#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/strdb.h"
-static real calc_mass(t_atoms *atoms, gmx_bool bGetMass, AtomProperties *aps)
+static real calc_mass(t_atoms* atoms, gmx_bool bGetMass, AtomProperties* aps)
{
real tmass;
int i;
{
if (bGetMass)
{
- aps->setAtomProperty(epropMass,
- std::string(*atoms->resinfo[atoms->atom[i].resind].name),
+ aps->setAtomProperty(epropMass, std::string(*atoms->resinfo[atoms->atom[i].resind].name),
std::string(*atoms->atomname[i]), &(atoms->atom[i].m));
}
tmass += atoms->atom[i].m;
return tmass;
}
-static real calc_geom(int isize, const int *index, rvec *x, rvec geom_center, rvec minval,
- rvec maxval, gmx_bool bDiam)
+static real calc_geom(int isize, const int* index, rvec* x, rvec geom_center, rvec minval, rvec maxval, gmx_bool bDiam)
{
- real diam2, d;
- int ii, i, j;
+ real diam2, d;
+ int ii, i, j;
clear_rvec(geom_center);
diam2 = 0;
return std::sqrt(diam2);
}
-static void center_conf(int natom, rvec *x, rvec center, rvec geom_cent)
+static void center_conf(int natom, rvec* x, rvec center, rvec geom_cent)
{
int i;
rvec shift;
rvec_sub(center, geom_cent, shift);
- printf(" shift :%7.3f%7.3f%7.3f (nm)\n", shift[XX], shift[YY],
- shift[ZZ]);
+ printf(" shift :%7.3f%7.3f%7.3f (nm)\n", shift[XX], shift[YY], shift[ZZ]);
for (i = 0; (i < natom); i++)
{
}
}
-static void read_bfac(const char *fn, int *n_bfac, double **bfac_val, int **bfac_nr)
+static void read_bfac(const char* fn, int* n_bfac, double** bfac_val, int** bfac_nr)
{
int i;
- char **bfac_lines;
+ char** bfac_lines;
*n_bfac = get_lines(fn, &bfac_lines);
snew(*bfac_val, *n_bfac);
{
sscanf(bfac_lines[i], "%d %lf", &(*bfac_nr)[i], &(*bfac_val)[i]);
}
-
}
-static void set_pdb_conf_bfac(int natoms, int nres, t_atoms *atoms, int n_bfac,
- double *bfac, int *bfac_nr, gmx_bool peratom)
+static void set_pdb_conf_bfac(int natoms, int nres, t_atoms* atoms, int n_bfac, double* bfac, int* bfac_nr, gmx_bool peratom)
{
real bfac_min, bfac_max;
int i, n;
{
fprintf(stderr,
"Range of values for B-factors too large (min %g, max %g) "
- "will scale down a factor 10\n", bfac_min, bfac_max);
+ "will scale down a factor 10\n",
+ bfac_min, bfac_max);
for (i = 0; (i < n_bfac); i++)
{
bfac[i] /= 10;
{
fprintf(stderr,
"Range of values for B-factors too small (min %g, max %g) "
- "will scale up a factor 10\n", bfac_min, bfac_max);
+ "will scale up a factor 10\n",
+ bfac_min, bfac_max);
for (i = 0; (i < n_bfac); i++)
{
bfac[i] *= 10;
if (!peratom)
{
- fprintf(stderr, "Will attach %d B-factors to %d residues\n", n_bfac,
- nres);
+ fprintf(stderr, "Will attach %d B-factors to %d residues\n", n_bfac, nres);
for (i = 0; (i < n_bfac); i++)
{
found = FALSE;
}
else
{
- fprintf(stderr, "Will attach %d B-factors to %d atoms\n", n_bfac,
- natoms);
+ fprintf(stderr, "Will attach %d B-factors to %d atoms\n", n_bfac, natoms);
for (i = 0; (i < n_bfac); i++)
{
atoms->pdbinfo[bfac_nr[i] - 1].bfac = bfac[i];
}
}
-static void pdb_legend(FILE *out, int natoms, int nres, t_atoms *atoms, rvec x[])
+static void pdb_legend(FILE* out, int natoms, int nres, t_atoms* atoms, rvec x[])
{
real bfac_min, bfac_max, xmin, ymin, zmin;
int i;
fprintf(stderr, "B-factors range from %g to %g\n", bfac_min, bfac_max);
for (i = 1; (i < 12); i++)
{
- fprintf(out,
- "%-6s%5d %-4.4s%3.3s %c%4d%c %8.3f%8.3f%8.3f%6.2f%6.2f\n",
- "ATOM ", natoms + 1 + i, "CA", "LEG", space, nres + 1, space,
- (xmin + (i * 0.12)) * 10, ymin * 10, zmin * 10, 1.0, bfac_min
- + ((i - 1.0) * (bfac_max - bfac_min) / 10));
+ fprintf(out, "%-6s%5d %-4.4s%3.3s %c%4d%c %8.3f%8.3f%8.3f%6.2f%6.2f\n", "ATOM ",
+ natoms + 1 + i, "CA", "LEG", space, nres + 1, space, (xmin + (i * 0.12)) * 10,
+ ymin * 10, zmin * 10, 1.0, bfac_min + ((i - 1.0) * (bfac_max - bfac_min) / 10));
}
}
-static void visualize_images(const char *fn, int ePBC, matrix box)
+static void visualize_images(const char* fn, int ePBC, matrix box)
{
t_atoms atoms;
- rvec *img;
- char *c, *ala;
+ rvec* img;
+ char * c, *ala;
int nat, i;
nat = NTRICIMG + 1;
sfree(img);
}
-static void visualize_box(FILE *out, int a0, int r0, matrix box, const rvec gridsize)
+static void visualize_box(FILE* out, int a0, int r0, matrix box, const rvec gridsize)
{
- int *edge;
+ int* edge;
rvec *vert, shift;
int nx, ny, nz, nbox, nat;
int i, j, x, y, z;
- int rectedge[24] =
- {
- 0, 1, 1, 3, 3, 2, 0, 2, 0, 4, 1, 5, 3, 7, 2, 6, 4, 5, 5, 7, 7, 6, 6,
- 4
- };
+ int rectedge[24] = { 0, 1, 1, 3, 3, 2, 0, 2, 0, 4, 1, 5, 3, 7, 2, 6, 4, 5, 5, 7, 7, 6, 6, 4 };
a0++;
r0++;
{
for (i = 0; i < DIM; i++)
{
- shift[i] = x * box[0][i] + y * box[1][i] + z
- * box[2][i];
+ shift[i] = x * box[0][i] + y * box[1][i] + z * box[2][i];
}
for (i = 0; i < NCUCVERT; i++)
{
for (i = 0; i < nat; i++)
{
- gmx_fprintf_pdb_atomline(out, epdbATOM, a0 + i, "C", ' ', "BOX", 'K' + i / NCUCVERT, r0 + i, ' ',
- 10*vert[i][XX], 10*vert[i][YY], 10*vert[i][ZZ], 1.0, 0.0, "");
+ gmx_fprintf_pdb_atomline(out, epdbATOM, a0 + i, "C", ' ', "BOX", 'K' + i / NCUCVERT,
+ r0 + i, ' ', 10 * vert[i][XX], 10 * vert[i][YY],
+ 10 * vert[i][ZZ], 1.0, 0.0, "");
}
edge = compact_unitcell_edges();
{
for (x = 0; x <= 1; x++)
{
- gmx_fprintf_pdb_atomline(out, epdbATOM, a0 + i, "C", ' ', "BOX", 'K' + i/8, r0+i, ' ',
- x * 10 * box[XX][XX], y * 10 * box[YY][YY], z * 10 * box[ZZ][ZZ], 1.0, 0.0, "");
+ gmx_fprintf_pdb_atomline(out, epdbATOM, a0 + i, "C", ' ', "BOX", 'K' + i / 8,
+ r0 + i, ' ', x * 10 * box[XX][XX], y * 10 * box[YY][YY],
+ z * 10 * box[ZZ][ZZ], 1.0, 0.0, "");
i++;
}
}
real ux, uy, uz, costheta, sintheta;
costheta = cos_angle(principal_axis, targetvec);
- sintheta = std::sqrt(1.0
-costheta*costheta); /* sign is always positive since 0<theta<pi */
+ sintheta = std::sqrt(1.0
- costheta * costheta); /* sign is always positive since 0<theta<pi */
/* Determine rotation from cross product with target vector */
cprod(principal_axis, targetvec, rotvec);
unitv(rotvec, rotvec);
- printf("Aligning %g %g %g to %g %g %g : xprod %g %g %g\n",
- principal_axis[XX], principal_axis[YY], principal_axis[ZZ], targetvec[XX], targetvec[YY], targetvec[ZZ],
+ printf("Aligning %g %g %g to %g %g %g : xprod %g %g %g\n", principal_axis[XX],
+ principal_axis[YY], principal_axis[ZZ], targetvec[XX], targetvec[YY], targetvec[ZZ],
rotvec[XX], rotvec[YY], rotvec[ZZ]);
ux = rotvec[XX];
uy = rotvec[YY];
uz = rotvec[ZZ];
- rotmatrix[0][0] = ux*ux + (1.0-ux*ux)*costheta;
- rotmatrix[0][1] = ux*uy*(1-costheta)-uz*sintheta;
- rotmatrix[0][2] = ux*uz*(1-costheta)+uy*sintheta;
- rotmatrix[1][0] = ux*uy*(1-costheta)+uz*sintheta;
- rotmatrix[1][1] = uy*uy + (1.0-uy*uy)*costheta;
- rotmatrix[1][2] = uy*uz*(1-costheta)-ux*sintheta;
- rotmatrix[2][0] = ux*uz*(1-costheta)-uy*sintheta;
- rotmatrix[2][1] = uy*uz*(1-costheta)+ux*sintheta;
- rotmatrix[2][2] = uz*uz + (1.0-uz*uz)*costheta;
-
- printf("Rotation matrix: \n%g %g %g\n%g %g %g\n%g %g %g\n",
- rotmatrix[0][0], rotmatrix[0][1], rotmatrix[0][2],
- rotmatrix[1][0], rotmatrix[1][1], rotmatrix[1][2],
- rotmatrix[2][0], rotmatrix[2][1], rotmatrix[2][2]);
+ rotmatrix[0][0] = ux * ux + (1.0 - ux * ux) * costheta;
+ rotmatrix[0][1] = ux * uy * (1 - costheta) - uz * sintheta;
+ rotmatrix[0][2] = ux * uz * (1 - costheta) + uy * sintheta;
+ rotmatrix[1][0] = ux * uy * (1 - costheta) + uz * sintheta;
+ rotmatrix[1][1] = uy * uy + (1.0 - uy * uy) * costheta;
+ rotmatrix[1][2] = uy * uz * (1 - costheta) - ux * sintheta;
+ rotmatrix[2][0] = ux * uz * (1 - costheta) - uy * sintheta;
+ rotmatrix[2][1] = uy * uz * (1 - costheta) + ux * sintheta;
+ rotmatrix[2][2] = uz * uz + (1.0 - uz * uz) * costheta;
+
+ printf("Rotation matrix: \n%g %g %g\n%g %g %g\n%g %g %g\n", rotmatrix[0][0], rotmatrix[0][1],
+ rotmatrix[0][2], rotmatrix[1][0], rotmatrix[1][1], rotmatrix[1][2], rotmatrix[2][0],
+ rotmatrix[2][1], rotmatrix[2][2]);
}
-static void renum_resnr(t_atoms *atoms, int isize, const int *index,
- int resnr_start)
+static void renum_resnr(t_atoms* atoms, int isize, const int* index, int resnr_start)
{
int i, resind_prev, resind;
}
}
-int gmx_editconf(int argc, char *argv[])
+int gmx_editconf(int argc, char* argv[])
{
- const char *desc[] =
- {
+ const char* desc[] = {
"[THISMODULE] converts generic structure format to [REF].gro[ref], [TT].g96[tt]",
"or [REF].pdb[ref].",
"[PAR]",
"Option [TT]-box[tt] requires only",
"one value for a cubic, rhombic dodecahedral, or truncated octahedral box.",
"[PAR]",
- "With [TT]-d[tt] and a [TT]triclinic[tt] box the size of the system in the [IT]x[it]-, [IT]y[it]-,",
+ "With [TT]-d[tt] and a [TT]triclinic[tt] box the size of the system in the [IT]x[it]-, ",
+ "[IT]y[it]-,",
"and [IT]z[it]-directions is used. With [TT]-d[tt] and [TT]cubic[tt],",
"[TT]dodecahedron[tt] or [TT]octahedron[tt] boxes, the dimensions are set",
"to the diameter of the system (largest distance between atoms) plus twice",
"",
"where [TT]veclen[tt] is the size of the cubic box times [SQRT]3[sqrt]/2."
};
- const char *bugs[] =
- {
- "For complex molecules, the periodicity removal routine may break down, "
+ const char* bugs[] = {
+ "For complex molecules, the periodicity removal routine may break down, ",
"in that case you can use [gmx-trjconv]."
};
- static real dist = 0.0;
- static gmx_bool bNDEF = FALSE, bRMPBC = FALSE, bCenter = FALSE, bReadVDW =
- FALSE, bCONECT = FALSE;
- static gmx_bool peratom = FALSE, bLegend = FALSE, bOrient = FALSE, bMead =
- FALSE, bGrasp = FALSE, bSig56 = FALSE;
- static rvec scale =
- { 1, 1, 1 }, newbox =
- { 0, 0, 0 }, newang =
- { 90, 90, 90 };
- static real rho = 1000.0, rvdw = 0.12;
- static rvec center =
- { 0, 0, 0 }, translation =
- { 0, 0, 0 }, rotangles =
- { 0, 0, 0 }, aligncenter =
- { 0, 0, 0 }, targetvec =
- { 0, 0, 0 };
- static const char *btype[] =
- { nullptr, "triclinic", "cubic", "dodecahedron", "octahedron", nullptr },
- *label = "A";
- static rvec visbox =
- { 0, 0, 0 };
- static int resnr_start = -1;
- t_pargs
- pa[] =
- {
- { "-ndef", FALSE, etBOOL,
- { &bNDEF }, "Choose output from default index groups" },
- { "-visbox", FALSE, etRVEC,
+ static real dist = 0.0;
+ static gmx_bool bNDEF = FALSE, bRMPBC = FALSE, bCenter = FALSE, bReadVDW = FALSE, bCONECT = FALSE;
+ static gmx_bool peratom = FALSE, bLegend = FALSE, bOrient = FALSE, bMead = FALSE,
+ bGrasp = FALSE, bSig56 = FALSE;
+ static rvec scale = { 1, 1, 1 }, newbox = { 0, 0, 0 }, newang = { 90, 90, 90 };
+ static real rho = 1000.0, rvdw = 0.12;
+ static rvec center = { 0, 0, 0 }, translation = { 0, 0, 0 }, rotangles = { 0, 0, 0 },
+ aligncenter = { 0, 0, 0 }, targetvec = { 0, 0, 0 };
+ static const char *btype[] = { nullptr, "triclinic", "cubic",
+ "dodecahedron", "octahedron", nullptr },
+ *label = "A";
+ static rvec visbox = { 0, 0, 0 };
+ static int resnr_start = -1;
+ t_pargs pa[] = {
+ { "-ndef", FALSE, etBOOL, { &bNDEF }, "Choose output from default index groups" },
+ { "-visbox",
+ FALSE,
+ etRVEC,
{ visbox },
"HIDDENVisualize a grid of boxes, -1 visualizes the 14 box images" },
- { "-bt", FALSE, etENUM,
- { btype }, "Box type for [TT]-box[tt] and [TT]-d[tt]" },
- { "-box", FALSE, etRVEC,
- { newbox }, "Box vector lengths (a,b,c)" },
- { "-angles", FALSE, etRVEC,
- { newang }, "Angles between the box vectors (bc,ac,ab)" },
- { "-d", FALSE, etREAL,
- { &dist }, "Distance between the solute and the box" },
- { "-c", FALSE, etBOOL,
+ { "-bt", FALSE, etENUM, { btype }, "Box type for [TT]-box[tt] and [TT]-d[tt]" },
+ { "-box", FALSE, etRVEC, { newbox }, "Box vector lengths (a,b,c)" },
+ { "-angles", FALSE, etRVEC, { newang }, "Angles between the box vectors (bc,ac,ab)" },
+ { "-d", FALSE, etREAL, { &dist }, "Distance between the solute and the box" },
+ { "-c",
+ FALSE,
+ etBOOL,
{ &bCenter },
"Center molecule in box (implied by [TT]-box[tt] and [TT]-d[tt])" },
- { "-center", FALSE, etRVEC,
- { center }, "Shift the geometrical center to (x,y,z)" },
- { "-aligncenter", FALSE, etRVEC,
- { aligncenter }, "Center of rotation for alignment" },
- { "-align", FALSE, etRVEC,
- { targetvec },
- "Align to target vector" },
- { "-translate", FALSE, etRVEC,
- { translation }, "Translation" },
- { "-rotate", FALSE, etRVEC,
+ { "-center", FALSE, etRVEC, { center }, "Shift the geometrical center to (x,y,z)" },
+ { "-aligncenter", FALSE, etRVEC, { aligncenter }, "Center of rotation for alignment" },
+ { "-align", FALSE, etRVEC, { targetvec }, "Align to target vector" },
+ { "-translate", FALSE, etRVEC, { translation }, "Translation" },
+ { "-rotate",
+ FALSE,
+ etRVEC,
{ rotangles },
"Rotation around the X, Y and Z axes in degrees" },
- { "-princ", FALSE, etBOOL,
- { &bOrient },
- "Orient molecule(s) along their principal axes" },
- { "-scale", FALSE, etRVEC,
- { scale }, "Scaling factor" },
- { "-density", FALSE, etREAL,
+ { "-princ", FALSE, etBOOL, { &bOrient }, "Orient molecule(s) along their principal axes" },
+ { "-scale", FALSE, etRVEC, { scale }, "Scaling factor" },
+ { "-density",
+ FALSE,
+ etREAL,
{ &rho },
"Density (g/L) of the output box achieved by scaling" },
- { "-pbc", FALSE, etBOOL,
- { &bRMPBC },
- "Remove the periodicity (make molecule whole again)" },
- { "-resnr", FALSE, etINT,
- { &resnr_start },
- " Renumber residues starting from resnr" },
- { "-grasp", FALSE, etBOOL,
+ { "-pbc", FALSE, etBOOL, { &bRMPBC }, "Remove the periodicity (make molecule whole again)" },
+ { "-resnr", FALSE, etINT, { &resnr_start }, " Renumber residues starting from resnr" },
+ { "-grasp",
+ FALSE,
+ etBOOL,
{ &bGrasp },
- "Store the charge of the atom in the B-factor field and the radius of the atom in the occupancy field" },
- {
- "-rvdw", FALSE, etREAL,
- { &rvdw },
- "Default Van der Waals radius (in nm) if one can not be found in the database or if no parameters are present in the topology file"
- },
- { "-sig56", FALSE, etBOOL,
+ "Store the charge of the atom in the B-factor field and the radius of the atom in the "
+ "occupancy field" },
+ { "-rvdw",
+ FALSE,
+ etREAL,
+ { &rvdw },
+ "Default Van der Waals radius (in nm) if one can not be found in the database or if no "
+ "parameters are present in the topology file" },
+ { "-sig56",
+ FALSE,
+ etBOOL,
{ &bSig56 },
"Use rmin/2 (minimum in the Van der Waals potential) rather than [GRK]sigma[grk]/2 " },
- {
- "-vdwread", FALSE, etBOOL,
- { &bReadVDW },
- "Read the Van der Waals radii from the file [TT]vdwradii.dat[tt] rather than computing the radii based on the force field"
- },
- { "-atom", FALSE, etBOOL,
- { &peratom }, "Force B-factor attachment per atom" },
- { "-legend", FALSE, etBOOL,
- { &bLegend }, "Make B-factor legend" },
- { "-label", FALSE, etSTR,
- { &label }, "Add chain label for all residues" },
- {
- "-conect", FALSE, etBOOL,
- { &bCONECT },
- "Add CONECT records to a [REF].pdb[ref] file when written. Can only be done when a topology is present"
- }
+ { "-vdwread",
+ FALSE,
+ etBOOL,
+ { &bReadVDW },
+ "Read the Van der Waals radii from the file [TT]vdwradii.dat[tt] rather than computing "
+ "the radii based on the force field" },
+ { "-atom", FALSE, etBOOL, { &peratom }, "Force B-factor attachment per atom" },
+ { "-legend", FALSE, etBOOL, { &bLegend }, "Make B-factor legend" },
+ { "-label", FALSE, etSTR, { &label }, "Add chain label for all residues" },
+ { "-conect",
+ FALSE,
+ etBOOL,
+ { &bCONECT },
+ "Add CONECT records to a [REF].pdb[ref] file when written. Can only be done when a "
+ "topology is present" }
};
#define NPA asize(pa)
- FILE *out;
- const char *infile, *outfile;
+ FILE* out;
+ const char * infile, *outfile;
int outftp, inftp, natom, i, j, n_bfac, itype, ntype;
- double *bfac = nullptr, c6, c12;
- int *bfac_nr = nullptr;
- t_topology *top = nullptr;
- char *grpname, *sgrpname, *agrpname;
+ double * bfac = nullptr, c6, c12;
+ int* bfac_nr = nullptr;
+ t_topology* top = nullptr;
+ char * grpname, *sgrpname, *agrpname;
int isize, ssize, numAlignmentAtoms;
- int *index, *sindex, *aindex;
- rvec *x, *v, gc, rmin, rmax, size;
+ int * index, *sindex, *aindex;
+ rvec * x, *v, gc, rmin, rmax, size;
int ePBC;
matrix box, rotmatrix, trans;
rvec princd, tmpvec;
gmx_bool bHaveV, bScale, bRho, bTranslate, bRotate, bCalcGeom, bCalcDiam;
real diam = 0, mass = 0, d, vdw;
gmx_conect conect;
- gmx_output_env_t *oenv;
- t_filenm fnm[] =
- {
- { efSTX, "-f", nullptr, ffREAD },
- { efNDX, "-n", nullptr, ffOPTRD },
- { efSTO, nullptr, nullptr, ffOPTWR },
- { efPQR, "-mead", "mead", ffOPTWR },
- { efDAT, "-bf", "bfact", ffOPTRD }
- };
+ gmx_output_env_t* oenv;
+ t_filenm fnm[] = { { efSTX, "-f", nullptr, ffREAD },
+ { efNDX, "-n", nullptr, ffOPTRD },
+ { efSTO, nullptr, nullptr, ffOPTWR },
+ { efPQR, "-mead", "mead", ffOPTWR },
+ { efDAT, "-bf", "bfact", ffOPTRD } };
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW, NFILE, fnm, NPA, pa,
- asize(desc), desc, asize(bugs), bugs, &oenv))
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW, NFILE, fnm, NPA, pa, asize(desc), desc,
+ asize(bugs), bugs, &oenv))
{
return 0;
}
- fprintf(stdout, "Note that major changes are planned in future for "
+ fprintf(stdout,
+ "Note that major changes are planned in future for "
"editconf, to improve usability and utility.\n");
bIndex = opt2bSet("-n", NFILE, fnm) || bNDEF;
}
if (bGrasp && (outftp != efPDB))
{
- gmx_fatal(FARGS, "Output file should be a .pdb file"
+ gmx_fatal(FARGS,
+ "Output file should be a .pdb file"
" when using the -grasp option\n");
}
if ((bMead || bGrasp) && (fn2ftp(infile) != efTPR))
{
- gmx_fatal(FARGS, "Input file should be a .tpr file"
+ gmx_fatal(FARGS,
+ "Input file should be a .tpr file"
" when using the -mead option\n");
}
- t_symtab symtab;
- char *name;
- t_atoms atoms;
+ t_symtab symtab;
+ char* name;
+ t_atoms atoms;
open_symtab(&symtab);
readConfAndAtoms(infile, &symtab, &name, &atoms, &ePBC, &x, &v, box);
natom = atoms.nr;
if (ePBC != epbcNONE)
{
real vol = det(box);
- printf("Volume: %g nm^3, corresponds to roughly %d electrons\n",
- vol, 100*(static_cast<int>(vol*4.5)));
+ printf("Volume: %g nm^3, corresponds to roughly %d electrons\n", vol,
+ 100 * (static_cast<int>(vol * 4.5)));
}
if (bMead || bGrasp || bCONECT)
/* Determine the Van der Waals radius from the force field */
if (bReadVDW)
{
- if (!aps.setAtomProperty(epropVDW,
- *top->atoms.resinfo[top->atoms.atom[i].resind].name,
+ if (!aps.setAtomProperty(epropVDW, *top->atoms.resinfo[top->atoms.atom[i].resind].name,
*top->atoms.atomname[i], &vdw))
{
vdw = rvdw;
else
{
itype = top->atoms.atom[i].type;
- c12 = top->idef.iparams[itype*ntype+itype].lj.c12;
- c6 = top->idef.iparams[itype*ntype+itype].lj.c6;
+ c12 = top->idef.iparams[itype * ntype + itype].lj.c12;
+ c6 = top->idef.iparams[itype * ntype + itype].lj.c6;
if ((c6 != 0) && (c12 != 0))
{
real sig6;
if (bSig56)
{
- sig6 = 2*c12/c6;
+ sig6 = 2 * c12 / c6;
}
else
{
- sig6 = c12/c6;
+ sig6 = c12 / c6;
}
- vdw = 0.5*gmx::sixthroot(sig6);
+ vdw = 0.5 * gmx::sixthroot(sig6);
}
else
{
if (bIndex)
{
fprintf(stderr, "\nSelect a group for determining the system size:\n");
- get_index(&atoms, ftp2fn_null(efNDX, NFILE, fnm),
- 1, &ssize, &sindex, &sgrpname);
+ get_index(&atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &ssize, &sindex, &sgrpname);
}
else
{
}
diam = calc_geom(ssize, sindex, x, gc, rmin, rmax, bCalcDiam);
rvec_sub(rmax, rmin, size);
- printf(" system size :%7.3f%7.3f%7.3f (nm)\n",
- size[XX], size[YY], size[ZZ]);
+ printf(" system size :%7.3f%7.3f%7.3f (nm)\n", size[XX], size[YY], size[ZZ]);
if (bCalcDiam)
{
printf(" diameter :%7.3f (nm)\n", diam);
}
printf(" center :%7.3f%7.3f%7.3f (nm)\n", gc[XX], gc[YY], gc[ZZ]);
- printf(" box vectors :%7.3f%7.3f%7.3f (nm)\n",
- norm(box[XX]), norm(box[YY]), norm(box[ZZ]));
+ printf(" box vectors :%7.3f%7.3f%7.3f (nm)\n", norm(box[XX]), norm(box[YY]), norm(box[ZZ]));
printf(" box angles :%7.2f%7.2f%7.2f (degrees)\n",
- norm2(box[ZZ]) == 0 ? 0 :
- RAD2DEG*gmx_angle(box[YY], box[ZZ]),
- norm2(box[ZZ]) == 0 ? 0 :
- RAD2DEG*gmx_angle(box[XX], box[ZZ]),
- norm2(box[YY]) == 0 ? 0 :
- RAD2DEG*gmx_angle(box[XX], box[YY]));
+ norm2(box[ZZ]) == 0 ? 0 : RAD2DEG * gmx_angle(box[YY], box[ZZ]),
+ norm2(box[ZZ]) == 0 ? 0 : RAD2DEG * gmx_angle(box[XX], box[ZZ]),
+ norm2(box[YY]) == 0 ? 0 : RAD2DEG * gmx_angle(box[XX], box[YY]));
printf(" box volume :%7.2f (nm^3)\n", det(box));
}
if (bOrient)
{
- int *index;
- char *grpnames;
+ int* index;
+ char* grpnames;
/* Get a group for principal component analysis */
fprintf(stderr, "\nSelect group for the determining the orientation\n");
real vol, dens;
vol = det(box);
- dens = (mass*AMU)/(vol*NANO*NANO*NANO);
+ dens = (mass * AMU) / (vol * NANO * NANO * NANO);
fprintf(stderr, "Volume of input %g (nm^3)\n", vol);
fprintf(stderr, "Mass of input %g (a.m.u.)\n", mass);
fprintf(stderr, "Density of input %g (g/l)\n", dens);
if (vol == 0 || mass == 0)
{
- gmx_fatal(FARGS, "Cannot scale density with "
- "zero mass (%g) or volume (%g)\n", mass, vol);
+ gmx_fatal(FARGS,
+ "Cannot scale density with "
+ "zero mass (%g) or volume (%g)\n",
+ mass, vol);
}
- scale[XX] = scale[YY] = scale[ZZ] = std::cbrt(dens/rho);
+ scale[XX] = scale[YY] = scale[ZZ] = std::cbrt(dens / rho);
fprintf(stderr, "Scaling all box vectors by %g\n", scale[XX]);
}
scale_conf(atoms.nr, x, box, scale);
if (bIndex)
{
fprintf(stderr, "\nSelect a group that you want to align:\n");
- get_index(&atoms, ftp2fn_null(efNDX, NFILE, fnm),
- 1, &numAlignmentAtoms, &aindex, &agrpname);
+ get_index(&atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &numAlignmentAtoms, &aindex, &agrpname);
}
else
{
aindex[i] = i;
}
}
- printf("Aligning %d atoms (out of %d) to %g %g %g, center of rotation %g %g %g\n", numAlignmentAtoms, natom,
- targetvec[XX], targetvec[YY], targetvec[ZZ],
+ printf("Aligning %d atoms (out of %d) to %g %g %g, center of rotation %g %g %g\n",
+ numAlignmentAtoms, natom, targetvec[XX], targetvec[YY], targetvec[ZZ],
aligncenter[XX], aligncenter[YY], aligncenter[ZZ]);
/*subtract out pivot point*/
for (i = 0; i < numAlignmentAtoms; i++)
unitv(targetvec, targetvec);
printf("Using %g %g %g as principal axis\n", trans[0][2], trans[1][2], trans[2][2]);
- tmpvec[XX] = trans[0][2]; tmpvec[YY] = trans[1][2]; tmpvec[ZZ] = trans[2][2];
+ tmpvec[XX] = trans[0][2];
+ tmpvec[YY] = trans[1][2];
+ tmpvec[ZZ] = trans[2][2];
calc_rotmatrix(tmpvec, targetvec, rotmatrix);
/* rotmatrix finished */
if (bIndex)
{
fprintf(stderr, "\nSelect a group that you want to translate:\n");
- get_index(&atoms, ftp2fn_null(efNDX, NFILE, fnm),
- 1, &ssize, &sindex, &sgrpname);
+ get_index(&atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &ssize, &sindex, &sgrpname);
}
else
{
ssize = atoms.nr;
sindex = nullptr;
}
- printf("Translating %d atoms (out of %d) by %g %g %g nm\n", ssize, natom,
- translation[XX], translation[YY], translation[ZZ]);
+ printf("Translating %d atoms (out of %d) by %g %g %g nm\n", ssize, natom, translation[XX],
+ translation[YY], translation[ZZ]);
if (sindex)
{
for (i = 0; i < ssize; i++)
if (bRotate)
{
/* Rotate */
- printf("Rotating %g, %g, %g degrees around the X, Y and Z axis respectively\n", rotangles[XX], rotangles[YY], rotangles[ZZ]);
+ printf("Rotating %g, %g, %g degrees around the X, Y and Z axis respectively\n",
+ rotangles[XX], rotangles[YY], rotangles[ZZ]);
for (i = 0; i < DIM; i++)
{
rotangles[i] *= DEG2RAD;
rvec_sub(rmax, rmin, size);
if (bScale || bOrient || bRotate)
{
- printf("new system size : %6.3f %6.3f %6.3f\n",
- size[XX], size[YY], size[ZZ]);
+ printf("new system size : %6.3f %6.3f %6.3f\n", size[XX], size[YY], size[ZZ]);
}
}
{
for (i = 0; i < DIM; i++)
{
- newbox[i] = size[i]+2*dist;
+ newbox[i] = size[i] + 2 * dist;
}
}
if (!bSetAng)
}
else
{
- d = diam+2*dist;
+ d = diam + 2 * dist;
}
if (btype[0][0] == 'c')
{
{
box[XX][XX] = d;
box[YY][YY] = d;
- box[ZZ][XX] = d/2;
- box[ZZ][YY] = d/2;
- box[ZZ][ZZ] = d*std::sqrt(2.0)/2.0;
+ box[ZZ][XX] = d / 2;
+ box[ZZ][YY] = d / 2;
+ box[ZZ][ZZ] = d * std::sqrt(2.0) / 2.0;
}
else
{
box[XX][XX] = d;
- box[YY][XX] = d/3;
- box[YY][YY] = d*std::sqrt(2.0)*2.0/3.0;
- box[ZZ][XX] = -d/3;
- box[ZZ][YY] = d*std::sqrt(2.0)/3.0;
- box[ZZ][ZZ] = d*std::sqrt(6.0)/3.0;
+ box[YY][XX] = d / 3;
+ box[YY][YY] = d * std::sqrt(2.0) * 2.0 / 3.0;
+ box[ZZ][XX] = -d / 3;
+ box[ZZ][YY] = d * std::sqrt(2.0) / 3.0;
+ box[ZZ][ZZ] = d * std::sqrt(6.0) / 3.0;
}
break;
}
}
if (bOrient || bScale || bDist || bSetSize)
{
- printf("new box vectors :%7.3f%7.3f%7.3f (nm)\n",
- norm(box[XX]), norm(box[YY]), norm(box[ZZ]));
+ printf("new box vectors :%7.3f%7.3f%7.3f (nm)\n", norm(box[XX]), norm(box[YY]), norm(box[ZZ]));
printf("new box angles :%7.2f%7.2f%7.2f (degrees)\n",
- norm2(box[ZZ]) == 0 ? 0 :
- RAD2DEG*gmx_angle(box[YY], box[ZZ]),
- norm2(box[ZZ]) == 0 ? 0 :
- RAD2DEG*gmx_angle(box[XX], box[ZZ]),
- norm2(box[YY]) == 0 ? 0 :
- RAD2DEG*gmx_angle(box[XX], box[YY]));
+ norm2(box[ZZ]) == 0 ? 0 : RAD2DEG * gmx_angle(box[YY], box[ZZ]),
+ norm2(box[ZZ]) == 0 ? 0 : RAD2DEG * gmx_angle(box[XX], box[ZZ]),
+ norm2(box[YY]) == 0 ? 0 : RAD2DEG * gmx_angle(box[XX], box[YY]));
printf("new box volume :%7.2f (nm^3)\n", det(box));
}
printf("\nWARNING: Your box is triclinic with non-orthogonal axes. In this case, the\n"
"distance from the solute to a box surface along the corresponding normal\n"
"vector might be somewhat smaller than your specified value %f.\n"
- "You can check the actual value with g_mindist -pi\n", dist);
+ "You can check the actual value with g_mindist -pi\n",
+ dist);
}
else if (!opt2parg_bSet("-bt", NPA, pa))
{
- printf("\nWARNING: No boxtype specified - distance condition applied in each dimension.\n"
+ printf("\nWARNING: No boxtype specified - distance condition applied in each "
+ "dimension.\n"
"If the molecule rotates the actual distance will be smaller. You might want\n"
"to use a cubic box instead, or why not try a dodecahedron today?\n");
}
if (bIndex)
{
fprintf(stderr, "\nSelect a group for output:\n");
- get_index(&atoms, opt2fn_null("-n", NFILE, fnm),
- 1, &isize, &index, &grpname);
+ get_index(&atoms, opt2fn_null("-n", NFILE, fnm), 1, &isize, &index, &grpname);
if (resnr_start >= 0)
{
out = gmx_ffopen(outfile, "w");
if (bMead)
{
- fprintf(out, "REMARK "
+ fprintf(out,
+ "REMARK "
"The B-factors in this file hold atomic radii\n");
- fprintf(out, "REMARK "
+ fprintf(out,
+ "REMARK "
"The occupancy in this file hold atomic charges\n");
}
else if (bGrasp)
{
fprintf(out, "GRASP PDB FILE\nFORMAT NUMBER=1\n");
- fprintf(out, "REMARK "
+ fprintf(out,
+ "REMARK "
"The B-factors in this file hold atomic charges\n");
- fprintf(out, "REMARK "
+ fprintf(out,
+ "REMARK "
"The occupancy in this file hold atomic radii\n");
}
else if (opt2bSet("-bf", NFILE, fnm))
{
read_bfac(opt2fn("-bf", NFILE, fnm), &n_bfac, &bfac, &bfac_nr);
- set_pdb_conf_bfac(atoms.nr, atoms.nres, &atoms,
- n_bfac, bfac, bfac_nr, peratom);
+ set_pdb_conf_bfac(atoms.nr, atoms.nres, &atoms, n_bfac, bfac, bfac_nr, peratom);
}
if (opt2parg_bSet("-label", NPA, pa))
{
/* Need to bypass the regular write_pdbfile because I don't want to change
* all instances to include the boolean flag for writing out PQR files.
*/
- int *index;
+ int* index;
snew(index, atoms.nr);
for (int i = 0; i < atoms.nr; i++)
{
}
if (visbox[0] > 0)
{
- visualize_box(out, bLegend ? atoms.nr+12 : atoms.nr,
+ visualize_box(out, bLegend ? atoms.nr + 12 : atoms.nr,
bLegend ? atoms.nres = 12 : atoms.nres, box, visbox);
}
gmx_ffclose(out);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff