* 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 "insert-molecules.h"
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+#include "insert-molecules.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "smalloc.h"
-#include "string2.h"
-#include "gromacs/math/utilities.h"
-#include "gromacs/fileio/confio.h"
-#include "macros.h"
-#include "gromacs/random/random.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/fileio/confio.h"
+#include "gromacs/fileio/xvgr.h"
#include "gromacs/gmxlib/conformation-utilities.h"
-#include "addconf.h"
-#include "read-conformation.h"
-#include "pbc.h"
-#include "xvgr.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/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/random/random.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"
static gmx_bool in_box(t_pbc *pbc, rvec x)
{
* allPairsDistOk is probably even faster than the other code.
*/
static gmx_bool
-allPairsDistOk(t_atoms *atoms, rvec *x, real *r,
+allPairsDistOk(t_atoms *atoms, rvec *x, real *exclusionDistances,
int ePBC, matrix box,
- t_atoms *atoms_insrt, rvec *x_n, real *r_insrt)
+ t_atoms *atoms_insrt, rvec *x_n, real *exclusionDistances_insrt)
{
int i, j;
rvec dx;
{
pbc_dx(&pbc, x[i], x_n[j], dx);
n2 = norm2(dx);
- r2 = sqr(r[i]+r_insrt[j]);
+ r2 = sqr(exclusionDistances[i]+exclusionDistances_insrt[j]);
if (n2 < r2)
{
return FALSE;
};
static char *insert_mols(const char *mol_insrt, int nmol_insrt, int ntry, int seed,
- t_atoms *atoms, rvec **x, real **r, int ePBC, matrix box,
+ t_atoms *atoms, rvec **x, real **exclusionDistances, int ePBC, matrix box,
gmx_atomprop_t aps,
- real r_distance, real r_scale, real rshell,
+ real defaultDistance, real scaleFactor, real rshell,
const output_env_t oenv,
const char* posfn, const rvec deltaR, int enum_rot,
gmx_bool bCheckAllPairDist)
static char *title_insrt;
t_atoms atoms_insrt;
rvec *x_insrt, *x_n;
- real *r_insrt;
+ real *exclusionDistances_insrt;
int ePBC_insrt;
matrix box_insrt;
int i, mol, onr, ncol;
set_pbc(&pbc, ePBC, box);
/* read number of atoms of insert molecules */
- get_stx_coordnum(mol_insrt, &atoms_insrt.nr);
- if (atoms_insrt.nr == 0)
{
- gmx_fatal(FARGS, "No molecule in %s, please check your input\n", mol_insrt);
+ int natoms;
+ get_stx_coordnum(mol_insrt, &natoms);
+ if (natoms == 0)
+ {
+ gmx_fatal(FARGS, "No molecule in %s, please check your input\n", mol_insrt);
+ }
+ init_t_atoms(&atoms_insrt, natoms, FALSE);
}
/* allocate memory for atom coordinates of insert molecules */
snew(x_insrt, atoms_insrt.nr);
- snew(r_insrt, atoms_insrt.nr);
snew(atoms_insrt.resinfo, atoms_insrt.nr);
snew(atoms_insrt.atomname, atoms_insrt.nr);
snew(atoms_insrt.atom, atoms_insrt.nr);
title_insrt, atoms_insrt.nr, atoms_insrt.nres);
srenew(atoms_insrt.resinfo, atoms_insrt.nres);
- /* initialise van der waals arrays for inserted molecules */
- mk_vdw(&atoms_insrt, r_insrt, aps, r_distance, r_scale);
+ /* initialise distance arrays for inserted molecules */
+ exclusionDistances_insrt = makeExclusionDistances(&atoms_insrt, aps, defaultDistance, scaleFactor);
/* With -ip, take nmol_insrt from file posfn */
if (posfn != NULL)
srenew(atoms->atomname, (atoms->nr+atoms_insrt.nr*nmol_insrt));
srenew(atoms->atom, (atoms->nr+atoms_insrt.nr*nmol_insrt));
srenew(*x, (atoms->nr+atoms_insrt.nr*nmol_insrt));
- srenew(*r, (atoms->nr+atoms_insrt.nr*nmol_insrt));
+ srenew(*exclusionDistances, (atoms->nr+atoms_insrt.nr*nmol_insrt));
trial = mol = 0;
while ((mol < nmol_insrt) && (trial < ntry*nmol_insrt))
* even faster than add_conf() when inserting a small molecule into a moderately
* small system.
*/
- if (bCheckAllPairDist && !allPairsDistOk(atoms, *x, *r, ePBC, box, &atoms_insrt, x_n, r_insrt))
+ if (bCheckAllPairDist && !allPairsDistOk(atoms, *x, *exclusionDistances, ePBC, box, &atoms_insrt, x_n, exclusionDistances_insrt))
{
continue;
}
- add_conf(atoms, x, NULL, r, FALSE, ePBC, box, TRUE,
- &atoms_insrt, x_n, NULL, r_insrt, FALSE, rshell, 0, oenv);
+ add_conf(atoms, x, NULL, exclusionDistances, FALSE, ePBC, box, TRUE,
+ &atoms_insrt, x_n, NULL, exclusionDistances_insrt, FALSE, rshell, 0, oenv);
if (atoms->nr == (atoms_insrt.nr+onr))
{
srenew(atoms->atomname, atoms->nr);
srenew(atoms->atom, atoms->nr);
srenew(*x, atoms->nr);
- srenew(*r, atoms->nr);
+ srenew(*exclusionDistances, atoms->nr);
fprintf(stderr, "\n");
/* print number of molecules added */
fprintf(stderr, "Added %d molecules (out of %d requested) of %s\n",
mol, nmol_insrt, *atoms_insrt.resinfo[0].name);
+ sfree(x_n);
+ sfree(exclusionDistances_insrt);
+ done_atom(&atoms_insrt);
+
return title_insrt;
}
"By default, the insertion positions are random (with initial seed",
"specified by [TT]-seed[tt]). The program iterates until [TT]-nmol[tt]",
"molecules have been inserted in the box. Molecules are not inserted",
- "where the distance between any existing atom and any atom of ",
- "the inserted 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].[PAR]",
+ "where the distance between any existing atom and any atom of the",
+ "inserted molecule is less than the sum based on 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 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]",
"A total of [TT]-nmol[tt] * [TT]-try[tt] insertion attempts are made",
"before giving up. Increase [TT]-try[tt] if you have several small",
/* parameter data */
gmx_bool bProt, bBox;
const char *conf_prot, *confout;
- real *r;
- char *title_ins = NULL;
+ real *exclusionDistances = NULL;
+ char *title_ins = NULL;
gmx_atomprop_t aps;
/* protein configuration data */
char *title = NULL;
- t_atoms atoms;
+ t_atoms *atoms;
rvec *x = NULL;
int ePBC = -1;
matrix box;
};
#define NFILE asize(fnm)
- static int nmol_ins = 0, nmol_try = 10, seed = 1997, enum_rot;
- static real r_distance = 0.105, r_scale = 0.57;
- static rvec new_box = {0.0, 0.0, 0.0}, deltaR = {0.0, 0.0, 0.0};
- static gmx_bool bCheckAllPairDist = FALSE;
+ static int nmol_ins = 0, nmol_try = 10, seed = 1997, enum_rot;
+ static real defaultDistance = 0.105, scaleFactor = 0.57;
+ static rvec new_box = {0.0, 0.0, 0.0}, deltaR = {0.0, 0.0, 0.0};
+ static gmx_bool bCheckAllPairDist = FALSE;
output_env_t oenv;
const char *enum_rot_string[] = {NULL, "xyz", "z", "none", NULL};
t_pargs pa[] = {
"Try inserting [TT]-nmol[tt] times [TT]-try[tt] times" },
{ "-seed", FALSE, etINT, {&seed},
"Random generator seed"},
- { "-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." },
{ "-dr", FALSE, etRVEC, {deltaR},
"Allowed displacement in x/y/z from positions in [TT]-ip[tt] file" },
{ "-rot", FALSE, etENUM, {enum_rot_string},
"Avoid momory leaks during neighbor searching with option -ci. May be slow for large systems." },
};
- 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 */
+ /* Generate a solute configuration */
conf_prot = opt2fn("-f", NFILE, fnm);
- title = read_conformation(conf_prot, &atoms, &x, NULL, &r, &ePBC, box,
- aps, r_distance, r_scale);
- if (atoms.nr == 0)
+ title = readConformation(conf_prot, atoms, &x, NULL,
+ &ePBC, box);
+ exclusionDistances = makeExclusionDistances(atoms, aps, defaultDistance, scaleFactor);
+ 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;
/* add nmol_ins molecules of atoms_ins
in random orientation at random place */
title_ins = insert_mols(insertionMoleculeFileName, nmol_ins, nmol_try, seed,
- &atoms, &x, &r, ePBC, box, aps,
- r_distance, r_scale, 0,
+ atoms, &x, &exclusionDistances, ePBC, box, aps,
+ defaultDistance, scaleFactor, 0,
oenv, opt2fn_null("-ip", NFILE, fnm), deltaR, enum_rot,
bCheckAllPairDist);
fprintf(stderr, "Writing generated configuration to %s\n", confout);
if (bProt)
{
- write_sto_conf(confout, title, &atoms, x, NULL, ePBC, box);
+ write_sto_conf(confout, title, atoms, x, NULL, ePBC, box);
/* print box sizes and box type to stderr */
fprintf(stderr, "%s\n", title);
}
else
{
- write_sto_conf(confout, title_ins, &atoms, x, NULL, ePBC, box);
+ write_sto_conf(confout, title_ins, atoms, x, NULL, ePBC, box);
}
/* print size of generated configuration */
fprintf(stderr, "\nOutput configuration contains %d atoms in %d residues\n",
- atoms.nr, atoms.nres);
+ atoms->nr, atoms->nres);
gmx_atomprop_destroy(aps);
+ sfree(exclusionDistances);
+ sfree(x);
+ done_atom(atoms);
+ sfree(atoms);
return 0;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff