?? simulation.cpp
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// Simulation.cpp: implementation of the Simulation class.
//
//////////////////////////////////////////////////////////////////////
#include "stdafx.h"
#include "Perm.h"
#include "Simulation.h"
#include <TIME.H>
using namespace std;
#ifdef _DEBUG
#undef THIS_FILE
static char THIS_FILE[]=__FILE__;
#define new DEBUG_NEW
#endif
//////////////////////////////////////////////////////////////////////
// Construction/Destruction
//////////////////////////////////////////////////////////////////////
Simulation::Simulation(ProteinSeq &tempseq, GlobePar &temppara):
sequence(tempseq),parameter(temppara){
spaceSize = 2*sequence.getLength();
initialized = false;
bestRecoder = 0;
space =(char*)malloc(spaceSize*spaceSize*spaceSize*sizeof(char));
}
Simulation::~Simulation(){
free(space);
}
/***Start the simulation. Take care that parameter.averageOfWei should be
initialized. There are two methods to initialize the parameter.averageOfWei
1.use GlobePar's initial
2.use Simulation's initializtion***/
void Simulation::run(){
startTime = time((time_t *)NULL);
resetTemp();
resetMatrix();
putFirstTwoPoint();
recursion();
endTime = time((time_t *)NULL);
parameter.c0 += parameter.step;
}
/***return time used to computing***/
long Simulation::usedTime() const{
return (endTime-startTime);
}
/***The two function are used to get the special node in the matric***/
inline char Simulation::getSpaceNode(int x, int y, int z) const{
return *(space+x*spaceSize*spaceSize+y*spaceSize+z);
}
inline void Simulation::setSpaceNode(int x, int y, int z, const char node){
*(space+x*spaceSize*spaceSize+y*spaceSize+z) = node;
}
/***reset the temp result***/
void Simulation::resetTemp(){
tempResult.clear();
tempWeight.clear();
tempEnergy.clear();
tempTotalEnergy = 0;
}
/***set the Matric to zero***/
void Simulation::resetMatrix(){
//there is a probelm
register int i,j,k;
for(i=0; i<spaceSize; i++)
for(j=0; j<spaceSize; j++)
for(k=0; k<spaceSize; k++ )
setSpaceNode(i,j,k,'0');
}
/***compute the quality of the different directions***/
void Simulation::computingQuality(Quality &quality){
quality.resetQuality();
register int x,y,z;
register char next_point = sequence.getSequence().GetAt(tempResult.size());
x = tempResult.back().x;
y = tempResult.back().y;
z = tempResult.back().z;
//the parameter in equation used to compute the quailty
int next_Kfree;
int e_increase;
//compute the different direction and get the result;
// 1. compute the parameter.directions[0]----forward
if(getSpaceNode(x+1,y,z) == '0'){
quality.k_free++;
next_Kfree = 0;
e_increase = 0;
if(getSpaceNode(x+2,y,z) == '0') //forward
next_Kfree++;
if(getSpaceNode(x+1,y+1,z) == '0') //right
next_Kfree++;
if(getSpaceNode(x+1,y-1,z) == '0') //left
next_Kfree++;
if(getSpaceNode(x+1,y,z+1) == '0') //up
next_Kfree++;
if(getSpaceNode(x+1,y,z-1) == '0') //down
next_Kfree++;
if( next_point == 'H'){
if(getSpaceNode(x+2,y,z) == 'H') //forward
e_increase++;
if(getSpaceNode(x+1,y+1,z) == 'H') //right
e_increase++;
if(getSpaceNode(x+1,y-1,z) == 'H') //left
e_increase++;
if(getSpaceNode(x+1,y,z+1) == 'H') //up
e_increase++;
if(getSpaceNode(x+1,y,z-1) == 'H') //down
e_increase++;
}
quality.energy[0] = e_increase;
quality.quality[0] = (next_Kfree + 0.5)*pow(parameter.Exp, e_increase);
}
// 2. compute the paramter.direction[1]----back
if(getSpaceNode(x-1,y,z) == '0' ){
quality.k_free++;
next_Kfree = 0;
e_increase = 0;
if(getSpaceNode(x-2,y,z) == '0') //back
next_Kfree++;
if(getSpaceNode(x-1,y+1,z) == '0') //left
next_Kfree++;
if(getSpaceNode(x-1,y-1,z) == '0') //right
next_Kfree++;
if(getSpaceNode(x-1,y,z+1) == '0') //up
next_Kfree++;
if(getSpaceNode(x-1,y,z-1) == '0') //down
next_Kfree++;
if( next_point == 'H'){
if(getSpaceNode(x-2,y,z) == 'H') //forward
e_increase++;
if(getSpaceNode(x-1,y+1,z) == 'H') //right
e_increase++;
if(getSpaceNode(x-1,y-1,z) == 'H') //left
e_increase++;
if(getSpaceNode(x-1,y,z+1) == 'H') //up
e_increase++;
if(getSpaceNode(x-1,y,z-1) == 'H') //down
e_increase++;
}
quality.energy[1] = e_increase;
quality.quality[1] = (next_Kfree + 0.5)*pow(parameter.Exp, e_increase);
}
// 3. compute the paramter.direction[2]----right
if(getSpaceNode(x,y+1,z) == '0' ){
quality.k_free++;
next_Kfree = 0;
e_increase = 0;
if(getSpaceNode(x-1,y+1,z) == '0')
next_Kfree++;
if(getSpaceNode(x+1,y+1,z) == '0')
next_Kfree++;
if(getSpaceNode(x,y+2,z) == '0')
next_Kfree++;
if(getSpaceNode(x,y+1,z+1) == '0')
next_Kfree++;
if(getSpaceNode(x,y+1,z-1) == '0')
next_Kfree++;
if( next_point == 'H'){
if(getSpaceNode(x-1,y+1,z) == 'H')
e_increase++;
if(getSpaceNode(x+1,y+1,z) == 'H')
e_increase++;
if(getSpaceNode(x,y+2,z) == 'H')
e_increase++;
if(getSpaceNode(x,y+1,z+1) == 'H')
e_increase++;
if(getSpaceNode(x,y+1,z-1) == 'H')
e_increase++;
}
quality.energy[2] = e_increase;
quality.quality[2] = (next_Kfree + 0.5)*pow(parameter.Exp, e_increase);
}
// 4. compute the paramter.direction[3]----left
if(getSpaceNode(x,y-1,z) == '0' ){
quality.k_free++;
next_Kfree = 0;
e_increase = 0;
if(getSpaceNode(x,y-2,z) == '0')
next_Kfree++;
if(getSpaceNode(x+1,y-1,z) == '0')
next_Kfree++;
if(getSpaceNode(x-1,y-1,z) == '0')
next_Kfree++;
if(getSpaceNode(x,y-1,z+1) == '0')
next_Kfree++;
if(getSpaceNode(x,y-1,z-1) == '0')
next_Kfree++;
if( next_point == 'H'){
if(getSpaceNode(x,y-2,z) == 'H')
e_increase++;
if(getSpaceNode(x+1,y-1,z) == 'H')
e_increase++;
if(getSpaceNode(x-1,y-1,z) == 'H')
e_increase++;
if(getSpaceNode(x,y-1,z+1) == 'H')
e_increase++;
if(getSpaceNode(x,y-1,z-1) == 'H')
e_increase++;
}
quality.energy[3] = e_increase;
quality.quality[3] = (next_Kfree + 0.5)*pow(parameter.Exp, e_increase);
}
// 5. compute the paramter.direction[4]----up
if(getSpaceNode(x,y,z+1) == '0' ){
quality.k_free++;
next_Kfree = 0;
e_increase = 0;
if(getSpaceNode(x,y,z+2) == '0')
next_Kfree++;
if(getSpaceNode(x+1,y,z+1) == '0')
next_Kfree++;
if(getSpaceNode(x-1,y,z+1) == '0')
next_Kfree++;
if(getSpaceNode(x,y+1,z+1) == '0')
next_Kfree++;
if(getSpaceNode(x,y-1,z+1) == '0')
next_Kfree++;
if( next_point == 'H'){
if(getSpaceNode(x,y,z+2) == 'H')
e_increase++;
if(getSpaceNode(x+1,y,z+1) == 'H')
e_increase++;
if(getSpaceNode(x-1,y,z+1) == 'H')
e_increase++;
if(getSpaceNode(x,y+1,z+1) == 'H')
e_increase++;
if(getSpaceNode(x,y-1,z+1) == 'H')
e_increase++;
}
quality.energy[4] = e_increase;
quality.quality[4] = (next_Kfree + 0.5)*pow(parameter.Exp, e_increase);
}
// 6. compute the paramter.direction[5]----down
if(getSpaceNode(x,y,z-1) == '0' ){
quality.k_free++;
next_Kfree = 0;
e_increase = 0;
if(getSpaceNode(x,y,z-2) == '0')
next_Kfree++;
if(getSpaceNode(x+1,y,z-1) == '0')
next_Kfree++;
if(getSpaceNode(x-1,y,z-1) == '0')
next_Kfree++;
if(getSpaceNode(x,y+1,z-1) == '0')
next_Kfree++;
if(getSpaceNode(x,y-1,z-1) == '0')
next_Kfree++;
if( next_point == 'H'){
if(getSpaceNode(x,y,z-2) == 'H')
e_increase++;
if(getSpaceNode(x+1,y,z-1) == 'H')
e_increase++;
if(getSpaceNode(x-1,y,z-1) == 'H')
e_increase++;
if(getSpaceNode(x,y+1,z-1) == 'H')
e_increase++;
if(getSpaceNode(x,y-1,z-1) == 'H')
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