Commit 01a19a3d authored by Pilar Cossio-Tejada's avatar Pilar Cossio-Tejada
Browse files

Polishing & including priors without FFTALGO

parent 470535fe
/* ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
< BioEM software for Bayesian inference of Electron Microscopy images>
Copyright (C) 2014 Pilar Cossio, David Rohr and Gerhard Hummer.
Copyright (C) 2016 Pilar Cossio, David Rohr, Fabio Baruffa, Markus Rampp,
Volker Lindenstruth and Gerhard Hummer.
Max Planck Institute of Biophysics, Frankfurt, Germany.
See license statement for terms of distribution.
......@@ -93,6 +94,7 @@ int bioem_param::readParameters(const char* fileinput)
yespriorAngles=false;
ignorepointsout=false;
printrotmod=false;
ignorePDB=false;
NotUn_angles=0;
priorMod=1; //Default
......@@ -334,6 +336,11 @@ int bioem_param::readParameters(const char* fileinput)
ignoreCCoff = true;
cout << "Ignoring Cross-Correlation offset \n";
}
else if (strcmp(token, "IGNORE_PDB") == 0) //Ignore PDB extension
{
ignorePDB = true;
cout << "Ignoring PDB extension in model file \n";
}
else if (strcmp(token, "NO_PROJECT_RADIUS") == 0) //If projecting CA with amino-acid radius
{
doaaradius = false;
......
#include "timer.h"
#ifdef _WIN32
#include <windows.h>
#include <winbase.h>
#else
#include <time.h>
#endif
HighResTimer::HighResTimer()
{
ElapsedTime = 0;
running = 0;
}
HighResTimer::~HighResTimer() {}
void HighResTimer::Start()
{
#ifdef _WIN32
__int64 istart;
QueryPerformanceCounter((LARGE_INTEGER*)&istart);
StartTime = (double) istart;
#else
timespec tv;
clock_gettime(CLOCK_REALTIME, &tv);
StartTime = (double) tv.tv_sec * 1.0E9 + (double) tv.tv_nsec;
#endif
running = 1;
}
void HighResTimer::ResetStart()
{
ElapsedTime = 0;
Start();
}
void HighResTimer::Stop()
{
if (running == 0) return;
running = 0;
double EndTime = 0;
#ifdef _WIN32
__int64 iend;
QueryPerformanceCounter((LARGE_INTEGER*) &iend);
EndTime = (double) iend;
#else
timespec tv;
clock_gettime(CLOCK_REALTIME, &tv);
EndTime = (double) tv.tv_sec * 1.0E9 + (double) tv.tv_nsec;
#endif
ElapsedTime += EndTime - StartTime;
}
void HighResTimer::Reset()
{
ElapsedTime = 0;
StartTime = 0;
running = 0;
}
double HighResTimer::GetElapsedTime()
{
return ElapsedTime / Frequency;
}
double HighResTimer::GetCurrentElapsedTime()
{
if (running == 0) return(GetElapsedTime());
double CurrentTime = 0;
#ifdef _WIN32
__int64 iend;
QueryPerformanceCounter((LARGE_INTEGER*) &iend);
CurrentTime = (double) iend;
#else
timespec tv;
clock_gettime(CLOCK_REALTIME, &tv);
CurrentTime = (double) tv.tv_sec * 1.0E9 + (double) tv.tv_nsec;
#endif
return((CurrentTime - StartTime + ElapsedTime) / Frequency);
}
double HighResTimer::GetFrequency()
{
#ifdef _WIN32
__int64 ifreq;
QueryPerformanceFrequency((LARGE_INTEGER*)&ifreq);
return((double) ifreq);
#else
return(1.0E9);
#endif
}
double HighResTimer::Frequency = HighResTimer::GetFrequency();
\ No newline at end of file
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