const char* program_name = "contact_profile";

bool optsOK = true;

gmx::initForCommandLine(&argc,&argv);

copyright(program_name);

cout << " Computes the standard atomic contacts for structures in" << endl;

cout << " the given xtc file. A topology PDB file and atom index file" << endl;

cout << " should be provided for determining the atoms to compare." << endl;

cout << " The resulting sparse contact distance profiles are" << endl;

cout << " in sparse vector format (index-file and data-file)." << endl;

cout << endl;

cout << " Use -h or --help to see the complete list of options." << endl;

cout << endl;

// Option vars...

int nthreads = 0;

double sigma;

double eps;

string top_filename;

string xtc_filename;

string ndx_filename;

const char* ndx_filename_ptr = NULL;

string index_filename;

string data_filename;

// Declare the supported options.

po::options_description cmdline_options;

po::options_description program_options("Program options");

program_options.add_options()

("help,h", "show this help message and exit")

("threads,t", po::value<int>(&nthreads)->default_value(omp_get_max_threads()>omp_get_num_procs()?omp_get_num_procs():omp_get_max_threads()), "Input: Number of threads to start (int)")

("epsilon,e", po::value<double>(&eps)->default_value(9.0), "Input: Contact cutoff (real)")

// ("sigma,q", po::value<double>(&sigma)->default_value(1), "Input: Standard deviation of gaussian kernel (real)")

("topology-file,p", po::value<string>(&top_filename)->default_value("topology.pdb"), "Input: Topology file [.pdb,.gro,.tpr] (string:filename)")

("xtc-file,x", po::value<string>(&xtc_filename)->default_value("traj.xtc"), "Input: Trajectory file (string:filename)")

("ndx-file,n", po::value<string>(&ndx_filename), "Input: K-nn distances file (string:filename)")

("index-file,i", po::value<string>(&index_filename)->default_value("reference.svi"), "Output: Sparse vector indices file (string:filename)")

("data-file,d", po::value<string>(&data_filename)->default_value("reference.svd"), "Output: Sparse vector data file (string:filename)")

;

cmdline_options.add(program_options);

po::variables_map vm;

po::store(po::parse_command_line(argc, argv, cmdline_options), vm);

po::notify(vm);

if (vm.count("help")) {

cout << "usage: " << program_name << " [options]" << endl;

cout << cmdline_options << endl;

return 1;

}

if (vm.count("ndx-file")) {

ndx_filename_ptr = ndx_filename.c_str();

}

if (!optsOK) {

return -1;

}

cout << "Running with the following options:" << endl;

cout << "threads = " << nthreads << endl;

cout << "topology-file = " << top_filename << endl;

cout << "xtc-file = " << xtc_filename << endl;

cout << "ndx-file = " << ndx_filename << endl;

cout << "index-file = " << index_filename << endl;

cout << "data-file = " << data_filename << endl;

cout << endl;

// Local vars

int step = 1;

float time = 0.0;

matrix box;

float prec = 0.001;

char buf[256];

t_topology top;

int ePBC;

int natoms = 0;

int nframes= 0;

int update_interval = 1;

t_fileio *ref_file;

rvec *mycoords = NULL;

gmx_bool bOK = 1;

double *contact = NULL;

vector<coord_array> *ref_coords = NULL;

::real *weights = NULL;

int gnx1,gnx2;

atom_id *index1,*index2;

char *grpname1,*grpname2;

ofstream index;

ofstream data;

// Remove C stdout (silly GROMACS warnings going every which stream!)

int myout = dup(1);

dup2(2,1);

// Setup threads

omp_set_num_threads(nthreads);

// Get number of atoms and check xtc

cout << "Reading topology information from " << top_filename << " ... ";

read_tps_conf(top_filename.c_str(), buf, &top, &ePBC, &mycoords,

NULL, box, TRUE);

cout << "done." << endl;

delete [] mycoords;

ref_file = open_xtc(xtc_filename.c_str(),"r");

read_first_xtc(ref_file,&natoms, &step, &time, box, &mycoords, &prec, &bOK);

close_xtc(ref_file);

if (natoms != top.atoms.nr) {

cout << "*** ERROR ***" << endl;

cout << "Number of atoms in topology file ("

<< top.atoms.nr << ") "

<< "does not match the number of atoms "

<< "in the XTC file (" << xtc_filename << " : " << natoms << ")."

<< endl;

exit(4);

}

// Get atom selections

cout << "Please select two (non-overlapping) groups for contact profiling..." << endl;

get_index(&top.atoms,ndx_filename_ptr,1,&gnx1,&index1,&grpname1);

cout << endl;

get_index(&top.atoms,ndx_filename_ptr,1,&gnx2,&index2,&grpname2);

cout << endl;

cout << "Total grid size is " << gnx1 << " x " << gnx2 << " = " << (gnx1*gnx2) << endl;

// Read coordinates and weight-center all structures

cout << "Reading reference coordinates from file: " << xtc_filename << " ... ";

ref_coords = new vector<coord_array>;

ref_file = open_xtc(xtc_filename.c_str(),"r");

mycoords = new rvec[natoms];

while (read_next_xtc(ref_file, natoms, &step, &time, box, mycoords, &prec, &bOK)) {

ref_coords->push_back(mycoords);

mycoords = new rvec[natoms];

}

close_xtc(ref_file);

delete [] mycoords;

mycoords = NULL;

nframes = ref_coords->size();

cout << "done." << endl;

// Allocate vectors for storing the distances for a structure

contact = new double[gnx1*gnx2];

weights = new ::real[gnx1*gnx2];

for (int x = 0; x < natoms; x++) weights[x] = top.atoms.atom[x].m;

#pragma omp parallel for

for (int i = 0; i < gnx1; i++)

for (int j = 0; j < gnx2; j++) {

weights[(i*gnx2)+j] = top.atoms.atom[index1[i]].m * top.atoms.atom[index2[j]].m;

}

// Restore C stdout.

dup2(myout,1);

index.open(index_filename.c_str());

data.open(data_filename.c_str());

// Timer for ETA

time_t start = std::time(0);

time_t last = start;

// Compute fits

for (int frame = 0; frame < nframes; frame++) {

// Update user of progress

if (std::time(0) - last > update_interval) {

last = std::time(0);

time_t eta = start + ((last-start) * nframes / frame);

cout << "\rFrame: " << frame << ", will finish "

<< string(std::ctime(&eta)).substr(0,20);

cout.flush();

}

// Do Work

#pragma omp parallel for

for (int i = 0; i < gnx1*gnx2; i++)

contact[i] = 0.0;

#pragma omp parallel for

for (int i = 0; i < gnx1; i++) {

int ii = index1[i];

for (int j = 0; j < gnx2; j++) {

int jj = index2[j];

double d = 0.0;

for (int k = 0; k < 3; k++)

d += (((*ref_coords)[frame][ii][k] - (*ref_coords)[frame][jj][k]) *

((*ref_coords)[frame][ii][k] - (*ref_coords)[frame][jj][k]));

d = sqrt(d) * 10.0;

// d = exp(-(d*d) / (2.0 * weights[(i*gnx2)+j]));

// if (d > eps)

// contact[(i*gnx2)+j] = d;

if (d < eps)

contact[(i*gnx2)+j] = 1.0;

} // j

} // i

double sum = 0.0;

#pragma omp parallel for reduction(+:sum)

for (int i = 0; i < gnx1*gnx2; i++)

sum += contact[i];

sum = 1.0; // No normalization...

int total = 0;

#pragma omp parallel for reduction(+:total)

for (int i = 0; i < gnx1*gnx2; i++)

if (contact[i] > 0) {

contact[i] /= sum;

total++;

}

index.write((char*) &total, sizeof(int) / sizeof(char));

for (int i = 0; i < gnx1*gnx2; i++)

if (contact[i] > 0.0) {

index.write((char*) &i, sizeof(int) / sizeof(char));

data.write((char*) &contact[i], sizeof(double) / sizeof(char));

}

// cout << frame << " " << total << endl;

} // frame

cout << endl << endl;

index.close();

data.close();

// Clean coordinates

for (vector<coord_array>::iterator itr = ref_coords->begin();

itr != ref_coords->end(); itr++) delete [] (*itr);

delete ref_coords;

delete [] contact;

delete [] weights;

return 0;