*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
fprintf(stderr,
"Do you REALLY want to truncate this trajectory (%s) at:\n"
"frame %d, time %g, bytes %ld ??? (type YES if so)\n",
- fn, j, t, static_cast<long int>(fpos));
+ fn,
+ j,
+ t,
+ static_cast<long int>(fpos));
if (1 != scanf("%s", yesno))
{
gmx_fatal(FARGS, "Error reading user input");
"[PAR]",
"The following formats are supported for input and output:",
- "[REF].xtc[ref], [REF].trr[ref], [REF].gro[ref], [TT].g96[tt]",
- "and [REF].pdb[ref].",
+ "[REF].xtc[ref], [REF].trr[ref], [REF].gro[ref], [TT].g96[tt],",
+ "[REF].pdb[ref] and [REF].tng[ref].",
"The file formats are detected from the file extension.",
"The precision of the [REF].xtc[ref] output is taken from the",
"input file for [REF].xtc[ref], [REF].gro[ref] and [REF].pdb[ref],",
"output can be single or double precision, depending on the precision",
"of the [THISMODULE] binary.",
"Note that velocities are only supported in",
- "[REF].trr[ref], [REF].gro[ref] and [TT].g96[tt] files.[PAR]",
+ "[REF].trr[ref], [REF].tng[ref], [REF].gro[ref] and [TT].g96[tt] files.[PAR]",
"Option [TT]-sep[tt] can be used to write every frame to a separate",
"[TT].gro, .g96[tt] or [REF].pdb[ref] file. By default, all frames all written to ",
"out the water from a trajectory of a protein in water.",
"[BB]ALWAYS[bb] put the original trajectory on tape!",
"We recommend to use the portable [REF].xtc[ref] format for your analysis",
- "to save disk space and to have portable files.[PAR]",
+ "to save disk space and to have portable files. When writing [REF].tng[ref]",
+ "output the file will contain one molecule type of the correct count",
+ "if the selection name matches the molecule name and the selected atoms",
+ "match all atoms of that molecule. Otherwise the whole selection will",
+ "be treated as one single molecule containing all the selected atoms.[PAR]",
"There are two options for fitting the trajectory to a reference",
"either for essential dynamics analysis, etc.",
const char* fit[efNR + 1] = { nullptr, "none", "rot+trans", "rotxy+transxy",
"translation", "transxy", "progressive", nullptr };
- static gmx_bool bSeparate = FALSE, bVels = TRUE, bForce = FALSE, bCONECT = FALSE;
- static gmx_bool bCenter = FALSE;
- static int skip_nr = 1, ndec = 3, nzero = 0;
- static real tzero = 0, delta_t = 0, timestep = 0, ttrunc = -1, tdump = -1, split_t = 0;
- static rvec newbox = { 0, 0, 0 }, shift = { 0, 0, 0 }, trans = { 0, 0, 0 };
- static char* exec_command = nullptr;
- static real dropunder = 0, dropover = 0;
- static gmx_bool bRound = FALSE;
+ gmx_bool bSeparate = FALSE, bVels = TRUE, bForce = FALSE, bCONECT = FALSE;
+ gmx_bool bCenter = FALSE;
+ int skip_nr = 1, ndec = 3, nzero = 0;
+ real tzero = 0, delta_t = 0, timestep = 0, ttrunc = -1, tdump = -1, split_t = 0;
+ rvec newbox = { 0, 0, 0 }, shift = { 0, 0, 0 }, trans = { 0, 0, 0 };
+ char* exec_command = nullptr;
+ real dropunder = 0, dropover = 0;
+ gmx_bool bRound = FALSE;
t_pargs pa[] = {
{ "-skip", FALSE, etINT, { &skip_nr }, "Only write every nr-th frame" },
FALSE,
etBOOL,
{ &bCONECT },
- "Add conect records when writing [REF].pdb[ref] files. Useful "
+ "Add CONECT PDB records when writing [REF].pdb[ref] files. Useful "
"for visualization of non-standard molecules, e.g. "
"coarse grained ones" }
};
real* w_rls = nullptr;
int m, i, d, frame, outframe, natoms, nout, ncent, newstep = 0, model_nr;
#define SKIP 10
- t_topology* top = nullptr;
- gmx_conect gc = nullptr;
- int ePBC = -1;
- t_atoms * atoms = nullptr, useatoms;
+ t_topology* top = nullptr;
+ gmx_conect gc = nullptr;
+ PbcType pbcType = PbcType::Unset;
+ t_atoms * atoms = nullptr, useatoms;
matrix top_box;
int * index = nullptr, *cindex = nullptr;
char* grpnm = nullptr;
{ efXVG, "-drop", "drop", ffOPTRD } };
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_VIEW | PCA_TIME_UNIT,
- NFILE, fnm, NPA, pa, asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(&argc,
+ argv,
+ PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_VIEW | PCA_TIME_UNIT,
+ NFILE,
+ fnm,
+ NPA,
+ pa,
+ asize(desc),
+ desc,
+ 0,
+ nullptr,
+ &oenv))
{
return 0;
}
"WARNING: Option for unitcell representation (-ur %s)\n"
" only has effect in combination with -pbc %s, %s or %s.\n"
" Ingoring unitcell representation.\n\n",
- unitcell_opt[0], pbc_opt[2], pbc_opt[3], pbc_opt[4]);
+ unitcell_opt[0],
+ pbc_opt[2],
+ pbc_opt[3],
+ pbc_opt[4]);
}
}
if (bFit && bPBC)
if (bTPS)
{
snew(top, 1);
- read_tps_conf(top_file, top, &ePBC, &xp, nullptr, top_box, bReset || bPBCcomRes);
+ read_tps_conf(top_file, top, &pbcType, &xp, nullptr, top_box, bReset || bPBCcomRes);
std::strncpy(top_title, *top->name, 255);
top_title[255] = '\0';
atoms = &top->atoms;
if (0 == top->mols.nr && (bCluster || bPBCcomMol))
{
- gmx_fatal(FARGS, "Option -pbc %s requires a .tpr file for the -s option",
- pbc_opt[pbc_enum]);
+ gmx_fatal(FARGS, "Option -pbc %s requires a .tpr file for the -s option", pbc_opt[pbc_enum]);
}
/* top_title is only used for gro and pdb,
}
if (bRmPBC)
{
- gpbc = gmx_rmpbc_init(&top->idef, ePBC, top->atoms.nr);
+ gpbc = gmx_rmpbc_init(&top->idef, pbcType, top->atoms.nr);
}
}
read_first_frame(oenv, &trxin, in_file, &fr, flags);
}
- set_trxframe_ePBC(&fr, ePBC);
+ setTrxFramePbcType(&fr, pbcType);
natoms = fr.natoms;
if (bSetTime)
"Index[%d] %d is larger than the number of atoms in the\n"
"trajectory file (%d). There is a mismatch in the contents\n"
"of your -f, -s and/or -n files.",
- i, index[i] + 1, natoms);
+ i,
+ index[i] + 1,
+ natoms);
}
bCopy = bCopy || (i != index[i]);
}
switch (ftp)
{
case efTNG:
- trxout = trjtools_gmx_prepare_tng_writing(
- out_file, filemode[0], trxin, nullptr, nout, mtop.get(),
- gmx::arrayRefFromArray(index, nout), grpnm);
+ trxout = trjtools_gmx_prepare_tng_writing(out_file,
+ filemode[0],
+ trxin,
+ nullptr,
+ nout,
+ mtop.get(),
+ gmx::arrayRefFromArray(index, nout),
+ grpnm);
break;
case efXTC:
case efTRR:
}
else if (bCluster)
{
- calc_pbc_cluster(ecenter, ifit, top, ePBC, fr.x, ind_fit, fr.box);
+ calc_pbc_cluster(ecenter, ifit, top, pbcType, fr.x, ind_fit, fr.box);
}
if (bPFit)
if (bTDump)
{
- fprintf(stderr, "\nDumping frame at t= %g %s\n",
+ fprintf(stderr,
+ "\nDumping frame at t= %g %s\n",
output_env_conv_time(oenv, frout_time),
output_env_get_time_unit(oenv).c_str());
}
else
{
/* round() is not C89 compatible, so we do this: */
- bDoIt = bRmod(std::floor(frout_time + 0.5), std::floor(tzero + 0.5),
+ bDoIt = bRmod(std::floor(frout_time + 0.5),
+ std::floor(tzero + 0.5),
std::floor(delta_t + 0.5));
}
}
/* print sometimes */
if (((outframe % SKIP) == 0) || (outframe < SKIP))
{
- fprintf(stderr, " -> frame %6d time %8.3f \r", outframe,
+ fprintf(stderr,
+ " -> frame %6d time %8.3f \r",
+ outframe,
output_env_conv_time(oenv, frout_time));
fflush(stderr);
}
switch (unitcell_enum)
{
case euRect:
- put_atoms_in_box(ePBC, fr.box, positionsArrayRef);
+ put_atoms_in_box(pbcType, fr.box, positionsArrayRef);
break;
case euTric:
put_atoms_in_triclinic_unitcell(ecenter, fr.box, positionsArrayRef);
break;
case euCompact:
- put_atoms_in_compact_unitcell(ePBC, ecenter, fr.box, positionsArrayRef);
+ put_atoms_in_compact_unitcell(
+ pbcType, ecenter, fr.box, positionsArrayRef);
break;
}
}
if (bPBCcomRes)
{
- put_residue_com_in_box(unitcell_enum, ecenter, natoms, atoms->atom,
- ePBC, fr.box, fr.x);
+ put_residue_com_in_box(
+ unitcell_enum, ecenter, natoms, atoms->atom, pbcType, fr.box, fr.x);
}
if (bPBCcomMol)
{
- put_molecule_com_in_box(unitcell_enum, ecenter, &top->mols, natoms,
- atoms->atom, ePBC, fr.box, fr.x);
+ put_molecule_com_in_box(
+ unitcell_enum, ecenter, &top->mols, natoms, atoms->atom, pbcType, fr.box, fr.x);
}
/* Copy the input trxframe struct to the output trxframe struct */
frout = fr;
/* round() is not C89 compatible, so we do this: */
bSplitHere = bSplit
&& bRmod(std::floor(frout.time + 0.5),
- std::floor(tzero + 0.5), std::floor(split_t + 0.5));
+ std::floor(tzero + 0.5),
+ std::floor(split_t + 0.5));
}
if (bSeparate || bSplitHere)
{
switch (ftp)
{
case efGRO:
- write_hconf_p(out, title.c_str(), &useatoms, frout.x,
- frout.bV ? frout.v : nullptr, frout.box);
+ write_hconf_p(out,
+ title.c_str(),
+ &useatoms,
+ frout.x,
+ frout.bV ? frout.v : nullptr,
+ frout.box);
break;
case efPDB:
fprintf(out, "REMARK GENERATED BY TRJCONV\n");
{
model_nr++;
}
- write_pdbfile(out, title.c_str(), &useatoms, frout.x,
- frout.ePBC, frout.box, ' ', model_nr, gc);
+ write_pdbfile(out,
+ title.c_str(),
+ &useatoms,
+ frout.x,
+ frout.pbcType,
+ frout.box,
+ ' ',
+ model_nr,
+ gc);
break;
case efG96:
const char* outputTitle = "";
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff