FFTW includedir: ${FFTW_INCLUDEDIR}")
message(STATUS "CUDA libraries: ${CUDA_CUDA_LIBRARY}")
message(STATUS "CUDA libraries: ${CUDA_LIBRARIES}")
message(STATUS "CUDA: ${BIOEM_CUDA_STATUS}")
message(STATUS "OpenMP: ${BIOEM_OPENMP_STATUS}")
message(STATUS "MPI: ${BIOEM_MPI_STATUS}")
if (PRINT_CMAKE_VARIABLES)
get_cmake_property(_variableNames VARIABLES)
foreach (_variableName ${_variableNames})
message(STATUS "${_variableName}=${${_variableName}}")
endforeach()
get_cmake_property(_variableNames VARIABLES)
foreach (_variableName ${_variableNames})
message(STATUS "${_variableName}=${${_variableName}}")
endforeach()
endif()
bioem.cpp
View file @ 9768552f
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bioem_algorithm.h
View file @ 9768552f
This diff is collapsed.
map.cpp
View file @ 9768552f
......@@ -5,6 +5,12 @@
See license statement for terms of distribution.
Note: This program contains subroutine "read_MRC" of the Situs 2.7.2 program.
Ref: Willy Wriggers. Using Situs for the Integration of Multi-Resolution Structures.
Biophysical Reviews, 2010, Vol. 2, pp. 21-27.
with a GPL lisences version XX.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/
#include <fstream>
......@@ -35,6 +41,7 @@ int bioem_RefMap::readRefMaps(bioem_param& param, const char* filemap)
int allocsize = 0;
if (param.loadMap)
{
//************** Loading Map from Binary file *******
FILE* fp = fopen("maps.dump", "rb");
if (fp == NULL)
{
......@@ -50,12 +57,14 @@ int bioem_RefMap::readRefMaps(bioem_param& param, const char* filemap)
}
else if(readMRC)
{
//************** Reading MRC file *******
ntotRefMap=0;
if(readMultMRC)
{
cout << "Opening File with MRC list names: " << filemap << "\n";
//************** Reading Multiple MRC files *************
cout << "Opening File with MRC list names: " << filemap << "\n";
ifstream input(filemap);
if (!input.good())
......@@ -74,9 +83,9 @@ int bioem_RefMap::readRefMaps(bioem_param& param, const char* filemap)
input.getline(line,511);
char tmpVals[100] = {0};
string strline(line);
string strline(line);
// cout << "MRC File name:" << strline << "\n";
// cout << "MRC File name:" << strline << "\n";
strncpy (tmpVals,line,99);
......@@ -87,10 +96,10 @@ int bioem_RefMap::readRefMaps(bioem_param& param, const char* filemap)
if(strcmp(tmpm,"XXX")!=0)
{
indifile=strline.c_str();
indifile=strline.c_str();
size_t foundpos= strline.find("mrc");
size_t endpos = strline.find_last_not_of(" \t");
// size_t foundpos= strline.find("mrc");
// size_t endpos = strline.find_last_not_of(" \t");
//Reading Multiple MRC
......@@ -106,15 +115,15 @@ int bioem_RefMap::readRefMaps(bioem_param& param, const char* filemap)
else
{
string strfilename(filemap);
string strfilename(filemap);
size_t foundpos= strfilename.find("mrc");
size_t endpos = strfilename.find_last_not_of(" \t");
size_t foundpos= strfilename.find("mrc");
size_t endpos = strfilename.find_last_not_of(" \t");
if(foundpos > endpos){
cout << "Warining:::: mrc extension NOT dectected in file name::" << filemap <<" \n";
cout << "Warining:::: Are you sure you want to read an MRC? \n";
}
if(foundpos > endpos){
cout << "Warining:::: mrc extension NOT dectected in file name::" << filemap <<" \n";
cout << "Warining:::: Are you sure you want to read an MRC? \n";
}
read_MRC(filemap,param);
cout << "\n++++++++++++++++++++++++++++++++++++++++++ \n";
......@@ -123,6 +132,7 @@ int bioem_RefMap::readRefMaps(bioem_param& param, const char* filemap)
}
else
{
//************** Reading Text file *************
int nummap = -1;
int lasti = 0;
int lastj = 0;
......@@ -201,7 +211,7 @@ int bioem_RefMap::readRefMaps(bioem_param& param, const char* filemap)
maps[nummap * refMapSize + i * numPixels + j] = (myfloat_t) z;
lasti = i;
lastj = j;
// cout << countpix << " " << param.param_device.NumberPixels*param.param_device.NumberPixels << "\n";
// cout << countpix << " " << param.param_device.NumberPixels*param.param_device.NumberPixels << "\n";
}
else
{
......@@ -221,20 +231,21 @@ int bioem_RefMap::readRefMaps(bioem_param& param, const char* filemap)
cout << "Particle Maps read from Standard File: " << ntotRefMap << "\n";
}
//Dumping Maps
//************* If Dumping Maps *********************
if (param.dumpMap)
{
FILE* fp = fopen("maps.dump", "w+b");
if (fp == NULL)
{
cout << "Error opening dump file\n";
exit(1);
}
fwrite(&ntotRefMap, sizeof(ntotRefMap), 1, fp);
fwrite(maps, sizeof(myfloat_t) * refMapSize, ntotRefMap, fp);
fclose(fp);
}
{
FILE* fp = fopen("maps.dump", "w+b");
if (fp == NULL)
{
cout << "Error opening dump file\n";
exit(1);
}
fwrite(&ntotRefMap, sizeof(ntotRefMap), 1, fp);
fwrite(maps, sizeof(myfloat_t) * refMapSize, ntotRefMap, fp);
fclose(fp);
}
//*********** To Debug with few Maps ********************
if (getenv("BIOEM_DEBUG_NMAPS"))
{
......@@ -250,7 +261,7 @@ int bioem_RefMap::readRefMaps(bioem_param& param, const char* filemap)
int bioem_RefMap::PreCalculateMapsFFT(bioem_param& param)
{
// **************************************************************************************
// ********** Routine that pre-calculates Kernels for Convolution **********************
// ********** Routine that pre-calculates Reference maps FFT for Convolution/ Comparison **********************
// ************************************************************************************
RefMapsFFT = new mycomplex_t[ntotRefMap * param.FFTMapSize];
......@@ -320,17 +331,19 @@ int bioem_RefMap::precalculate(bioem_param& param, bioem& bio)
void bioem_Probability::init(size_t maps, size_t angles, size_t cc, bioem& bio)
{
//********** Initializing pointers *******************
nMaps = maps;
nAngles = angles;
nCC = cc;
ptr = bio.malloc_device_host(get_size(maps, angles, cc, bio.param.param_device.writeAngles, bio.param.param_device.writeCC));
cout << "Allocation #Maps " << maps << " #Angles " << angles << " #cross.cor " << cc << "\n";
//<< " == " << get_size(maps, angles, cc, bio.param.param_device.writeAngles, bio.param.param_device.writeCC)<< "\n";
//<< " == " << get_size(maps, angles, cc, bio.param.param_device.writeAngles, bio.param.param_device.writeCC)<< "\n";
set_pointers();
}
void bioem_Probability::copyFrom(bioem_Probability* from, bioem& bio)
{
bioem_Probability_map& pProbMap = getProbMap(0);
bioem_Probability_map& pProbMapFrom = from->getProbMap(0);
memcpy(&pProbMap, &pProbMapFrom, from->nMaps * sizeof(bioem_Probability_map));
......@@ -358,6 +371,12 @@ void bioem_Probability::copyFrom(bioem_Probability* from, bioem& bio)
int bioem_RefMap::read_MRC(const char* filename,bioem_param& param)
{
/* subroutine "read_MRC" of the Situs 2.7.2 program.
Ref: Willy Wriggers. Using Situs for the Integration of Multi-Resolution Structures.
Biophysical Reviews, 2010, Vol. 2, pp. 21-27.*/
myfloat_t st,st2;
unsigned long count;
FILE *fin;
......@@ -453,7 +472,7 @@ int bioem_RefMap::read_MRC(const char* filename,bioem_param& param)
if(nr!=param.param_device.NumberPixels || nc!=param.param_device.NumberPixels )
{
cout << "PROBLEM INCONSISTENT NUMBER OF PIXELS IN MAPS AND INPUTFILE ( " << param.param_device.NumberPixels << ", i " << nc << ", j " << nr << ")" << "\n";
if(!param.notsqure) exit(1);
if(!param.notsqure) exit(1);
}
if (ntotRefMap == 0)
......@@ -498,25 +517,25 @@ int bioem_RefMap::read_MRC(const char* filename,bioem_param& param)
}
else
{
if(!param.notsqure){
maps[(nmap + ntotRefMap) * refMapSize + i * numPixels + j] = (myfloat_t) currfloat;
st += currfloat;
st2 += currfloat*currfloat;
} else {
if( i > 595 && i < 675 && j > 1250 && j< 1330 && nmap >230 && nmap <310)cout << "map1: " << i << " "<< j << " " << nmap << " " << currfloat <<"\n";
}
if(!param.notsqure){
maps[(nmap + ntotRefMap) * refMapSize + i * numPixels + j] = (myfloat_t) currfloat;
st += currfloat;
st2 += currfloat*currfloat;
} else {
if( i > 595 && i < 675 && j > 1250 && j< 1330 && nmap >230 && nmap <310)cout << "map1: " << i << " "<< j << " " << nmap << " " << currfloat <<"\n";
}
}
}
if(param.notsqure)exit(1);
if(param.notsqure)exit(1);
//Normaling maps to zero mean and unit standard deviation
if(!param.notnormmap){
st /= float(nr*nc);
st2 = sqrt(st2 / float(nr * nc) - st * st);
for ( int j = 0 ; j < nr ; j ++ ) for ( int i = 0 ; i < nc ; i ++ ){
maps[(nmap + ntotRefMap) * refMapSize + i * numPixels + j] = maps[(nmap + ntotRefMap) * refMapSize + i * numPixels + j] / st2 - st/st2;
//cout <<"MAP:: " << i << " " << j << " " << maps[(nmap + ntotRefMap) * refMapSize + i * numPixels + j] << "\n";
}
}
st /= float(nr*nc);
st2 = sqrt(st2 / float(nr * nc) - st * st);
for ( int j = 0 ; j < nr ; j ++ ) for ( int i = 0 ; i < nc ; i ++ ){
maps[(nmap + ntotRefMap) * refMapSize + i * numPixels + j] = maps[(nmap + ntotRefMap) * refMapSize + i * numPixels + j] / st2 - st/st2;
//cout <<"MAP:: " << i << " " << j << " " << maps[(nmap + ntotRefMap) * refMapSize + i * numPixels + j] << "\n";
}
}
}
ntotRefMap += ns ;
// cout << ntotRefMap << "\n";
......
model.cpp
View file @ 9768552f
/* ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
< BioEM software for Bayesian inference of Electron Microscopy images>
Copyright (C) 2014 Pilar Cossio, David Rohr and Gerhard Hummer.
Max Planck Institute of Biophysics, Frankfurt, Germany.
< BioEM software for Bayesian inference of Electron Microscopy images>
Copyright (C) 2014 Pilar Cossio, David Rohr and Gerhard Hummer.
Max Planck Institute of Biophysics, Frankfurt, Germany.
See license statement for terms of distribution.
See license statement for terms of distribution.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/
......@@ -20,289 +20,291 @@ using namespace std;
bioem_model::bioem_model()
{
points = NULL;
points = NULL;
}
bioem_model::~bioem_model()
{
if (points) free(points);
if (points) free(points);
}
int bioem_model::readModel(bioem_param& param, const char* filemodel)
{
// **************************************************************************************
// ***************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");
ofstream exampleReadCoor;
exampleReadCoor.open ("COORDREAD");
exampleReadCoor << "Text --- Number ---- x ---- y ---- z ---- radius ---- density\n";
exampleReadCoor << "Text --- Number ---- x ---- y ---- z ---- radius ---- number of electron\n";
int allocsize = 0;
int allocsize = 0;
std::ifstream input(filemodel);
if(readPDB)
{
ifstream input(filemodel);
if (!input.good())
{
cout << "PDB Failed to open file" << endl ; // pdbfilename << " ("<<filename<<")\n";
exit(0);
}
char line[512] = {0};
char tmpLine[512] = {0};
int numres = 0;
NormDen = 0.0;
string strfilename(filemodel);
std::ifstream input(filemodel);
if(readPDB)
{
//************** Reading PDB files **********************
size_t foundpos= strfilename.find(".pdb");
size_t endpos = strfilename.find_last_not_of(" \t");
ifstream input(filemodel);
if (!input.good())
{
cout << "PDB Failed to open file" << endl ; // pdbfilename << " ("<<filename<<")\n";
exit(0);
}
if(foundpos > endpos){
cout << "Warining:::: .pdb extension NOT dectected in file name \n";
cout << "Warining:::: Are you sure you want to read a PDB? \n";
}
char line[512] = {0};
char tmpLine[512] = {0};
int numres = 0;
NormDen = 0.0;
string strfilename(filemodel);
// cout << " HERE " << filemodel ;
// for eachline in the file
while (!input.eof())
{
input.getline(line, 511);
strncpy(tmpLine, line, strlen(line));
char *token = strtok(tmpLine, " ");
if (strcmp(token, "ATOM") == 0) // Optional,Mandatory if standard residues exist
{
/*
1-6 "ATOM "
7 - 11 Integer serial Atom serial number.
13 - 16 Atom name Atom name.
17 Character altLoc Alternate location indicator.
18 - 20 Residue name resName Residue name.
22 Character chainID Chain identifier.
23 - 26 Integer resSeq Residue sequence number.
27 AChar iCode Code for insertion of residues.
31 - 38 Real(8.3) x Orthogonal coordinates for X in
39 - 46 Real(8.3) y Orthogonal coordinates for Y in
47 - 54 Real(8.3) z Orthogonal coordinates for Z in
*/
char name[5] = {0};
char resName[4] = {0};
float x = 0.0;
float y = 0.0;
float z = 0.0;
char tmp[6] = {0};
// parse name
strncpy(tmp, line + 12, 4);
sscanf (tmp, "%s", name);
// parse resName
strncpy(tmp, line + 17, 3);
sscanf (tmp, "%s", resName);
// parse x, y, z
char tmpVals[36] = {0};
strncpy (tmpVals, line + 30, 8);
sscanf (tmpVals, "%f", &x);
strncpy (tmpVals, line + 38, 8);
sscanf (tmpVals, "%f", &y);
strncpy (tmpVals, line + 46, 8);
sscanf (tmpVals, "%f", &z);
if (strcmp(name, "CA") == 0)
{
if (allocsize == 0)
{
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
points[numres].radius = getAminoAcidRad(resName);
points[numres].density = getAminoAcidDensity(resName);
NormDen += points[numres].density;
size_t foundpos= strfilename.find(".pdb");
size_t endpos = strfilename.find_last_not_of(" \t");
//Getting the coordinates
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].radius << " " << points[numres].density << "\n";
numres++;
}
}
if(foundpos > endpos){
cout << "Warining:::: .pdb extension NOT dectected in file name \n";
cout << "Warining:::: Are you sure you want to read a PDB? \n";
}
}
nPointsModel = numres;
cout << "Protein structure read from PDB\n";
}
else //Reading model from FILE FORMAT x,y,z,rad,density
// cout << " HERE " << filemodel ;
// for eachline in the file
while (!input.eof())
{
char line[128];
int numres = 0;
NormDen = 0.0;
string strfilename(filemodel);
size_t foundpos= strfilename.find(".pdb");
size_t endpos = strfilename.find_last_not_of(" \t");
if(foundpos < endpos){
cout << "Warining:::: .pdb dectected in file name whilst using text read \n";
cout << "Warining:::: Are you sure you do not need --ReadPDB? \n";
}
FILE *file = fopen ( filemodel , "r" );
if (file == NULL)
{
cout << "Error opening file " << filemodel << "\n";
exit(1);
}
while ( fgets ( line, sizeof line, file ) != NULL )
input.getline(line, 511);
strncpy(tmpLine, line, strlen(line));
char *token = strtok(tmpLine, " ");
if (strcmp(token, "ATOM") == 0) // Optional,Mandatory if standard residues exist
{
/*
1-6 "ATOM "