#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/groio.h"
#include "gromacs/fileio/pdbio.h"
-#include "gromacs/fileio/tngio_for_tools.h"
+#include "gromacs/fileio/tngio.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trrio.h"
#include "gromacs/fileio/trxio.h"
in = gmx_trr_open(fn, "r");
fp = gmx_fio_getfp(in);
- if (fp == NULL)
+ if (fp == nullptr)
{
fprintf(stderr, "Sorry, can not trunc %s, truncation of this filetype is not supported\n", fn);
gmx_trr_close(in);
bStop = FALSE;
while (!bStop && gmx_trr_read_frame_header(in, &sh, &bOK))
{
- gmx_trr_read_frame_data(in, &sh, NULL, NULL, NULL, NULL);
+ gmx_trr_read_frame_data(in, &sh, nullptr, nullptr, nullptr, nullptr);
fpos = gmx_ftell(fp);
t = sh.t;
if (t >= t0)
const char *input_file,
const char *output_file)
{
- gmx_mtop_t *mtop = NULL;
+ gmx_mtop_t *mtop = nullptr;
if (fn2bTPX(tps_file) &&
efTNG != fn2ftp(input_file) &&
{
int temp_natoms = -1;
snew(mtop, 1);
- read_tpx(tps_file, NULL, NULL, &temp_natoms,
- NULL, NULL, mtop);
+ read_tpx(tps_file, nullptr, nullptr, &temp_natoms,
+ nullptr, nullptr, mtop);
}
return mtop;
};
const char *pbc_opt[epNR + 1] =
{
- NULL, "none", "mol", "res", "atom", "nojump", "cluster", "whole",
- NULL
+ nullptr, "none", "mol", "res", "atom", "nojump", "cluster", "whole",
+ nullptr
};
int unitcell_enum;
const char *unitcell_opt[euNR+1] =
- { NULL, "rect", "tric", "compact", NULL };
+ { nullptr, "rect", "tric", "compact", nullptr };
enum
{
ecSel, ecTric, ecRect, ecZero, ecNR
};
const char *center_opt[ecNR+1] =
- { NULL, "tric", "rect", "zero", NULL };
+ { nullptr, "tric", "rect", "zero", nullptr };
int ecenter;
int fit_enum;
};
const char *fit[efNR + 1] =
{
- NULL, "none", "rot+trans", "rotxy+transxy", "translation", "transxy",
- "progressive", NULL
+ nullptr, "none", "rot+trans", "rotxy+transxy", "translation", "transxy",
+ "progressive", nullptr
};
static gmx_bool bSeparate = FALSE, bVels = TRUE, bForce = FALSE, bCONECT = 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 = NULL;
+ static char *exec_command = nullptr;
static real dropunder = 0, dropover = 0;
static gmx_bool bRound = FALSE;
};
#define NPA asize(pa)
- FILE *out = NULL;
- t_trxstatus *trxout = NULL;
+ FILE *out = nullptr;
+ t_trxstatus *trxout = nullptr;
t_trxstatus *trxin;
int file_nr;
t_trxframe fr, frout;
int flags;
- rvec *xmem = NULL, *vmem = NULL, *fmem = NULL;
- rvec *xp = NULL, x_shift, hbox;
- real *w_rls = NULL;
+ rvec *xmem = nullptr, *vmem = nullptr, *fmem = nullptr;
+ rvec *xp = nullptr, x_shift, hbox;
+ real *w_rls = nullptr;
int m, i, d, frame, outframe, natoms, nout, ncent, newstep = 0, model_nr;
#define SKIP 10
t_topology top;
- gmx_mtop_t *mtop = NULL;
- gmx_conect gc = NULL;
+ gmx_mtop_t *mtop = nullptr;
+ gmx_conect gc = nullptr;
int ePBC = -1;
- t_atoms *atoms = NULL, useatoms;
+ t_atoms *atoms = nullptr, useatoms;
matrix top_box;
int *index, *cindex;
char *grpnm;
int ifit, my_clust = -1;
int *ind_fit;
char *gn_fit;
- t_cluster_ndx *clust = NULL;
- t_trxstatus **clust_status = NULL;
- int *clust_status_id = NULL;
+ t_cluster_ndx *clust = nullptr;
+ t_trxstatus **clust_status = nullptr;
+ int *clust_status_id = nullptr;
int ntrxopen = 0;
- int *nfwritten = NULL;
+ int *nfwritten = nullptr;
int ndrop = 0, ncol, drop0 = 0, drop1 = 0, dropuse = 0;
double **dropval;
real tshift = 0, t0 = -1, dt = 0.001, prec;
gmx_bool bFit, bPFit, bReset;
int nfitdim;
- gmx_rmpbc_t gpbc = NULL;
+ gmx_rmpbc_t gpbc = nullptr;
gmx_bool bRmPBC, bPBCWhole, bPBCcomRes, bPBCcomMol, bPBCcomAtom, bPBC, bNoJump, bCluster;
gmx_bool bCopy, bDoIt, bIndex, bTDump, bSetTime, bTPS = FALSE, bDTset = FALSE;
gmx_bool bExec, bTimeStep = FALSE, bDumpFrame = FALSE, bSetPrec, bNeedPrec;
gmx_bool bHaveFirstFrame, bHaveNextFrame, bSetBox, bSetUR, bSplit = FALSE;
gmx_bool bSubTraj = FALSE, bDropUnder = FALSE, bDropOver = FALSE, bTrans = FALSE;
gmx_bool bWriteFrame, bSplitHere;
- const char *top_file, *in_file, *out_file = NULL;
+ const char *top_file, *in_file, *out_file = nullptr;
char out_file2[256], *charpt;
- char *outf_base = NULL;
- const char *outf_ext = NULL;
+ char *outf_base = nullptr;
+ const char *outf_ext = nullptr;
char top_title[256], title[256], filemode[5];
gmx_output_env_t *oenv;
t_filenm fnm[] = {
- { efTRX, "-f", NULL, ffREAD },
- { efTRO, "-o", NULL, ffWRITE },
- { efTPS, NULL, NULL, ffOPTRD },
- { efNDX, NULL, NULL, ffOPTRD },
+ { efTRX, "-f", nullptr, ffREAD },
+ { efTRO, "-o", nullptr, ffWRITE },
+ { efTPS, nullptr, nullptr, ffOPTRD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
{ efNDX, "-fr", "frames", ffOPTRD },
{ efNDX, "-sub", "cluster", ffOPTRD },
{ efXVG, "-drop", "drop", ffOPTRD }
PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_VIEW |
PCA_TIME_UNIT,
NFILE, fnm, NPA, pa, asize(desc), desc,
- 0, NULL, &oenv))
+ 0, nullptr, &oenv))
{
return 0;
}
if (bSeparate || bSplit)
{
outf_ext = std::strrchr(out_file, '.');
- if (outf_ext == NULL)
+ if (outf_ext == nullptr)
{
gmx_fatal(FARGS, "Output file name '%s' does not contain a '.'", out_file);
}
gmx_fatal(FARGS, "Can only use the sub option with output file types "
"xtc and trr");
}
- clust = cluster_index(NULL, opt2fn("-sub", NFILE, fnm));
+ clust = cluster_index(nullptr, opt2fn("-sub", NFILE, fnm));
/* Check for number of files disabled, as FOPEN_MAX is not the correct
* number to check for. In my linux box it is only 16.
snew(nfwritten, clust->clust->nr);
for (i = 0; (i < clust->clust->nr); i++)
{
- clust_status[i] = NULL;
+ clust_status[i] = nullptr;
clust_status_id[i] = -1;
}
bSeparate = bSplit = FALSE;
if (bTPS)
{
- read_tps_conf(top_file, &top, &ePBC, &xp, NULL, top_box,
+ read_tps_conf(top_file, &top, &ePBC, &xp, nullptr, top_box,
bReset || bPBCcomRes);
std::strncpy(top_title, *top.name, 255);
top_title[255] = '\0';
}
/* get frame number index */
- frindex = NULL;
+ frindex = nullptr;
if (opt2bSet("-fr", NFILE, fnm))
{
printf("Select groups of frame number indices:\n");
gmx_rmpbc(gpbc, top.atoms.nr, top_box, xp);
}
copy_rvec(xp[index[0]], x_shift);
- reset_x_ndim(nfitdim, ifit, ind_fit, atoms->nr, NULL, xp, w_rls);
+ reset_x_ndim(nfitdim, ifit, ind_fit, atoms->nr, nullptr, xp, w_rls);
rvec_dec(x_shift, xp[index[0]]);
}
else
/* get memory for stuff to go in .pdb file, and initialize
* the pdbinfo structure part if the input has it.
*/
- init_t_atoms(&useatoms, atoms->nr, (atoms->pdbinfo != NULL));
+ init_t_atoms(&useatoms, atoms->nr, atoms->havePdbInfo);
sfree(useatoms.resinfo);
useatoms.resinfo = atoms->resinfo;
for (i = 0; (i < nout); i++)
{
useatoms.atomname[i] = atoms->atomname[index[i]];
useatoms.atom[i] = atoms->atom[index[i]];
- if (atoms->pdbinfo != NULL)
+ if (atoms->havePdbInfo)
{
useatoms.pdbinfo[i] = atoms->pdbinfo[index[i]];
}
filemode[0],
trxin,
&trxout,
- NULL,
+ nullptr,
nout,
mtop,
index,
break;
case efXTC:
case efTRR:
- out = NULL;
+ out = nullptr;
if (!bSplit && !bSubTraj)
{
trxout = open_trx(out_file, filemode);
gmx_rmpbc_trxfr(gpbc, &fr);
}
- reset_x_ndim(nfitdim, ifit, ind_fit, natoms, NULL, fr.x, w_rls);
+ reset_x_ndim(nfitdim, ifit, ind_fit, natoms, nullptr, fr.x, w_rls);
do_fit(natoms, w_rls, xp, fr.x);
}
/* store this set of coordinates for future use */
if (bPFit || bNoJump)
{
- if (xp == NULL)
+ if (xp == nullptr)
{
snew(xp, natoms);
}
if (bReset)
{
- reset_x_ndim(nfitdim, ifit, ind_fit, natoms, NULL, fr.x, w_rls);
+ reset_x_ndim(nfitdim, ifit, ind_fit, natoms, nullptr, fr.x, w_rls);
if (bFit)
{
do_fit_ndim(nfitdim, natoms, w_rls, xp, fr.x);
clust->clust->index[my_clust]))
{
close_trx(clust_status[my_clust]);
- clust_status[my_clust] = NULL;
+ clust_status[my_clust] = nullptr;
clust_status_id[my_clust] = -2;
ntrxopen--;
if (ntrxopen < 0)
{
case efGRO:
write_hconf_p(out, title, &useatoms,
- frout.x, frout.bV ? frout.v : NULL, frout.box);
+ frout.x, frout.bV ? frout.v : nullptr, frout.box);
break;
case efPDB:
fprintf(out, "REMARK GENERATED BY TRJCONV\n");
frout.bStep = TRUE;
frout.bTime = TRUE;
}
- write_g96_conf(out, &frout, -1, NULL);
+ write_g96_conf(out, &frout, -1, nullptr);
}
if (bSeparate || bSplitHere)
{
gmx_ffclose(out);
- out = NULL;
+ out = nullptr;
}
break;
default:
{
close_trx(trxout);
}
- else if (out != NULL)
+ else if (out != nullptr)
{
gmx_ffclose(out);
}
sfree(mtop);
- do_view(oenv, out_file, NULL);
+ do_view(oenv, out_file, nullptr);
return 0;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff