/** 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();
}
int main(int argc, char**argv) {
// Set up the command-line options and parse them
CLOptions clopt = CLOptions(argc, argv);
if (clopt.Parse())
return 1;
// Check the input
if (clopt.CheckInput()) {
cerr << "Error: Input errors detected! See messages above." << endl;
return 1;
}
// test_clopt(clopt); /* Uncomment to test command-line parsing */
int nres = 0; // number of residues (for consistency tests)
/* Set up the cpin and print some diagnostic information (only necessary if
* we're not fixing REMD files
*/
Cpin my_cpin;
if (clopt.REMDPrefix().empty()) {
if ( clopt.Cpin().empty() ) {
#ifdef REDOX
cerr << "Error: No cein file provided!" << endl;
#else
cerr << "Error: No cpin file provided!" << endl;
#endif
return 1;
}
if ( my_cpin.Parse(clopt.Cpin()) )
return 1;
nres = (int) my_cpin.getTrescnt();
if (nres <= 0) {
cerr << "Error: Did not detect any residues in " <<
clopt.Cpin() << endl;
return 1;
}
if (clopt.Debug()) {
cout << "There are " << nres << " titratable residues defined in " <<
my_cpin.getFilename() << ":" << endl;
cout << "They are:" << endl;
for (Cpin::ResIterator it = my_cpin.begin(); it != my_cpin.end(); it++) {
cout << "\t" << setw(3) << it->getResname() << left << " " <<
setw(3) << it->getResnum() << " (" << it->numStates()
<< " states) [ ";
for (int j = 0; j < it->numStates(); j++) {
#ifdef REDOX
if (it->isProtonated(j))
cout << "R ";
else
cout << "O ";
#else
if (it->isProtonated(j))
cout << "P ";
else
cout << "D ";
#endif
}
cout << "]" << endl;
}
}
} // if clopt.REMDPrefix().empty()
// Set up the cpouts
CpoutList cpouts;
for (CLOptions::cpout_iterator it = clopt.begin(); it != clopt.end(); it++) {
CpoutFile c = CpoutFile(&my_cpin, *it);
// Skip over invalid cpouts
if (!c.Valid()) {
#ifdef REDOX
cerr << "Error: Ceout file " << *it << " is invalid! Skipping." << endl;
#else
cerr << "Error: Cpout file " << *it << " is invalid! Skipping." << endl;
#endif
continue;
}
// For REMD fixing where a cpin is unnecessary, make sure all cpouts have
// the same number of residues, so set nres to the first cpout's Nres
if (nres <= 0) nres = c.Nres();
// Skip over cpouts with a residue mismatch
if (c.Nres() != nres) {
#ifdef REDOX
cerr << "Error: Ceout file " << *it << " has " << c.Nres() <<
#else
cerr << "Error: Cpout file " << *it << " has " << c.Nres() <<
#endif
" residues. I expected " << my_cpin.getTrescnt() <<
". Skipping." << endl;
continue;
}
if (clopt.Debug())
#ifdef REDOX
cout << "Added [[ " << *it << " ]] to ceout list." << endl;
#else
cout << "Added [[ " << *it << " ]] to cpout list." << endl;
#endif
cpouts.push_back(c);
}
if (clopt.Debug())
#ifdef REDOX
cout << "Analyzing " << clopt.Cpouts().size() << " ceouts." << endl;
if (cpouts.size() != clopt.Cpouts().size()) {
cerr << "Error: Number of Ceout files " << cpouts.size() <<
#else
cout << "Analyzing " << clopt.Cpouts().size() << " cpouts." << endl;
if (cpouts.size() != clopt.Cpouts().size()) {
cerr << "Error: Number of Cpout files " << cpouts.size() <<
#endif
" does not equal number specified: " << clopt.Cpouts().size() << endl;
return 1;
}
// Special-case REMD re-ordering
if (!clopt.REMDPrefix().empty())
return sort_remd_files(cpouts, clopt.REMDPrefix(), clopt.Overwrite());
#ifdef REDOX
ProtTraj stats = ProtTraj(&my_cpin, cpouts[0].pH(), cpouts[0].GetRecord(), cpouts[0].Temperature());
#else
ProtTraj stats = ProtTraj(&my_cpin, cpouts[0].pH(), cpouts[0].GetRecord());
#endif
for (cpout_iterator it = cpouts.begin(); it != cpouts.end(); it++) {
// If we are here, then warn if we are about to use a REMD file
if (!clopt.Expert())
it->WarnRemd();
stats.LoadCpout(*it);
}
// Do the normal calcpka-style output if requested
if (clopt.Calcpka()) {
if (clopt.Output().empty())
stats.PrintCalcpka(cout);
else {
ofstream fd; fd.open(clopt.Output().c_str());
stats.PrintCalcpka(fd);
fd.close();
}
}
// Do chunk analysis
if (clopt.ChunkWindow() > 0)
stats.PrintChunks(clopt.ChunkWindow(), clopt.ChunkOutput(),
clopt.PrintProtonated() && !clopt.pKa(), clopt.pKa());
// Do cumulative analysis
if (clopt.doCumulative())
stats.PrintCumulative(clopt.CumulativeOutput(), clopt.Interval(),
clopt.PrintProtonated() && !clopt.pKa(), clopt.pKa());
// Do running averages
if (clopt.RunningAvgWindow() > 0)
stats.PrintRunningAvg(clopt.RunningAvgWindow(), clopt.Interval(),
clopt.RunningAvgOutput(),
clopt.PrintProtonated() && !clopt.pKa(), clopt.pKa());
// Do protonation fraction dump
if (clopt.Population().size() > 0)
stats.PrintProtPop(clopt.Population());
// Do conditional probabilities
if (clopt.CondProbs().size() > 0) {
for (CLOptions::prob_iterator it = clopt.condbegin();
it != clopt.condend(); it++)
if (it->Set(my_cpin) == ConditionalProb::ERR) {
cerr << "Quitting due to errors above." << endl;
return 1;
}
stats.PrintCondProb(clopt.ConditionalOutput(), clopt.CondProbs());
}
// Do conditional probability time series (we already set the conditional
// probabilities above, so no need to do it again)
if (clopt.CondProbs().size() > 0 && !clopt.ConditionalChunkOut().empty())
stats.PrintCondTimeseries(clopt.ConditionalChunkOut(), clopt.Interval(),
clopt.CondProbs());
if (clopt.Debug()) cout << "All done!" << endl;
return 0;
}
