*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017,2018,2019, 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.
#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-typedef struct {
+typedef struct
+{
int nlj, nqq;
- int *lj;
- int *qq;
+ int* lj;
+ int* qq;
} t_liedata;
-static t_liedata *analyze_names(int nre, gmx_enxnm_t *names, const char *ligand)
+static t_liedata* analyze_names(int nre, gmx_enxnm_t* names, const char* ligand)
{
int i;
- t_liedata *ld;
+ t_liedata* ld;
char self[256];
/* Skip until we come to pressure */
snew(ld, 1);
for (; (i < nre); i++)
{
- if ((std::strstr(names[i].name, ligand) != nullptr) &&
- (std::strstr(names[i].name, self) == nullptr))
+ if ((std::strstr(names[i].name, ligand) != nullptr) && (std::strstr(names[i].name, self) == nullptr))
{
if (std::strstr(names[i].name, "LJ") != nullptr)
{
ld->nlj++;
srenew(ld->lj, ld->nlj);
- ld->lj[ld->nlj-1] = i;
+ ld->lj[ld->nlj - 1] = i;
}
else if (std::strstr(names[i].name, "Coul") != nullptr)
{
ld->nqq++;
srenew(ld->qq, ld->nqq);
- ld->qq[ld->nqq-1] = i;
+ ld->qq[ld->nqq - 1] = i;
}
}
}
return ld;
}
-static real calc_lie(t_liedata *ld, t_energy ee[], real lie_lj, real lie_qq,
- real fac_lj, real fac_qq)
+static real calc_lie(t_liedata* ld, t_energy ee[], real lie_lj, real lie_qq, real fac_lj, real fac_qq)
{
int i;
real lj_tot, qq_tot;
}
/* And now the great LIE formula: */
- return fac_lj*(lj_tot-lie_lj)+fac_qq*(qq_tot-lie_qq);
+ return fac_lj * (lj_tot - lie_lj) + fac_qq * (qq_tot - lie_qq);
}
-int gmx_lie(int argc, char *argv[])
+int gmx_lie(int argc, char* argv[])
{
- const char *desc[] = {
+ const char* desc[] = {
"[THISMODULE] computes a free energy estimate based on an energy analysis",
"from nonbonded energies. One needs an energy file with the following components:",
"Coul-(A-B) LJ-SR (A-B) etc.[PAR]",
"are necessary for supplying suitable values for -Elj and -Eqq."
};
static real lie_lj = 0, lie_qq = 0, fac_lj = 0.181, fac_qq = 0.5;
- static const char *ligand = "none";
+ static const char* ligand = "none";
t_pargs pa[] = {
- { "-Elj", FALSE, etREAL, {&lie_lj},
+ { "-Elj",
+ FALSE,
+ etREAL,
+ { &lie_lj },
"Lennard-Jones interaction between ligand and solvent" },
- { "-Eqq", FALSE, etREAL, {&lie_qq},
- "Coulomb interaction between ligand and solvent" },
- { "-Clj", FALSE, etREAL, {&fac_lj},
+ { "-Eqq", FALSE, etREAL, { &lie_qq }, "Coulomb interaction between ligand and solvent" },
+ { "-Clj",
+ FALSE,
+ etREAL,
+ { &fac_lj },
"Factor in the LIE equation for Lennard-Jones component of energy" },
- { "-Cqq", FALSE, etREAL, {&fac_qq},
+ { "-Cqq",
+ FALSE,
+ etREAL,
+ { &fac_qq },
"Factor in the LIE equation for Coulomb component of energy" },
- { "-ligand", FALSE, etSTR, {&ligand},
- "Name of the ligand in the energy file" }
+ { "-ligand", FALSE, etSTR, { &ligand }, "Name of the ligand in the energy file" }
};
#define NPA asize(pa)
- FILE *out;
+ FILE* out;
int nre, nframes = 0, ct = 0;
ener_file_t fp;
- t_liedata *ld;
- gmx_enxnm_t *enm = nullptr;
- t_enxframe *fr;
+ t_liedata* ld;
+ gmx_enxnm_t* enm = nullptr;
+ t_enxframe* fr;
real lie;
double lieaver = 0, lieav2 = 0;
- gmx_output_env_t *oenv;
+ gmx_output_env_t* oenv;
- t_filenm fnm[] = {
- { efEDR, "-f", "ener", ffREAD },
- { efXVG, "-o", "lie", ffWRITE }
- };
+ t_filenm fnm[] = { { efEDR, "-f", "ener", ffREAD }, { efXVG, "-o", "lie", ffWRITE } };
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
- NFILE, fnm, NPA, pa, asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, NPA, pa,
+ asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
ld = analyze_names(nre, enm, ligand);
snew(fr, 1);
- out = xvgropen(ftp2fn(efXVG, NFILE, fnm), "LIE free energy estimate",
- "Time (ps)", "DGbind (kJ/mol)", oenv);
+ out = xvgropen(ftp2fn(efXVG, NFILE, fnm), "LIE free energy estimate", "Time (ps)",
+ "DGbind (kJ/mol)", oenv);
while (do_enx(fp, fr))
{
ct = check_times(fr->t);
if (ct == 0)
{
- lie = calc_lie(ld, fr->ener, lie_lj, lie_qq, fac_lj, fac_qq);
+ lie = calc_lie(ld, fr->ener, lie_lj, lie_qq, fac_lj, fac_qq);
lieaver += lie;
- lieav2 += lie*lie;
+ lieav2 += lie * lie;
nframes++;
fprintf(out, "%10g %10g\n", fr->t, lie);
}
if (nframes > 0)
{
- printf("DGbind = %.3f (%.3f)\n", lieaver/nframes,
- std::sqrt(lieav2/nframes-gmx::square(lieaver/nframes)));
+ printf("DGbind = %.3f (%.3f)\n", lieaver / nframes,
+ std::sqrt(lieav2 / nframes - gmx::square(lieaver / nframes)));
}
do_view(oenv, ftp2fn(efXVG, NFILE, fnm), "-nxy");
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff