static void do_sham(const char *fn, const char *ndx,
const char *xpmP, const char *xpm, const char *xpm2,
const char *xpm3, const char *xpm4, const char *pdb,
const char *logf,
int n, int neig, real **eig,
gmx_bool bGE, int nenerT, real **enerT,
int nmap, real *mapindex, real **map,
real Tref,
real pmax, real gmax,
real *emin, real *emax, int nlevels, real pmin,
const char *mname, gmx_bool bSham, int *idim, int *ibox,
gmx_bool bXmin, real *xmin, gmx_bool bXmax, real *xmax)
{
FILE *fp;
real *min_eig, *max_eig;
real *axis_x, *axis_y, *axis_z, *axis = NULL;
double *P;
real **PP, *W, *E, **WW, **EE, *S, **SS, *M, **MM, *bE;
rvec xxx;
char *buf;
double *bfac, efac, bref, Pmax, Wmin, Wmax, Winf, Emin, Emax, Einf, Smin, Smax, Sinf, Mmin, Mmax, Minf;
real *delta;
int i, j, k, imin, len, index, d, *nbin, *bindex, bi;
int *nxyz, maxbox;
t_blocka *b;
gmx_bool bOutside;
unsigned int flags;
t_rgb rlo = { 0, 0, 0 };
t_rgb rhi = { 1, 1, 1 };
/* Determine extremes for the eigenvectors */
snew(min_eig, neig);
snew(max_eig, neig);
snew(nxyz, neig);
snew(bfac, neig);
snew(delta, neig);
for (i = 0; (i < neig); i++)
{
/* Check for input constraints */
min_eig[i] = max_eig[i] = eig[i][0];
for (j = 0; (j < n); j++)
{
min_eig[i] = min(min_eig[i], eig[i][j]);
max_eig[i] = max(max_eig[i], eig[i][j]);
delta[i] = (max_eig[i]-min_eig[i])/(2.0*ibox[i]);
}
/* Add some extra space, half a bin on each side, unless the
* user has set the limits.
*/
if (bXmax)
{
if (max_eig[i] > xmax[i])
{
gmx_warning("Your xmax[%d] value %f is smaller than the largest data point %f", i, xmax[i], max_eig[i]);
}
max_eig[i] = xmax[i];
}
else
{
max_eig[i] += delta[i];
}
if (bXmin)
{
if (min_eig[i] < xmin[i])
{
gmx_warning("Your xmin[%d] value %f is larger than the smallest data point %f", i, xmin[i], min_eig[i]);
}
min_eig[i] = xmin[i];
}
else
{
min_eig[i] -= delta[i];
}
bfac[i] = ibox[i]/(max_eig[i]-min_eig[i]);
}
/* Do the binning */
bref = 1/(BOLTZ*Tref);
snew(bE, n);
if (bGE || nenerT == 2)
{
Emin = 1e8;
for (j = 0; (j < n); j++)
{
if (bGE)
{
bE[j] = bref*enerT[0][j];
}
else
{
bE[j] = (bref - 1/(BOLTZ*enerT[1][j]))*enerT[0][j];
}
Emin = min(Emin, bE[j]);
}
}
else
{
Emin = 0;
}
len = 1;
for (i = 0; (i < neig); i++)
{
len = len*ibox[i];
}
printf("There are %d bins in the %d-dimensional histogram. Beta-Emin = %g\n",
len, neig, Emin);
snew(P, len);
snew(W, len);
snew(E, len);
snew(S, len);
snew(M, len);
snew(nbin, len);
snew(bindex, n);
/* Loop over projections */
for (j = 0; (j < n); j++)
{
/* Loop over dimensions */
bOutside = FALSE;
for (i = 0; (i < neig); i++)
{
nxyz[i] = bfac[i]*(eig[i][j]-min_eig[i]);
if (nxyz[i] < 0 || nxyz[i] >= ibox[i])
{
bOutside = TRUE;
}
}
if (!bOutside)
{
index = indexn(neig, ibox, nxyz);
range_check(index, 0, len);
/* Compute the exponential factor */
if (enerT)
{
efac = exp(-bE[j]+Emin);
}
else
{
efac = 1;
}
/* Apply the bin volume correction for a multi-dimensional distance */
for (i = 0; i < neig; i++)
{
if (idim[i] == 2)
{
efac /= eig[i][j];
}
else if (idim[i] == 3)
{
efac /= sqr(eig[i][j]);
}
else if (idim[i] == -1)
{
efac /= sin(DEG2RAD*eig[i][j]);
}
}
/* Update the probability */
P[index] += efac;
/* Update the energy */
if (enerT)
{
E[index] += enerT[0][j];
}
/* Statistics: which "structure" in which bin */
nbin[index]++;
bindex[j] = index;
}
}
/* Normalize probability */
normalize_p_e(len, P, nbin, E, pmin);
Pmax = 0;
/* Compute boundaries for the Free energy */
Wmin = 1e8;
imin = -1;
Wmax = -1e8;
/* Recompute Emin: it may have changed due to averaging */
Emin = 1e8;
Emax = -1e8;
for (i = 0; (i < len); i++)
{
if (P[i] != 0)
{
Pmax = max(P[i], Pmax);
W[i] = -BOLTZ*Tref*log(P[i]);
if (W[i] < Wmin)
{
Wmin = W[i];
imin = i;
}
Emin = min(E[i], Emin);
Emax = max(E[i], Emax);
Wmax = max(W[i], Wmax);
}
}
if (pmax > 0)
{
Pmax = pmax;
}
if (gmax > 0)
{
Wmax = gmax;
}
else
{
Wmax -= Wmin;
}
Winf = Wmax+1;
Einf = Emax+1;
Smin = Emin-Wmax;
Smax = Emax-Smin;
Sinf = Smax+1;
/* Write out the free energy as a function of bin index */
fp = ffopen(fn, "w");
for (i = 0; (i < len); i++)
{
if (P[i] != 0)
{
W[i] -= Wmin;
S[i] = E[i]-W[i]-Smin;
fprintf(fp, "%5d %10.5e %10.5e %10.5e\n", i, W[i], E[i], S[i]);
}
else
{
W[i] = Winf;
E[i] = Einf;
S[i] = Sinf;
}
}
ffclose(fp);
/* Organize the structures in the bins */
snew(b, 1);
snew(b->index, len+1);
snew(b->a, n);
b->index[0] = 0;
for (i = 0; (i < len); i++)
{
b->index[i+1] = b->index[i]+nbin[i];
nbin[i] = 0;
}
for (i = 0; (i < n); i++)
{
bi = bindex[i];
b->a[b->index[bi]+nbin[bi]] = i;
nbin[bi]++;
}
/* Consistency check */
/* This no longer applies when we allow the plot to be smaller
than the sampled space.
for(i=0; (i<len); i++) {
if (nbin[i] != (b->index[i+1] - b->index[i]))
gmx_fatal(FARGS,"nbin[%d] = %d, should be %d",i,nbin[i],
b->index[i+1] - b->index[i]);
}
*/
/* Write the index file */
fp = ffopen(ndx, "w");
for (i = 0; (i < len); i++)
{
if (nbin[i] > 0)
{
fprintf(fp, "[ %d ]\n", i);
for (j = b->index[i]; (j < b->index[i+1]); j++)
{
fprintf(fp, "%d\n", b->a[j]+1);
}
}
}
ffclose(fp);
snew(axis_x, ibox[0]+1);
snew(axis_y, ibox[1]+1);
snew(axis_z, ibox[2]+1);
maxbox = max(ibox[0], max(ibox[1], ibox[2]));
snew(PP, maxbox*maxbox);
snew(WW, maxbox*maxbox);
snew(EE, maxbox*maxbox);
snew(SS, maxbox*maxbox);
for (i = 0; (i < min(neig, 3)); i++)
{
switch (i)
{
case 0: axis = axis_x; break;
case 1: axis = axis_y; break;
case 2: axis = axis_z; break;
default: break;
}
for (j = 0; j <= ibox[i]; j++)
{
axis[j] = min_eig[i] + j/bfac[i];
}
}
if (map)
{
snew(M, len);
snew(MM, maxbox*maxbox);
for (i = 0; (i < ibox[0]); i++)
{
MM[i] = &(M[i*ibox[1]]);
}
Mmin = 1e8;
Mmax = -1e8;
for (i = 0; (i < nmap); i++)
{
Mmin = min(Mmin, map[0][i]);
Mmax = max(Mmax, map[0][i]);
}
Minf = Mmax*1.05;
for (i = 0; (i < len); i++)
{
M[i] = Minf;
}
for (i = 0; (i < nmap); i++)
{
index = gmx_nint(mapindex[i]);
if (index >= len)
{
gmx_fatal(FARGS, "Number of bins in file from -mdata option does not correspond to current analysis");
}
if (P[index] != 0)
{
M[index] = map[0][i];
}
}
}
else
{
MM = NULL;
Minf = NOTSET;
}
pick_minima(logf, ibox, neig, len, W);
if (gmax <= 0)
{
gmax = Winf;
}
flags = MAT_SPATIAL_X | MAT_SPATIAL_Y;
if (neig == 2)
{
/* Dump to XPM file */
snew(PP, ibox[0]);
for (i = 0; (i < ibox[0]); i++)
{
snew(PP[i], ibox[1]);
for (j = 0; j < ibox[1]; j++)
{
PP[i][j] = P[i*ibox[1]+j];
}
WW[i] = &(W[i*ibox[1]]);
EE[i] = &(E[i*ibox[1]]);
SS[i] = &(S[i*ibox[1]]);
}
fp = ffopen(xpmP, "w");
write_xpm(fp, flags, "Probability Distribution", "", "PC1", "PC2",
ibox[0], ibox[1], axis_x, axis_y, PP, 0, Pmax, rlo, rhi, &nlevels);
ffclose(fp);
fp = ffopen(xpm, "w");
write_xpm(fp, flags, "Gibbs Energy Landscape", "G (kJ/mol)", "PC1", "PC2",
ibox[0], ibox[1], axis_x, axis_y, WW, 0, gmax, rlo, rhi, &nlevels);
ffclose(fp);
fp = ffopen(xpm2, "w");
write_xpm(fp, flags, "Enthalpy Landscape", "H (kJ/mol)", "PC1", "PC2",
ibox[0], ibox[1], axis_x, axis_y, EE,
emin ? *emin : Emin, emax ? *emax : Einf, rlo, rhi, &nlevels);
ffclose(fp);
fp = ffopen(xpm3, "w");
write_xpm(fp, flags, "Entropy Landscape", "TDS (kJ/mol)", "PC1", "PC2",
ibox[0], ibox[1], axis_x, axis_y, SS, 0, Sinf, rlo, rhi, &nlevels);
ffclose(fp);
if (map)
{
fp = ffopen(xpm4, "w");
write_xpm(fp, flags, "Custom Landscape", mname, "PC1", "PC2",
ibox[0], ibox[1], axis_x, axis_y, MM, 0, Minf, rlo, rhi, &nlevels);
ffclose(fp);
}
}
else if (neig == 3)
{
/* Dump to PDB file */
fp = ffopen(pdb, "w");
for (i = 0; (i < ibox[0]); i++)
{
xxx[XX] = 3*(i+0.5-ibox[0]/2);
for (j = 0; (j < ibox[1]); j++)
{
xxx[YY] = 3*(j+0.5-ibox[1]/2);
for (k = 0; (k < ibox[2]); k++)
{
xxx[ZZ] = 3*(k+0.5-ibox[2]/2);
index = index3(ibox, i, j, k);
if (P[index] > 0)
{
fprintf(fp, "%-6s%5u %-4.4s%3.3s %4d %8.3f%8.3f%8.3f%6.2f%6.2f\n",
"ATOM", (index+1) %10000, "H", "H", (index+1)%10000,
xxx[XX], xxx[YY], xxx[ZZ], 1.0, W[index]);
}
}
}
}
ffclose(fp);
write_xplor("out.xplor", W, ibox, min_eig, max_eig);
if (map)
{
write_xplor("user.xplor", M, ibox, min_eig, max_eig);
}
nxyz[XX] = imin/(ibox[1]*ibox[2]);
nxyz[YY] = (imin-nxyz[XX]*ibox[1]*ibox[2])/ibox[2];
nxyz[ZZ] = imin % ibox[2];
for (i = 0; (i < ibox[0]); i++)
{
snew(WW[i], maxbox);
for (j = 0; (j < ibox[1]); j++)
{
WW[i][j] = W[index3(ibox, i, j, nxyz[ZZ])];
}
}
snew(buf, strlen(xpm)+4);
sprintf(buf, "%s", xpm);
sprintf(&buf[strlen(xpm)-4], "12.xpm");
fp = ffopen(buf, "w");
write_xpm(fp, flags, "Gibbs Energy Landscape", "W (kJ/mol)", "PC1", "PC2",
ibox[0], ibox[1], axis_x, axis_y, WW, 0, gmax, rlo, rhi, &nlevels);
ffclose(fp);
for (i = 0; (i < ibox[0]); i++)
{
for (j = 0; (j < ibox[2]); j++)
{
WW[i][j] = W[index3(ibox, i, nxyz[YY], j)];
}
}
sprintf(&buf[strlen(xpm)-4], "13.xpm");
fp = ffopen(buf, "w");
write_xpm(fp, flags, "SHAM Energy Landscape", "kJ/mol", "PC1", "PC3",
ibox[0], ibox[2], axis_x, axis_z, WW, 0, gmax, rlo, rhi, &nlevels);
ffclose(fp);
for (i = 0; (i < ibox[1]); i++)
{
for (j = 0; (j < ibox[2]); j++)
{
WW[i][j] = W[index3(ibox, nxyz[XX], i, j)];
}
}
sprintf(&buf[strlen(xpm)-4], "23.xpm");
fp = ffopen(buf, "w");
write_xpm(fp, flags, "SHAM Energy Landscape", "kJ/mol", "PC2", "PC3",
ibox[1], ibox[2], axis_y, axis_z, WW, 0, gmax, rlo, rhi, &nlevels);
ffclose(fp);
sfree(buf);
}
if (map)
{
sfree(MM);
sfree(M);
}
}
static void update_topol(char *topinout,int p_num,int n_num,
const char *p_name,const char *n_name,char *grpname)
{
#define TEMP_FILENM "temp.top"
FILE *fpin,*fpout;
char buf[STRLEN],buf2[STRLEN],*temp;
int line,i,nsol;
bool bMolecules;
printf("\nProcessing topology\n");
fpin = ffopen(topinout,"r");
fpout= ffopen(TEMP_FILENM,"w");
line=0;
bMolecules = FALSE;
while (fgets(buf, STRLEN, fpin)) {
line++;
strcpy(buf2,buf);
if ((temp=strchr(buf2,'\n')) != NULL)
temp[0]='\0';
ltrim(buf2);
if (buf2[0]=='[') {
buf2[0]=' ';
if ((temp=strchr(buf2,'\n')) != NULL)
temp[0]='\0';
rtrim(buf2);
if (buf2[strlen(buf2)-1]==']') {
buf2[strlen(buf2)-1]='\0';
ltrim(buf2);
rtrim(buf2);
bMolecules=(strcasecmp(buf2,"molecules")==0);
}
}
if (bMolecules) {
/* check if this is a line with solvent molecules */
sscanf(buf,"%s",buf2);
if (strcasecmp(buf2,grpname)==0) {
sscanf(buf,"%*s %d",&i);
nsol = i-p_num-n_num;
if (nsol < 0)
gmx_incons("Not enough water");
else {
printf("Replacing %d solute molecules in topology file (%s) "
" by %d %s and %d %s ions.\n",
nsol,topinout,p_num,p_name,n_num,n_name);
fprintf(fpout,"%-10s %d\n",grpname,nsol);
fprintf(fpout,"%-10s %d\n",p_name,p_num);
fprintf(fpout,"%-10s %d\n",n_name,n_num);
}
} else
fprintf(fpout,"%s",buf);
} else
fprintf(fpout,"%s",buf);
}
fclose(fpin);
fclose(fpout);
/* use ffopen to generate backup of topinout */
fpout=ffopen(topinout,"w");
fclose(fpout);
rename(TEMP_FILENM,topinout);
#undef TEMP_FILENM
}
int gmx_editconf(int argc, char *argv[])
{
const char *desc[] = {
"editconf converts generic structure format to [TT].gro[tt], [TT].g96[tt]",
"or [TT].pdb[tt].",
"[PAR]",
"The box can be modified with options [TT]-box[tt], [TT]-d[tt] and",
"[TT]-angles[tt]. Both [TT]-box[tt] and [TT]-d[tt]",
"will center the system in the box, unless [TT]-noc[tt] is used.",
"[PAR]",
"Option [TT]-bt[tt] determines the box type: [TT]triclinic[tt] is a",
"triclinic box, [TT]cubic[tt] is a rectangular box with all sides equal",
"[TT]dodecahedron[tt] represents a rhombic dodecahedron and "
"[TT]octahedron[tt] is a truncated octahedron.",
"The last two are special cases of a triclinic box.",
"The length of the three box vectors of the truncated octahedron is the",
"shortest distance between two opposite hexagons.",
"The volume of a dodecahedron is 0.71 and that of a truncated octahedron",
"is 0.77 of that of a cubic box with the same periodic image distance.",
"[PAR]",
"Option [TT]-box[tt] requires only",
"one value for a cubic box, dodecahedron and a truncated octahedron.",
"[PAR]",
"With [TT]-d[tt] and a [TT]triclinic[tt] box the size of the system in the x, y",
"and z 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",
"the specified distance.",
"[PAR]",
"Option [TT]-angles[tt] is only meaningful with option [TT]-box[tt] and",
"a triclinic box and can not be used with option [TT]-d[tt].",
"[PAR]",
"When [TT]-n[tt] or [TT]-ndef[tt] is set, a group",
"can be selected for calculating the size and the geometric center,",
"otherwise the whole system is used.",
"[PAR]",
"[TT]-rotate[tt] rotates the coordinates and velocities.",
"[PAR]",
"[TT]-princ[tt] aligns the principal axes of the system along the",
"coordinate axes, this may allow you to decrease the box volume,",
"but beware that molecules can rotate significantly in a nanosecond.",
"[PAR]",
"Scaling is applied before any of the other operations are",
"performed. Boxes and coordinates can be scaled to give a certain density (option",
"[TT]-density[tt]). Note that this may be inaccurate in case a gro",
"file is given as input. A special feature of the scaling option, when the",
"factor -1 is given in one dimension, one obtains a mirror image,",
"mirrored in one of the plains, when one uses -1 in three dimensions",
"a point-mirror image is obtained.[PAR]",
"Groups are selected after all operations have been applied.[PAR]",
"Periodicity can be removed in a crude manner.",
"It is important that the box sizes at the bottom of your input file",
"are correct when the periodicity is to be removed.",
"[PAR]",
"When writing [TT].pdb[tt] files, B-factors can be",
"added with the [TT]-bf[tt] option. B-factors are read",
"from a file with with following format: first line states number of",
"entries in the file, next lines state an index",
"followed by a B-factor. The B-factors will be attached per residue",
"unless an index is larger than the number of residues or unless the",
"[TT]-atom[tt] option is set. Obviously, any type of numeric data can",
"be added instead of B-factors. [TT]-legend[tt] will produce",
"a row of CA atoms with B-factors ranging from the minimum to the",
"maximum value found, effectively making a legend for viewing.",
"[PAR]",
"With the option -mead a special pdb (pqr) file for the MEAD electrostatics",
"program (Poisson-Boltzmann solver) can be made. A further prerequisite",
"is that the input file is a run input file.",
"The B-factor field is then filled with the Van der Waals radius",
"of the atoms while the occupancy field will hold the charge.",
"[PAR]",
"The option -grasp is similar, but it puts the charges in the B-factor",
"and the radius in the occupancy.",
"[PAR]",
"Finally with option [TT]-label[tt] editconf can add a chain identifier",
"to a pdb file, which can be useful for analysis with e.g. rasmol."
"[PAR]",
"To convert a truncated octrahedron file produced by a package which uses",
"a cubic box with the corners cut off (such as Gromos) use:[BR]",
"[TT]editconf -f <in> -rotate 0 45 35.264 -bt o -box <veclen> -o <out>[tt][BR]",
"where [TT]veclen[tt] is the size of the cubic box times sqrt(3)/2."
};
const char *bugs[] = {
"For complex molecules, the periodicity removal routine may break down, "
"in that case you can use trjconv"
};
static real dist=0.0,rbox=0.0,to_diam=0.0;
static bool bNDEF=FALSE,bRMPBC=FALSE,bCenter=FALSE,bReadVDW=FALSE,bCONECT=FALSE;
static 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};
static const char *btype[]={ NULL, "triclinic", "cubic", "dodecahedron", "octahedron", NULL },*label="A";
static rvec visbox={0,0,0};
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 -box and -d" },
{ "-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 -box and -d)" },
{ "-center", FALSE, etRVEC, {center}, "Coordinates of geometrical center"},
{ "-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, {&rho},
"Density (g/l) of the output box achieved by scaling" },
{ "-pbc", FALSE, etBOOL, {&bRMPBC},
"Remove the periodicity (make molecule whole again)" },
{ "-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, etREAL, {&bSig56},
"Use rmin/2 (minimum in the Van der Waals potential) rather than sigma/2 " },
{ "-vdwread",FALSE, etBOOL, {&bReadVDW},
"Read the Van der Waals radii from the file vdwradii.dat 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 pdb file when written. Can only be done when a topology is present" }
};
#define NPA asize(pa)
FILE *out;
char *infile,*outfile,title[STRLEN];
int outftp,inftp,natom,i,j,n_bfac,itype,ntype;
double *bfac=NULL,c6,c12;
int *bfac_nr=NULL;
t_topology *top=NULL;
t_atoms atoms;
char *grpname,*sgrpname;
int isize,ssize,tsize;
atom_id *index,*sindex,*tindex;
rvec *x,*v,gc,min,max,size;
int ePBC;
matrix box;
bool bIndex,bSetSize,bSetAng,bCubic,bDist,bSetCenter;
bool bHaveV,bScale,bRho,bTranslate,bRotate,bCalcGeom,bCalcDiam;
real xs,ys,zs,xcent,ycent,zcent,diam=0,mass=0,d,vdw;
gmx_atomprop_t aps;
gmx_conect conect;
t_filenm fnm[] = {
{ efSTX, "-f", NULL, ffREAD },
{ efNDX, "-n", NULL, ffOPTRD },
{ efSTO, NULL, NULL, ffOPTWR },
{ efPQR, "-mead", "mead", ffOPTWR },
{ efDAT, "-bf", "bfact", ffOPTRD }
};
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_CAN_VIEW,NFILE,fnm,NPA,pa,
asize(desc),desc,asize(bugs),bugs);
bIndex = opt2bSet("-n",NFILE,fnm) || bNDEF;
bMead = opt2bSet("-mead",NFILE,fnm);
bSetSize = opt2parg_bSet("-box" ,NPA,pa);
bSetAng = opt2parg_bSet("-angles" ,NPA,pa);
bSetCenter= opt2parg_bSet("-center" ,NPA,pa);
bDist = opt2parg_bSet("-d" ,NPA,pa);
/* Only automatically turn on centering without -noc */
if ((bDist || bSetSize || bSetCenter) && !opt2parg_bSet("-c",NPA,pa)) {
bCenter = TRUE;
}
bScale = opt2parg_bSet("-scale" ,NPA,pa);
bRho = opt2parg_bSet("-density",NPA,pa);
bTranslate= opt2parg_bSet("-translate",NPA,pa);
bRotate = opt2parg_bSet("-rotate",NPA,pa);
if (bScale && bRho)
fprintf(stderr,"WARNING: setting -density overrides -scale\n");
bScale = bScale || bRho;
bCalcGeom = bCenter || bRotate || bOrient || bScale;
bCalcDiam = btype[0][0]=='c' || btype[0][0]=='d' || btype[0][0]=='o';
infile = ftp2fn(efSTX,NFILE,fnm);
if (bMead)
outfile = ftp2fn(efPQR,NFILE,fnm);
else
outfile = ftp2fn(efSTO,NFILE,fnm);
outftp = fn2ftp(outfile);
inftp = fn2ftp(infile);
aps = gmx_atomprop_init();
if (bMead && bGrasp) {
printf("Incompatible options -mead and -grasp. Turning off -grasp\n");
bGrasp = FALSE;
}
if (bGrasp && (outftp != efPDB))
gmx_fatal(FARGS,"Output file should be a .pdb file"
" when using the -grasp option\n");
if ((bMead || bGrasp) && !((fn2ftp(infile) == efTPR) ||
(fn2ftp(infile) == efTPA) ||
(fn2ftp(infile) == efTPB)))
gmx_fatal(FARGS,"Input file should be a .tp[abr] file"
" when using the -mead option\n");
get_stx_coordnum(infile,&natom);
init_t_atoms(&atoms,natom,TRUE);
snew(x,natom);
snew(v,natom);
read_stx_conf(infile,title,&atoms,x,v,&ePBC,box);
if (fn2ftp(infile) == efPDB)
{
get_pdb_atomnumber(&atoms,aps);
}
printf("Read %d atoms\n",atoms.nr);
/* Get the element numbers if available in a pdb file */
if (fn2ftp(infile) == efPDB)
get_pdb_atomnumber(&atoms,aps);
if (ePBC != epbcNONE) {
real vol = det(box);
printf("Volume: %g nm^3, corresponds to roughly %d electrons\n",
vol,100*((int)(vol*4.5)));
}
if (bMead || bGrasp || bCONECT)
top = read_top(infile,NULL);
if (bMead || bGrasp) {
if (atoms.nr != top->atoms.nr)
gmx_fatal(FARGS,"Atom numbers don't match (%d vs. %d)",atoms.nr,top->atoms.nr);
snew(atoms.pdbinfo,top->atoms.nr);
ntype = top->idef.atnr;
for(i=0; (i<atoms.nr); i++) {
/* Determine the Van der Waals radius from the force field */
if (bReadVDW) {
if (!gmx_atomprop_query(aps,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;
if ((c6 != 0) && (c12 != 0)) {
real sig6;
if (bSig56)
sig6 = 2*c12/c6;
else
sig6 = c12/c6;
vdw = 0.5*pow(sig6,1.0/6.0);
}
else
vdw = rvdw;
}
/* Factor of 10 for nm -> Angstroms */
vdw *= 10;
if (bMead) {
atoms.pdbinfo[i].occup = top->atoms.atom[i].q;
atoms.pdbinfo[i].bfac = vdw;
}
else {
atoms.pdbinfo[i].occup = vdw;
atoms.pdbinfo[i].bfac = top->atoms.atom[i].q;
}
}
}
bHaveV=FALSE;
for (i=0; (i<natom) && !bHaveV; i++)
for (j=0; (j<DIM) && !bHaveV; j++)
bHaveV=bHaveV || (v[i][j]!=0);
printf("%selocities found\n",bHaveV?"V":"No v");
if (visbox[0] > 0) {
if (bIndex)
gmx_fatal(FARGS,"Sorry, can not visualize box with index groups");
if (outftp != efPDB)
gmx_fatal(FARGS,"Sorry, can only visualize box with a pdb file");
} else if (visbox[0] == -1)
visualize_images("images.pdb",ePBC,box);
/* remove pbc */
if (bRMPBC)
rm_gropbc(&atoms,x,box);
if (bCalcGeom) {
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);
} else {
ssize = atoms.nr;
sindex = NULL;
}
diam=calc_geom(ssize,sindex,x,gc,min,max,bCalcDiam);
rvec_sub(max, min, size);
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 angles :%7.2f%7.2f%7.2f (degrees)\n",
norm2(box[ZZ])==0 ? 0 :
RAD2DEG*acos(cos_angle_no_table(box[YY],box[ZZ])),
norm2(box[ZZ])==0 ? 0 :
RAD2DEG*acos(cos_angle_no_table(box[XX],box[ZZ])),
norm2(box[YY])==0 ? 0 :
RAD2DEG*acos(cos_angle_no_table(box[XX],box[YY])));
printf(" box volume :%7.2f (nm^3)\n",det(box));
}
if (bRho || bOrient)
mass = calc_mass(&atoms,!fn2bTPX(infile),aps);
if (bOrient) {
atom_id *index;
char *grpnames;
/* Get a group for principal component analysis */
fprintf(stderr,"\nSelect group for the determining the orientation\n");
get_index(&atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&isize,&index,&grpnames);
/* Orient the principal axes along the coordinate axes */
orient_princ(&atoms,isize,index,natom,x,bHaveV ? v : NULL, NULL);
sfree(index);
sfree(grpnames);
}
if ( bScale ) {
/* scale coordinates and box */
if (bRho) {
/* Compute scaling constant */
real vol,dens;
vol = det(box);
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);
scale[XX] = scale[YY] = scale[ZZ] = pow(dens/rho,1.0/3.0);
fprintf(stderr,"Scaling all box vectors by %g\n",scale[XX]);
}
scale_conf(atoms.nr,x,box,scale);
}
if (bTranslate) {
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);
} else {
ssize = atoms.nr;
sindex = NULL;
}
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++)
rvec_inc(x[sindex[i]],translation);
}
else {
for(i=0; i<natom; i++)
rvec_inc(x[i],translation);
}
}
if (bRotate) {
/* Rotate */
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;
rotate_conf(natom,x,v,rotangles[XX],rotangles[YY],rotangles[ZZ]);
}
if (bCalcGeom) {
/* recalc geometrical center and max and min coordinates and size */
calc_geom(ssize,sindex,x,gc,min,max,FALSE);
rvec_sub(max, min, size);
if (bScale || bOrient || bRotate)
printf("new system size : %6.3f %6.3f %6.3f\n",
size[XX],size[YY],size[ZZ]);
}
if (bSetSize || bDist || (btype[0][0]=='t' && bSetAng)) {
ePBC = epbcXYZ;
if (!(bSetSize || bDist))
for (i=0; i<DIM; i++)
newbox[i] = norm(box[i]);
clear_mat(box);
/* calculate new boxsize */
switch(btype[0][0]){
case 't':
if (bDist)
for(i=0; i<DIM; i++)
newbox[i] = size[i]+2*dist;
if (!bSetAng) {
box[XX][XX] = newbox[XX];
box[YY][YY] = newbox[YY];
box[ZZ][ZZ] = newbox[ZZ];
} else {
svmul(DEG2RAD,newang,newang);
box[XX][XX] = newbox[XX];
box[YY][XX] = newbox[YY]*cos(newang[ZZ]);
box[YY][YY] = newbox[YY]*sin(newang[ZZ]);
box[ZZ][XX] = newbox[ZZ]*cos(newang[YY]);
box[ZZ][YY] = newbox[ZZ]
*(cos(newang[XX])-cos(newang[YY])*cos(newang[ZZ]))/sin(newang[ZZ]);
box[ZZ][ZZ] = sqrt(sqr(newbox[ZZ])
-box[ZZ][XX]*box[ZZ][XX]-box[ZZ][YY]*box[ZZ][YY]);
}
break;
case 'c':
case 'd':
case 'o':
if (bSetSize)
d = newbox[0];
else
d = diam+2*dist;
if (btype[0][0] == 'c')
for(i=0; i<DIM; i++)
box[i][i] = d;
else if (btype[0][0] == 'd') {
box[XX][XX] = d;
box[YY][YY] = d;
box[ZZ][XX] = d/2;
box[ZZ][YY] = d/2;
box[ZZ][ZZ] = d*sqrt(2)/2;
} else {
box[XX][XX] = d;
box[YY][XX] = d/3;
box[YY][YY] = d*sqrt(2)*2/3;
box[ZZ][XX] = -d/3;
box[ZZ][YY] = d*sqrt(2)/3;
box[ZZ][ZZ] = d*sqrt(6)/3;
}
break;
}
}
/* calculate new coords for geometrical center */
if (!bSetCenter)
calc_box_center(ecenterDEF,box,center);
/* center molecule on 'center' */
if (bCenter)
center_conf(natom,x,center,gc);
/* print some */
if (bCalcGeom) {
calc_geom(ssize,sindex,x, gc, min, max, FALSE);
printf("new center :%7.3f%7.3f%7.3f (nm)\n",gc[XX],gc[YY],gc[ZZ]);
}
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 angles :%7.2f%7.2f%7.2f (degrees)\n",
norm2(box[ZZ])==0 ? 0 :
RAD2DEG*acos(cos_angle_no_table(box[YY],box[ZZ])),
norm2(box[ZZ])==0 ? 0 :
RAD2DEG*acos(cos_angle_no_table(box[XX],box[ZZ])),
norm2(box[YY])==0 ? 0 :
RAD2DEG*acos(cos_angle_no_table(box[XX],box[YY])));
printf("new box volume :%7.2f (nm^3)\n",det(box));
}
if (check_box(epbcXYZ,box))
printf("\nWARNING: %s\n",check_box(epbcXYZ,box));
if (bDist && btype[0][0]=='t')
{
if(TRICLINIC(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);
}
else
{
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 (bCONECT && (outftp == efPDB) && (inftp == efTPR))
conect = gmx_conect_generate(top);
else
conect = NULL;
if (bIndex) {
fprintf(stderr,"\nSelect a group for output:\n");
get_index(&atoms,opt2fn_null("-n",NFILE,fnm),
1,&isize,&index,&grpname);
if (opt2bSet("-bf",NFILE,fnm))
gmx_fatal(FARGS,"combination not implemented: -bf -n or -bf -ndef");
else {
if (outftp == efPDB) {
out=ffopen(outfile,"w");
write_pdbfile_indexed(out,title,&atoms,x,ePBC,box,' ',1,isize,index,conect);
fclose(out);
}
else
write_sto_conf_indexed(outfile,title,&atoms,x,bHaveV?v:NULL,ePBC,box,
isize,index);
}
}
else {
if ((outftp == efPDB) || (outftp == efPQR)) {
out=ffopen(outfile,"w");
if (bMead) {
set_pdb_wide_format(TRUE);
fprintf(out,"REMARK "
"The B-factors in this file hold atomic radii\n");
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 "
"The B-factors in this file hold atomic charges\n");
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);
}
if (opt2parg_bSet("-label",NPA,pa)) {
for(i=0; (i<atoms.nr); i++)
atoms.resinfo[atoms.atom[i].resind].chain=label[0];
}
write_pdbfile(out,title,&atoms,x,ePBC,box,0,-1,conect);
if (bLegend)
pdb_legend(out,atoms.nr,atoms.nres,&atoms,x);
if (visbox[0] > 0)
visualize_box(out,bLegend ? atoms.nr+12 : atoms.nr,
bLegend? atoms.nres=12 : atoms.nres,box,visbox);
fclose(out);
}
else
write_sto_conf(outfile,title,&atoms,x,bHaveV?v:NULL,ePBC,box);
}
gmx_atomprop_destroy(aps);
do_view(outfile,NULL);
thanx(stderr);
return 0;
}
static void pick_minima(const char *logfile, int *ibox, int ndim, int len, real W[])
{
FILE *fp;
int i, j, k, nmin;
t_minimum *mm, this_min;
int *this_point;
int loopmax, loopcounter;
snew(mm, len);
nmin = 0;
fp = ffopen(logfile, "w");
/* Loop over each element in the array of dimenion ndim seeking
* minima with respect to every dimension. Specialized loops for
* speed with ndim == 2 and ndim == 3. */
switch (ndim)
{
case 0:
/* This is probably impossible to reach anyway. */
break;
case 2:
for (i = 0; (i < ibox[0]); i++)
{
for (j = 0; (j < ibox[1]); j++)
{
/* Get the index of this point in the flat array */
this_min.index = index2(ibox, i, j);
this_min.ener = W[this_min.index];
if (is_local_minimum_from_below(&this_min, i, 0, index2(ibox, i-1, j ), W) &&
is_local_minimum_from_above(&this_min, i, ibox[0]-1, index2(ibox, i+1, j ), W) &&
is_local_minimum_from_below(&this_min, j, 0, index2(ibox, i, j-1), W) &&
is_local_minimum_from_above(&this_min, j, ibox[1]-1, index2(ibox, i, j+1), W))
{
add_minimum(fp, nmin, &this_min, mm);
nmin++;
}
}
}
break;
case 3:
for (i = 0; (i < ibox[0]); i++)
{
for (j = 0; (j < ibox[1]); j++)
{
for (k = 0; (k < ibox[2]); k++)
{
/* Get the index of this point in the flat array */
this_min.index = index3(ibox, i, j, k);
this_min.ener = W[this_min.index];
if (is_local_minimum_from_below(&this_min, i, 0, index3(ibox, i-1, j, k ), W) &&
is_local_minimum_from_above(&this_min, i, ibox[0]-1, index3(ibox, i+1, j, k ), W) &&
is_local_minimum_from_below(&this_min, j, 0, index3(ibox, i, j-1, k ), W) &&
is_local_minimum_from_above(&this_min, j, ibox[1]-1, index3(ibox, i, j+1, k ), W) &&
is_local_minimum_from_below(&this_min, k, 0, index3(ibox, i, j, k-1), W) &&
is_local_minimum_from_above(&this_min, k, ibox[2]-1, index3(ibox, i, j, k+1), W))
{
add_minimum(fp, nmin, &this_min, mm);
nmin++;
}
}
}
}
break;
default:
/* Note this treats ndim == 1 and ndim > 3 */
/* Set up an ndim-dimensional vector to loop over the points
* on the grid. (0,0,0, ... 0) is an acceptable place to
* start. */
snew(this_point, ndim);
/* Determine the number of points of the ndim-dimensional
* grid. */
loopmax = ibox[0];
for (i = 1; i < ndim; i++)
{
loopmax *= ibox[i];
}
loopcounter = 0;
while (loopmax > loopcounter)
{
gmx_bool bMin = TRUE;
/* Get the index of this_point in the flat array */
this_min.index = indexn(ndim, ibox, this_point);
this_min.ener = W[this_min.index];
/* Is this_point a minimum from above and below in each
* dimension? */
for (i = 0; bMin && (i < ndim); i++)
{
/* Save the index of this_point within the curent
* dimension so we can change that index in the
* this_point array for use with indexn(). */
int index = this_point[i];
this_point[i]--;
bMin = bMin &&
is_local_minimum_from_below(&this_min, index, 0, indexn(ndim, ibox, this_point), W);
this_point[i] += 2;
bMin = bMin &&
is_local_minimum_from_above(&this_min, index, ibox[i]-1, indexn(ndim, ibox, this_point), W);
this_point[i]--;
}
if (bMin)
{
add_minimum(fp, nmin, &this_min, mm);
nmin++;
}
/* update global loop counter */
loopcounter++;
/* Avoid underflow of this_point[i] */
if (loopmax > loopcounter)
{
/* update this_point non-recursively */
i = ndim-1;
this_point[i]++;
while (ibox[i] == this_point[i])
{
this_point[i] = 0;
i--;
/* this_point[i] cannot underflow because
* loopmax > loopcounter. */
this_point[i]++;
}
}
}
sfree(this_point);
break;
}
qsort(mm, nmin, sizeof(mm[0]), comp_minima);
fprintf(fp, "Minima sorted after energy\n");
for (i = 0; (i < nmin); i++)
{
print_minimum(fp, i, &mm[i]);
}
ffclose(fp);
sfree(mm);
}
int
ncio_open(const char *path,
int ioflags,
off_t igeto, size_t igetsz, size_t *sizehintp,
ncio **nciopp, void **const igetvpp)
{
ncio *nciop;
const char *ControlString;
int oflags = fIsSet(ioflags, NC_WRITE) ? O_RDWR : O_RDONLY;
int fd;
int status;
struct ffsw stat;
if(path == NULL || *path == 0)
return EINVAL;
nciop = ncio_new(path, ioflags);
if(nciop == NULL)
return ENOMEM;
if ((ControlString = ncio_ffio_assign(path)) == (const char *)NULL) {
/* an error occured - just punt */
status = errno;
goto unwind_new;
}
#ifdef NOFFFLUSH
/* test whether the global layer is being called for
* this file ... if so then can't call FFIO ffflush()
* RKO 06/26/98
*/
if (strstr(ControlString,"global") != (char *) NULL) {
/* use no ffflush version */
*((ncio_syncfunc **)&nciop->sync)
= ncio_ffio_sync_noffflush;
}
#endif
/* Orig: fd = ffopens(path, oflags, 0, 0, &stat, ControlString); */
fd = ffopen(path, oflags, 0, 0, &stat);
if(fd < 0)
{
status = errno;
goto unwind_new;
}
*((int *)&nciop->fd) = fd; /* cast away const */
if(*sizehintp < NCIO_MINBLOCKSIZE || *sizehintp > NCIO_MAXBLOCKSIZE)
{
/* Use default */
*sizehintp = blksize(fd);
}
else
{
*sizehintp = M_RNDUP(*sizehintp);
}
status = ncio_ffio_init2(nciop, sizehintp);
if(status != ENOERR)
goto unwind_open;
if(igetsz != 0)
{
status = nciop->get(nciop,
igeto, igetsz,
0,
igetvpp);
if(status != ENOERR)
goto unwind_open;
}
*nciopp = nciop;
return ENOERR;
unwind_open:
(void) ffclose(fd);
/*FALLTHRU*/
unwind_new:
ncio_free(nciop);
return status;
}
int gmx_helix(int argc,char *argv[])
{
const char *desc[] = {
"g_helix computes all kind of helix properties. First, the peptide",
"is checked to find the longest helical part. This is determined by",
"Hydrogen bonds and Phi/Psi angles.",
"That bit is fitted",
"to an ideal helix around the Z-axis and centered around the origin.",
"Then the following properties are computed:[PAR]",
"[BB]1.[bb] Helix radius (file radius.xvg). This is merely the",
"RMS deviation in two dimensions for all Calpha atoms.",
"it is calced as sqrt((SUM i(x^2(i)+y^2(i)))/N), where N is the number",
"of backbone atoms. For an ideal helix the radius is 0.23 nm[BR]",
"[BB]2.[bb] Twist (file twist.xvg). The average helical angle per",
"residue is calculated. For alpha helix it is 100 degrees,",
"for 3-10 helices it will be smaller,",
"for 5-helices it will be larger.[BR]",
"[BB]3.[bb] Rise per residue (file rise.xvg). The helical rise per",
"residue is plotted as the difference in Z-coordinate between Ca",
"atoms. For an ideal helix this is 0.15 nm[BR]",
"[BB]4.[bb] Total helix length (file len-ahx.xvg). The total length",
"of the",
"helix in nm. This is simply the average rise (see above) times the",
"number of helical residues (see below).[BR]",
"[BB]5.[bb] Number of helical residues (file n-ahx.xvg). The title says",
"it all.[BR]",
"[BB]6.[bb] Helix Dipole, backbone only (file dip-ahx.xvg).[BR]",
"[BB]7.[bb] RMS deviation from ideal helix, calculated for the Calpha",
"atoms only (file rms-ahx.xvg).[BR]",
"[BB]8.[bb] Average Calpha-Calpha dihedral angle (file phi-ahx.xvg).[BR]",
"[BB]9.[bb] Average Phi and Psi angles (file phipsi.xvg).[BR]",
"[BB]10.[bb] Ellipticity at 222 nm according to [IT]Hirst and Brooks[it]",
"[PAR]"
};
static const char *ppp[efhNR+2] = {
NULL, "RAD", "TWIST", "RISE", "LEN", "NHX", "DIP", "RMS", "CPHI",
"RMSA", "PHI", "PSI", "HB3", "HB4", "HB5", "CD222", NULL
};
static gmx_bool bCheck=FALSE,bFit=TRUE,bDBG=FALSE,bEV=FALSE;
static int rStart=0,rEnd=0,r0=1;
t_pargs pa [] = {
{ "-r0", FALSE, etINT, {&r0},
"The first residue number in the sequence" },
{ "-q", FALSE, etBOOL,{&bCheck},
"Check at every step which part of the sequence is helical" },
{ "-F", FALSE, etBOOL,{&bFit},
"Toggle fit to a perfect helix" },
{ "-db", FALSE, etBOOL,{&bDBG},
"Print debug info" },
{ "-prop", FALSE, etENUM, {ppp},
"Select property to weight eigenvectors with. WARNING experimental stuff" },
{ "-ev", FALSE, etBOOL,{&bEV},
"Write a new 'trajectory' file for ED" },
{ "-ahxstart", FALSE, etINT, {&rStart},
"First residue in helix" },
{ "-ahxend", FALSE, etINT, {&rEnd},
"Last residue in helix" }
};
typedef struct {
FILE *fp,*fp2;
gmx_bool bfp2;
const char *filenm;
const char *title;
const char *xaxis;
const char *yaxis;
real val;
} t_xvgrfile;
t_xvgrfile xf[efhNR] = {
{ NULL, NULL, TRUE, "radius", "Helix radius", NULL, "r (nm)" , 0.0 },
{ NULL, NULL, TRUE, "twist", "Twist per residue", NULL, "Angle (deg)", 0.0 },
{ NULL, NULL, TRUE, "rise", "Rise per residue", NULL, "Rise (nm)", 0.0 },
{ NULL, NULL, FALSE, "len-ahx", "Length of the Helix", NULL, "Length (nm)", 0.0 },
{ NULL, NULL, FALSE, "dip-ahx", "Helix Backbone Dipole", NULL, "rq (nm e)", 0.0 },
{ NULL, NULL, TRUE, "rms-ahx", "RMS Deviation from Ideal Helix", NULL, "RMS (nm)", 0.0 },
{ NULL, NULL, FALSE, "rmsa-ahx","Average RMSD per Residue", "Residue", "RMS (nm)", 0.0 },
{ NULL, NULL,FALSE, "cd222", "Ellipticity at 222 nm", NULL, "nm", 0.0 },
{ NULL, NULL, TRUE, "pprms", "RMS Distance from \\8a\\4-helix", NULL, "deg" , 0.0 },
{ NULL, NULL, TRUE, "caphi", "Average Ca-Ca Dihedral", NULL, "\\8F\\4(deg)", 0.0 },
{ NULL, NULL, TRUE, "phi", "Average \\8F\\4 angles", NULL, "deg" , 0.0 },
{ NULL, NULL, TRUE, "psi", "Average \\8Y\\4 angles", NULL, "deg" , 0.0 },
{ NULL, NULL, TRUE, "hb3", "Average n-n+3 hbond length", NULL, "nm" , 0.0 },
{ NULL, NULL, TRUE, "hb4", "Average n-n+4 hbond length", NULL, "nm" , 0.0 },
{ NULL, NULL, TRUE, "hb5", "Average n-n+5 hbond length", NULL, "nm" , 0.0 },
{ NULL, NULL,FALSE, "JCaHa", "J-Coupling Values", "Residue", "Hz" , 0.0 },
{ NULL, NULL,FALSE, "helicity","Helicity per Residue", "Residue", "% of time" , 0.0 }
};
output_env_t oenv;
FILE *otrj;
char buf[54],prop[256];
t_trxstatus *status;
int natoms,nre,nres;
t_bb *bb;
int i,j,ai,m,nall,nbb,nca,teller,nSel=0;
atom_id *bbindex,*caindex,*allindex;
t_topology *top;
int ePBC;
rvec *x,*xref,*xav;
real t;
real rms,fac;
matrix box;
gmx_rmpbc_t gpbc=NULL;
gmx_bool bRange;
t_filenm fnm[] = {
{ efTPX, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffREAD },
{ efTRX, "-f", NULL, ffREAD },
{ efG87, "-to", NULL, ffOPTWR },
{ efSTO, "-cz", "zconf",ffWRITE },
{ efSTO, "-co", "waver",ffWRITE }
};
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&oenv);
bRange=(opt2parg_bSet("-ahxstart",asize(pa),pa) &&
opt2parg_bSet("-ahxend",asize(pa),pa));
top=read_top(ftp2fn(efTPX,NFILE,fnm),&ePBC);
natoms=read_first_x(oenv,&status,opt2fn("-f",NFILE,fnm),&t,&x,box);
if (opt2bSet("-to",NFILE,fnm)) {
otrj=opt2FILE("-to",NFILE,fnm,"w");
strcpy(prop,ppp[0]);
fprintf(otrj,"%s Weighted Trajectory: %d atoms, NO box\n",prop,natoms);
}
else
otrj=NULL;
if (natoms != top->atoms.nr)
gmx_fatal(FARGS,"Sorry can only run when the number of atoms in the run input file (%d) is equal to the number in the trajectory (%d)",
top->atoms.nr,natoms);
bb=mkbbind(ftp2fn(efNDX,NFILE,fnm),&nres,&nbb,r0,&nall,&allindex,
top->atoms.atomname,top->atoms.atom,top->atoms.resinfo);
snew(bbindex,natoms);
snew(caindex,nres);
fprintf(stderr,"nall=%d\n",nall);
/* Open output files, default x-axis is time */
for(i=0; (i<efhNR); i++) {
sprintf(buf,"%s.xvg",xf[i].filenm);
remove(buf);
xf[i].fp=xvgropen(buf,xf[i].title,
xf[i].xaxis ? xf[i].xaxis : "Time (ps)",
xf[i].yaxis,oenv);
if (xf[i].bfp2) {
sprintf(buf,"%s.out",xf[i].filenm);
remove(buf);
xf[i].fp2=ffopen(buf,"w");
}
}
/* Read reference frame from tpx file to compute helix length */
snew(xref,top->atoms.nr);
read_tpx(ftp2fn(efTPX,NFILE,fnm),
NULL,NULL,&natoms,xref,NULL,NULL,NULL);
calc_hxprops(nres,bb,xref,box);
do_start_end(nres,bb,xref,&nbb,bbindex,&nca,caindex,bRange,rStart,rEnd);
sfree(xref);
if (bDBG) {
fprintf(stderr,"nca=%d, nbb=%d\n",nca,nbb);
pr_bb(stdout,nres,bb);
}
gpbc = gmx_rmpbc_init(&top->idef,ePBC,natoms,box);
snew(xav,natoms);
teller=0;
do {
if ((teller++ % 10) == 0)
fprintf(stderr,"\rt=%.2f",t);
gmx_rmpbc(gpbc,natoms,box,x);
calc_hxprops(nres,bb,x,box);
if (bCheck)
do_start_end(nres,bb,x,&nbb,bbindex,&nca,caindex,FALSE,0,0);
if (nca >= 5) {
rms=fit_ahx(nres,bb,natoms,nall,allindex,x,nca,caindex,box,bFit);
if (teller == 1) {
write_sto_conf(opt2fn("-cz",NFILE,fnm),"Helix fitted to Z-Axis",
&(top->atoms),x,NULL,ePBC,box);
}
xf[efhRAD].val = radius(xf[efhRAD].fp2,nca,caindex,x);
xf[efhTWIST].val = twist(xf[efhTWIST].fp2,nca,caindex,x);
xf[efhRISE].val = rise(nca,caindex,x);
xf[efhLEN].val = ahx_len(nca,caindex,x,box);
xf[efhCD222].val = ellipticity(nres,bb);
xf[efhDIP].val = dip(nbb,bbindex,x,top->atoms.atom);
xf[efhRMS].val = rms;
xf[efhCPHI].val = ca_phi(nca,caindex,x,box);
xf[efhPPRMS].val = pprms(xf[efhPPRMS].fp2,nres,bb);
for(j=0; (j<=efhCPHI); j++)
fprintf(xf[j].fp, "%10g %10g\n",t,xf[j].val);
av_phipsi(xf[efhPHI].fp,xf[efhPSI].fp,xf[efhPHI].fp2,xf[efhPSI].fp2,
t,nres,bb);
av_hblen(xf[efhHB3].fp,xf[efhHB3].fp2,
xf[efhHB4].fp,xf[efhHB4].fp2,
xf[efhHB5].fp,xf[efhHB5].fp2,
t,nres,bb);
if (otrj)
dump_otrj(otrj,nall,allindex,x,xf[nSel].val,xav);
}
} while (read_next_x(oenv,status,&t,natoms,x,box));
fprintf(stderr,"\n");
gmx_rmpbc_done(gpbc);
close_trj(status);
if (otrj) {
ffclose(otrj);
fac=1.0/teller;
for(i=0; (i<nall); i++) {
ai=allindex[i];
for(m=0; (m<DIM); m++)
xav[ai][m]*=fac;
}
write_sto_conf_indexed(opt2fn("-co",NFILE,fnm),
"Weighted and Averaged conformation",
&(top->atoms),xav,NULL,ePBC,box,nall,allindex);
}
for(i=0; (i<nres); i++) {
if (bb[i].nrms > 0) {
fprintf(xf[efhRMSA].fp,"%10d %10g\n",r0+i,bb[i].rmsa/bb[i].nrms);
}
fprintf(xf[efhAHX].fp,"%10d %10g\n",r0+i,(bb[i].nhx*100.0)/(real )teller);
fprintf(xf[efhJCA].fp,"%10d %10g\n",
r0+i,140.3+(bb[i].jcaha/(double)teller));
}
for(i=0; (i<efhNR); i++) {
ffclose(xf[i].fp);
if (xf[i].bfp2)
ffclose(xf[i].fp2);
do_view(oenv,xf[i].filenm,"-nxy");
}
thanx(stderr);
return 0;
}
int main(int argc, char *argv[])
{
t_symtab tab;
static char *desc[] = {
"[TT]hexamer[tt] takes a single input coordinate file and makes five symmetry",
"related copies."
};
#define NPA asize(pa)
t_filenm fnm[] = {
{ efSTX, "-f", NULL, ffREAD },
{ efPDB, "-o", NULL, ffWRITE }
};
#define NFILE asize(fnm)
gmx_bool bCenter = FALSE;
gmx_bool bTrimer = FALSE;
gmx_bool bAlternate = FALSE;
real rDist = 0,rAngleZ = 0,rAngleX = 0, alterz = 0;
t_pargs pa[] = {
{ "-center", FALSE, etBOOL, {&bCenter},
"Center molecule on Z-axis first" },
{ "-trimer", FALSE, etBOOL, {&bTrimer},
"Make trimer rather than hexamer" },
{ "-alternate",FALSE, etBOOL, {&bAlternate},
"Turn every other molecule upside down" },
{ "-alterz", FALSE, etREAL, {&alterz},
"Add this amount to Z-coordinate in every other molecule" },
{ "-radius", FALSE, etREAL, {&rDist},
"Distance of protein axis from Z-axis (implies [TT]-center[tt])" },
{ "-anglez", FALSE, etREAL, {&rAngleZ},
"Initial angle of rotation around Z-axis of protein" },
{ "-anglex", FALSE, etREAL, {&rAngleX},
"Initial angle of rotation around X-axis of protein" }
};
#define NPA asize(pa)
FILE *fp;
int i,iout,now,natom;
rvec *xin,*vin,*xout;
matrix box;
t_atoms atoms,aout;
char *infile,*outfile,title[256],buf[32];
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,0,NFILE,fnm,NPA,pa,
asize(desc),desc,0,NULL);
bCenter = bCenter || (rDist > 0) || bAlternate;
infile = ftp2fn(efSTX,NFILE,fnm);
outfile = ftp2fn(efPDB,NFILE,fnm);
get_stx_coordnum(infile,&natom);
init_t_atoms(&atoms,natom,TRUE);
snew(xin,natom);
snew(xout,natom);
snew(vin,natom);
read_stx_conf(infile,title,&atoms,xin,vin,box);
printf("Read %d atoms\n",atoms.nr);
if (bCenter)
prep_x(atoms.nr,xin,rDist,rAngleZ,rAngleX);
fp = ffopen(outfile,"w");
for(i=0; (i<(bTrimer ? 3 : 6)); i++) {
rotate_x(atoms.nr,xin,i*(bTrimer ? 120.0 : 60.0),xout,TRUE,
bAlternate && ((i % 2) != 0),alterz*(((i % 2) == 0) ? 0 : 1));
sprintf(buf,"Rotated %d degrees",i*(bTrimer ? 120 : 60));
write_pdbfile(fp,buf,&atoms,xout,box,'A'+i,1+i);
}
ffclose(fp);
thanx(stderr);
return 0;
}
int f_fcst_ave(ARG2) {
struct ave_struct *save;
int i, pdt, new_type;
int year, month, day, hour, minute, second;
int tyear, tmonth, tday, thour, tminute, tsecond;
int missing;
char string[10];
// initialization
if (mode == -1) {
save_translation = decode = 1;
// allocate static structure
*local = save = (struct ave_struct *) malloc( sizeof(struct ave_struct));
if (save == NULL) fatal_error("memory allocation fcst_ave","");
i = sscanf(arg1, "%d%2s", &save->dt,string);
if (i != 2) fatal_error("fcst_ave: delta-time: (int)(2 characters) %s", arg1);
save->dt_unit = -1;
if (strcmp(string,"hr") == 0) save->dt_unit = 1;
else if (strcmp(string,"dy") == 0) save->dt_unit = 2;
else if (strcmp(string,"mo") == 0) save->dt_unit = 3;
else if (strcmp(string,"yr") == 0) save->dt_unit = 4;
if (save->dt_unit == -1) fatal_error("fcst_ave: unsupported time unit %s", string);
if ((save->output = ffopen(arg2, file_append ? "ab" : "wb")) == NULL) {
fatal_error("fcst_ave: could not open file %s", arg2);
}
save->has_val = 0;
save->n = NULL;
save->sum = NULL;
init_sec(save->first_sec);
init_sec(save->next_sec);
return 0;
}
save = (struct ave_struct *) *local;
if (mode == -2) { // cleanup
if (save->has_val == 1) {
do_ave(save);
}
ffclose(save->output);
free_ave_struct(save);
return 0;
}
// if data
if (mode >= 0) {
// 1/2015 use_scale = 0;
pdt = GB2_ProdDefTemplateNo(sec);
if (mode == 98) fprintf(stderr,"fcst_ave: pdt=%d\n",pdt);
// only support pdt == 0, 1 and 8
if (pdt != 0 && pdt != 1 && pdt != 8) return 0;
// first time through .. save data and return
if (save->has_val == 0) { // new data: write and save
init_ave_struct(save,ndata);
add_to_ave_struct(save, sec, data, ndata, 0);
// copy sec
copy_sec(sec, save->first_sec);
copy_sec(sec, save->next_sec);
// get reference time and save it
get_time(sec[1]+12,&save->ref_year, &save->ref_month, &save->ref_day, &save->ref_hour, &save->ref_minute, &save->ref_second);
if (start_ft(sec, &save->fcst_year, &save->fcst_month, &save->fcst_day, &save->fcst_hour,
&save->fcst_minute, &save->fcst_second) != 0) {
fatal_error("fcst_ave: could not determine the start FT time","");
}
// get verf time and save it
if (verftime(sec, &save->year2, &save->month2, &save->day2, &save->hour2, &save->minute2, &save->second2) != 0) {
fatal_error("fcst_ave: could not determine the verification time","");
}
save->has_val = 1;
return 0;
}
// check to see if new variable
new_type = 0;
// get the reference time of field
get_time(sec[1]+12, &year, &month, &day, &hour, &minute, &second);
// see if reference time has not changed
if (year != save->ref_year) new_type = 1;
else if (month != save->ref_month) new_type = 1;
else if (day != save->ref_day) new_type = 1;
else if (hour != save->ref_hour) new_type = 1;
else if (minute != save->ref_minute) new_type = 1;
else if (second != save->ref_second) new_type = 1;
if (new_type == 0) {
if (same_sec0(sec,save->first_sec) == 0 ||
same_sec1_not_time(sec,save->first_sec) == 0 ||
same_sec3(sec,save->first_sec) == 0 ||
same_sec4_not_time(sec,save->first_sec) == 0)
new_type = 1;
if (mode == 98) fprintf(stderr, "fcst_ave: testsec %d %d %d %d\n", same_sec0(sec,save->first_sec),
same_sec1_not_time(sec,save->first_sec),
same_sec3(sec,save->first_sec),
same_sec4_not_time(sec,save->first_sec));
}
if (mode == 98) fprintf(stderr, "fcst_ave: new_type %d\n", new_type);
// unlike f_ave, assume no missing .. it is a fcst not observations
// check to see if verification date is expected value
if (new_type == 0) {
tyear = save->fcst_year;
tmonth = save->fcst_month;
tday = save->fcst_day;
thour = save->fcst_hour;
tminute = save->fcst_minute;
tsecond = save->fcst_second;
add_time(&tyear, &tmonth, &tday, &thour, &tminute, &tsecond, save->dt, save->dt_unit);
if (start_ft(sec, &year, &month, &day, &hour, &minute, &second) != 0)
fatal_error("fcst_ave: could not determine the start_ft time","");
if (cmp_time(year,month,day,hour,minute,second,tyear,tmonth,tday,thour,tminute,tsecond)) {
new_type = 1;
if (mode == 98) fprintf(stderr, "fcst_ave: unexpected verf time, new_type=1\n");
}
else {
save->fcst_year = year;
save->fcst_month = month;
save->fcst_day = day;
save->fcst_hour = hour;
save->fcst_minute = minute;
save->fcst_second = second;
}
}
// check to see if verification date is expected value
missing = 0;
if (new_type == 0) {
if (verftime(sec, &year, &month, &day, &hour, &minute, &second) != 0)
fatal_error("fcst_ave: could not determine the verification time","");
tyear = save->year2;
tmonth = save->month2;
tday = save->day2;
thour = save->hour2;
tminute = save->minute2;
tsecond = save->second2;
add_time(&tyear, &tmonth, &tday, &thour, &tminute, &tsecond, save->dt, save->dt_unit);
if (cmp_time(year,month,day,hour,minute,second,tyear,tmonth,tday,thour,tminute,tsecond) != 0) new_type = 1;
else {
save->year2 = year;
save->month2 = month;
save->day2 = day;
save->hour2 = hour;
save->minute2 = minute;
save->second2 = second;
}
}
// if data is the same as the previous, update the sum
if (mode == 98) fprintf(stderr, "fcst_ave ave: before update_sum new_type %d\n", new_type);
if (new_type == 0) { // update sum
if (mode == 98) fprintf(stderr, "fcst_ave: update sum\n");
add_to_ave_struct(save, sec, data, ndata, missing);
return 0;
}
// new field, do grib output and save current data
do_ave(save);
init_ave_struct(save, ndata);
add_to_ave_struct(save, sec, data, ndata, 0);
copy_sec(sec, save->first_sec);
copy_sec(sec, save->next_sec);
// get reference time and save it
get_time(sec[1]+12,&save->ref_year, &save->ref_month, &save->ref_day, &save->ref_hour, &save->ref_minute, &save->ref_second);
if (start_ft(sec, &save->fcst_year, &save->fcst_month, &save->fcst_day, &save->fcst_hour,
&save->fcst_minute, &save->fcst_second) != 0) {
fatal_error("fcst_ave: could not determine the start FT time","");
}
// get verf time and save it
if (verftime(sec, &save->year2, &save->month2, &save->day2, &save->hour2, &save->minute2, &save->second2) != 0) {
fatal_error("fcst_ave: could not determine the verification time","");
}
save->has_val = 1;
return 0;
}
return 0;
}
int gmx_make_edi(int argc, char *argv[])
{
static const char *desc[] = {
"[TT]make_edi[tt] generates an essential dynamics (ED) sampling input file to be used with [TT]mdrun[tt]",
"based on eigenvectors of a covariance matrix ([TT]g_covar[tt]) or from a",
"normal modes analysis ([TT]g_nmeig[tt]).",
"ED sampling can be used to manipulate the position along collective coordinates",
"(eigenvectors) of (biological) macromolecules during a simulation. Particularly,",
"it may be used to enhance the sampling efficiency of MD simulations by stimulating",
"the system to explore new regions along these collective coordinates. A number",
"of different algorithms are implemented to drive the system along the eigenvectors",
"([TT]-linfix[tt], [TT]-linacc[tt], [TT]-radfix[tt], [TT]-radacc[tt], [TT]-radcon[tt]),",
"to keep the position along a certain (set of) coordinate(s) fixed ([TT]-linfix[tt]),",
"or to only monitor the projections of the positions onto",
"these coordinates ([TT]-mon[tt]).[PAR]",
"References:[BR]",
"A. Amadei, A.B.M. Linssen, B.L. de Groot, D.M.F. van Aalten and ",
"H.J.C. Berendsen; An efficient method for sampling the essential subspace ",
"of proteins., J. Biomol. Struct. Dyn. 13:615-626 (1996)[BR]",
"B.L. de Groot, A. Amadei, D.M.F. van Aalten and H.J.C. Berendsen; ",
"Towards an exhaustive sampling of the configurational spaces of the ",
"two forms of the peptide hormone guanylin,",
"J. Biomol. Struct. Dyn. 13 : 741-751 (1996)[BR]",
"B.L. de Groot, A.Amadei, R.M. Scheek, N.A.J. van Nuland and H.J.C. Berendsen; ",
"An extended sampling of the configurational space of HPr from E. coli",
"Proteins: Struct. Funct. Gen. 26: 314-322 (1996)",
"[PAR]You will be prompted for one or more index groups that correspond to the eigenvectors,",
"reference structure, target positions, etc.[PAR]",
"[TT]-mon[tt]: monitor projections of the coordinates onto selected eigenvectors.[PAR]",
"[TT]-linfix[tt]: perform fixed-step linear expansion along selected eigenvectors.[PAR]",
"[TT]-linacc[tt]: perform acceptance linear expansion along selected eigenvectors.",
"(steps in the desired directions will be accepted, others will be rejected).[PAR]",
"[TT]-radfix[tt]: perform fixed-step radius expansion along selected eigenvectors.[PAR]",
"[TT]-radacc[tt]: perform acceptance radius expansion along selected eigenvectors.",
"(steps in the desired direction will be accepted, others will be rejected).",
"[BB]Note:[bb] by default the starting MD structure will be taken as origin of the first",
"expansion cycle for radius expansion. If [TT]-ori[tt] is specified, you will be able",
"to read in a structure file that defines an external origin.[PAR]",
"[TT]-radcon[tt]: perform acceptance radius contraction along selected eigenvectors",
"towards a target structure specified with [TT]-tar[tt].[PAR]",
"NOTE: each eigenvector can be selected only once. [PAR]",
"[TT]-outfrq[tt]: frequency (in steps) of writing out projections etc. to [TT].xvg[tt] file[PAR]",
"[TT]-slope[tt]: minimal slope in acceptance radius expansion. A new expansion",
"cycle will be started if the spontaneous increase of the radius (in nm/step)",
"is less than the value specified.[PAR]",
"[TT]-maxedsteps[tt]: maximum number of steps per cycle in radius expansion",
"before a new cycle is started.[PAR]",
"Note on the parallel implementation: since ED sampling is a 'global' thing",
"(collective coordinates etc.), at least on the 'protein' side, ED sampling",
"is not very parallel-friendly from an implementation point of view. Because",
"parallel ED requires some extra communication, expect the performance to be",
"lower as in a free MD simulation, especially on a large number of nodes and/or",
"when the ED group contains a lot of atoms. [PAR]",
"Please also note that if your ED group contains more than a single protein,",
"then the [TT].tpr[tt] file must contain the correct PBC representation of the ED group.",
"Take a look on the initial RMSD from the reference structure, which is printed",
"out at the start of the simulation; if this is much higher than expected, one",
"of the ED molecules might be shifted by a box vector. [PAR]",
"All ED-related output of [TT]mdrun[tt] (specify with [TT]-eo[tt]) is written to a [TT].xvg[tt] file",
"as a function of time in intervals of OUTFRQ steps.[PAR]",
"[BB]Note[bb] that you can impose multiple ED constraints and flooding potentials in",
"a single simulation (on different molecules) if several [TT].edi[tt] files were concatenated",
"first. The constraints are applied in the order they appear in the [TT].edi[tt] file. ",
"Depending on what was specified in the [TT].edi[tt] input file, the output file contains for each ED dataset[PAR]",
"[TT]*[tt] the RMSD of the fitted molecule to the reference structure (for atoms involved in fitting prior to calculating the ED constraints)[BR]",
"[TT]*[tt] projections of the positions onto selected eigenvectors[BR]",
"[PAR][PAR]",
"FLOODING:[PAR]",
"with [TT]-flood[tt], you can specify which eigenvectors are used to compute a flooding potential,",
"which will lead to extra forces expelling the structure out of the region described",
"by the covariance matrix. If you switch -restrain the potential is inverted and the structure",
"is kept in that region.",
"[PAR]",
"The origin is normally the average structure stored in the [TT]eigvec.trr[tt] file.",
"It can be changed with [TT]-ori[tt] to an arbitrary position in configuration space.",
"With [TT]-tau[tt], [TT]-deltaF0[tt], and [TT]-Eflnull[tt] you control the flooding behaviour.",
"Efl is the flooding strength, it is updated according to the rule of adaptive flooding.",
"Tau is the time constant of adaptive flooding, high [GRK]tau[grk] means slow adaption (i.e. growth). ",
"DeltaF0 is the flooding strength you want to reach after tau ps of simulation.",
"To use constant Efl set [TT]-tau[tt] to zero.",
"[PAR]",
"[TT]-alpha[tt] is a fudge parameter to control the width of the flooding potential. A value of 2 has been found",
"to give good results for most standard cases in flooding of proteins.",
"[GRK]alpha[grk] basically accounts for incomplete sampling, if you sampled further the width of the ensemble would",
"increase, this is mimicked by [GRK]alpha[grk] > 1.",
"For restraining, [GRK]alpha[grk] < 1 can give you smaller width in the restraining potential.",
"[PAR]",
"RESTART and FLOODING:",
"If you want to restart a crashed flooding simulation please find the values deltaF and Efl in",
"the output file and manually put them into the [TT].edi[tt] file under DELTA_F0 and EFL_NULL."
};
/* Save all the params in this struct and then save it in an edi file.
* ignoring fields nmass,massnrs,mass,tmass,nfit,fitnrs,edo
*/
static t_edipar edi_params;
enum {
evStepNr = evRADFIX + 1
};
static const char* evSelections[evNr] = {NULL, NULL, NULL, NULL, NULL, NULL};
static const char* evOptions[evNr] = {"-linfix", "-linacc", "-flood", "-radfix", "-radacc", "-radcon", "-mon"};
static const char* evParams[evStepNr] = {NULL, NULL};
static const char* evStepOptions[evStepNr] = {"-linstep", "-accdir", "-not_used", "-radstep"};
static const char* ConstForceStr;
static real * evStepList[evStepNr];
static real radfix = 0.0;
static real deltaF0 = 150;
static real deltaF = 0;
static real tau = .1;
static real constEfl = 0.0;
static real alpha = 1;
static int eqSteps = 0;
static int * listen[evNr];
static real T = 300.0;
const real kB = 2.5 / 300.0; /* k_boltzmann in MD units */
static gmx_bool bRestrain = FALSE;
static gmx_bool bHesse = FALSE;
static gmx_bool bHarmonic = FALSE;
t_pargs pa[] = {
{ "-mon", FALSE, etSTR, {&evSelections[evMON]},
"Indices of eigenvectors for projections of x (e.g. 1,2-5,9) or 1-100:10 means 1 11 21 31 ... 91" },
{ "-linfix", FALSE, etSTR, {&evSelections[0]},
"Indices of eigenvectors for fixed increment linear sampling" },
{ "-linacc", FALSE, etSTR, {&evSelections[1]},
"Indices of eigenvectors for acceptance linear sampling" },
{ "-radfix", FALSE, etSTR, {&evSelections[3]},
"Indices of eigenvectors for fixed increment radius expansion" },
{ "-radacc", FALSE, etSTR, {&evSelections[4]},
"Indices of eigenvectors for acceptance radius expansion" },
{ "-radcon", FALSE, etSTR, {&evSelections[5]},
"Indices of eigenvectors for acceptance radius contraction" },
{ "-flood", FALSE, etSTR, {&evSelections[2]},
"Indices of eigenvectors for flooding"},
{ "-outfrq", FALSE, etINT, {&edi_params.outfrq},
"Freqency (in steps) of writing output in [TT].xvg[tt] file" },
{ "-slope", FALSE, etREAL, { &edi_params.slope},
"Minimal slope in acceptance radius expansion"},
{ "-linstep", FALSE, etSTR, {&evParams[0]},
"Stepsizes (nm/step) for fixed increment linear sampling (put in quotes! \"1.0 2.3 5.1 -3.1\")"},
{ "-accdir", FALSE, etSTR, {&evParams[1]},
"Directions for acceptance linear sampling - only sign counts! (put in quotes! \"-1 +1 -1.1\")"},
{ "-radstep", FALSE, etREAL, {&radfix},
"Stepsize (nm/step) for fixed increment radius expansion"},
{ "-maxedsteps", FALSE, etINT, {&edi_params.maxedsteps},
"Maximum number of steps per cycle" },
{ "-eqsteps", FALSE, etINT, {&eqSteps},
"Number of steps to run without any perturbations "},
{ "-deltaF0", FALSE, etREAL, {&deltaF0},
"Target destabilization energy for flooding"},
{ "-deltaF", FALSE, etREAL, {&deltaF},
"Start deltaF with this parameter - default 0, nonzero values only needed for restart"},
{ "-tau", FALSE, etREAL, {&tau},
"Coupling constant for adaption of flooding strength according to deltaF0, 0 = infinity i.e. constant flooding strength"},
{ "-Eflnull", FALSE, etREAL, {&constEfl},
"The starting value of the flooding strength. The flooding strength is updated "
"according to the adaptive flooding scheme. For a constant flooding strength use [TT]-tau[tt] 0. "},
{ "-T", FALSE, etREAL, {&T},
"T is temperature, the value is needed if you want to do flooding "},
{ "-alpha", FALSE, etREAL, {&alpha},
"Scale width of gaussian flooding potential with alpha^2 "},
{ "-restrain", FALSE, etBOOL, {&bRestrain},
"Use the flooding potential with inverted sign -> effects as quasiharmonic restraining potential"},
{ "-hessian", FALSE, etBOOL, {&bHesse},
"The eigenvectors and eigenvalues are from a Hessian matrix"},
{ "-harmonic", FALSE, etBOOL, {&bHarmonic},
"The eigenvalues are interpreted as spring constant"},
{ "-constF", FALSE, etSTR, {&ConstForceStr},
"Constant force flooding: manually set the forces for the eigenvectors selected with -flood "
"(put in quotes! \"1.0 2.3 5.1 -3.1\"). No other flooding parameters are needed when specifying the forces directly."}
};
#define NPA asize(pa)
rvec *xref1;
int nvec1, *eignr1 = NULL;
rvec *xav1, **eigvec1 = NULL;
t_atoms *atoms = NULL;
int nav; /* Number of atoms in the average structure */
char *grpname;
const char *indexfile;
int i;
atom_id *index, *ifit;
int nfit; /* Number of atoms in the reference/fit structure */
int ev_class; /* parameter _class i.e. evMON, evRADFIX etc. */
int nvecs;
real *eigval1 = NULL; /* in V3.3 this is parameter of read_eigenvectors */
const char *EdiFile;
const char *TargetFile;
const char *OriginFile;
const char *EigvecFile;
output_env_t oenv;
/*to read topology file*/
t_topology top;
int ePBC;
char title[STRLEN];
matrix topbox;
rvec *xtop;
gmx_bool bTop, bFit1;
t_filenm fnm[] = {
{ efTRN, "-f", "eigenvec", ffREAD },
{ efXVG, "-eig", "eigenval", ffOPTRD },
{ efTPS, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efSTX, "-tar", "target", ffOPTRD},
{ efSTX, "-ori", "origin", ffOPTRD},
{ efEDI, "-o", "sam", ffWRITE }
};
#define NFILE asize(fnm)
edi_params.outfrq = 100; edi_params.slope = 0.0; edi_params.maxedsteps = 0;
parse_common_args(&argc, argv, 0,
NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv);
indexfile = ftp2fn_null(efNDX, NFILE, fnm);
EdiFile = ftp2fn(efEDI, NFILE, fnm);
TargetFile = opt2fn_null("-tar", NFILE, fnm);
OriginFile = opt2fn_null("-ori", NFILE, fnm);
for (ev_class = 0; ev_class < evNr; ++ev_class)
{
if (opt2parg_bSet(evOptions[ev_class], NPA, pa))
{
/*get list of eigenvectors*/
nvecs = sscan_list(&(listen[ev_class]), opt2parg_str(evOptions[ev_class], NPA, pa), evOptions[ev_class]);
if (ev_class < evStepNr-2)
{
/*if apropriate get list of stepsizes for these eigenvectors*/
if (opt2parg_bSet(evStepOptions[ev_class], NPA, pa))
{
evStepList[ev_class] =
scan_vecparams(opt2parg_str(evStepOptions[ev_class], NPA, pa), evStepOptions[ev_class], nvecs);
}
else /*if list is not given fill with zeros */
{
snew(evStepList[ev_class], nvecs);
for (i = 0; i < nvecs; i++)
{
evStepList[ev_class][i] = 0.0;
}
}
}
else if (ev_class == evRADFIX && opt2parg_bSet(evStepOptions[ev_class], NPA, pa))
{
snew(evStepList[ev_class], nvecs);
for (i = 0; i < nvecs; i++)
{
evStepList[ev_class][i] = radfix;
}
}
else if (ev_class == evFLOOD)
{
snew(evStepList[ev_class], nvecs);
/* Are we doing constant force flooding? In that case, we read in
* the fproj values from the command line */
if (opt2parg_bSet("-constF", NPA, pa))
{
evStepList[ev_class] = scan_vecparams(opt2parg_str("-constF", NPA, pa), "-constF", nvecs);
}
}
else
{
}; /*to avoid ambiguity */
}
else /* if there are no eigenvectors for this option set list to zero */
{
listen[ev_class] = NULL;
snew(listen[ev_class], 1);
listen[ev_class][0] = 0;
}
}
/* print the interpreted list of eigenvectors - to give some feedback*/
for (ev_class = 0; ev_class < evNr; ++ev_class)
{
printf("Eigenvector list %7s consists of the indices: ", evOptions[ev_class]);
i = 0;
while (listen[ev_class][i])
{
printf("%d ", listen[ev_class][i++]);
}
printf("\n");
}
EigvecFile = NULL;
EigvecFile = opt2fn("-f", NFILE, fnm);
/*read eigenvectors from eigvec.trr*/
read_eigenvectors(EigvecFile, &nav, &bFit1,
&xref1, &edi_params.fitmas, &xav1, &edi_params.pcamas, &nvec1, &eignr1, &eigvec1, &eigval1);
bTop = read_tps_conf(ftp2fn(efTPS, NFILE, fnm),
title, &top, &ePBC, &xtop, NULL, topbox, 0);
atoms = &top.atoms;
printf("\nSelect an index group of %d elements that corresponds to the eigenvectors\n", nav);
get_index(atoms, indexfile, 1, &i, &index, &grpname); /*if indexfile != NULL parameter 'atoms' is ignored */
if (i != nav)
{
gmx_fatal(FARGS, "you selected a group with %d elements instead of %d",
i, nav);
}
printf("\n");
if (xref1 == NULL)
{
if (bFit1)
{
/* if g_covar used different coordinate groups to fit and to do the PCA */
printf("\nNote: the structure in %s should be the same\n"
" as the one used for the fit in g_covar\n", ftp2fn(efTPS, NFILE, fnm));
printf("\nSelect the index group that was used for the least squares fit in g_covar\n");
}
else
{
printf("\nNote: Apparently no fitting was done in g_covar.\n"
" However, you need to select a reference group for fitting in mdrun\n");
}
get_index(atoms, indexfile, 1, &nfit, &ifit, &grpname);
snew(xref1, nfit);
for (i = 0; i < nfit; i++)
{
copy_rvec(xtop[ifit[i]], xref1[i]);
}
}
else
{
nfit = nav;
ifit = index;
}
if (opt2parg_bSet("-constF", NPA, pa))
{
/* Constant force flooding is special: Most of the normal flooding
* options are not needed. */
edi_params.flood.bConstForce = TRUE;
}
else
{
/* For normal flooding read eigenvalues and store them in evSteplist[evFLOOD] */
if (listen[evFLOOD][0] != 0)
{
read_eigenvalues(listen[evFLOOD], opt2fn("-eig", NFILE, fnm), evStepList[evFLOOD], bHesse, kB*T);
}
edi_params.flood.tau = tau;
edi_params.flood.deltaF0 = deltaF0;
edi_params.flood.deltaF = deltaF;
edi_params.presteps = eqSteps;
edi_params.flood.kT = kB*T;
edi_params.flood.bHarmonic = bHarmonic;
if (bRestrain)
{
/* Trick: invert sign of Efl and alpha2 then this will give the same sign in the exponential and inverted sign outside */
edi_params.flood.constEfl = -constEfl;
edi_params.flood.alpha2 = -sqr(alpha);
}
else
{
edi_params.flood.constEfl = constEfl;
edi_params.flood.alpha2 = sqr(alpha);
}
}
edi_params.ned = nav;
/*number of system atoms */
edi_params.nini = atoms->nr;
/*store reference and average structure in edi_params*/
make_t_edx(&edi_params.sref, nfit, xref1, ifit );
make_t_edx(&edi_params.sav, nav, xav1, index);
/* Store target positions in edi_params */
if (opt2bSet("-tar", NFILE, fnm))
{
if (0 != listen[evFLOOD][0])
{
fprintf(stderr, "\nNote: Providing a TARGET structure has no effect when using flooding.\n"
" You may want to use -ori to define the flooding potential center.\n\n");
}
get_structure(atoms, indexfile, TargetFile, &edi_params.star, nfit, ifit, nav, index);
}
else
{
make_t_edx(&edi_params.star, 0, NULL, index);
}
/* Store origin positions */
if (opt2bSet("-ori", NFILE, fnm))
{
get_structure(atoms, indexfile, OriginFile, &edi_params.sori, nfit, ifit, nav, index);
}
else
{
make_t_edx(&edi_params.sori, 0, NULL, index);
}
/* Write edi-file */
write_the_whole_thing(ffopen(EdiFile, "w"), &edi_params, eigvec1, nvec1, listen, evStepList);
thanx(stderr);
return 0;
}
int f_ncep_norm(ARG1) {
struct local_struct {
float *val;
int has_val;
unsigned char *clone_sec[9];
FILE *output;
};
struct local_struct *save;
int j, pdt, fhr_1, fhr_2, dt1, dt2, new_type, is_ave;
unsigned int i;
float *d1, *data_tmp;
if (mode == -1) { // initialization
save_translation = decode = 1;
// allocate static variables
*local = save = (struct local_struct *) malloc( sizeof(struct local_struct));
if (save == NULL) fatal_error("memory allocation f_normalize","");
if ((save->output = (void *) ffopen(arg1, file_append ? "ab" : "wb")) == NULL) {
fatal_error("f_ncep_norm: could not open file %s", arg1);
}
save->has_val = 0;
init_sec(save->clone_sec);
return 0;
}
save = *local;
if (mode == -2) { // cleanup
if (save->has_val == 1) {
free(save->val);
free_sec(save->clone_sec);
free(save);
}
return 0;
}
if (mode >= 0) { // processing
// only hande PDT = 8
pdt = GB2_ProdDefTemplateNo(sec);
if (pdt != 8) return 0;
// only process averages or accumulations
// check for code table 4.8
j = code_table_4_10(sec);
if (mode == 99) fprintf(stderr,"\nncep_norm: code table 4.10 (ave/acc/etc)=%d\n",j);
if (j == 0) is_ave = 1; // average
else if (j == 1) is_ave = 0; // accumulation
else return 0; // only process average or accumulations
// only process when fcst time units == ave/acc time units
if (sec[4][17] != sec[4][48]) {
if (int4(sec[4]+18) != 0) {
return 0;
}
}
fhr_2 = int4(sec[4]+18); // start time
dt2 = int4(sec[4]+49); // delta-time
if (dt2 == 0) return 0; // dt == 0
if (save->has_val == 0) { // new data: write and save
if ((data_tmp = (float *) malloc(ndata * sizeof(float))) == NULL)
fatal_error("memory allocation - data_tmp","");
undo_output_order(data, data_tmp, ndata);
grib_wrt(sec, data_tmp, ndata, nx, ny, use_scale, dec_scale, bin_scale,
wanted_bits, max_bits, grib_type, save->output);
/*
if (grib_type == simple) grib_out(sec, data_tmp, ndata, save->output);
else if (grib_type == jpeg) jpeg_grib_out(sec, data_tmp, ndata, nx,
ny, use_scale, dec_scale, bin_scale, save->output);
else if (grib_type == ieee) ieee_grib_out(sec, data_tmp, ndata,
save->output);
else fatal_error("NCEP_norm: unsupported grib type output","");
*/
if (flush_mode) fflush(save->output);
free(data_tmp);
if (save->has_val == 1) { // copy data to save
free(save->val); // save = new field
free_sec(save->clone_sec);
}
copy_sec(sec, save->clone_sec);
copy_data(data,ndata,&(save->val));
save->has_val = 1;
if (mode == 99) fprintf(stderr," ncep_norm: saved as new field\n");
return 0;
}
new_type = 0;
fhr_1 = int4(save->clone_sec[4]+18); // start time of save message
dt1 = int4(save->clone_sec[4]+49); // delta time
if (mode == 99) fprintf(stderr,"ncep_norm: is_ave = %d\n fhr_1 %d dt1 %d fhr_2 %d dt2 %d\n",is_ave,
fhr_1, dt1, fhr_2, dt2);
if (fhr_1 != fhr_2) new_type = 1;
if (new_type == 0) {
if (same_sec0(sec,save->clone_sec) == 0 ||
same_sec1(sec,save->clone_sec) == 0 ||
same_sec3(sec,save->clone_sec) == 0 ||
same_sec4_diff_ave_period(sec,save->clone_sec) == 0) {
new_type = 1;
}
}
if (new_type == 1) { // fields dont match: write and save
if ((data_tmp = (float *) malloc(ndata * sizeof(float))) == NULL)
fatal_error("memory allocation - data_tmp","");
undo_output_order(data, data_tmp, ndata);
grib_wrt(sec, data_tmp, ndata, nx, ny, use_scale, dec_scale, bin_scale,
wanted_bits, max_bits, grib_type, save->output);
/*
if (grib_type == simple) grib_out(sec, data_tmp, ndata, save->output);
else if (grib_type == jpeg) jpeg_grib_out(sec, data_tmp, ndata, nx,
ny, use_scale, dec_scale, bin_scale, save->output);
else if (grib_type == ieee) ieee_grib_out(sec, data_tmp, ndata,
save->output);
*/
if (flush_mode) fflush(save->output);
free(data_tmp);
if (save->has_val == 1) { // copy data to save
free(save->val); // save = new field
free_sec(save->clone_sec);
}
copy_sec(sec, save->clone_sec);
copy_data(data,ndata,&(save->val));
save->has_val = 1;
if (mode == 99) fprintf(stderr," ncep_norm: saved as new type/sequence\n");
return 0;
}
/* now do stuff */
if (dt1 == dt2) return 0; // same ending time
// change metadata
int_char(dt2-dt1, save->clone_sec[4]+49); // dt = dt2 - dt1
save->clone_sec[4][17] = sec[4][48]; // new forecast time unit
int_char(dt1+fhr_1, save->clone_sec[4]+18); // fhr = fhr + dt1
for (i = 34; i < 41; i++) { // ending time from pds2
save->clone_sec[4][i] = sec[4][i];
}
if (mode == 99) {
if (is_ave)
fprintf(stderr," process: factor: NEW*%g - OLD*%g\n", dt2/ (double) (dt2 - dt1),
dt1/ (double) (dt2-dt1));
else fprintf(stderr," process: current-last\n");
}
// change floating point data
d1= save->val;
for (i = 0; i < ndata; i++) {
if (!UNDEFINED_VAL(data[i]) && !UNDEFINED_VAL(*d1) ) {
if (is_ave) {
*d1 = (data[i]*dt2 - *d1*dt1) / (double) (dt2 - dt1);
}
else { // accumulation
*d1 = data[i] - *d1;
}
}
else *d1 = UNDEFINED;
d1++;
}
// write grib output
if ((data_tmp = (float *) malloc(ndata * sizeof(float))) == NULL)
fatal_error("memory allocation - data_tmp","");
undo_output_order(save->val, data_tmp, ndata);
grib_wrt(save->clone_sec, data_tmp, ndata, nx, ny, use_scale, dec_scale, bin_scale,
wanted_bits, max_bits, grib_type, save->output);
/*
if (grib_type == simple) grib_out(save->clone_sec, data_tmp, ndata, save->output);
else if (grib_type == jpeg) jpeg_grib_out(save->clone_sec, data_tmp, ndata, nx,
ny, use_scale, dec_scale, bin_scale, save->output);
else if (grib_type == ieee) ieee_grib_out(save->clone_sec, data_tmp, ndata,
save->output);
else if (grib_type == complex1) complex_grib_out(save->clone_sec, data_tmp, ndata,
use_scale, dec_scale, bin_scale, wanted_bits, max_bits, 1, save->output);
else if (grib_type == complex2) complex_grib_out(save->clone_sec, data_tmp, ndata,
use_scale, dec_scale, bin_scale, wanted_bits, max_bits, 2, save->output);
else if (grib_type == complex3) complex_grib_out(save->clone_sec, data_tmp, ndata,
use_scale, dec_scale, bin_scale, wanted_bits, max_bits, 3, save->output);
else fatal_error("NCEP_norm: unsupported grib output type","");
*/
if (flush_mode) fflush(save->output);
free(data_tmp);
// save data
free(save->val); // save = new field
free_sec(save->clone_sec);
copy_sec(sec, save->clone_sec);
copy_data(data,ndata,&(save->val));
return 0;
}
return 0;
}
void init_debug (char *dbgfile)
{
no_buffers();
debug=ffopen(dbgfile,"w");
bDebug = TRUE;
}
int gmx_spatial(int argc,char *argv[])
{
const char *desc[] = {
"[TT]g_spatial[tt] calculates the spatial distribution function and ",
"outputs it in a form that can be read by VMD as Gaussian98 cube format. ",
"This was developed from template.c (GROMACS-3.3). ",
"For a system of 32,000 atoms and a 50 ns trajectory, the SDF can be generated ",
"in about 30 minutes, with most of the time dedicated to the two runs through ",
"[TT]trjconv[tt] that are required to center everything properly. ",
"This also takes a whole bunch of space (3 copies of the [TT].xtc[tt] file). ",
"Still, the pictures are pretty and very informative when the fitted selection is properly made. ",
"3-4 atoms in a widely mobile group (like a free amino acid in solution) works ",
"well, or select the protein backbone in a stable folded structure to get the SDF ",
"of solvent and look at the time-averaged solvation shell. ",
"It is also possible using this program to generate the SDF based on some arbitrary ",
"Cartesian coordinate. To do that, simply omit the preliminary [TT]trjconv[tt] steps. \n",
"USAGE: \n",
"1. Use [TT]make_ndx[tt] to create a group containing the atoms around which you want the SDF \n",
"2. [TT]trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc none[tt] \n",
"3. [TT]trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans[tt] \n",
"4. run [TT]g_spatial[tt] on the [TT].xtc[tt] output of step #3. \n",
"5. Load [TT]grid.cube[tt] into VMD and view as an isosurface. \n",
"[BB]Note[bb] that systems such as micelles will require [TT]trjconv -pbc cluster[tt] between steps 1 and 2\n",
"WARNINGS:[BR]",
"The SDF will be generated for a cube that contains all bins that have some non-zero occupancy. ",
"However, the preparatory [TT]-fit rot+trans[tt] option to [TT]trjconv[tt] implies that your system will be rotating ",
"and translating in space (in order that the selected group does not). Therefore the values that are ",
"returned will only be valid for some region around your central group/coordinate that has full overlap ",
"with system volume throughout the entire translated/rotated system over the course of the trajectory. ",
"It is up to the user to ensure that this is the case. \n",
"BUGS:[BR]",
"When the allocated memory is not large enough, a segmentation fault may occur. This is usually detected ",
"and the program is halted prior to the fault while displaying a warning message suggesting the use of the [TT]-nab[tt] (Number of Additional Bins)",
"option. However, the program does not detect all such events. If you encounter a segmentation fault, run it again ",
"with an increased [TT]-nab[tt] value. \n",
"RISKY OPTIONS:[BR]",
"To reduce the amount of space and time required, you can output only the coords ",
"that are going to be used in the first and subsequent run through [TT]trjconv[tt]. ",
"However, be sure to set the [TT]-nab[tt] option to a sufficiently high value since ",
"memory is allocated for cube bins based on the initial coordinates and the [TT]-nab[tt] ",
"option value. \n"
};
static gmx_bool bPBC=FALSE;
static gmx_bool bSHIFT=FALSE;
static int iIGNOREOUTER=-1; /*Positive values may help if the surface is spikey */
static gmx_bool bCUTDOWN=TRUE;
static real rBINWIDTH=0.05; /* nm */
static gmx_bool bCALCDIV=TRUE;
static int iNAB=4;
t_pargs pa[] = {
{ "-pbc", FALSE, etBOOL, {&bPBC},
"Use periodic boundary conditions for computing distances" },
{ "-div", FALSE, etBOOL, {&bCALCDIV},
"Calculate and apply the divisor for bin occupancies based on atoms/minimal cube size. Set as TRUE for visualization and as FALSE ([TT]-nodiv[tt]) to get accurate counts per frame" },
{ "-ign", FALSE, etINT, {&iIGNOREOUTER},
"Do not display this number of outer cubes (positive values may reduce boundary speckles; -1 ensures outer surface is visible)" },
/* { "-cut", bCUTDOWN, etBOOL, {&bCUTDOWN},*/
/* "Display a total cube that is of minimal size" }, */
{ "-bin", FALSE, etREAL, {&rBINWIDTH},
"Width of the bins in nm" },
{ "-nab", FALSE, etINT, {&iNAB},
"Number of additional bins to ensure proper memory allocation" }
};
double MINBIN[3];
double MAXBIN[3];
t_topology top;
int ePBC;
char title[STRLEN];
t_trxframe fr;
rvec *xtop,*shx[26];
matrix box,box_pbc;
t_trxstatus *status;
int flags = TRX_READ_X;
t_pbc pbc;
t_atoms *atoms;
int natoms;
char *grpnm,*grpnmp;
atom_id *index,*indexp;
int i,nidx,nidxp;
int v;
int j,k;
long ***bin=(long ***)NULL;
long nbin[3];
FILE *flp;
long x,y,z,minx,miny,minz,maxx,maxy,maxz;
long numfr, numcu;
long tot,max,min;
double norm;
output_env_t oenv;
gmx_rmpbc_t gpbc=NULL;
t_filenm fnm[] = {
{ efTPS, NULL, NULL, ffREAD }, /* this is for the topology */
{ efTRX, "-f", NULL, ffREAD }, /* and this for the trajectory */
{ efNDX, NULL, NULL, ffOPTRD }
};
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
/* This is the routine responsible for adding default options,
* calling the X/motif interface, etc. */
parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&oenv);
read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,&xtop,NULL,box,TRUE);
sfree(xtop);
atoms=&(top.atoms);
printf("Select group to generate SDF:\n");
get_index(atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&nidx,&index,&grpnm);
printf("Select group to output coords (e.g. solute):\n");
get_index(atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&nidxp,&indexp,&grpnmp);
/* The first time we read data is a little special */
natoms=read_first_frame(oenv,&status,ftp2fn(efTRX,NFILE,fnm),&fr,flags);
/* Memory Allocation */
MINBIN[XX]=MAXBIN[XX]=fr.x[0][XX];
MINBIN[YY]=MAXBIN[YY]=fr.x[0][YY];
MINBIN[ZZ]=MAXBIN[ZZ]=fr.x[0][ZZ];
for(i=1; i<top.atoms.nr; ++i) {
if(fr.x[i][XX]<MINBIN[XX])MINBIN[XX]=fr.x[i][XX];
if(fr.x[i][XX]>MAXBIN[XX])MAXBIN[XX]=fr.x[i][XX];
if(fr.x[i][YY]<MINBIN[YY])MINBIN[YY]=fr.x[i][YY];
if(fr.x[i][YY]>MAXBIN[YY])MAXBIN[YY]=fr.x[i][YY];
if(fr.x[i][ZZ]<MINBIN[ZZ])MINBIN[ZZ]=fr.x[i][ZZ];
if(fr.x[i][ZZ]>MAXBIN[ZZ])MAXBIN[ZZ]=fr.x[i][ZZ];
}
for (i=ZZ; i>=XX; --i){
MAXBIN[i]=(ceil((MAXBIN[i]-MINBIN[i])/rBINWIDTH)+(double)iNAB)*rBINWIDTH+MINBIN[i];
MINBIN[i]-=(double)iNAB*rBINWIDTH;
nbin[i]=(long)ceil((MAXBIN[i]-MINBIN[i])/rBINWIDTH);
}
bin=(long ***)malloc(nbin[XX]*sizeof(long **));
if(!bin)mequit();
for(i=0; i<nbin[XX]; ++i){
bin[i]=(long **)malloc(nbin[YY]*sizeof(long *));
if(!bin[i])mequit();
for(j=0; j<nbin[YY]; ++j){
bin[i][j]=(long *)calloc(nbin[ZZ],sizeof(long));
if(!bin[i][j])mequit();
}
}
copy_mat(box,box_pbc);
numfr=0;
minx=miny=minz=999;
maxx=maxy=maxz=0;
if (bPBC)
gpbc = gmx_rmpbc_init(&top.idef,ePBC,natoms,box);
/* This is the main loop over frames */
do {
/* Must init pbc every step because of pressure coupling */
copy_mat(box,box_pbc);
if (bPBC) {
gmx_rmpbc_trxfr(gpbc,&fr);
set_pbc(&pbc,ePBC,box_pbc);
}
for(i=0; i<nidx; i++) {
if(fr.x[index[i]][XX]<MINBIN[XX]||fr.x[index[i]][XX]>MAXBIN[XX]||
fr.x[index[i]][YY]<MINBIN[YY]||fr.x[index[i]][YY]>MAXBIN[YY]||
fr.x[index[i]][ZZ]<MINBIN[ZZ]||fr.x[index[i]][ZZ]>MAXBIN[ZZ])
{
printf("There was an item outside of the allocated memory. Increase the value given with the -nab option.\n");
printf("Memory was allocated for [%f,%f,%f]\tto\t[%f,%f,%f]\n",MINBIN[XX],MINBIN[YY],MINBIN[ZZ],MAXBIN[XX],MAXBIN[YY],MAXBIN[ZZ]);
printf("Memory was required for [%f,%f,%f]\n",fr.x[index[i]][XX],fr.x[index[i]][YY],fr.x[index[i]][ZZ]);
exit(1);
}
x=(long)ceil((fr.x[index[i]][XX]-MINBIN[XX])/rBINWIDTH);
y=(long)ceil((fr.x[index[i]][YY]-MINBIN[YY])/rBINWIDTH);
z=(long)ceil((fr.x[index[i]][ZZ]-MINBIN[ZZ])/rBINWIDTH);
++bin[x][y][z];
if(x<minx)minx=x;
if(x>maxx)maxx=x;
if(y<miny)miny=y;
if(y>maxy)maxy=y;
if(z<minz)minz=z;
if(z>maxz)maxz=z;
}
numfr++;
/* printf("%f\t%f\t%f\n",box[XX][XX],box[YY][YY],box[ZZ][ZZ]); */
} while(read_next_frame(oenv,status,&fr));
if (bPBC)
gmx_rmpbc_done(gpbc);
if(!bCUTDOWN){
minx=miny=minz=0;
maxx=nbin[XX];
maxy=nbin[YY];
maxz=nbin[ZZ];
}
/* OUTPUT */
flp=ffopen("grid.cube","w");
fprintf(flp,"Spatial Distribution Function\n");
fprintf(flp,"test\n");
fprintf(flp,"%5d%12.6f%12.6f%12.6f\n",nidxp,(MINBIN[XX]+(minx+iIGNOREOUTER)*rBINWIDTH)*10./bohr,(MINBIN[YY]+(miny+iIGNOREOUTER)*rBINWIDTH)*10./bohr,(MINBIN[ZZ]+(minz+iIGNOREOUTER)*rBINWIDTH)*10./bohr);
fprintf(flp,"%5ld%12.6f%12.6f%12.6f\n",maxx-minx+1-(2*iIGNOREOUTER),rBINWIDTH*10./bohr,0.,0.);
fprintf(flp,"%5ld%12.6f%12.6f%12.6f\n",maxy-miny+1-(2*iIGNOREOUTER),0.,rBINWIDTH*10./bohr,0.);
fprintf(flp,"%5ld%12.6f%12.6f%12.6f\n",maxz-minz+1-(2*iIGNOREOUTER),0.,0.,rBINWIDTH*10./bohr);
for(i=0; i<nidxp; i++){
v=2;
if(*(top.atoms.atomname[indexp[i]][0])=='C')v=6;
if(*(top.atoms.atomname[indexp[i]][0])=='N')v=7;
if(*(top.atoms.atomname[indexp[i]][0])=='O')v=8;
if(*(top.atoms.atomname[indexp[i]][0])=='H')v=1;
if(*(top.atoms.atomname[indexp[i]][0])=='S')v=16;
fprintf(flp,"%5d%12.6f%12.6f%12.6f%12.6f\n",v,0.,(double)fr.x[indexp[i]][XX]*10./bohr,(double)fr.x[indexp[i]][YY]*10./bohr,(double)fr.x[indexp[i]][ZZ]*10./bohr);
}
tot=0;
for(k=0;k<nbin[XX];k++) {
if(!(k<minx||k>maxx))continue;
for(j=0;j<nbin[YY];j++) {
if(!(j<miny||j>maxy))continue;
for(i=0;i<nbin[ZZ];i++) {
if(!(i<minz||i>maxz))continue;
if(bin[k][j][i]!=0){
printf("A bin was not empty when it should have been empty. Programming error.\n");
printf("bin[%d][%d][%d] was = %ld\n",k,j,i,bin[k][j][i]);
exit(1);
}
}
}
}
min=999;
max=0;
for(k=0;k<nbin[XX];k++) {
if(k<minx+iIGNOREOUTER||k>maxx-iIGNOREOUTER)continue;
for(j=0;j<nbin[YY];j++) {
if(j<miny+iIGNOREOUTER||j>maxy-iIGNOREOUTER)continue;
for(i=0;i<nbin[ZZ];i++) {
if(i<minz+iIGNOREOUTER||i>maxz-iIGNOREOUTER)continue;
tot+=bin[k][j][i];
if(bin[k][j][i]>max)max=bin[k][j][i];
if(bin[k][j][i]<min)min=bin[k][j][i];
}
}
}
numcu=(maxx-minx+1-(2*iIGNOREOUTER))*(maxy-miny+1-(2*iIGNOREOUTER))*(maxz-minz+1-(2*iIGNOREOUTER));
if(bCALCDIV){
norm=((double)numcu*(double)numfr) / (double)tot;
}else{
norm=1.0;
}
for(k=0;k<nbin[XX];k++) {
if(k<minx+iIGNOREOUTER||k>maxx-iIGNOREOUTER)continue;
for(j=0;j<nbin[YY];j++) {
if(j<miny+iIGNOREOUTER||j>maxy-iIGNOREOUTER)continue;
for(i=0;i<nbin[ZZ];i++) {
if(i<minz+iIGNOREOUTER||i>maxz-iIGNOREOUTER)continue;
fprintf(flp,"%12.6f ",norm*(double)bin[k][j][i]/(double)numfr);
}
fprintf(flp,"\n");
}
fprintf(flp,"\n");
}
ffclose(flp);
/* printf("x=%d to %d\n",minx,maxx); */
/* printf("y=%d to %d\n",miny,maxy); */
/* printf("z=%d to %d\n",minz,maxz); */
if(bCALCDIV){
printf("Counts per frame in all %ld cubes divided by %le\n",numcu,1.0/norm);
printf("Normalized data: average %le, min %le, max %le\n",1.0,norm*(double)min/(double)numfr,norm*(double)max/(double)numfr);
}else{
printf("grid.cube contains counts per frame in all %ld cubes\n",numcu);
printf("Raw data: average %le, min %le, max %le\n",1.0/norm,(double)min/(double)numfr,(double)max/(double)numfr);
}
thanx(stderr);
return 0;
}
static void pick_minima(const char *logfile,int *ibox,int ndim,int len,real W[])
{
FILE *fp;
int i,j,k,ijk,nmin;
gmx_bool bMin;
t_minimum *mm;
snew(mm,len);
nmin = 0;
fp = ffopen(logfile,"w");
for(i=0; (i<ibox[0]); i++) {
for(j=0; (j<ibox[1]); j++) {
if (ndim == 3) {
for(k=0; (k<ibox[2]); k++) {
ijk = index3(ibox,i,j,k);
bMin = (((i == 0) || ((i > 0) &&
(W[ijk] < W[index3(ibox,i-1,j,k)]))) &&
((i == ibox[0]-1) || ((i < ibox[0]-1) &&
(W[ijk] < W[index3(ibox,i+1,j,k)]))) &&
((j == 0) || ((j > 0) &&
(W[ijk] < W[index3(ibox,i,j-1,k)]))) &&
((j == ibox[1]-1) || ((j < ibox[1]-1) &&
(W[ijk] < W[index3(ibox,i,j+1,k)]))) &&
((k == 0) || ((k > 0) &&
(W[ijk] < W[index3(ibox,i,j,k-1)]))) &&
((k == ibox[2]-1) || ((k < ibox[2]-1) &&
(W[ijk] < W[index3(ibox,i,j,k+1)]))));
if (bMin) {
fprintf(fp,"Minimum %d at index %6d energy %10.3f\n",
nmin,ijk,W[ijk]);
mm[nmin].index = ijk;
mm[nmin].ener = W[ijk];
nmin++;
}
}
}
else {
ijk = index2(ibox,i,j);
bMin = (((i == 0) || ((i > 0) &&
(W[ijk] < W[index2(ibox,i-1,j)]))) &&
((i == ibox[0]-1) || ((i < ibox[0]-1) &&
(W[ijk] < W[index2(ibox,i+1,j)]))) &&
((j == 0) || ((j > 0) &&
(W[ijk] < W[index2(ibox,i,j-1)]))) &&
((j == ibox[1]-1) || ((j < ibox[1]-1) &&
(W[ijk] < W[index2(ibox,i,j+1)]))));
if (bMin) {
fprintf(fp,"Minimum %d at index %6d energy %10.3f\n",
nmin,ijk,W[ijk]);
mm[nmin].index = ijk;
mm[nmin].ener = W[ijk];
nmin++;
}
}
}
}
qsort(mm,nmin,sizeof(mm[0]),comp_minima);
fprintf(fp,"Minima sorted after energy\n");
for(i=0; (i<nmin); i++) {
fprintf(fp,"Minimum %d at index %6d energy %10.3f\n",
i,mm[i].index,mm[i].ener);
}
ffclose(fp);
sfree(mm);
}
int
gmx_select(int argc, char *argv[])
{
const char *desc[] = {
"g_select writes out basic data about dynamic selections.",
"It can be used for some simple analyses, or the output can",
"be combined with output from other programs and/or external",
"analysis programs to calculate more complex things.",
"Any combination of the output options is possible, but note",
"that [TT]-om[tt] only operates on the first selection.[PAR]",
"With [TT]-os[tt], calculates the number of positions in each",
"selection for each frame. With [TT]-norm[tt], the output is",
"between 0 and 1 and describes the fraction from the maximum",
"number of positions (e.g., for selection 'resname RA and x < 5'",
"the maximum number of positions is the number of atoms in",
"RA residues). With [TT]-cfnorm[tt], the output is divided",
"by the fraction covered by the selection.",
"[TT]-norm[tt] and [TT]-cfnorm[tt] can be specified independently",
"of one another.[PAR]",
"With [TT]-oc[tt], the fraction covered by each selection is",
"written out as a function of time.[PAR]",
"With [TT]-oi[tt], the selected atoms/residues/molecules are",
"written out as a function of time. In the output, the first",
"column contains the frame time, the second contains the number",
"of positions, followed by the atom/residue/molecule numbers.",
"If more than one selection is specified, the size of the second",
"group immediately follows the last number of the first group",
"and so on. With [TT]-dump[tt], the frame time and the number",
"of positions is omitted from the output. In this case, only one",
"selection can be given.[PAR]",
"With [TT]-on[tt], the selected atoms are written as a index file",
"compatible with make_ndx and the analyzing tools. Each selection",
"is written as a selection group and for dynamic selections a",
"group is written for each frame.[PAR]",
"For residue numbers, the output of [TT]-oi[tt] can be controlled",
"with [TT]-resnr[tt]: [TT]number[tt] (default) prints the residue",
"numbers as they appear in the input file, while [TT]index[tt] prints",
"unique numbers assigned to the residues in the order they appear",
"in the input file, starting with 1. The former is more intuitive,",
"but if the input contains multiple residues with the same number,",
"the output can be less useful.[PAR]",
"With [TT]-om[tt], a mask is printed for the first selection",
"as a function of time. Each line in the output corresponds to",
"one frame, and contains either 0/1 for each atom/residue/molecule",
"possibly selected. 1 stands for the atom/residue/molecule being",
"selected for the current frame, 0 for not selected.",
"With [TT]-dump[tt], the frame time is omitted from the output.",
};
gmx_bool bDump = FALSE;
gmx_bool bFracNorm = FALSE;
gmx_bool bTotNorm = FALSE;
const char *routt[] = {NULL, "number", "index", NULL};
t_pargs pa[] = {
{"-dump", FALSE, etBOOL, {&bDump},
"Do not print the frame time (-om, -oi) or the index size (-oi)"},
{"-norm", FALSE, etBOOL, {&bTotNorm},
"Normalize by total number of positions with -os"},
{"-cfnorm", FALSE, etBOOL, {&bFracNorm},
"Normalize by covered fraction with -os"},
{"-resnr", FALSE, etENUM, {routt},
"Residue number output type"},
};
t_filenm fnm[] = {
{efXVG, "-os", "size.xvg", ffOPTWR},
{efXVG, "-oc", "cfrac.xvg", ffOPTWR},
{efDAT, "-oi", "index.dat", ffOPTWR},
{efDAT, "-om", "mask.dat", ffOPTWR},
{efNDX, "-on", "index.ndx", ffOPTWR},
};
#define NFILE asize(fnm)
gmx_ana_traj_t *trj;
t_topology *top;
int ngrps;
gmx_ana_selection_t **sel;
char **grpnames;
t_dsdata d;
const char *fnSize, *fnFrac, *fnIndex, *fnNdx, *fnMask;
int g;
int rc;
output_env_t oenv;
CopyRight(stderr, argv[0]);
gmx_ana_traj_create(&trj, 0);
gmx_ana_set_nanagrps(trj, -1);
parse_trjana_args(trj, &argc, argv, 0,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL,
&oenv);
gmx_ana_get_nanagrps(trj, &ngrps);
gmx_ana_get_anagrps(trj, &sel);
gmx_ana_init_coverfrac(trj, CFRAC_SOLIDANGLE);
/* Get output file names */
fnSize = opt2fn_null("-os", NFILE, fnm);
fnFrac = opt2fn_null("-oc", NFILE, fnm);
fnIndex = opt2fn_null("-oi", NFILE, fnm);
fnNdx = opt2fn_null("-on", NFILE, fnm);
fnMask = opt2fn_null("-om", NFILE, fnm);
/* Write out sizes if nothing specified */
if (!fnFrac && !fnIndex && !fnMask && !fnNdx)
{
fnSize = opt2fn("-os", NFILE, fnm);
}
if ( bDump && ngrps > 1)
{
gmx_fatal(FARGS, "Only one index group allowed with -dump");
}
if (fnNdx && sel[0]->p.m.type != INDEX_ATOM)
{
gmx_fatal(FARGS, "Only atom selection allowed with -on");
}
if (fnMask && ngrps > 1)
{
fprintf(stderr, "warning: the mask (-om) will only be written for the first group\n");
}
if (fnMask && !sel[0]->bDynamic)
{
fprintf(stderr, "warning: will not write the mask (-om) for a static selection\n");
fnMask = NULL;
}
/* Initialize reference calculation for masks */
if (fnMask)
{
gmx_ana_get_topology(trj, FALSE, &top, NULL);
snew(d.mmap, 1);
gmx_ana_indexmap_init(d.mmap, sel[0]->g, top, sel[0]->p.m.type);
}
/* Initialize calculation data */
d.bDump = bDump;
d.bFracNorm = bFracNorm;
d.routt = routt[0];
snew(d.size, ngrps);
for (g = 0; g < ngrps; ++g)
{
d.size[g] = bTotNorm ? sel[g]->p.nr : 1;
}
/* Open output files */
d.sfp = d.cfp = d.ifp = d.mfp = NULL;
d.block = NULL;
gmx_ana_get_grpnames(trj, &grpnames);
if (fnSize)
{
d.sfp = xvgropen(fnSize, "Selection size", "Time (ps)", "Number",oenv);
xvgr_selections(d.sfp, trj);
xvgr_legend(d.sfp, ngrps, (const char**)grpnames, oenv);
}
if (fnFrac)
{
d.cfp = xvgropen(fnFrac, "Covered fraction", "Time (ps)", "Fraction",
oenv);
xvgr_selections(d.cfp, trj);
xvgr_legend(d.cfp, ngrps, (const char**)grpnames, oenv);
}
if (fnIndex)
{
d.ifp = ffopen(fnIndex, "w");
xvgr_selections(d.ifp, trj);
}
if (fnNdx)
{
d.block = new_blocka();
d.gnames = NULL;
}
if (fnMask)
{
d.mfp = ffopen(fnMask, "w");
xvgr_selections(d.mfp, trj);
}
/* Do the analysis and write out results */
gmx_ana_do(trj, 0, &print_data, &d);
/* Close the files */
if (d.sfp)
{
ffclose(d.sfp);
}
if (d.cfp)
{
ffclose(d.cfp);
}
if (d.ifp)
{
ffclose(d.ifp);
}
if (d.block)
{
write_index(fnNdx, d.block, d.gnames);
}
if (d.mfp)
{
ffclose(d.mfp);
}
thanx(stderr);
return 0;
}
int f_csv(ARG1) {
char new_inv_out[STRING_SIZE];
char name[100], desc[100], unit[100];
FILE *out;
unsigned int j;
char vt[20],rt[20];
int year, month, day, hour, minute, second;
/* initialization phase */
if (mode == -1) {
WxText = decode = latlon = 1;
if ((*local = (void *) ffopen(arg1,file_append ? "a" : "w")) == NULL)
fatal_error("csv could not open file %s", arg1);
return 0;
}
/* cleanup phase */
if (mode == -2) {
ffclose((FILE *) *local);
return 0;
}
/* processing phase */
if (lat == NULL || lon == NULL) {
fprintf(stderr,"csv: latitude/longitude not defined, record skipped\n");
return 0;
}
out = (FILE *) *local;
/*Collect runtime and validtime into vt and rt*/
reftime(sec, &year, &month, &day, &hour, &minute, &second);
sprintf(rt, "%4.4d-%2.2d-%2.2d %2.2d:%2.2d:%2.2d", year,month,day,hour,minute,second);
vt[0] = 0;
if (verftime(sec, &year, &month, &day, &hour, &minute, &second) == 0) {
sprintf(vt,"%4.4d-%2.2d-%2.2d %2.2d:%2.2d:%2.2d", year,month,day,hour,minute,second);
}
/*Get levels, parameter name, description and unit*/
*new_inv_out = 0;
f_lev(call_ARG0(new_inv_out,NULL));
if (strcmp(new_inv_out, "reserved")==0) return 0;
// getName(sec, mode, NULL, name, desc, unit);
getExtName(sec, mode, NULL, name, desc, unit,".","_");
// fprintf(stderr,"Start processing of %s at %s\n", name, new_inv_out);
// fprintf(stderr,"Gridpoints in data: %d\n", ndata);
// fprintf(stderr,"Description: %s, Unit %s\n", desc,unit);
/* Lage if-setning rundt hele som sjekker om alt eller deler skal ut*/
if (WxNum > 0) {
for (j = 0; j < ndata; j++) {
if (!UNDEFINED_VAL(data[j])) {
fprintf(out,"\"%s\",\"%s\",\"%s\",\"%s\",%g,%g,\"%s\"\n",rt,vt,name,
new_inv_out,lon[j] > 180.0 ? lon[j]-360.0 : lon[j],lat[j],WxLabel(data[j]));
}
}
}
else {
for (j = 0; j < ndata; j++) {
if (!UNDEFINED_VAL(data[j])) {
fprintf(out,"\"%s\",\"%s\",\"%s\",\"%s\",%g,%g,%lg\n",rt,vt,name,
new_inv_out,lon[j] > 180.0 ? lon[j]-360.0 : lon[j],lat[j],data[j]);
}
}
}
if (flush_mode) fflush(out);
return 0;
}
int gmx_rmsf(int argc,char *argv[])
{
static char *desc[] = {
"g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard ",
"deviation) of atomic positions ",
"after (optionally) fitting to a reference frame.[PAR]",
"With option [TT]-oq[tt] the RMSF values are converted to B-factor",
"values, which are written to a pdb file with the coordinates, of the",
"structure file, or of a pdb file when [TT]-q[tt] is specified.",
"Option [TT]-ox[tt] writes the B-factors to a file with the average",
"coordinates.[PAR]",
"With the option [TT]-od[tt] the root mean square deviation with",
"respect to the reference structure is calculated.[PAR]",
"With the option [TT]aniso[tt] g_rmsf will compute anisotropic",
"temperature factors and then it will also output average coordinates",
"and a pdb file with ANISOU records (corresonding to the [TT]-oq[tt]",
"or [TT]-ox[tt] option). Please note that the U values",
"are orientation dependent, so before comparison with experimental data",
"you should verify that you fit to the experimental coordinates.[PAR]",
"When a pdb input file is passed to the program and the [TT]-aniso[tt]",
"flag is set",
"a correlation plot of the Uij will be created, if any anisotropic",
"temperature factors are present in the pdb file.[PAR]",
"With option [TT]-dir[tt] the average MSF (3x3) matrix is diagonalized.",
"This shows the directions in which the atoms fluctuate the most and",
"the least."
};
static bool bRes=FALSE,bAniso=FALSE,bdevX=FALSE,bFit=TRUE;
t_pargs pargs[] = {
{ "-res", FALSE, etBOOL, {&bRes},
"Calculate averages for each residue" },
{ "-aniso",FALSE, etBOOL, {&bAniso},
"Compute anisotropic termperature factors" },
{ "-fit", FALSE, etBOOL, {&bFit},
"Do a least squares superposition before computing RMSF. Without this you must make sure that the reference structure and the trajectory match." }
};
int step,nre,natom,natoms,i,g,m,teller=0;
real t,lambda,*w_rls,*w_rms;
t_tpxheader header;
t_inputrec ir;
t_topology top;
int ePBC;
t_atoms *pdbatoms,*refatoms;
bool bCont;
matrix box,pdbbox;
rvec *x,*pdbx,*xref;
int status,npdbatoms,res0;
char buf[256],*label;
char title[STRLEN];
FILE *fp; /* the graphics file */
char *devfn,*dirfn;
int resnr;
bool bReadPDB;
atom_id *index;
int isize;
char *grpnames;
real bfac,pdb_bfac,*Uaver;
double **U,*xav;
atom_id aid;
rvec *rmsd_x=NULL;
real *rmsf,invcount,totmass;
int d;
real count=0;
rvec xcm;
char *leg[2] = { "MD", "X-Ray" };
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efPDB, "-q", NULL, ffOPTRD },
{ efPDB, "-oq", "bfac", ffOPTWR },
{ efPDB, "-ox", "xaver", ffOPTWR },
{ efXVG, "-o", "rmsf", ffWRITE },
{ efXVG, "-od", "rmsdev", ffOPTWR },
{ efXVG, "-oc", "correl", ffOPTWR },
{ efLOG, "-dir", "rmsf", ffOPTWR }
};
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE ,
NFILE,fnm,asize(pargs),pargs,asize(desc),desc,0,NULL);
bReadPDB = ftp2bSet(efPDB,NFILE,fnm);
devfn = opt2fn_null("-od",NFILE,fnm);
dirfn = opt2fn_null("-dir",NFILE,fnm);
read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,&xref,NULL,box,TRUE);
snew(w_rls,top.atoms.nr);
fprintf(stderr,"Select group(s) for root mean square calculation\n");
get_index(&top.atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&isize,&index,&grpnames);
/* Set the weight */
for(i=0; i<isize; i++)
w_rls[index[i]]=top.atoms.atom[index[i]].m;
/* Malloc the rmsf arrays */
snew(xav,isize*DIM);
snew(U,isize);
for(i=0; i<isize; i++)
snew(U[i],DIM*DIM);
snew(rmsf,isize);
if (devfn)
snew(rmsd_x, isize);
if (bReadPDB) {
get_stx_coordnum(opt2fn("-q",NFILE,fnm),&npdbatoms);
snew(pdbatoms,1);
snew(refatoms,1);
init_t_atoms(pdbatoms,npdbatoms,TRUE);
init_t_atoms(refatoms,npdbatoms,TRUE);
snew(pdbx,npdbatoms);
/* Read coordinates twice */
read_stx_conf(opt2fn("-q",NFILE,fnm),title,pdbatoms,pdbx,NULL,NULL,pdbbox);
read_stx_conf(opt2fn("-q",NFILE,fnm),title,refatoms,pdbx,NULL,NULL,pdbbox);
} else {
pdbatoms = &top.atoms;
refatoms = &top.atoms;
pdbx = xref;
npdbatoms = pdbatoms->nr;
snew(pdbatoms->pdbinfo,npdbatoms);
copy_mat(box,pdbbox);
}
if (bFit)
sub_xcm(xref,isize,index,top.atoms.atom,xcm,FALSE);
natom = read_first_x(&status,ftp2fn(efTRX,NFILE,fnm),&t,&x,box);
/* Now read the trj again to compute fluctuations */
teller = 0;
do {
if (bFit) {
/* Remove periodic boundary */
rm_pbc(&(top.idef),ePBC,natom,box,x,x);
/* Set center of mass to zero */
sub_xcm(x,isize,index,top.atoms.atom,xcm,FALSE);
/* Fit to reference structure */
do_fit(natom,w_rls,xref,x);
}
/* Calculate Anisotropic U Tensor */
for(i=0; i<isize; i++) {
aid = index[i];
for(d=0; d<DIM; d++) {
xav[i*DIM + d] += x[aid][d];
for(m=0; m<DIM; m++)
U[i][d*DIM + m] += x[aid][d]*x[aid][m];
}
}
if (devfn) {
/* Calculate RMS Deviation */
for(i=0;(i<isize);i++) {
aid = index[i];
for(d=0;(d<DIM);d++) {
rmsd_x[i][d] += sqr(x[aid][d]-xref[aid][d]);
}
}
}
count += 1.0;
teller++;
} while(read_next_x(status,&t,natom,x,box));
close_trj(status);
invcount = 1.0/count;
snew(Uaver,DIM*DIM);
totmass = 0;
for(i=0; i<isize; i++) {
for(d=0; d<DIM; d++)
xav[i*DIM + d] *= invcount;
for(d=0; d<DIM; d++)
for(m=0; m<DIM; m++) {
U[i][d*DIM + m] = U[i][d*DIM + m]*invcount
- xav[i*DIM + d]*xav[i*DIM + m];
Uaver[3*d+m] += top.atoms.atom[index[i]].m*U[i][d*DIM + m];
}
totmass += top.atoms.atom[index[i]].m;
}
for(d=0; d<DIM*DIM; d++)
Uaver[d] /= totmass;
if (bAniso) {
for(i=0; i<isize; i++) {
aid = index[i];
pdbatoms->pdbinfo[aid].bAnisotropic = TRUE;
pdbatoms->pdbinfo[aid].uij[U11] = 1e6*U[i][XX*DIM + XX];
pdbatoms->pdbinfo[aid].uij[U22] = 1e6*U[i][YY*DIM + YY];
pdbatoms->pdbinfo[aid].uij[U33] = 1e6*U[i][ZZ*DIM + ZZ];
pdbatoms->pdbinfo[aid].uij[U12] = 1e6*U[i][XX*DIM + YY];
pdbatoms->pdbinfo[aid].uij[U13] = 1e6*U[i][XX*DIM + ZZ];
pdbatoms->pdbinfo[aid].uij[U23] = 1e6*U[i][YY*DIM + ZZ];
}
}
if (bRes) {
average_residues(rmsf,isize,index,w_rls,&top.atoms);
label = "Residue";
} else
label = "Atom";
for(i=0; i<isize; i++)
rmsf[i] = U[i][XX*DIM + XX] + U[i][YY*DIM + YY] + U[i][ZZ*DIM + ZZ];
if (dirfn) {
fprintf(stdout,"\n");
print_dir(stdout,Uaver);
fp = ffopen(dirfn,"w");
print_dir(fp,Uaver);
fclose(fp);
}
for(i=0; i<isize; i++)
sfree(U[i]);
sfree(U);
/* Write RMSF output */
if (bReadPDB) {
bfac = 8.0*M_PI*M_PI/3.0*100;
fp = xvgropen(ftp2fn(efXVG,NFILE,fnm),"B-Factors",
label,"(A\\b\\S\\So\\N\\S2\\N)");
xvgr_legend(fp,2,leg);
for(i=0;(i<isize);i++) {
if (!bRes || i+1==isize ||
top.atoms.atom[index[i]].resnr!=top.atoms.atom[index[i+1]].resnr) {
resnr = top.atoms.atom[index[i]].resnr;
pdb_bfac = find_pdb_bfac(pdbatoms,*(top.atoms.resname[resnr]),resnr,
*(top.atoms.atomname[index[i]]));
fprintf(fp,"%5d %10.5f %10.5f\n",
bRes ? top.atoms.atom[index[i]].resnr+1 : i+1,rmsf[i]*bfac,
pdb_bfac);
}
}
fclose(fp);
} else {
fp = xvgropen(ftp2fn(efXVG,NFILE,fnm),"RMS fluctuation",label,"(nm)");
for(i=0; i<isize; i++)
if (!bRes || i+1==isize ||
top.atoms.atom[index[i]].resnr!=top.atoms.atom[index[i+1]].resnr)
fprintf(fp,"%5d %8.4f\n",
bRes ? top.atoms.atom[index[i]].resnr+1 : i+1,sqrt(rmsf[i]));
fclose(fp);
}
for(i=0; i<isize; i++)
pdbatoms->pdbinfo[index[i]].bfac = 800*M_PI*M_PI/3.0*rmsf[i];
if (devfn) {
for(i=0; i<isize; i++)
rmsf[i] = (rmsd_x[i][XX]+rmsd_x[i][YY]+rmsd_x[i][ZZ])/count;
if (bRes)
average_residues(rmsf,isize,index,w_rls,&top.atoms);
/* Write RMSD output */
fp = xvgropen(devfn,"RMS Deviation",label,"(nm)");
for(i=0; i<isize; i++)
if (!bRes || i+1==isize ||
top.atoms.atom[index[i]].resnr!=top.atoms.atom[index[i+1]].resnr)
fprintf(fp,"%5d %8.4f\n",
bRes ? top.atoms.atom[index[i]].resnr+1 : i+1,sqrt(rmsf[i]));
fclose(fp);
}
if (opt2bSet("-oq",NFILE,fnm)) {
/* Write a pdb file with B-factors and optionally anisou records */
for(i=0; i<isize; i++)
rvec_inc(xref[index[i]],xcm);
write_sto_conf_indexed(opt2fn("-oq",NFILE,fnm),title,pdbatoms,pdbx,
NULL,ePBC,pdbbox,isize,index);
}
if (opt2bSet("-ox",NFILE,fnm)) {
/* Misuse xref as a temporary array */
for(i=0; i<isize; i++)
for(d=0; d<DIM; d++)
xref[index[i]][d] = xcm[d] + xav[i*DIM + d];
/* Write a pdb file with B-factors and optionally anisou records */
write_sto_conf_indexed(opt2fn("-ox",NFILE,fnm),title,pdbatoms,xref,NULL,
ePBC,pdbbox,isize,index);
}
if (bAniso) {
correlate_aniso(opt2fn("-oc",NFILE,fnm),refatoms,pdbatoms);
do_view(opt2fn("-oc",NFILE,fnm),"-nxy");
}
do_view(opt2fn("-o",NFILE,fnm),"-nxy");
if (devfn)
do_view(opt2fn("-od",NFILE,fnm),"-nxy");
thanx(stderr);
return 0;
}
int polarInAPBS(t_PolKey *param, char *fnPQR, char *fnPolAPBS, gmx_bool bDECOMP) {
FILE *fIn;
fIn = ffopen(fnPolAPBS, "w");
fprintf(fIn, "read\n mol pqr %s\nend\n", fnPQR);
/*
if(param->bParallel) {
fprintf(fIn, "\nelec name mol1\n mg-para\n");
fprintf(fIn, " dime %d %d %d\n", param->dime[XX], param->dime[YY], param->dime[ZZ]);
fprintf(fIn, " pdime %d %d %d\n", param->pdime[XX], param->pdime[YY], param->pdime[ZZ]);
fprintf(fIn, " ofrac %g\n", param->ofrac);
}*/
fprintf(fIn, "\nelec name mol1\n mg-auto\n");
fprintf(fIn, " dime %d %d %d\n", param->dime[XX], param->dime[YY], param->dime[ZZ]);
fprintf(fIn, " cglen %6.3lf %6.3lf %6.3lf\n", param->cglen[XX], param->cglen[YY], param->cglen[ZZ]);
fprintf(fIn, " fglen %6.3lf %6.3lf %6.3lf\n", param->fglen[XX], param->fglen[YY], param->fglen[ZZ]);
fprintf(fIn, " cgcent %6.3lf %6.3lf %6.3lf\n", param->cgcent[XX], param->cgcent[YY], param->cgcent[ZZ]);
fprintf(fIn, " fgcent %6.3lf %6.3lf %6.3lf\n", param->fgcent[XX], param->fgcent[YY], param->fgcent[ZZ]);
fprintf(fIn, " mol 1\n");
fprintf(fIn, " %s\n", PBsolver[param->pbsolver]);
fprintf(fIn, " bcfl %s\n", bcfl_words[param->bcfl]);
fprintf(fIn, " ion %.1g %.3g %.3g\n", param->pcharge, param->pconc, param->prad);
fprintf(fIn, " ion %.1g %.3g %.3g\n", param->ncharge, param->nconc, param->nrad);
fprintf(fIn, " pdie %g\n", param->pdie);
fprintf(fIn, " sdie %g\n", param->sdie);
fprintf(fIn, " srfm %s\n", srfm_words[param->srfm]);
fprintf(fIn, " chgm %s\n", chgm_words[param->chgm]);
fprintf(fIn, " sdens %g\n", param->sdens);
fprintf(fIn, " srad %g\n", param->srad);
fprintf(fIn, " swin %g\n", param->swin);
fprintf(fIn, " temp %g\n", param->temp);
if(bDECOMP)
fprintf(fIn, " calcenergy comps\n");
else
fprintf(fIn, " calcenergy total\n");
fprintf(fIn, "end\n");
/*
if(param->bParallel) {
fprintf(fIn, "\nelec name mol2\n mg-para\n");
fprintf(fIn, " dime %d %d %d\n", param->dime[XX], param->dime[YY], param->dime[ZZ]);
fprintf(fIn, " pdime %d %d %d\n", param->pdime[XX], param->pdime[YY], param->pdime[ZZ]);
fprintf(fIn, " ofrac %g\n", param->ofrac);
}*/
fprintf(fIn, "\nelec name mol2\n mg-auto\n");
fprintf(fIn, " dime %d %d %d\n", param->dime[XX], param->dime[YY], param->dime[ZZ]);
fprintf(fIn, " cglen %6.3lf %6.3lf %6.3lf\n", param->cglen[XX], param->cglen[YY], param->cglen[ZZ]);
fprintf(fIn, " fglen %6.3lf %6.3lf %6.3lf\n", param->fglen[XX], param->fglen[YY], param->fglen[ZZ]);
fprintf(fIn, " cgcent %6.3lf %6.3lf %6.3lf\n", param->cgcent[XX], param->cgcent[YY], param->cgcent[ZZ]);
fprintf(fIn, " fgcent %6.3lf %6.3lf %6.3lf\n", param->fgcent[XX], param->fgcent[YY], param->fgcent[ZZ]);
fprintf(fIn, " mol 1\n");
fprintf(fIn, " %s\n", PBsolver[param->pbsolver]);
fprintf(fIn, " bcfl %s\n", bcfl_words[param->bcfl]);
fprintf(fIn, " ion %.1g %.3g %.3g\n", param->pcharge, param->pconc, param->prad);
fprintf(fIn, " ion %.1g %.3g %.3g\n", param->ncharge, param->nconc, param->nrad);
fprintf(fIn, " pdie %g\n", param->pdie);
fprintf(fIn, " sdie %g\n", param->vdie);
fprintf(fIn, " srfm %s\n", srfm_words[param->srfm]);
fprintf(fIn, " chgm %s\n", chgm_words[param->chgm]);
fprintf(fIn, " sdens %g\n", param->sdens);
fprintf(fIn, " srad %g\n", param->srad);
fprintf(fIn, " swin %g\n", param->swin);
fprintf(fIn, " temp %g\n", param->temp);
if(bDECOMP)
fprintf(fIn, " calcenergy comps\n");
else
fprintf(fIn, " calcenergy total\n");
fprintf(fIn, "end\n");
fprintf(fIn, "print elecEnergy mol1 - mol2 end\n");
fprintf(fIn, "quit\n");
ffclose(fIn);
return 0;
}
