void CLjz153View::OnPic1()
{
// TODO: Add your command handler code here
CFileDialog pic1( TRUE, _T( ".bmp" ), _T( "test.bmp" ), OFN_FILEMUSTEXIST | OFN_HIDEREADONLY, _T( "应用程序(bmp)|*.bmp|所有文件|*||" ) );
if ( pic1.DoModal() == IDOK )
{
CString path = pic1.GetPathName(); //获取路径
//AfxMessageBox(path);
char* name = path.GetBuffer(path.GetLength());
path.ReleaseBuffer();
lpBitsInfo = LoadBmpFile(name);
Invalidate();
picNum++;
}
}
int main(int argn, char* args[])
{
static char *desc[] = {
"This script will read the xtc trajectory from an MD simulation",
"performed by GROMACS and output all data related to the analysis",
"of preferential interactions.",
"[PAR]",
"Generated: Thu Aug 20 16:49:21 EDT 2015.[BR]",
"Last updated: Thu Aug 27 17:26:01 EDT 2015.",
"[PAR]",
"Future Developments:[BR]",
"[BB]1.[bb] Partition calculation into groups (constituent amino acids).[BR]",
"[BB]2.[bb] Calculate residence times.[BR]",
"[BB]3.[bb] Include a measure for geometric orientation.[BR]",
"[BB]4.[bb] Calculate molecular distributions.[BR]",
"[BB]5.[bb] Parallelize it.",
"[PAR]",
"Remember to check the dependencie of the results on the number of block",
" used by using [TT]-block[tt].",
"Also, check that your simulation has been properly equilibrated by using [TT]-f0[tt].",
"In terms of reducing the computational cost of the analysis, use the option",
"[TT]-skip[tt] to only use every nr[TT]-th[tt] frame from the trajectory."
};
unsigned int protein_sequence=20; /* parse tpr.itp for info */
unsigned int N_co=4; /* look at topology for number of co-solvents */
unsigned int num_sol=7906; /* look at topology as well */
unsigned int skip_nr=1;
unsigned int granularity=2*100;
unsigned int f0=0;
bool bIndex=false;
t_pargs pa[] = {
{"-start", FALSE, etINT, {&f0}, "Start after n-th frame."},
{"-skip", FALSE, etINT, {&skip_nr}, "Only write every nr-th frame."},
{"-grid", FALSE, etINT, {&granularity}, "Number points to calculate."},
{"-seq", FALSE, etINT,{&protein_sequence}, "Number of amino acids in protein sequence."},
{"-Nco", FALSE, etINT,{&N_co}, "Number of cosolvent molecules."},
{"-Sol", FALSE, etINT,{&num_sol}, "Number of water molecules."}
};
char title[STRLEN];
t_topology top;
int ePBC;
rvec *xtop;
matrix box;
t_filenm fnm[] = { /* See filenm.h */
{ efTOP, NULL, NULL, ffREAD },
{ efTPS, NULL, NULL, ffREAD }, /* topology */
{ efTRX, "-f", NULL, ffREAD }, /* trajcetory */
{ efNDX, "-n", NULL, ffOPTRD } /* index file */
};
#define NFILE asize(fnm)
/* Interface. Adds default options. */
CopyRight(stderr,args[0]);
parse_common_args(&argn,args,PCA_CAN_TIME | PCA_CAN_VIEW, NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
read_tps_conf( ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, &xtop, NULL, box, TRUE);
sfree(xtop);
/*******************************************************************************************************************/
/*
int iter;
for (iter=0;iter<top.atoms.nr/100;++iter)
{
printf("Atom name: %s\tAtom charge: %f\n", *(top.atoms.atomname[iter]), top.atoms.atom[iter].q );
printf("Atom type: %d\tAtomic Residue NUmber: %d\n", top.atoms.atom[iter].type, top.atoms.atom[iter].resnr );
printf("Chain Identifier: %u\tNr of residues names: %d\n", top.atoms.atom[iter].ptype, top.atoms.nres );
printf("Residue name: %s\n\n", *(top.atoms.resname[iter]) );
}
*/
/*******************************************************************************************************************/
int status;
t_trxframe fr;
int flags = TRX_READ_X;
/* Count Number of Frames */
unsigned int bframes=0, frames=0;
int bwrite;
read_first_frame(&status, ftp2fn(efTRX,NFILE,fnm), &fr, flags);
do {
bwrite = bframes % skip_nr;
++bframes;
if ((bframes>f0) && (bwrite==0)){ ++frames; }
} while ( read_next_frame(status,&fr) );
/* Preparing Block Analysis */
bIndex = ftp2bSet(efNDX,NFILE,fnm);
std::vector<int> blocks_list;
if (bIndex)
{
FILE *fp = ffopen(opt2fn("-n",NFILE,fnm),"r");
int numblock;
while(fscanf(fp,"%d",&numblock)!=EOF)
{
blocks_list.push_back(numblock);
}
fclose(fp);
} else {
blocks_list.push_back(1);
}
/* Actual Calculation */
std::vector<Info> protein;
std::vector<Info> cosolvent;
std::vector<Info> solvent;
std::vector<double> cutoff, coefficients;
double molals=0, molars=0;
/* BLOCK AVERAGE */
typedef std::vector<double> Row;
typedef std::vector<Row> Matrix;
unsigned int num_blocks;
/////////////
//////////// std::ofstream test_partition("partition.txt");
for (unsigned int iter=0; iter<blocks_list.size(); ++iter)
{
num_blocks = blocks_list[iter];
unsigned int partition = (frames)/num_blocks;
unsigned int frame_counter=0;
std::vector<double> positions(granularity), averages(granularity), averages_sqr(granularity), sigma(granularity);
Matrix values(num_blocks,Row(granularity)), values_sqr(num_blocks,Row(granularity));
unsigned int frame=0, twrite=0;
read_first_frame(&status, ftp2fn(efTRX,NFILE,fnm), &fr, flags);
do
{
twrite = frame % skip_nr; /* if twrite==0 then read frame. */
++frame;
if ((frame > f0) && (twrite==0))
{
/* READING */
unsigned int protein_co=protein_sequence+N_co;
unsigned int solvated=protein_co+num_sol;
for (unsigned int n=0; n<top.atoms.nr; ++n)
{
/* Parsing */
Info atomo;
atomo.setAtom( (std::string) *(top.atoms.atomname[n]) );
atomo.setResnum( (unsigned int) top.atoms.atom[n].resnr );
atomo.setResname( (std::string) *(top.atoms.resname[atomo.getResnum()]) );
atomo.setCoords( (double) fr.x[n][XX], (double) fr.x[n][YY], (double) fr.x[n][ZZ] );
/* Testing for partition of groups */
/////// atomo.print(test_partition);
/* Appending */
// if
if ( atomo.getAtom()[0]!='H') // atomo.atom[0]!='H')
{
if ( atomo.getResnum() < protein_sequence ){
protein.push_back(atomo);
} else if ( (atomo.getResnum() >= protein_sequence) && (atomo.getResnum() < protein_co) ){
cosolvent.push_back(atomo);
} else if ( (atomo.getResnum() >= protein_co) && (atomo.getResnum() < solvated) ){
// if (atomo.getResname().compare("SOL")!=0)
// we want to avoid inputing number of waters for analysis
solvent.push_back(atomo);
}
}
}
/* MAIN */
double box_size = fr.box[0][0];
/* Local calculation for cosolvents */
std::vector<double> close_co; /* Stores Distances of closest */
for (unsigned int i=0; i<N_co; ++i)
{
std::vector<double> local_co;
double minimum_calculated = box_size*box_size;
unsigned int Nco_size=cosolvent.size()/N_co;
for (unsigned int n=(i*Nco_size); n<((i+1)*Nco_size); ++n)
{
for (unsigned int j=0; j<protein.size(); ++j)
{
double dist = cosolvent[n].distance(protein[j],box_size);
if (dist < minimum_calculated ){ minimum_calculated = dist; }
}
local_co.push_back(minimum_calculated);
}
close_co.push_back( *min_element(local_co.begin(), local_co.end()) );
}
/* Local calculation for water */
std::vector<double> local_wat;
for (unsigned int i=0; i<solvent.size(); ++i)
{
double minimum_calculated = box_size*box_size;
for (unsigned int j=0; j<protein.size(); ++j)
{
double dist = solvent[i].distance(protein[j],box_size);
if (dist < minimum_calculated){ minimum_calculated = dist; }
}
local_wat.push_back(minimum_calculated);
}
/* Preferential Interaction Coefficient */
double N_wat = solvent.size();
linspace(0,box_size,granularity,cutoff);
for (unsigned int x=0; x<granularity; ++x)
{
unsigned int n3=0, n1=0;
for (unsigned int i=0; i<close_co.size(); ++i){ if (close_co[i] < (cutoff[x]*cutoff[x])) ++n3; }
for (unsigned int i=0; i<local_wat.size(); ++i){ if (local_wat[i] < (cutoff[x]*cutoff[x])) ++n1; }
coefficients.push_back(pref_coef(N_co, N_wat, n3, n1));
}
molals+= molality(N_co, (int) N_wat);
molars+= molarity(N_co, box_size);
/* Storage */
for (unsigned int i=0; i<granularity; ++i){ positions[i] += cutoff[i]; }
for (unsigned int j=0; j<granularity; ++j)
{
values[(int) (frame_counter/(partition+1))][j] += coefficients[j];
values_sqr[(int) (frame_counter/(partition+1))][j] += coefficients[j]*coefficients[j];
}
cutoff.clear();
coefficients.clear();
protein.clear();
cosolvent.clear();
solvent.clear();
++frame_counter;
}
} while ( read_next_frame(status,&fr) );
//thanx(stderr);
/* FINAL REUSLTS */
double normalization = partition;
molals /= (num_blocks*normalization);
molars /= (num_blocks*normalization);
for (unsigned int i=0; i<granularity; ++i){ positions[i] /= (num_blocks*normalization); }
for (unsigned int i=0; i<num_blocks; ++i)
{
for (unsigned int j=0; j<granularity; ++j)
{
values[i][j] /= normalization;
values_sqr[i][j] /= normalization;
}
}
/* AVERAGES */
for (unsigned int i=0; i<granularity; ++i)
{
for (unsigned int j=0; j<num_blocks; ++j)
{
averages[i] += values[j][i];
averages_sqr[i] += values_sqr[j][i];
}
averages[i] /= (double) num_blocks;
averages_sqr[i] /= (double) num_blocks;
}
/* STANDARD DEVIATIONS */
for (unsigned int i=0; i<granularity; ++i)
{
sigma[i] += sqrt( averages_sqr[i] - averages[i]*averages[i] );
}
/* OUTPUT */
std::ofstream distances("dimensions.dat");
for (unsigned int i=0; i<granularity/2; ++i){ distances << std::setw(1) << positions[i] <<'\n'; }
distances.close();
std::string output1="preferential_val.dat";
std::string output2="preferential_sig.dat";
std::string result;
std::ostringstream convert;
convert << num_blocks; //skip;
result = convert.str();
output1.insert(16,result);
output2.insert(16,result);
std::ofstream pic1(output1.c_str());
std::ofstream pic2(output2.c_str());
for (unsigned int i=0; i<granularity/2; ++i)
{
pic1 << std::setw(10)<< averages[i] <<'\n';
pic2 << std::setw(10)<< sigma[i] <<'\n';
}
pic1.close();
pic2.close();
std::ofstream concentrations("concentrations.dat");
concentrations<< std::setw(10) << "Molality" <<'\t'<< std::setw(10) << "Molarity" <<'\n';
concentrations<< std::setw(10) << molals <<'\t'<< std::setw(10) << molars << '\n';
concentrations.close();
std::cout << "ANALYSIS COMPLETED!" <<'\n';
std::cout<<"Total number of frames: "<<frame_counter<<'\n';
}
//////////////// test_partition.close();
thanx(stderr);
return 0;
}
int compare( const void *arg1, const void *arg2 )
{
try {
const I_MapItem *i1 = *reinterpret_cast<I_MapItem**>(const_cast<void*>(arg1));
const I_MapItem *i2 = *reinterpret_cast<I_MapItem**>(const_cast<void*>(arg2));
C_TextPtr text1(const_cast<I_MapItem*>(i1));
C_TextPtr text2(const_cast<I_MapItem*>(i2));
if (text1 && !text2) {
return 1;
}
else if (text2 && !text1) {
return -1;
}
C_PicturePtr pic1(const_cast<I_MapItem*>(i1));
C_PicturePtr pic2(const_cast<I_MapItem*>(i2));
if (pic1 && !pic2) {
return 1;
}
else if (pic2 && !pic1) {
return -1;
}
C_PositionPtr p1(const_cast<I_MapItem*>(i1));
C_PositionPtr p2(const_cast<I_MapItem*>(i2));
if (p1 && p2) {
C_Area area1(p1.GetPoints());
C_Area area2(p2.GetPoints());
int n = 0;
int cnt1 = area1.GetLength();
int cnt2 = area2.GetLength();
if (0 == cnt1) {
return -1;
}
if (0 == cnt2) {
return 1;
}
POINT3D *ptr1 = area1[cnt1 - 1];
POINT3D *ptr2 = area2[cnt2 - 1];
if (ptr1->x < 0 && ptr2->x > 0) {
n = -1;
}
else if (ptr1->x > 0 && ptr2->x < 0) {
n = 1;
}
else if (ptr1->y < ptr2->y) {
n = -1;
}
else if (ptr1->y > ptr2->y) {
n = 1;
}
if (0 == n) {
if (cnt1 < cnt2) {
n = -1;
}
else if (cnt1 > cnt2) {
n = 1;
}
}
if (0 != n) {
return n;
}
}
C_UniquePtr u1(const_cast<I_MapItem*>(i1));
C_UniquePtr u2(const_cast<I_MapItem*>(i2));
if (!u1 && !u2) {
return 0;
}
else if (!u1) {
return -1;
}
else if (!u2) {
return 1;
}
else {
BSTR bs1 = NULL;
BSTR bs2 = NULL;
u1->get_UID(&bs1);
u2->get_UID(&bs2);
int n = ::wcscmp(bs1, bs2);
String::FreeBSTR(&bs1);
String::FreeBSTR(&bs2);
return n;
}
}
catch (C_STLNonStackException const &exception) {
exception.Log(_T("Exception in Items.cpp (compare)"));
}
return 0;
}
