void list_xtc(const char *fn)
{
t_fileio *xd;
int indent;
char buf[256];
rvec *x;
matrix box;
int nframe, natoms, step;
real prec, time;
gmx_bool bOK;
xd = open_xtc(fn, "r");
read_first_xtc(xd, &natoms, &step, &time, box, &x, &prec, &bOK);
nframe = 0;
do
{
sprintf(buf, "%s frame %d", fn, nframe);
indent = 0;
indent = pr_title(stdout, indent, buf);
pr_indent(stdout, indent);
fprintf(stdout, "natoms=%10d step=%10d time=%12.7e prec=%10g\n",
natoms, step, time, prec);
pr_rvecs(stdout, indent, "box", box, DIM);
pr_rvecs(stdout, indent, "x", x, natoms);
nframe++;
}
while (read_next_xtc(xd, natoms, &step, &time, box, x, &prec, &bOK));
if (!bOK)
{
fprintf(stderr, "\nWARNING: Incomplete frame at time %g\n", time);
}
sfree(x);
close_xtc(xd);
}
void ReadGromacs::readFileXtc()
{
int xd, indent;
char buf[256];
rvec *x;
matrix box;
int nframe, natoms, step;
real prec, time;
bool bOK;
float *d;
float *e;
float *f;
coDoPoints **outanimationpoints = NULL;
coDoSet *setpoints = NULL;
const char *filename = xtcFileParam->getValue();
xd = open_xtc((char *)"traj.xtc", (char *)"r");
read_first_xtc(xd, &natoms, &step, &time, box, &x, &prec, &bOK);
outanimationpoints = new coDoPoints *[100];
for (int h = 0; h < 100; h++)
{
outanimationpoints[h] = new coDoPoints(pointsAnimationOutput->getObjName(), natoms);
}
nframe = 0;
do
{
indent = 0;
outanimationpoints[nframe]->getAddresses(&d, &e, &f);
for (int i = 0; i < natoms; i++)
{
d[i] = x[i][0];
e[i] = x[i][1];
f[i] = x[i][2];
}
nframe++;
} while (read_next_xtc(xd, natoms, &step, &time, box, x, &prec, &bOK));
setpoints = new coDoSet(pointsAnimationOutput->getObjName(), (coDistributedObject **)outanimationpoints);
pointsAnimationOutput->setCurrentObject(setpoints);
}
void list_xtc(char *fn, bool bXVG)
{
int xd,indent;
char buf[256];
rvec *x;
matrix box;
int nframe,natoms,step;
real prec,time;
bool bOK;
xd = open_xtc(fn,"r");
read_first_xtc(xd,&natoms,&step,&time,box,&x,&prec,&bOK);
nframe=0;
do {
if (bXVG) {
int i,d;
fprintf(stdout,"%g",time);
for(i=0; i<natoms; i++)
for(d=0; d<DIM; d++)
fprintf(stdout," %g",x[i][d]);
fprintf(stdout,"\n");
} else {
sprintf(buf,"%s frame %d",fn,nframe);
indent=0;
indent=pr_title(stdout,indent,buf);
pr_indent(stdout,indent);
fprintf(stdout,"natoms=%10d step=%10d time=%12.7e prec=%10g\n",
natoms,step,time,prec);
pr_rvecs(stdout,indent,"box",box,DIM);
pr_rvecs(stdout,indent,"x",x,natoms);
}
nframe++;
} while (read_next_xtc(xd,natoms,&step,&time,box,x,&prec,&bOK));
if (!bOK)
fprintf(stderr,"\nWARNING: Incomplete frame at time %g\n",time);
close_xtc(xd);
}
bool read_first_frame(const gmx_output_env_t *oenv, t_trxstatus **status,
const char *fn, t_trxframe *fr, int flags)
{
t_fileio *fio = nullptr;
gmx_bool bFirst, bOK;
int ftp = fn2ftp(fn);
clear_trxframe(fr, TRUE);
bFirst = TRUE;
snew((*status), 1);
status_init( *status );
initcount(*status);
(*status)->flags = flags;
if (efTNG == ftp)
{
/* Special treatment for TNG files */
gmx_tng_open(fn, 'r', &(*status)->tng);
}
else
{
fio = (*status)->fio = gmx_fio_open(fn, "r");
}
switch (ftp)
{
case efTRR:
break;
case efCPT:
read_checkpoint_trxframe(fio, fr);
bFirst = FALSE;
break;
case efG96:
{
/* Can not rewind a compressed file, so open it twice */
if (!(*status)->persistent_line)
{
/* allocate the persistent line */
snew((*status)->persistent_line, STRLEN+1);
}
t_symtab *symtab = nullptr;
read_g96_conf(gmx_fio_getfp(fio), fn, nullptr, fr, symtab, (*status)->persistent_line);
gmx_fio_close(fio);
clear_trxframe(fr, FALSE);
if (flags & (TRX_READ_X | TRX_NEED_X))
{
snew(fr->x, fr->natoms);
}
if (flags & (TRX_READ_V | TRX_NEED_V))
{
snew(fr->v, fr->natoms);
}
(*status)->fio = gmx_fio_open(fn, "r");
break;
}
case efXTC:
if (read_first_xtc(fio, &fr->natoms, &fr->step, &fr->time, fr->box, &fr->x,
&fr->prec, &bOK) == 0)
{
GMX_RELEASE_ASSERT(!bOK, "Inconsistent results - OK status from read_first_xtc, but 0 atom coords read");
fr->not_ok = DATA_NOT_OK;
}
if (fr->not_ok)
{
fr->natoms = 0;
printincomp(*status, fr);
}
else
{
fr->bPrec = (fr->prec > 0);
fr->bStep = TRUE;
fr->bTime = TRUE;
fr->bX = TRUE;
fr->bBox = TRUE;
printcount(*status, oenv, fr->time, FALSE);
}
bFirst = FALSE;
break;
case efTNG:
fr->step = -1;
if (!gmx_read_next_tng_frame((*status)->tng, fr, nullptr, 0))
{
fr->not_ok = DATA_NOT_OK;
fr->natoms = 0;
printincomp(*status, fr);
}
else
{
printcount(*status, oenv, fr->time, FALSE);
}
bFirst = FALSE;
break;
case efPDB:
pdb_first_x(*status, gmx_fio_getfp(fio), fr);
if (fr->natoms)
{
printcount(*status, oenv, fr->time, FALSE);
}
bFirst = FALSE;
break;
case efGRO:
if (gro_first_x_or_v(gmx_fio_getfp(fio), fr))
{
printcount(*status, oenv, fr->time, FALSE);
}
bFirst = FALSE;
break;
default:
#if GMX_USE_PLUGINS
fprintf(stderr, "The file format of %s is not a known trajectory format to GROMACS.\n"
"Please make sure that the file is a trajectory!\n"
"GROMACS will now assume it to be a trajectory and will try to open it using the VMD plug-ins.\n"
"This will only work in case the VMD plugins are found and it is a trajectory format supported by VMD.\n", fn);
gmx_fio_fp_close(fio); /*only close the file without removing FIO entry*/
if (!read_first_vmd_frame(fn, &(*status)->vmdplugin, fr))
{
gmx_fatal(FARGS, "Not supported in read_first_frame: %s", fn);
}
#else
gmx_fatal(FARGS, "Not supported in read_first_frame: %s. Please make sure that the file is a trajectory.\n"
"GROMACS is not compiled with plug-in support. Thus it cannot read non-GROMACS trajectory formats using the VMD plug-ins.\n"
"Please compile with plug-in support if you want to read non-GROMACS trajectory formats.\n", fn);
#endif
break;
}
(*status)->tf = fr->time;
/* Return FALSE if we read a frame that's past the set ending time. */
if (!bFirst && (!(flags & TRX_DONT_SKIP) && check_times(fr->time) > 0))
{
(*status)->t0 = fr->time;
return FALSE;
}
if (bFirst ||
(!(flags & TRX_DONT_SKIP) && check_times(fr->time) < 0))
{
/* Read a frame when no frame was read or the first was skipped */
if (!read_next_frame(oenv, *status, fr))
{
return FALSE;
}
}
(*status)->t0 = fr->time;
/* We need the number of atoms for random-access XTC searching, even when
* we don't have access to the actual frame data.
*/
(*status)->natoms = fr->natoms;
return (fr->natoms > 0);
}
int read_first_frame(const output_env_t oenv, t_trxstatus **status,
const char *fn, t_trxframe *fr, int flags)
{
t_fileio *fio;
gmx_bool bFirst, bOK;
int dummy = 0;
clear_trxframe(fr, TRUE);
fr->flags = flags;
bFirst = TRUE;
snew((*status), 1);
status_init( *status );
(*status)->nxframe = 1;
initcount(*status);
fio = (*status)->fio = gmx_fio_open(fn, "r");
switch (gmx_fio_getftp(fio))
{
case efTRJ:
case efTRR:
break;
case efCPT:
read_checkpoint_trxframe(fio, fr);
bFirst = FALSE;
break;
case efG96:
/* Can not rewind a compressed file, so open it twice */
if (!(*status)->persistent_line)
{
/* allocate the persistent line */
snew((*status)->persistent_line, STRLEN+1);
}
read_g96_conf(gmx_fio_getfp(fio), fn, fr, (*status)->persistent_line);
gmx_fio_close(fio);
clear_trxframe(fr, FALSE);
if (flags & (TRX_READ_X | TRX_NEED_X))
{
snew(fr->x, fr->natoms);
}
if (flags & (TRX_READ_V | TRX_NEED_V))
{
snew(fr->v, fr->natoms);
}
fio = (*status)->fio = gmx_fio_open(fn, "r");
break;
case efG87:
fr->natoms = xyz_first_x(*status, gmx_fio_getfp(fio), oenv, &fr->time,
&fr->x, fr->box);
if (fr->natoms)
{
fr->bTime = TRUE;
fr->bX = TRUE;
fr->bBox = TRUE;
printcount(*status, oenv, fr->time, FALSE);
}
bFirst = FALSE;
break;
case efXTC:
if (read_first_xtc(fio, &fr->natoms, &fr->step, &fr->time, fr->box, &fr->x,
&fr->prec, &bOK) == 0)
{
if (bOK)
{
gmx_fatal(FARGS, "No XTC!\n");
}
else
{
fr->not_ok = DATA_NOT_OK;
}
}
if (fr->not_ok)
{
fr->natoms = 0;
printincomp(*status, fr);
}
else
{
fr->bPrec = (fr->prec > 0);
fr->bStep = TRUE;
fr->bTime = TRUE;
fr->bX = TRUE;
fr->bBox = TRUE;
printcount(*status, oenv, fr->time, FALSE);
}
bFirst = FALSE;
break;
case efPDB:
pdb_first_x(*status, gmx_fio_getfp(fio), fr);
if (fr->natoms)
{
printcount(*status, oenv, fr->time, FALSE);
}
bFirst = FALSE;
break;
case efGRO:
if (gro_first_x_or_v(gmx_fio_getfp(fio), fr))
{
printcount(*status, oenv, fr->time, FALSE);
}
bFirst = FALSE;
break;
default:
#ifdef GMX_USE_PLUGINS
fprintf(stderr, "The file format of %s is not a known trajectory format to GROMACS.\n"
"Please make sure that the file is a trajectory!\n"
"GROMACS will now assume it to be a trajectory and will try to open it using the VMD plug-ins.\n"
"This will only work in case the VMD plugins are found and it is a trajectory format supported by VMD.\n", fn);
gmx_fio_fp_close(fio); /*only close the file without removing FIO entry*/
if (!read_first_vmd_frame(fn, fr))
{
gmx_fatal(FARGS, "Not supported in read_first_frame: %s", fn);
}
#else
gmx_fatal(FARGS, "Not supported in read_first_frame: %s. Please make sure that the file is a trajectory.\n"
"GROMACS is not compiled with plug-in support. Thus it cannot read non-GROMACS trajectory formats using the VMD plug-ins.\n"
"Please compile with plug-in support if you want to read non-GROMACS trajectory formats.\n", fn);
#endif
break;
}
/* Return FALSE if we read a frame that's past the set ending time. */
if (!bFirst && (!(fr->flags & TRX_DONT_SKIP) && check_times(fr->time) > 0))
{
fr->t0 = fr->time;
return FALSE;
}
if (bFirst ||
(!(fr->flags & TRX_DONT_SKIP) && check_times(fr->time) < 0))
{
/* Read a frame when no frame was read or the first was skipped */
if (!read_next_frame(oenv, *status, fr))
{
return FALSE;
}
}
fr->t0 = fr->time;
return (fr->natoms > 0);
}
int main(int argc, char* argv[]) {
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;
}
int read_first_frame(const output_env_t oenv,t_trxstatus **status,
const char *fn,t_trxframe *fr,int flags)
{
t_fileio *fio;
gmx_bool bFirst,bOK;
int dummy=0;
clear_trxframe(fr,TRUE);
fr->flags = flags;
bFirst = TRUE;
snew((*status), 1);
status_init( *status );
(*status)->nxframe=1;
initcount(*status);
fio = (*status)->fio =gmx_fio_open(fn,"r");
switch (gmx_fio_getftp(fio))
{
case efTRJ:
case efTRR:
break;
case efCPT:
read_checkpoint_trxframe(fio,fr);
bFirst = FALSE;
break;
case efG96:
/* Can not rewind a compressed file, so open it twice */
read_g96_conf(gmx_fio_getfp(fio),fn,fr);
gmx_fio_close(fio);
clear_trxframe(fr,FALSE);
if (flags & (TRX_READ_X | TRX_NEED_X))
snew(fr->x,fr->natoms);
if (flags & (TRX_READ_V | TRX_NEED_V))
snew(fr->v,fr->natoms);
fio = (*status)->fio =gmx_fio_open(fn,"r");
break;
case efG87:
fr->natoms=xyz_first_x(*status, gmx_fio_getfp(fio),oenv,&fr->time,
&fr->x,fr->box);
if (fr->natoms) {
fr->bTime = TRUE;
fr->bX = TRUE;
fr->bBox = TRUE;
printcount(*status,oenv,fr->time,FALSE);
}
bFirst = FALSE;
break;
case efXTC:
if (read_first_xtc(fio,&fr->natoms,&fr->step,&fr->time,fr->box,&fr->x,
&fr->prec,&bOK) == 0) {
if (bOK) {
gmx_fatal(FARGS,"No XTC!\n");
} else {
fr->not_ok = DATA_NOT_OK;
}
}
if (fr->not_ok) {
fr->natoms = 0;
printincomp(*status,fr);
} else {
fr->bPrec = (fr->prec > 0);
fr->bStep = TRUE;
fr->bTime = TRUE;
fr->bX = TRUE;
fr->bBox = TRUE;
printcount(*status,oenv,fr->time,FALSE);
}
bFirst = FALSE;
break;
case efPDB:
pdb_first_x(*status, gmx_fio_getfp(fio),fr);
if (fr->natoms)
printcount(*status,oenv,fr->time,FALSE);
bFirst = FALSE;
break;
case efGRO:
if (gro_first_x_or_v(gmx_fio_getfp(fio),fr))
printcount(*status,oenv,fr->time,FALSE);
bFirst = FALSE;
break;
default:
#ifdef GMX_DLOPEN
gmx_fio_fp_close(fio); /*only close the file without removing FIO entry*/
if (!read_first_vmd_frame(&dummy,fn,fr,flags))
{
gmx_fatal(FARGS,"Not supported in read_first_frame: %s",fn);
}
#else
gmx_fatal(FARGS,"Not supported in read_first_frame: %s",fn);
#endif
break;
}
/* Return FALSE if we read a frame that's past the set ending time. */
if (!bFirst && (!(fr->flags & TRX_DONT_SKIP) && check_times(fr->time) > 0)) {
fr->t0 = fr->time;
return FALSE;
}
if (bFirst ||
(!(fr->flags & TRX_DONT_SKIP) && check_times(fr->time) < 0))
/* Read a frame when no frame was read or the first was skipped */
if (!read_next_frame(oenv,*status,fr))
return FALSE;
fr->t0 = fr->time;
return (fr->natoms > 0);
}