int main(int argc, char **argv)
{
cout << "usage: pdbgen <indexfile> <boxdim> [0/1: reverse drms cal] [1: outputcrowders crowders]" << endl;
AminoAcids aminoAcidData;
cout << "Loading amino acid data. ";
aminoAcidData.loadAminoAcidData(AMINOACIDDATASOURCE);
cout << "Done." << endl;
cout << "Loading pair lookup table. " << endl;
aminoAcidData.loadLJPotentialData(LJPDSOURCE);
cout << "Done." << endl;
vector<Replica> Conformations;
Replica initalReplica;
initalReplica.setAminoAcidData(aminoAcidData);
initalReplica.reserveConiguousMoleculeArray(30);
Replica reference;
reference.setAminoAcidData(aminoAcidData);
char *indexfilename = new char[256];
char *savefilename = new char[256];
char *datafilename = new char[256];
char *drmsEfilename = new char[256];
float boundary(atof(argv[2]));
cout << "File: " << argv[1] << endl;
cout << "Bounding box size: " << boundary << "A**3" << endl;
bool printCrowders(false);
bool reversedrms=false;
if (argc > 3)
{
if (argv[3][0]=='1')
reversedrms = true;
}
if (argc > 4)
{
if (argv[4][0]=='1')
printCrowders = true;
}
strcpy(indexfilename,argv[1]);
char * strstrresult = strstr(indexfilename,"fileindex");
if (strstrresult==NULL)
{
cout << "You must provide and index file as the input" << endl;
exit(0);
}
ifstream indexfile(indexfilename);
if (!indexfile.good())
{
cout << "Failed to open file: " << indexfilename << endl;
exit(0);
}
char line[512] = {0};
int loadcount = 0;
float max_d = 0;
while (!indexfile.eof())
{
indexfile.getline(line,512);
int index;
char crowder;
int result = sscanf(line,"%d %s %c",&index,datafilename,&crowder);
if (result==3)
{
if (crowder=='N' || (crowder=='Y' && printCrowders))
{
cout << "load : " << datafilename << endl;
initalReplica.loadMolecule(datafilename);
reference.loadMolecule(datafilename);
if (loadcount > 0)
{
Vector3f c = initalReplica.molecules[initalReplica.moleculeCount-1].position;
for(int i=0;i<initalReplica.molecules[initalReplica.moleculeCount-1].residueCount;i++)
{
Vector3f r = initalReplica.molecules[initalReplica.moleculeCount-1].Residues[i].position;
max_d = max((c-r).magnitude(),max_d);
}
}
loadcount++;
}
}
}
cout << "finished loading" << endl;
indexfile.close();
memset(datafilename,0,256);
strncpy(datafilename,indexfilename,strlen(indexfilename)-strlen("fileindex"));
strcat(datafilename,"boundconformations");
memset(drmsEfilename,0,256);
strncpy(drmsEfilename,indexfilename,strlen(indexfilename)-strlen("fileindex"));
strcat(drmsEfilename,"drms.dat");
int iteration;
float energy; // system energy
float temperature;
float energyC; // complex energy
int samples = 0;
ifstream datafile(datafilename);
if (!datafile.good())
{
cout << "Failed to open file: " << datafilename << endl;
exit(0);
}
else
{
cout << "loading data: "<< datafilename << endl;
}
//ofstream drmslog(drmsEfilename);
//drmslog.precision(7);
//first 2 lines contain nothing
datafile.getline(line,512);
datafile.getline(line,512);
// next lines are in sets of the number of non crowders
// 501000; -9.18593; 5.3; 297.6
// 0 0: -0.258606 -0.929792 -0.256388 -0.053619 7.369041 103.941734 91.936638
// 0 1: -0.055370 -0.464538 -0.429429 0.772482 7.673889 89.995583 96.419502
char savename[256];
int instanceNo = 0;
while (!datafile.eof())
{
datafile.getline(line,512);
//cout << "line: "<< line << endl;
//int result = sscanf(line,"%d; %f; %f; %f;",&iteration,&energy,&distance,&temperature);
int result = sscanf(line,"%d; %f (%f); %f;",&iteration,&energy,&energyC,&temperature);
//int result = sscanf(line,"%d; %f; %f;",&iteration,&energy,&temperature);
initalReplica.temperature = temperature;
initalReplica.potential = energy;
if (abs(temperature-300.0f)<1.0f && iteration>10000000) // if the instance is at 300K and more than 1m iterations are done
{
Quaternion rotation0;
Vector3f vrotation0;
Vector3f position0;
Replica instance;
instance.copy(initalReplica);
for (int i=0;i<instance.moleculeCount;i++)
{
datafile.getline(line,512);
Quaternion rotationi;
Vector3f positioni;
Vector3f vrotationi;
int mno;
int crowderyn;
//cout << line << endl;
char * token = strtok(line, ":");
sscanf(token,"%d %d",&crowderyn,&mno); // new format
if (crowderyn==1 && !printCrowders)
continue; // ignore crowders
rotationi.w = atof(strtok(NULL, " "));
rotationi.x = atof(strtok(NULL, " "));
rotationi.y = atof(strtok(NULL, " "));
rotationi.z = atof(strtok(NULL, " "));
positioni.x = atof(strtok(NULL, " "));
positioni.y = atof(strtok(NULL, " "));
positioni.z = atof(strtok(NULL, " "));
rotationi.normalize();
instance.molecules[i].setRotation(rotationi);
if (crowderyn==0) // only two in the simulation
{
Vector3f v = positioni - instance.molecules[0].position;
positioni.x -= boundary * round(v.x/boundary);
positioni.y -= boundary * round(v.y/boundary);
positioni.z -= boundary * round(v.z/boundary);
}
instance.molecules[i].setPosition(positioni);
}
memset(savename,0,256);
instanceNo++;
sprintf(savename, "pdbgen_results/sample_%d_%0.1fK_%5.2f.pdb",instanceNo,temperature,energy);
//if (energy < -70.0)
instance.saveAsSinglePDB(savename);
//double drms(DRMS(&instance,&reference,reversedrms));
//drmslog << energy << " " << drms << endl;
cout << "Saved frame " << instanceNo << ": " << savename << endl;
}
}
datafile.close();
//drmslog.close();
cout << "Exiting..." << endl;
return 0;
}
