int main(int argc, char *argv[]){
FILE *fptr;
if (!(fptr = fopen(argv[1], "r"))){
printf("Couldn't open file.");
return 1;
}
char buf[1000]; //line size limitation, lame
begin();
char * ip;
while (fgets(buf,1000, fptr)!=NULL){
ip = buf;
while (*ip){
curr_state = bead(*ip++);
}
}
printf("%s\n", c_file);
fclose(fptr);
return 0;
}
void MultiChain::record() {
//h_config = H5Gopen(h_file,"MultiChain");
typedef Bead::RealType PosType;
typedef Bead::Buffer_t Buffer_t;
Buffer_t chain_buffer,bead_buffer;
(*(this->begin()))->registerData(bead_buffer);
chain_buffer.rewind();
copyToBuffer(chain_buffer);
HDFAttribIO<Buffer_t> mcout(chain_buffer);
mcout.overwrite(h_config,"state");
std::deque<Bead*>::iterator bead_it(this->begin());
std::deque<Bead*>::iterator bead_end(this->end());
//create the group and increment counter
char GrpName[128];
int ibead=0;
while(bead_it != bead_end) {
sprintf(GrpName,"bead%04d",ibead);
hid_t bead_id = H5Gopen(h_config,GrpName);
bead_buffer.rewind();
Bead& bead(**bead_it);
bead.copyToBuffer(bead_buffer);
HDFAttribIO<Buffer_t> bout(bead_buffer);
bout.overwrite(bead_id,"state");
H5Gclose(bead_id);
++bead_it;
++ibead;
}
}
void PDBtoCG::make_using_alpha_carbon()
{
int imp_all(0);
for(std::vector<PDBChnSptr>::iterator iter = pure_pdb_style.begin();
iter != pure_pdb_style.end(); ++iter)
{
bool filled(false);
int counter(0);
CGChnSptr chain(new CGChain);
for(PDBChain::iterator aiter = (*iter)->begin();
aiter != (*iter)->end(); ++aiter)
{
if(is_C_alpha((*aiter)->get_name()))
{
++counter;
Realvec pos((*aiter)->get_x(),
(*aiter)->get_y(),
(*aiter)->get_z());
BeadSptr bead(make_cg(*aiter, pos, imp_all, counter));
chain->push_back(bead);
if(!filled) filled = true;
}
}
if(filled) cg_style_chain.push_back(chain);
imp_all += counter;
}
return;
}
/**
* - MultiChain
* -- Version
* -- NumberOfBeads
* -- state: number of beads, grotwh direction etc, see MultiChain::copyToBuffer
* -- bead0000
* -- state: everything is stored in a buffer using PooledData<t>
* R, Drift, Multiple Gradients,
* properties, weights etc, see Bead::copyToBuffer
*/
void MultiChain::open(const string& aroot) {
hid_t h_file=-1;
string h5file=aroot+".config.h5";
h_file = H5Fopen(h5file.c_str(),H5F_ACC_RDWR,H5P_DEFAULT);
h_config = H5Gcreate(h_file,"MultiChain",0);
int m_version=1;
HDFAttribIO<int> v(m_version);
v.write(h_config,"Version");
int nc=Beads.size();
HDFAttribIO<int> c(nc);
c.write(h_config,"NumberOfBeads");
//typedef Bead::PosType PosType;
typedef Bead::RealType PosType;
typedef Bead::Buffer_t Buffer_t;
Buffer_t chain_buffer,bead_buffer;
(*(this->begin()))->registerData(bead_buffer);
nc=bead_buffer.size();
HDFAttribIO<int> c2(nc);
c2.write(h_config,"BufferSize");
chain_buffer.rewind();
copyToBuffer(chain_buffer);
HDFAttribIO<Buffer_t> mcout(chain_buffer);
mcout.write(h_config,"state");
std::deque<Bead*>::iterator bead_it(this->begin());
std::deque<Bead*>::iterator bead_end(this->end());
//create the group and increment counter
char GrpName[128];
int ibead=0;
while(bead_it != bead_end) {
sprintf(GrpName,"bead%04d",ibead);
hid_t bead_id = H5Gcreate(h_config,GrpName,0);
bead_buffer.rewind();
Bead& bead(**bead_it);
bead.copyToBuffer(bead_buffer);
HDFAttribIO<Buffer_t> bout(bead_buffer);
bout.write(bead_id,"state");
H5Gclose(bead_id);
++bead_it;
++ibead;
}
if(h_file>-1) H5Fclose(h_file);
}
BeadSptr PDBtoCG::make_cg(AtomSptr& atom, Realvec pos, int imp_all, int imp_local)
{
BeadSptr bead(new CGBead);
bead->set_headder("ATOM ");//header
bead->set_imp(imp_all + imp_local);//imp
bead->set_beadname("CA");//bead
bead->set_seq(atom->get_resName());//seq
bead->set_chainID(atom->get_chainID());//ID
bead->set_iResNum(atom->get_resSeq()); //resNum
bead->set_coordx(pos[0]);
bead->set_coordy(pos[1]);
bead->set_coordz(pos[2]);
return bead;
}
chain::chain(int N, vector<chain>* Chains,mt19937 *engine,list<pair<int,int>> ***Zellen, double * xVal, double * yVal, double * zVal,int *xTimes,int *yTimes,int *zTimes)
{
engineX=engine;
this->Zellen=Zellen;
uniform_real_distribution<> distribution(0, 1);
auto rnd = bind(distribution, ref(*engineX));
uniform_real_distribution<> PIdistribution(0, PI);
auto rndPI = bind(PIdistribution, ref(*engineX));
uniform_real_distribution<> NEGdistribution(-1, 1);
auto rndWAY = bind(NEGdistribution, ref(*engineX));
uniform_int_distribution<> INTdistribution(0, N-1);
auto INTrnd = bind(INTdistribution, ref(*engineX));
// cout << "Konstruktor Chain" << endl;
this->Chains=Chains;
// cout << "Pushe in Chains" << endl;
// Chains->push_back(*this);
this->N=N;
vektor<double> x;
// x=vektor<double>(rnd()*XMAX,rnd()*YMAX,rnd()*ZMAX);
// x=vektor<double>(.5*XMAX,.5*YMAX,.5*ZMAX);
// if(k==0) x=vektor<double>(.5*XMAX+1.5*x0,.5*YMAX+x0/2+.1,.5*ZMAX-1.*x0);
// else x=vektor<double>(.5*XMAX+x0,.5*YMAX-x0/2,.5*ZMAX-.5*x0);
// cout << "..." << endl;
// Beads.push_back(x);
// vektor<double> ex;
for(int i=0;i<N;i++)
{
// cout << "Bead " << i << endl;
// double phi=2*rndPI();
// double theta=acos(1-2*rnd());
// ex=vektor<double>(sin(theta)*cos(phi),sin(theta)*sin(phi),cos(theta));
// ex=vektor<double>(sin(phi),cos(phi),1);
// if(k==0) ex=vektor<double>(-1,0,0);
// else ex=vektor<double>(0,0,-1);
// ex=vektor<double>(1,0,0);
// if(i<N/4) ex=vektor<double>(-1,0,0);
// if(i==N/4) ex=vektor<double>(0,-1,0);
// if(i>N/4 && i< N/2) ex=vektor<double>(1,0,1);
// if(i>=N/2 && i<3*N/4) ex=vektor<double>(0,0,-1);
// if(i==3*N/4 || i==3*N/4+1) ex=vektor<double>(0,1,0);
// if(i>3*N/4+1) ex=vektor<double>(0,0,1);
// ex=ex/ex.Betrag()*x0;
//vektor<double> x=Beads.at(i-1).ort-ex;
Beads.push_back(bead(xVal[i],yVal[i],zVal[i],xTimes[i],yTimes[i],zTimes[i]));
// Beads.at(i).verschiebe(ex);
}
for(int i=0;i<N-1;i++)
{
Bonds.push_back(bond(&Beads.at(i),&Beads.at(i+1)));
Zellen[int(Bonds.at(i).Schwerpunkt.x/(Zellgroesse))][int(Bonds.at(i).Schwerpunkt.y/(Zellgroesse))][int(Bonds.at(i).Schwerpunkt.z/(Zellgroesse))].push_back(make_pair(Chains->size(),i));
Bonds.at(i).self=Zellen[int(Bonds.at(i).Schwerpunkt.x/(Zellgroesse))][int(Bonds.at(i).Schwerpunkt.y/(Zellgroesse))][int(Bonds.at(i).Schwerpunkt.z/(Zellgroesse))].end();
Bonds.at(i).self--;
// cout << "Füge Schwerpunkt";
// Bonds.at(i).Schwerpunkt.Ausgabe();
// cout << "in Zelle" << int(Bonds.at(i).Schwerpunkt.x)/(Zellgroesse) << int(Bonds.at(i).Schwerpunkt.y)/(Zellgroesse) <<int(Bonds.at(i).Schwerpunkt.z)/(Zellgroesse) << "ein" << endl;
}
}
chain::chain(int N, vector<chain>* Chains,mt19937 *engine , list<pair<int,int>> ***Zellen)
{
engineX=engine;
this->Zellen=Zellen;
uniform_real_distribution<> distribution(0, 1);
auto rnd = bind(distribution, ref(*engineX));
uniform_real_distribution<> PIdistribution(0, PI);
auto rndPI = bind(PIdistribution, ref(*engineX));
uniform_real_distribution<> NEGdistribution(-1, 1);
auto rndWAY = bind(NEGdistribution, ref(*engineX));
// cout << "Konstruktor Chain" << endl;
this->Chains=Chains;
// cout << "Pushe in Chains" << endl;
// Chains->push_back(*this);
this->N=N;
vektor<double> x;
x=vektor<double>(rnd()*XMAX,rnd()*YMAX,rnd()*ZMAX);
// x=vektor<double>(.5*XMAX,.5*YMAX,.5*ZMAX);
// if(k==0) x=vektor<double>(.5*XMAX+1.5*x0,.5*YMAX+x0/2+.1,.5*ZMAX-1.*x0);
// else x=vektor<double>(.5*XMAX+x0,.5*YMAX-x0/2,.5*ZMAX-.5*x0);
// cout << "..." << endl;
Beads.push_back(x);
vektor<double> ex;
// int xtimes=0;
// int ytimes=0;
// int ztimes=0;
for(int i=1;i<N;i++)
{
// cout << "Bead " << i << endl;
double phi=2*rndPI();
double theta=acos(1-2*rnd());
ex=vektor<double>(sin(theta)*cos(phi),sin(theta)*sin(phi),cos(theta));
// ex=vektor<double>(sin(phi),cos(phi),1);
// if(k==0) ex=vektor<double>(-1,0,0);
// else ex=vektor<double>(0,0,-1);
// ex=vektor<double>(1,0,0);
// if(i<N/4) ex=vektor<double>(-1,0,0);
// if(i==N/4) ex=vektor<double>(0,-1,0);
// if(i>N/4 && i< N/2) ex=vektor<double>(1,0,1);
// if(i>=N/2 && i<3*N/4) ex=vektor<double>(0,0,-1);
// if(i==3*N/4 || i==3*N/4+1) ex=vektor<double>(0,1,0);
// if(i>3*N/4+1) ex=vektor<double>(0,0,1);
ex=ex/ex.Betrag()*x0;
//vektor<double> x=Beads.at(i-1).ort-ex;
Beads.push_back(bead(Beads.at(i-1).ort));
// vektor<double> newOrt=Beads.at(i-1).ort.add(ex);
// if (newOrt.x>XMAX) xtimes++;
// else if(newOrt.x<0) xtimes--;
// if (newOrt.y>YMAX) ytimes++;
// else if(newOrt.y<0) ytimes--;
// if (newOrt.x>XMAX) xtimes++;
// else if(newOrt.x<0) xtimes--;
Beads.at(i).verschiebe(ex);
Beads.at(i).xtimes+=Beads.at(i-1).xtimes;
Beads.at(i).ytimes+=Beads.at(i-1).ytimes;
Beads.at(i).ztimes+=Beads.at(i-1).ztimes;
}
for(int i=0;i<N-1;i++)
{
Bonds.push_back(bond(&Beads.at(i),&Beads.at(i+1)));
Zellen[int(Bonds.at(i).Schwerpunkt.x/(Zellgroesse))][int(Bonds.at(i).Schwerpunkt.y/(Zellgroesse))][int(Bonds.at(i).Schwerpunkt.z/(Zellgroesse))].push_back(make_pair(Chains->size(),i));
Bonds.at(i).self=Zellen[int(Bonds.at(i).Schwerpunkt.x/(Zellgroesse))][int(Bonds.at(i).Schwerpunkt.y/(Zellgroesse))][int(Bonds.at(i).Schwerpunkt.z/(Zellgroesse))].end();
Bonds.at(i).self--;
// cout << "Füge Schwerpunkt";
// Bonds.at(i).Schwerpunkt.Ausgabe();
// cout << "in Zelle" << int(Bonds.at(i).Schwerpunkt.x)/(Zellgroesse) << int(Bonds.at(i).Schwerpunkt.y)/(Zellgroesse) <<int(Bonds.at(i).Schwerpunkt.z)/(Zellgroesse) << "ein" << endl;
}
// cout << "maxSize=" << midBead.max_size() << endl;
}
bool MultiChain::read(hid_t grp){
hid_t hgrp = H5Gopen(grp,"MultiChain");
int m_version=1;
HDFAttribIO<int> v(m_version);
v.read(hgrp,"Version");
int nc(0);
HDFAttribIO<int> c(nc);
c.read(hgrp,"NumberOfBeads");
if(nc != Beads.size()) {
WARNMSG("The number of chains is different. Previous = " << nc << " Current = " << Beads.size())
}
typedef Bead::RealType PosType;
typedef Bead::Buffer_t Buffer_t;
Buffer_t chain_buffer,bead_buffer;
(*(this->begin()))->registerData(bead_buffer);
HDFAttribIO<int> c2(nc);
c2.read(hgrp,"BufferSize");
if(nc != bead_buffer.size()) {
ERRORMSG("The buffer size is different. Ignore restart data")
H5Gclose(hgrp);
return false;
}
chain_buffer.rewind();
copyToBuffer(chain_buffer);
HDFAttribIO<Buffer_t> mcin(chain_buffer);
mcin.read(hgrp,"state");
chain_buffer.rewind();
copyFromBuffer(chain_buffer);
std::deque<Bead*>::iterator bead_it(this->begin());
std::deque<Bead*>::iterator bead_end(this->end());
//create the group and increment counter
char GrpName[128];
int ibead=0;
while(bead_it != bead_end) {
sprintf(GrpName,"bead%04d",ibead);
hid_t bead_id = H5Gopen(hgrp,GrpName);
Bead& bead(**bead_it);
HDFAttribIO<Buffer_t> bout(bead_buffer);
bout.read(bead_id,"state");
bead_buffer.rewind();
bead.copyFromBuffer(bead_buffer);
H5Gclose(bead_id);
++bead_it;
++ibead;
}
H5Gclose(hgrp);
return true;
}
