* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "solvate.h"
+#include "gmxpre.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "solvate.h"
+#include <string.h>
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "smalloc.h"
-#include "string2.h"
-#include "gromacs/fileio/confio.h"
-#include "macros.h"
-#include "gromacs/fileio/futil.h"
-#include "atomprop.h"
-#include "names.h"
-#include "vec.h"
-#include "gmx_fatal.h"
#include "gromacs/commandline/pargs.h"
-#include "gromacs/gmxlib/conformation-utilities.h"
-#include "addconf.h"
-#include "read-conformation.h"
+#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/pdbio.h"
-#include "pbc.h"
+#include "gromacs/gmxlib/conformation-utilities.h"
+#include "gromacs/gmxpreprocess/addconf.h"
+#include "gromacs/gmxpreprocess/read-conformation.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/atomprop.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
#ifdef DEBUG
static void print_stat(rvec *x, int natoms, matrix box)
moltp = NOTSET;
for (j = 0; (j < nrmoltypes) && (moltp == NOTSET); j++)
{
- if (strcmp(*(atoms->resinfo[atoms->atom[i].resind].name),
- moltypes[j].name) == 0)
+ /* cppcheck-suppress nullPointer
+ * moltypes is guaranteed to be allocated because otherwise
+ * nrmoltypes is 0. */
+ if (strcmp(*(atoms->resinfo[atoms->atom[i].resind].name), moltypes[j].name) == 0)
{
moltp = j;
}
}
}
-static void add_solv(const char *fn, t_atoms *atoms, rvec **x, rvec **v, real **r,
+static void add_solv(const char *fn, t_atoms *atoms, rvec **x, rvec **v, real **exclusionDistances,
int ePBC, matrix box,
gmx_atomprop_t aps,
- real r_distance, real r_scale, int *atoms_added,
+ real defaultDistance, real scaleFactor, int *atoms_added,
int *residues_added, real rshell, int max_sol,
const output_env_t oenv)
{
char title_solvt[STRLEN];
t_atoms *atoms_solvt;
rvec *x_solvt, *v_solvt = NULL;
- real *r_solvt;
+ real *exclusionDistances_solvt;
int ePBC_solvt;
matrix box_solvt;
int onr, onres;
lfn = gmxlibfn(fn);
strncpy(filename, lfn, STRLEN);
sfree(lfn);
- snew(atoms_solvt, 1);
- get_stx_coordnum(filename, &(atoms_solvt->nr));
- if (atoms_solvt->nr == 0)
{
- gmx_fatal(FARGS, "No solvent in %s, please check your input\n", filename);
+ int natoms;
+ get_stx_coordnum(filename, &natoms);
+ if (0 == natoms)
+ {
+ gmx_fatal(FARGS, "No solvent in %s, please check your input\n", filename);
+ }
+ snew(atoms_solvt, 1);
+ init_t_atoms(atoms_solvt, natoms, FALSE);
}
snew(x_solvt, atoms_solvt->nr);
if (v)
{
snew(v_solvt, atoms_solvt->nr);
}
- snew(r_solvt, atoms_solvt->nr);
+ snew(exclusionDistances_solvt, atoms_solvt->nr);
snew(atoms_solvt->resinfo, atoms_solvt->nr);
snew(atoms_solvt->atomname, atoms_solvt->nr);
snew(atoms_solvt->atom, atoms_solvt->nr);
/* apply pbc for solvent configuration for whole molecules */
rm_res_pbc(atoms_solvt, x_solvt, box_solvt);
- /* initialise van der waals arrays for solvent configuration */
- mk_vdw(atoms_solvt, r_solvt, aps, r_distance, r_scale);
+ /* initialise distance arrays for solvent configuration */
+ exclusionDistances_solvt = makeExclusionDistances(atoms_solvt, aps, defaultDistance, scaleFactor);
/* calculate the box multiplication factors n_box[0...DIM] */
nmol = 1;
{
srenew(v_solvt, atoms_solvt->nr*nmol);
}
- srenew(r_solvt, atoms_solvt->nr*nmol);
+ srenew(exclusionDistances_solvt, atoms_solvt->nr*nmol);
/* generate a new solvent configuration */
- make_new_conformation(atoms_solvt, x_solvt, v_solvt, r_solvt, box_solvt, n_box);
+ make_new_conformation(atoms_solvt, x_solvt, v_solvt, exclusionDistances_solvt, box_solvt, n_box);
#ifdef DEBUG
print_stat(x_solvt, atoms_solvt->nr, box_solvt);
print_stat(x_solvt, atoms_solvt->nr, box_solvt);
#endif
/* Sort the solvent mixture, not the protein... */
- sort_molecule(&atoms_solvt, x_solvt, v_solvt, r_solvt);
+ sort_molecule(&atoms_solvt, x_solvt, v_solvt, exclusionDistances_solvt);
/* add the two configurations */
onr = atoms->nr;
onres = atoms->nres;
- add_conf(atoms, x, v, r, TRUE, ePBC, box, FALSE,
- atoms_solvt, x_solvt, v_solvt, r_solvt, TRUE, rshell, max_sol, oenv);
+ add_conf(atoms, x, v, exclusionDistances, TRUE, ePBC, box, FALSE,
+ atoms_solvt, x_solvt, v_solvt, exclusionDistances_solvt, TRUE, rshell, max_sol, oenv);
*atoms_added = atoms->nr-onr;
*residues_added = atoms->nres-onres;
sfree(x_solvt);
- sfree(r_solvt);
+ sfree(exclusionDistances_solvt);
+ done_atom(atoms_solvt);
+ sfree(atoms_solvt);
fprintf(stderr, "Generated solvent containing %d atoms in %d residues\n",
*atoms_added, *residues_added);
if (ftp2bSet(efTOP, NFILE, fnm) )
{
fprintf(stderr, "Processing topology\n");
- fpin = ffopen(topinout, "r");
- fpout = ffopen(TEMP_FILENM, "w");
+ fpin = gmx_ffopen(topinout, "r");
+ fpout = gmx_ffopen(TEMP_FILENM, "w");
line = 0;
bSystem = bMolecules = FALSE;
while (fgets(buf, STRLEN, fpin))
fprintf(fpout, "%s", buf);
}
}
- ffclose(fpin);
+ gmx_ffclose(fpin);
if (nsol)
{
fprintf(stdout, "Adding line for %d solvent molecules to "
"topology file (%s)\n", nsol, topinout);
fprintf(fpout, "%-15s %5d\n", "SOL", nsol);
}
- ffclose(fpout);
- /* use ffopen to generate backup of topinout */
- fpout = ffopen(topinout, "w");
- ffclose(fpout);
+ gmx_ffclose(fpout);
+ /* use gmx_ffopen to generate backup of topinout */
+ fpout = gmx_ffopen(topinout, "w");
+ gmx_ffclose(fpout);
rename(TEMP_FILENM, topinout);
}
#undef TEMP_FILENM
"to change the box dimensions and center the solute.",
"Solvent molecules are removed from the box where the ",
"distance between any atom of the solute molecule(s) and any atom of ",
- "the solvent molecule is less than the sum of the van der Waals radii of ",
- "both atoms. A database ([TT]vdwradii.dat[tt]) of van der Waals radii is ",
- "read by the program, and atoms not in the database are ",
- "assigned a default distance [TT]-vdwd[tt].",
- "Note that this option will also influence the distances between",
- "solvent molecules if they contain atoms that are not in the database.",
- "[PAR]",
+ "the solvent molecule is less than the sum of the scaled van der Waals",
+ "radii of both atoms. A database ([TT]vdwradii.dat[tt]) of van der",
+ "Waals radii is read by the program, and the resulting radii scaled",
+ "by [TT]-scale[tt]. If radii are not found in the database, those"
+ "atoms are assigned the (pre-scaled) distance [TT]-radius[tt].[PAR]",
"The default solvent is Simple Point Charge water (SPC), with coordinates ",
"from [TT]$GMXLIB/spc216.gro[tt]. These coordinates can also be used",
/* parameter data */
gmx_bool bProt, bBox;
const char *conf_prot, *confout;
- real *r;
+ real *exclusionDistances = NULL;
gmx_atomprop_t aps;
/* protein configuration data */
char *title = NULL;
- t_atoms atoms;
- rvec *x, *v = NULL;
+ t_atoms *atoms;
+ rvec *x = NULL, *v = NULL;
int ePBC = -1;
matrix box;
};
#define NFILE asize(fnm)
- static real r_distance = 0.105, r_shell = 0, r_scale = 0.57;
- static rvec new_box = {0.0, 0.0, 0.0};
- static gmx_bool bReadV = FALSE;
- static int max_sol = 0;
+ static real defaultDistance = 0.105, r_shell = 0, scaleFactor = 0.57;
+ static rvec new_box = {0.0, 0.0, 0.0};
+ static gmx_bool bReadV = FALSE;
+ static int max_sol = 0;
output_env_t oenv;
t_pargs pa[] = {
{ "-box", FALSE, etRVEC, {new_box},
"Box size (in nm)" },
- { "-vdwd", FALSE, etREAL, {&r_distance},
+ { "-radius", FALSE, etREAL, {&defaultDistance},
"Default van der Waals distance"},
- { "-vdwscale", FALSE, etREAL, {&r_scale},
- "HIDDENScale factor to multiply Van der Waals radii from the database in share/gromacs/top/vdwradii.dat. The default value of 0.57 yields density close to 1000 g/l for proteins in water." },
+ { "-scale", FALSE, etREAL, {&scaleFactor},
+ "Scale factor to multiply Van der Waals radii from the database in share/gromacs/top/vdwradii.dat. The default value of 0.57 yields density close to 1000 g/l for proteins in water." },
{ "-shell", FALSE, etREAL, {&r_shell},
"Thickness of optional water layer around solute" },
{ "-maxsol", FALSE, etINT, {&max_sol},
"Keep velocities from input solute and solvent" },
};
- if (!parse_common_args(&argc, argv, PCA_BE_NICE, NFILE, fnm, asize(pa), pa,
+ if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
asize(desc), desc, asize(bugs), bugs, &oenv))
{
return 0;
aps = gmx_atomprop_init();
+ snew(atoms, 1);
+ init_t_atoms(atoms, 0, FALSE);
if (bProt)
{
/* Generate a solute configuration */
conf_prot = opt2fn("-cp", NFILE, fnm);
- title = read_conformation(conf_prot, &atoms, &x, bReadV ? &v : NULL, &r, &ePBC, box,
- aps, r_distance, r_scale);
+ title = readConformation(conf_prot, atoms, &x,
+ bReadV ? &v : NULL, &ePBC, box);
+ exclusionDistances = makeExclusionDistances(atoms, aps, defaultDistance, scaleFactor);
+
if (bReadV && !v)
{
fprintf(stderr, "Note: no velocities found\n");
}
- if (atoms.nr == 0)
+ if (atoms->nr == 0)
{
fprintf(stderr, "Note: no atoms in %s\n", conf_prot);
bProt = FALSE;
}
}
- else
- {
- atoms.nr = 0;
- atoms.nres = 0;
- atoms.resinfo = NULL;
- atoms.atomname = NULL;
- atoms.atom = NULL;
- atoms.pdbinfo = NULL;
- x = NULL;
- r = NULL;
- }
if (bBox)
{
ePBC = epbcXYZ;
"or give explicit -box command line option");
}
- add_solv(solventFileName, &atoms, &x, v ? &v : NULL, &r, ePBC, box,
- aps, r_distance, r_scale, &atoms_added, &residues_added, r_shell, max_sol,
+ add_solv(solventFileName, atoms, &x, v ? &v : NULL, &exclusionDistances, ePBC, box,
+ aps, defaultDistance, scaleFactor, &atoms_added, &residues_added, r_shell, max_sol,
oenv);
/* write new configuration 1 to file confout */
fprintf(stderr, "Writing generated configuration to %s\n", confout);
if (bProt)
{
- write_sto_conf(confout, title, &atoms, x, v, ePBC, box);
+ write_sto_conf(confout, title, atoms, x, v, ePBC, box);
/* print box sizes and box type to stderr */
fprintf(stderr, "%s\n", title);
}
else
{
- write_sto_conf(confout, "Generated by gmx solvate", &atoms, x, v, ePBC, box);
+ write_sto_conf(confout, "Generated by gmx solvate", atoms, x, v, ePBC, box);
}
/* print size of generated configuration */
fprintf(stderr, "\nOutput configuration contains %d atoms in %d residues\n",
- atoms.nr, atoms.nres);
- update_top(&atoms, box, NFILE, fnm, aps);
+ atoms->nr, atoms->nres);
+ update_top(atoms, box, NFILE, fnm, aps);
gmx_atomprop_destroy(aps);
+ sfree(exclusionDistances);
+ sfree(x);
+ sfree(v);
+ done_atom(atoms);
+ sfree(atoms);
return 0;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff