static gmx_bool pdb_next_x(t_trxstatus *status, FILE *fp, t_trxframe *fr)
{
t_atoms atoms;
t_symtab *symtab;
matrix boxpdb;
// Initiate model_nr to -1 rather than NOTSET.
// It is not worthwhile introducing extra variables in the
// read_pdbfile call to verify that a model_nr was read.
int ePBC, model_nr = -1, na;
char title[STRLEN], *time, *step;
double dbl;
atoms.nr = fr->natoms;
atoms.atom = nullptr;
atoms.pdbinfo = nullptr;
/* the other pointers in atoms should not be accessed if these are NULL */
snew(symtab, 1);
open_symtab(symtab);
na = read_pdbfile(fp, title, &model_nr, &atoms, symtab, fr->x, &ePBC, boxpdb, TRUE, nullptr);
free_symtab(symtab);
sfree(symtab);
set_trxframe_ePBC(fr, ePBC);
if (nframes_read(status) == 0)
{
fprintf(stderr, " '%s', %d atoms\n", title, fr->natoms);
}
fr->bPrec = TRUE;
fr->prec = 10000;
fr->bX = TRUE;
fr->bBox = (boxpdb[XX][XX] != 0.0);
if (fr->bBox)
{
copy_mat(boxpdb, fr->box);
}
fr->step = 0;
step = std::strstr(title, " step= ");
fr->bStep = ((step != nullptr) && sscanf(step+7, "%" SCNd64, &fr->step) == 1);
dbl = 0.0;
time = std::strstr(title, " t= ");
fr->bTime = ((time != nullptr) && sscanf(time+4, "%lf", &dbl) == 1);
fr->time = dbl;
if (na == 0)
{
return FALSE;
}
else
{
if (na != fr->natoms)
{
gmx_fatal(FARGS, "Number of atoms in pdb frame %d is %d instead of %d",
nframes_read(status), na, fr->natoms);
}
return TRUE;
}
}
static gmx_bool pdb_next_x(t_trxstatus *status, FILE *fp,t_trxframe *fr)
{
t_atoms atoms;
matrix boxpdb;
int ePBC,model_nr,na;
char title[STRLEN],*time;
double dbl;
atoms.nr = fr->natoms;
atoms.atom=NULL;
atoms.pdbinfo=NULL;
/* the other pointers in atoms should not be accessed if these are NULL */
model_nr=NOTSET;
na=read_pdbfile(fp,title,&model_nr,&atoms,fr->x,&ePBC,boxpdb,TRUE,NULL);
set_trxframe_ePBC(fr,ePBC);
if (nframes_read(status)==0)
fprintf(stderr," '%s', %d atoms\n",title, fr->natoms);
fr->bPrec = TRUE;
fr->prec = 10000;
fr->bX = TRUE;
fr->bBox = (boxpdb[XX][XX] != 0.0);
if (fr->bBox) {
copy_mat(boxpdb,fr->box);
}
if (model_nr!=NOTSET) {
fr->bStep = TRUE;
fr->step = model_nr;
}
time=strstr(title," t= ");
if (time) {
fr->bTime = TRUE;
sscanf(time+4,"%lf",&dbl);
fr->time=(real)dbl;
} else {
fr->bTime = FALSE;
/* this is a bit dirty, but it will work: if no time is read from
comment line in pdb file, set time to current frame number */
if (fr->bStep)
fr->time=(real)fr->step;
else
fr->time=(real)nframes_read(status);
}
if (na == 0) {
return FALSE;
} else {
if (na != fr->natoms)
gmx_fatal(FARGS,"Number of atoms in pdb frame %d is %d instead of %d",
nframes_read(status),na,fr->natoms);
return TRUE;
}
}
/*!
* \param[in,out] d Trajectory analysis data structure.
* \returns 0 on success, a non-zero error code on error.
*/
static int
init_first_frame(gmx_ana_traj_t *d)
{
int i;
/* Return if we have already initialized the trajectory */
if (d->fr)
{
return 0;
}
d->frflags |= TRX_NEED_X;
snew(d->fr, 1);
if (!read_first_frame(&d->status, d->trjfile, d->fr, d->frflags))
{
gmx_input("could not read coordinates from trajectory");
return EIO;
}
if (d->top && d->fr->natoms > d->top->atoms.nr)
{
gmx_fatal(FARGS, "Trajectory (%d atoms) does not match topology (%d atoms)",
d->fr->natoms, d->top->atoms.nr);
return -1;
}
/* check index groups */
for (i = 0; i < d->ngrps; ++i)
{
gmx_ana_index_check(d->sel[i]->g, d->fr->natoms);
}
set_trxframe_ePBC(d->fr, d->ePBC);
return 0;
}
void
TrajectoryAnalysisRunnerCommon::initFirstFrame()
{
// Return if we have already initialized the trajectory.
if (impl_->fr)
{
return;
}
time_unit_t time_unit
= static_cast<time_unit_t>(impl_->settings_.timeUnit() + 1);
output_env_init(&impl_->oenv_, 0, NULL, time_unit, FALSE, exvgNONE, 0, 0);
int frflags = impl_->settings_.frflags();
frflags |= TRX_NEED_X;
snew(impl_->fr, 1);
const TopologyInformation &top = impl_->topInfo_;
if (hasTrajectory())
{
if (!read_first_frame(impl_->oenv_, &impl_->status_,
impl_->trjfile_.c_str(), impl_->fr, frflags))
{
GMX_THROW(FileIOError("Could not read coordinates from trajectory"));
}
impl_->bTrajOpen_ = true;
if (top.hasTopology() && impl_->fr->natoms > top.topology()->atoms.nr)
{
GMX_THROW(InconsistentInputError(formatString(
"Trajectory (%d atoms) does not match topology (%d atoms)",
impl_->fr->natoms, top.topology()->atoms.nr)));
}
// Check index groups if they have been initialized based on the topology.
/*
if (top)
{
for (int i = 0; i < impl_->sel->nr(); ++i)
{
gmx_ana_index_check(impl_->sel->sel(i)->indexGroup(),
impl_->fr->natoms);
}
}
*/
}
else
{
// Prepare a frame from topology information.
// TODO: Initialize more of the fields.
if (frflags & (TRX_NEED_V))
{
GMX_THROW(NotImplementedError("Velocity reading from a topology not implemented"));
}
if (frflags & (TRX_NEED_F))
{
GMX_THROW(InvalidInputError("Forces cannot be read from a topology"));
}
impl_->fr->flags = frflags;
impl_->fr->natoms = top.topology()->atoms.nr;
impl_->fr->bX = TRUE;
snew(impl_->fr->x, impl_->fr->natoms);
memcpy(impl_->fr->x, top.xtop_,
sizeof(*impl_->fr->x) * impl_->fr->natoms);
impl_->fr->bBox = TRUE;
copy_mat(const_cast<rvec *>(top.boxtop_), impl_->fr->box);
}
set_trxframe_ePBC(impl_->fr, top.ePBC());
if (top.hasTopology() && impl_->settings_.hasRmPBC())
{
impl_->gpbc_ = gmx_rmpbc_init(&top.topology()->idef, top.ePBC(),
impl_->fr->natoms, impl_->fr->box);
}
}
static gmx_bool pdb_next_x(t_trxstatus *status, FILE *fp, t_trxframe *fr)
{
t_atoms atoms;
t_symtab *symtab;
matrix boxpdb;
// Initiate model_nr to -1 rather than NOTSET.
// It is not worthwhile introducing extra variables in the
// read_pdbfile call to verify that a model_nr was read.
int ePBC, model_nr = -1, na;
char title[STRLEN], *time;
double dbl;
atoms.nr = fr->natoms;
atoms.atom = NULL;
atoms.pdbinfo = NULL;
/* the other pointers in atoms should not be accessed if these are NULL */
snew(symtab, 1);
open_symtab(symtab);
na = read_pdbfile(fp, title, &model_nr, &atoms, symtab, fr->x, &ePBC, boxpdb, TRUE, NULL);
free_symtab(symtab);
sfree(symtab);
set_trxframe_ePBC(fr, ePBC);
if (nframes_read(status) == 0)
{
fprintf(stderr, " '%s', %d atoms\n", title, fr->natoms);
}
fr->bPrec = TRUE;
fr->prec = 10000;
fr->bX = TRUE;
fr->bBox = (boxpdb[XX][XX] != 0.0);
if (fr->bBox)
{
copy_mat(boxpdb, fr->box);
}
if (model_nr != -1)
{
fr->bStep = TRUE;
fr->step = model_nr;
}
time = std::strstr(title, " t= ");
if (time)
{
fr->bTime = TRUE;
sscanf(time+4, "%lf", &dbl);
fr->time = (real)dbl;
}
else
{
fr->bTime = FALSE;
/* this is a bit dirty, but it will work: if no time is read from
comment line in pdb file, set time to current frame number */
if (fr->bStep)
{
fr->time = (real)fr->step;
}
else
{
fr->time = (real)nframes_read(status);
}
}
if (na == 0)
{
return FALSE;
}
else
{
if (na != fr->natoms)
{
gmx_fatal(FARGS, "Number of atoms in pdb frame %d is %d instead of %d",
nframes_read(status), na, fr->natoms);
}
return TRUE;
}
}
int gmx_insert_dummy_atom(int argc, char *argv[])
{
const char *desc[] = {
"\tAdd a dummy atom between atoms -a1 and -a2",
};
gmx_bool bVerbose = FALSE;
int a1=-1,a2=-1;
int insert_at=-1;
const char *tpr_file, *traj_file, *out_file;
t_pargs pa[] = {
{ "-a1", TRUE, etINT,
{&a1}, "Starting atom for bond vector--ie: CD in CNC"},
{ "-a2", TRUE, etINT,
{&a2}, "Ending atom for bond vector--ie: NE in CNC"},
{ "-insert_at", TRUE, etINT,
{&insert_at}, "Desired index for dummy atom. Default = 0"},
{ "-v", FALSE, etBOOL,
{&bVerbose}, "Be slightly more verbose"}
};
t_filenm fnm[] = {
{efTPS, NULL, NULL, ffREAD},
{efTRX, NULL, NULL, ffREAD},
{efTRO, "-o","tilt",ffWRITE},
};
#define NFILE asize(fnm)
#define NPA asize(pa)
output_env_t oenv;
int ngrps, nrefgrps;
t_topology top;
t_atoms *atoms=NULL;
t_trxframe fr,frout;
t_trxstatus *status;
rvec *xtop;
matrix box;
int ePBC;
int flags=TRX_READ_X;
char buffer[1024];
int ftp;
FILE *out_gro = NULL;
t_trxstatus *trxout = NULL;
CopyRight(stderr,argv[0]);
parse_common_args(&argc, argv,
PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_VIEW |
PCA_TIME_UNIT | PCA_BE_NICE | PCA_CAN_TIME,
NFILE, fnm, NPA, pa, asize(desc), desc,
0, NULL, &oenv);
/* Get inputs */
tpr_file = ftp2fn(efTPS, NFILE, fnm);
traj_file = opt2fn( "-f", NFILE, fnm);
out_file = opt2fn("-o", NFILE, fnm);
ftp = fn2ftp(out_file);
std::cout << "\n\n" << out_file << " " << ftp << std::endl;
/* Open inputs */
read_tps_conf(tpr_file, buffer, &top, &ePBC,
&xtop, NULL, box, TRUE);
sfree(xtop);
atoms = &top.atoms;
gmx_conect gc = NULL;
gc = gmx_conect_generate(&top);
/* Make sure -a1 and -a2 are included and increment by -1 to match internal numbering */
if ( a1<1 || a2<1 || a1==a2 || a1>top.atoms.nr || a2>top.atoms.nr ) {
gmx_fatal(FARGS, "\nAtom numbers -a1 and -a2 defining the bond vector must be specified and different\n");
}
a1--; a2--;
/* Read first frame */
gmx_bool bHaveFirstFrame = read_first_frame(oenv, &status, traj_file, &fr, flags);
if (bHaveFirstFrame) {
set_trxframe_ePBC(&fr,ePBC);
}
if (ftp == efGRO) {
out_gro = ffopen(out_file,"w");
}
else if (ftp == efXTC) {
trxout = open_trx(out_file,"w");
}
/* read file and loop through frames */
int frameN = 0;
do {
if (ftp == efGRO) {
fprintf(out_gro,"Dummy atom inserted into %s, FRAME %i\n",traj_file,frameN);
fprintf(out_gro,"%i\n",top.atoms.nr+1);
float CD[3] = { fr.x[a1][0], fr.x[a1][1], fr.x[a1][2] };
float NE[3] = { fr.x[a2][0], fr.x[a2][1], fr.x[a2][2] };
float MP[3] ;
for (int i=0;i<3;i++) {
MP[i] = (CD[i]+NE[i])*0.5;
}
// GRO format:
// RESID, RESNAME, ATOM, INDEX, X, Y, Z, vX, vY, vZ
//"%5d%-5s%5s%5d%8.3f%8.3f%8.3f%8.4f%8.4f%8.4f"
int index = 1;
if (insert_at <= 0) {
fprintf(out_gro,"%5d%-5s%5s%5d%8.4f%8.4f%8.4f%8.4f%8.4f%8.4f\n",
0,"TCHG","TCHG",0,MP[0],MP[1],MP[2],0.0f,0.0f,0.0f);
index++;
}
/* Loop over atoms */
int i;
int resid_offset = 0;
for (i=0;i<top.atoms.nr;i++){
if (insert_at == index) {
fprintf(out_gro,"%5d%-5s%5s%5d%8.4f%8.4f%8.4f%8.4f%8.4f%8.4f\n",
top.atoms.atom[i-1].resind+2,"TCHG","TCHG",index,MP[0],MP[1],MP[2],0.0f,0.0f,0.0f);
index++;
resid_offset++;
}
// Ignoring velocities since I'm using this with mdrun -rerun for
// force calculations only, which don't care about velocities
fprintf(out_gro,"%5d%-5s%5s%5d%8.4f%8.4f%8.4f%8.4f%8.4f%8.4f\n",
top.atoms.atom[i].resind+1 + resid_offset,
*top.atoms.resinfo[top.atoms.atom[i].resind].name,
*top.atoms.atomname[i],
index,
fr.x[i][0], fr.x[i][1], fr.x[i][2],
0.0f,0.0f,0.0f);
index++;
if (index > 99999) {
index = 0;
}
}
/* Get box information */
write_hconf_box(out_gro,1,box);
}
else if (ftp == efXTC) {
float CD[3] = { fr.x[a1][0], fr.x[a1][1], fr.x[a1][2] };
float NE[3] = { fr.x[a2][0], fr.x[a2][1], fr.x[a2][2] };
rvec MP ;
for (int i=0;i<3;i++) {
MP[i] = (CD[i]+NE[i])*0.5;
}
rvec * newX = new rvec [top.atoms.nr+1];
int i = 0;
int offset = 0;
if (insert_at <= 0) {
for (int j=0;j<3;j++) {
newX[i][j] = MP[j];
}
offset++;
}
for (i=0; i<top.atoms.nr; i++) {
if (insert_at == i) {
for (int j=0;j<3;j++) {
newX[i][j] = MP[j];
}
offset++;
}
for (int j=0;j<3;j++) {
newX[i+offset][j] = fr.x[i][j];
}
}
frout = fr;
frout.x = newX;
frout.natoms++;
write_trxframe(trxout,&frout,gc);
delete[] newX;
}
frameN++;
} while(read_next_frame(oenv, status, &fr));
if (trxout) {
close_trx(trxout);
}
if (out_gro) {
ffclose(out_gro);
}
return 0;
}
void
TrajectoryAnalysisRunnerCommon::Impl::initFirstFrame()
{
// Return if we have already initialized the trajectory.
if (fr != NULL)
{
return;
}
time_unit_t time_unit
= static_cast<time_unit_t>(settings_.timeUnit() + 1);
output_env_init(&oenv_, getProgramContext(), time_unit, FALSE, exvgNONE, 0);
int frflags = settings_.frflags();
frflags |= TRX_NEED_X;
snew(fr, 1);
if (hasTrajectory())
{
if (!read_first_frame(oenv_, &status_, trjfile_.c_str(), fr, frflags))
{
GMX_THROW(FileIOError("Could not read coordinates from trajectory"));
}
bTrajOpen_ = true;
if (topInfo_.hasTopology())
{
const int topologyAtomCount = topInfo_.topology()->atoms.nr;
if (fr->natoms > topologyAtomCount)
{
const std::string message
= formatString("Trajectory (%d atoms) does not match topology (%d atoms)",
fr->natoms, topologyAtomCount);
GMX_THROW(InconsistentInputError(message));
}
}
}
else
{
// Prepare a frame from topology information.
// TODO: Initialize more of the fields.
if (frflags & (TRX_NEED_V))
{
GMX_THROW(NotImplementedError("Velocity reading from a topology not implemented"));
}
if (frflags & (TRX_NEED_F))
{
GMX_THROW(InvalidInputError("Forces cannot be read from a topology"));
}
fr->natoms = topInfo_.topology()->atoms.nr;
fr->bX = TRUE;
snew(fr->x, fr->natoms);
memcpy(fr->x, topInfo_.xtop_,
sizeof(*fr->x) * fr->natoms);
fr->bBox = TRUE;
copy_mat(topInfo_.boxtop_, fr->box);
}
set_trxframe_ePBC(fr, topInfo_.ePBC());
if (topInfo_.hasTopology() && settings_.hasRmPBC())
{
gpbc_ = gmx_rmpbc_init(&topInfo_.topology()->idef, topInfo_.ePBC(),
fr->natoms);
}
}
