/// Prints a cumulative running average time series of the desired property
void ProtTraj::PrintCumulative(string const& fname, const int interval,
const bool print_prot, const bool print_pka) {
// Open up the file and write a header
ofstream fp(fname.c_str());
if (!fp.is_open())
throw FileIOError("Could not open " + fname + " for writing!");
fp << fixed << "#Time step ";
for (Cpin::ResIterator rit = cpin_->begin(); rit != cpin_->end(); rit++) {
stringstream iss;
iss << rit->getResname() << " " << rit->getResnum();
fp << setw(8) << iss.str() << " ";
}
fp << " Total Avg. Prot." << endl;
// Now go through the trajectory
vector<long long int> nprot(nres_, 0ll);
long long int totprot = 0ll;
int c = 0; // simple counter
for (int i = 1; i < nframes_ + 1; i++) {
{ // scope this
int j = 0;
for (Cpin::ResIterator rit = cpin_->begin(); rit != cpin_->end(); rit++) {
long long int protadd = (long long int) (rit->isProtonated(statelist_[i][j]));
nprot[j] += protadd;
totprot += (long long int) rit->numProtons(statelist_[i][j]);
j++;
}
}
if (c * time_step_ >= interval) {
c = 0;
// Now we print a point
int j = 0;
fp << setw(10) << (i-1)*time_step_ << " ";
for (Cpin::ResIterator rit = cpin_->begin(); rit != cpin_->end(); rit++) {
double fracprot = (double)nprot[j] / (double)(i+1);
if (print_prot) {
// We want the fraction protonated
fp << setprecision(5) << setw(8) << fracprot << " ";
}else if (print_pka) {
// We want the pKa
double pKa = pH_ - log10( (1.0 - fracprot) / fracprot );
fp << setprecision(4) << setw(8) << pKa << " ";
}else {
// We want the fraction deprotonated
fp << setprecision(5) << setw(8) << 1.0-fracprot << " ";
}
j++;
}
double fracprot = (double)totprot / (double)i;
fp << setprecision(6) << setw(17) << fracprot << endl;
}
c++; // heh
}
fp.close();
return;
}
/// Print the rolling/running average time series with a given window
void ProtTraj::PrintRunningAvg(const int window, const int interval,
string const& fname, const bool print_prot,
const bool print_pka) {
const int halfwin = window / (2 * time_step_);
// Open the file for writing and print a header
ofstream fp(fname.c_str());
if (!fp.is_open())
throw FileIOError("Could not open " + fname + " for writing!");
fp << fixed << "#Time step ";
for (Cpin::ResIterator rit = cpin_->begin(); rit != cpin_->end(); rit++) {
stringstream iss;
iss << rit->getResname() << " " << rit->getResnum();
fp << setw(8) << iss.str() << " ";
}
fp << " Total Avg. Prot." << endl;
for (int i = 1; i < nframes_ + 1; i+= interval/time_step_) {
vector<long long int> nprot(nres_, 0ll);
long long int totprot = 0ll;
// Loop over all frames we should include here
for (int j = MAX(0, i-halfwin); j < MIN(nframes_, i+halfwin); j++) {
// Loop over every residue
int k = 0;
for (Cpin::ResIterator rit = cpin_->begin(); rit != cpin_->end(); rit++) {
long long int protadd = (long long int) (rit->isProtonated(statelist_[j][k]));
nprot[k] += protadd;
totprot += (long long int) rit->numProtons(statelist_[j][k]);
k++;
}
}
// Print this frame to the output file
int j = 0;
int n = MIN(nframes_, i+halfwin) - MAX(0, i-halfwin);
fp << setw(10) << time_step_*i << " ";
for (Cpin::ResIterator rit = cpin_->begin(); rit != cpin_->end(); rit++) {
double fracprot = (double)nprot[j] / (double)n;
if (print_prot) {
// We want the fraction protonated
fp << setprecision(5) << setw(8) << fracprot << " ";
}else if (print_pka) {
// We want the pKa
double pKa = pH_ - log10( (1.0 - fracprot) / fracprot );
fp << setprecision(4) << setw(8) << pKa << " ";
}else {
// We want the fraction deprotonated
fp << setprecision(5) << setw(8) << 1.0-fracprot << " ";
}
j++;
}
double fracprot = (double)totprot / (double)n;
fp << setprecision(6) << setw(17) << fracprot << endl;
}
fp.close();
return;
}
/// Print a time series of the desired properties in 'chunks' of the simulation
void ProtTraj::PrintChunks(const int window, string const& fname,
const bool print_prot, const bool print_pka) {
// Open up the file and write a header (set fixed precision)
ofstream fp(fname.c_str());
if (!fp.is_open())
throw FileIOError("Could not open " + fname + " for writing!");
fp << fixed << "#Time step ";
for (Cpin::ResIterator rit = cpin_->begin(); rit != cpin_->end(); rit++) {
stringstream iss;
iss << rit->getResname() << " " << rit->getResnum();
fp << setw(8) << iss.str() << " ";
}
fp << " Total Avg. Prot." << endl;
int interval = window / time_step_;
int first = 0;
while (first < nframes_+1) {
vector<long long int> nprot(nres_, 0ll);
long long int totprot = 0ll;
int last = MIN(nframes_+1, first + interval);
for (int i = first; i < last; i++) {
int j = 0;
for (Cpin::ResIterator rit = cpin_->begin(); rit != cpin_->end(); rit++) {
long long int protadd = (long long int) (rit->isProtonated(statelist_[i][j]));
nprot[j] += protadd;
totprot += (long long int) rit->numProtons(statelist_[i][j]);
j++;
}
}
// Now write the information
int j = 0;
fp << setw(10) << time_step_*(first + interval / 2) << " ";
for (Cpin::ResIterator rit = cpin_->begin(); rit != cpin_->end(); rit++) {
double fracprot = (double)nprot[j] / (double)(last - first);
if (print_prot) {
// We want the fraction protonated
fp << setprecision(5) << setw(8) << fracprot << " ";
}else if (print_pka) {
// We want the pKa
double pKa = pH_ - log10( (1.0 - fracprot) / fracprot );
fp << setprecision(4) << setw(8) << pKa << " ";
}else {
// We want the fraction deprotonated
fp << setprecision(5) << setw(8) << 1.0-fracprot << " ";
}
j++;
}
double fracprot = (double)totprot/(double)(last - first);
fp << setprecision(6) << setw(17) << fracprot << endl;
first += interval;
}
// Now that I'm here (and done), close the file
fp.close();
return;
}
/** Print the population fraction of the entire simulation for each state and
* each residue
*/
void ProtTraj::PrintProtPop(string const& fname) {
// Set up the table of populations, initializing everything to zero
vector<StateCount> pop_counts;
// Now loop through every state and every residue, building pop_counts
for (Cpin::ResIterator rit = cpin_->begin(); rit != cpin_->end(); rit++) {
StateCount newstate;
newstate.nstates = 0;
for (int i = 0; i < rit->numStates(); i++) {
newstate.state_cnt.push_back(0ll);
newstate.prot_cnt.push_back(rit->numProtons(i));
newstate.nstates++;
}
pop_counts.push_back(newstate);
}
// Now loop through the entire trajectory, building the population list
for (int i = 1; i < nframes_ + 1; i++) {
ProtVector curst = statelist_[i];
for (int j = 0; j < nres_; j++)
pop_counts[j].state_cnt[ statelist_[i][j] ] += 1ll;
}
// Now print out the population counts
ofstream fp(fname.c_str());
if (!fp.is_open())
throw FileIOError("Could not open " + fname + " for writing!");
// Get the max number of states
int maxst = cpin_->getResidues()[0].numStates();
for (Cpin::ResIterator rit = cpin_->begin(); rit != cpin_->end(); rit++)
maxst = MAX(maxst, rit->numStates());
// Write the header
fp << right << fixed << setw(17) << "Residue Number" << " ";
for (int i = 0; i < maxst; i++)
fp << setw(9) << "State" << setw(3) << i << ' ';
fp << endl << setfill('-') << setw(maxst*13+18) << '-' << endl;
// Now loop through every residue and print out the populations
for (int i = 0; i < nres_; i++) {
stringstream iss;
iss << "Residue: " << cpin_->getResidues()[i].getResname() << " "
<< cpin_->getResidues()[i].getResnum();
fp << setfill(' ') << left << setw(17) << iss.str() << " ";
for (int j = 0; j < pop_counts[i].nstates; j++) {
double pop = (double) pop_counts[i].state_cnt[j] / (double) nframes_;
fp << setprecision(6) << setw(8) << pop << " (" << pop_counts[i].prot_cnt[j]
<< ") ";
}
fp << endl;
}
fp.close();
}
/// Prints the calcpka-style output
void ProtTraj::PrintCalcpka(ostream& fd, const int start) {
// First calculate the statistics
vector<long long int> nprot(nres_, 0ll);
vector<int> transitions(nres_, 0);
long long int totprot = 0ll;
// Start with the first point, but skip it in the iteration
last_point_ = statelist_[start];
for (int i = start + 1; i < nframes_ + 1; i++) {
int j = 0;
for (Cpin::ResIterator rit = cpin_->begin(); rit != cpin_->end(); rit++) {
transitions[j] += (int) (rit->isProtonated(last_point_[j]) !=
rit->isProtonated(statelist_[i][j]));
long long int protadd = (long long int) (rit->isProtonated(statelist_[i][j]));
nprot[j] += protadd;
totprot += (long long int) rit->numProtons(statelist_[i][j]);
j++;
}
// Reassign the last point to the current one before incrementing
last_point_ = statelist_[i];
}
// Now do the printing
fd.precision(3);
fd << fixed;
fd << "Solvent pH is " << setw(8) << pH_ << endl;
int i = 0;
for (Cpin::ResIterator rit = cpin_->begin(); rit != cpin_->end(); rit++) {
double pKa = pH_ - log10( (double) (nframes_-nprot[i]) / (double) nprot[i] );
float offset = (float) pKa - pH_;
fd << setw(3) << rit->getResname() << " " << setw(4) << left << rit->getResnum()
<< ": Offset " << right << setw(6) << offset << " Pred " << setw(6) << pKa
<< " Frac Prot " << setw(5) << (double) nprot[i] / (double) nframes_
<< " Transitions " << setw(9) << transitions[i] << endl;
i++;
}
fd << endl << "Average total molecular protonation: " << setw(7)
<< (double)totprot / (double)nframes_ << endl;
return;
}
