void ps_mat(char *outf,int nmat,t_matrix mat[],t_matrix mat2[],
bool bFrame,bool bDiag,bool bFirstDiag,
bool bTitle,bool bTitleOnce,bool bYonce,int elegend,
real size,real boxx,real boxy,char *m2p,char *m2pout,
int mapoffset)
{
char *libm2p;
char buf[256],*legend;
t_psdata out;
t_psrec psrec,*psr;
int W,H;
int i,j,x,y,col,leg=0;
real x0,y0,xx;
real w,h,dw,dh;
int nmap1=0,nmap2=0,leg_nmap;
t_mapping *map1=NULL,*map2=NULL,*leg_map;
bool bMap1,bNextMap1,bDiscrete;
libm2p = m2p ? strdup(libfn(m2p)) : m2p;
get_params(libm2p,m2pout,&psrec);
psr=&psrec;
if (psr->X.major <= 0 )
tick_spacing((mat[0].flags & MAT_SPATIAL_X) ? mat[0].nx + 1 : mat[0].nx,
mat[0].axis_x, psr->X.offset, 'X',
&(psr->X.major), &(psr->X.minor) );
if (psr->X.minor <= 0 )
psr->X.minor = psr->X.major / 2;
if (psr->Y.major <= 0)
tick_spacing((mat[0].flags & MAT_SPATIAL_Y) ? mat[0].ny + 1 : mat[0].ny,
mat[0].axis_y, psr->Y.offset, 'Y',
&(psr->Y.major), &(psr->Y.minor) );
if (psr->Y.minor <= 0)
psr->Y.minor = psr->Y.major / 2;
if (boxx>0) {
psr->xboxsize=boxx;
psr->yboxsize=boxx;
}
if (boxy>0)
psr->yboxsize=boxy;
if (psr->xboxsize==0) {
psr->xboxsize = size/mat[0].nx;
printf("Set the x-size of the box to %.3f\n",psr->xboxsize);
}
if (psr->yboxsize==0) {
psr->yboxsize = size/mat[0].nx;
printf("Set the y-size of the box to %.3f\n",psr->yboxsize);
}
nmap1=0;
for (i=0; (i<nmat); i++)
if (mat[i].nmap>nmap1) {
nmap1=mat[i].nmap;
map1=mat[i].map;
leg=i+1;
}
if (leg!=1)
printf("Selected legend of matrix # %d for display\n",leg);
if (mat2) {
nmap2=0;
for (i=0; (i<nmat); i++)
if (mat2[i].nmap>nmap2) {
nmap2=mat2[i].nmap;
map2=mat2[i].map;
leg=i+1;
}
if (leg!=1)
printf("Selected legend of matrix # %d for second display\n",leg);
}
if ( (mat[0].legend[0]==0) && psr->legend )
strcpy(mat[0].legend, psr->leglabel);
bTitle = bTitle && mat[nmat-1].title[0];
bTitleOnce = bTitleOnce && mat[nmat-1].title[0];
psr->bTitle = bTitle;
psr->bTitleOnce = bTitleOnce;
psr->bYonce = bYonce;
/* Set up size of box for nice colors */
box_dim(nmat,mat,mat2,psr,elegend,bFrame,&w,&h,&dw,&dh);
/* Set up bounding box */
W=w+dw;
H=h+dh;
/* Start box at */
x0=dw;
y0=dh;
x = W+psr->xoffs;
y = H+psr->yoffs;
if (bFrame) {
x += 5*DDD;
y += 4*DDD;
}
out=ps_open(outf,0,0,x,y);
ps_linewidth(out,psr->linewidth);
ps_init_rgb_box(out,psr->xboxsize,psr->yboxsize);
ps_init_rgb_nbox(out,psr->xboxsize,psr->yboxsize);
ps_translate(out,psr->xoffs,psr->yoffs);
if (bFrame) {
ps_comment(out,"Here starts the BOX drawing");
draw_boxes(out,x0,y0,w,nmat,mat,psr);
}
for(i=0; (i<nmat); i++) {
if (bTitle || (bTitleOnce && i==nmat-1) ) {
/* Print title, if any */
ps_rgb(out,BLACK);
ps_strfont(out,psr->titfont,psr->titfontsize);
if (!mat2 || (strcmp(mat[i].title,mat2[i].title) == 0))
strcpy(buf,mat[i].title);
else
sprintf(buf,"%s / %s",mat[i].title,mat2[i].title);
ps_ctext(out,x0+w/2,y0+box_height(&(mat[i]),psr)+psr->titfontsize,
buf,eXCenter);
}
sprintf(buf,"Here starts the filling of box #%d",i);
ps_comment(out,buf);
for(x=0; (x<mat[i].nx); x++) {
int nexty;
int nextcol;
xx=x0+x*psr->xboxsize;
ps_moveto(out,xx,y0);
y=0;
bMap1 = (!mat2 || (x<y || (x==y && bFirstDiag)));
if ((bDiag) || (x!=y))
col = mat[i].matrix[x][y];
else
col = -1;
for(nexty=1; (nexty<=mat[i].ny); nexty++) {
bNextMap1 = (!mat2 || (x<nexty || (x==nexty && bFirstDiag)));
/* TRUE: upper left -> map1 */
/* FALSE: lower right -> map2 */
if ((nexty==mat[i].ny) || (!bDiag && (x==nexty)))
nextcol = -1;
else
nextcol=mat[i].matrix[x][nexty];
if ( (nexty==mat[i].ny) || (col!=nextcol) || (bMap1!=bNextMap1) ) {
if (col >= 0)
if (bMap1)
ps_rgb_nbox(out,&(mat[i].map[col].rgb),nexty-y);
else
ps_rgb_nbox(out,&(mat2[i].map[col].rgb),nexty-y);
else
ps_moverel(out,0,psr->yboxsize);
y=nexty;
bMap1=bNextMap1;
col=nextcol;
}
}
}
y0+=box_height(&(mat[i]),psr)+box_dh(psr)+box_dh_top(IS_ONCE,psr);
}
if (psr->X.lineatzero || psr->Y.lineatzero) {
/* reset y0 for first box */
y0=dh;
ps_comment(out,"Here starts the zero lines drawing");
draw_zerolines(out,x0,y0,w,nmat,mat,psr);
}
if (elegend!=elNone) {
ps_comment(out,"Now it's legend time!");
ps_linewidth(out,psr->linewidth);
if ( mat2==NULL || elegend!=elSecond ) {
bDiscrete = mat[0].bDiscrete;
legend = mat[0].legend;
leg_nmap = nmap1;
leg_map = map1;
} else {
bDiscrete = mat2[0].bDiscrete;
legend = mat2[0].legend;
leg_nmap = nmap2;
leg_map = map2;
}
if (bDiscrete)
leg_discrete(out,psr->legfontsize,DDD,legend,
psr->legfontsize,psr->legfont,leg_nmap,leg_map);
else {
if ( elegend!=elBoth )
leg_continuous(out,x0+w/2,w/2,DDD,legend,
psr->legfontsize,psr->legfont,leg_nmap,leg_map,
mapoffset);
else
leg_bicontinuous(out,x0+w/2,w,DDD,mat[0].legend,mat2[0].legend,
psr->legfontsize,psr->legfont,nmap1,map1,nmap2,map2);
}
ps_comment(out,"Were there, dude");
}
ps_close(out);
}
static char *insert_mols(char *mol_insrt,int nmol_insrt,int ntry,int seed,
t_atoms *atoms,rvec **x,real **r,int ePBC,matrix box,
gmx_atomprop_t aps,real r_distance,real rshell)
{
t_pbc pbc;
static char *title_insrt;
t_atoms atoms_insrt;
rvec *x_insrt,*x_n;
real *r_insrt;
int ePBC_insrt;
matrix box_insrt;
int i,mol,onr;
real alfa,beta,gamma;
rvec offset_x;
int try;
set_pbc(&pbc,ePBC,box);
/* read number of atoms of insert molecules */
get_stx_coordnum(mol_insrt,&atoms_insrt.nr);
if (atoms_insrt.nr == 0)
gmx_fatal(FARGS,"No molecule in %s, please check your input\n",mol_insrt);
/* allocate memory for atom coordinates of insert molecules */
snew(x_insrt,atoms_insrt.nr);
snew(r_insrt,atoms_insrt.nr);
snew(atoms_insrt.resname,atoms_insrt.nr);
snew(atoms_insrt.atomname,atoms_insrt.nr);
snew(atoms_insrt.atom,atoms_insrt.nr);
atoms_insrt.pdbinfo = NULL;
snew(x_n,atoms_insrt.nr);
snew(title_insrt,STRLEN);
/* read residue number, residue names, atomnames, coordinates etc. */
fprintf(stderr,"Reading molecule configuration \n");
read_stx_conf(mol_insrt,title_insrt,&atoms_insrt,x_insrt,NULL,
&ePBC_insrt,box_insrt);
fprintf(stderr,"%s\nContaining %d atoms in %d residue\n",
title_insrt,atoms_insrt.nr,atoms_insrt.nres);
srenew(atoms_insrt.resname,atoms_insrt.nres);
/* initialise van der waals arrays of insert molecules */
mk_vdw(&atoms_insrt,r_insrt,aps,r_distance);
srenew(atoms->resname,(atoms->nres+nmol_insrt));
srenew(atoms->atomname,(atoms->nr+atoms_insrt.nr*nmol_insrt));
srenew(atoms->atom,(atoms->nr+atoms_insrt.nr*nmol_insrt));
srenew(*x,(atoms->nr+atoms_insrt.nr*nmol_insrt));
srenew(*r,(atoms->nr+atoms_insrt.nr*nmol_insrt));
try=mol=0;
while ((mol < nmol_insrt) && (try < ntry*nmol_insrt)) {
fprintf(stderr,"\rTry %d",try++);
for (i=0;(i<atoms_insrt.nr);i++) {
if (atoms_insrt.atom[i].resnr!=0)
gmx_fatal(FARGS,"more then one residue in insert molecules\n"
"program terminated\n");
copy_rvec(x_insrt[i],x_n[i]);
}
alfa=2*M_PI*rando(&seed);
beta=2*M_PI*rando(&seed);
gamma=2*M_PI*rando(&seed);
rotate_conf(atoms_insrt.nr,x_n,NULL,alfa,beta,gamma);
offset_x[XX]=box[XX][XX]*rando(&seed);
offset_x[YY]=box[YY][YY]*rando(&seed);
offset_x[ZZ]=box[ZZ][ZZ]*rando(&seed);
gen_box(0,atoms_insrt.nr,x_n,box_insrt,offset_x,TRUE);
if (!in_box(&pbc,x_n[0]) || !in_box(&pbc,x_n[atoms_insrt.nr-1]))
continue;
onr=atoms->nr;
add_conf(atoms,x,NULL,r,FALSE,ePBC,box,TRUE,
&atoms_insrt,x_n,NULL,r_insrt,FALSE,rshell,0);
if (atoms->nr==(atoms_insrt.nr+onr)) {
mol++;
fprintf(stderr," success (now %d atoms)!",atoms->nr);
}
}
srenew(atoms->resname, atoms->nres);
srenew(atoms->atomname, atoms->nr);
srenew(atoms->atom, atoms->nr);
srenew(*x, atoms->nr);
srenew(*r, atoms->nr);
fprintf(stderr,"\n");
/* print number of molecules added */
fprintf(stderr,"Added %d molecules (out of %d requested) of %s\n",
mol,nmol_insrt,*atoms_insrt.resname[0]);
return title_insrt;
}
static void add_solv(char *fn,t_atoms *atoms,rvec **x,rvec **v,real **r,
int ePBC,matrix box,
gmx_atomprop_t aps,real r_distance,int *atoms_added,
int *residues_added,real rshell,int max_sol)
{
int i,nmol;
ivec n_box;
char filename[STRLEN];
char title_solvt[STRLEN];
t_atoms *atoms_solvt;
rvec *x_solvt,*v_solvt=NULL;
real *r_solvt;
int ePBC_solvt;
matrix box_solvt;
int onr,onres;
strncpy(filename,libfn(fn),STRLEN);
snew(atoms_solvt,1);
get_stx_coordnum(filename,&(atoms_solvt->nr));
if (atoms_solvt->nr == 0)
gmx_fatal(FARGS,"No solvent in %s, please check your input\n",filename);
snew(x_solvt,atoms_solvt->nr);
if (v) snew(v_solvt,atoms_solvt->nr);
snew(r_solvt,atoms_solvt->nr);
snew(atoms_solvt->resname,atoms_solvt->nr);
snew(atoms_solvt->atomname,atoms_solvt->nr);
snew(atoms_solvt->atom,atoms_solvt->nr);
atoms_solvt->pdbinfo = NULL;
fprintf(stderr,"Reading solvent configuration%s\n",
v_solvt?" and velocities":"");
read_stx_conf(filename,title_solvt,atoms_solvt,x_solvt,v_solvt,
&ePBC_solvt,box_solvt);
fprintf(stderr,"\"%s\"\n",title_solvt);
fprintf(stderr,"solvent configuration contains %d atoms in %d residues\n",
atoms_solvt->nr,atoms_solvt->nres);
fprintf(stderr,"\n");
/* apply pbc for solvent configuration for whole molecules */
rm_res_pbc(atoms_solvt,x_solvt,box_solvt);
/* initialise van der waals arrays of solvent configuration */
mk_vdw(atoms_solvt,r_solvt,aps,r_distance);
/* calculate the box multiplication factors n_box[0...DIM] */
nmol=1;
for (i=0; (i < DIM);i++) {
n_box[i] = 1;
while (n_box[i]*box_solvt[i][i] < box[i][i])
n_box[i]++;
nmol*=n_box[i];
}
fprintf(stderr,"Will generate new solvent configuration of %dx%dx%d boxes\n",
n_box[XX],n_box[YY],n_box[ZZ]);
/* realloc atoms_solvt for the new solvent configuration */
srenew(atoms_solvt->resname,atoms_solvt->nres*nmol);
srenew(atoms_solvt->atomname,atoms_solvt->nr*nmol);
srenew(atoms_solvt->atom,atoms_solvt->nr*nmol);
srenew(x_solvt,atoms_solvt->nr*nmol);
if (v_solvt) srenew(v_solvt,atoms_solvt->nr*nmol);
srenew(r_solvt,atoms_solvt->nr*nmol);
/* generate a new solvent configuration */
genconf(atoms_solvt,x_solvt,v_solvt,r_solvt,box_solvt,n_box);
#ifdef DEBUG
print_stat(x_solvt,atoms_solvt->nr,box_solvt);
#endif
#ifdef DEBUG
print_stat(x_solvt,atoms_solvt->nr,box_solvt);
#endif
/* Sort the solvent mixture, not the protein... */
sort_molecule(&atoms_solvt,x_solvt,v_solvt,r_solvt);
/* add the two configurations */
onr=atoms->nr;
onres=atoms->nres;
add_conf(atoms,x,v,r,TRUE,ePBC,box,FALSE,
atoms_solvt,x_solvt,v_solvt,r_solvt,TRUE,rshell,max_sol);
*atoms_added=atoms->nr-onr;
*residues_added=atoms->nres-onres;
sfree(x_solvt);
sfree(r_solvt);
fprintf(stderr,"Generated solvent containing %d atoms in %d residues\n",
*atoms_added,*residues_added);
}
static void add_solv(char *fn,t_atoms *atoms,rvec **x,rvec **v,real **r,
int ePBC,matrix box,
gmx_atomprop_t aps,real r_distance,int *atoms_added,
int *residues_added,real rshell,int max_sol)
{
int i,nmol;
ivec n_box;
char filename[STRLEN];
char title_solvt[STRLEN];
t_atoms *atoms_solvt;
rvec *x_solvt,*v_solvt=NULL;
real *r_solvt;
int ePBC_solvt;
matrix box_solvt;
int onr,onres;
strncpy(filename,libfn(fn),STRLEN);
snew(atoms_solvt,1);
get_stx_coordnum(filename,&(atoms_solvt->nr));
if (atoms_solvt->nr == 0)
gmx_fatal(FARGS,"No solvent in %s, please check your input\n",filename);
snew(x_solvt,atoms_solvt->nr);
if (v) snew(v_solvt,atoms_solvt->nr);
snew(r_solvt,atoms_solvt->nr);
snew(atoms_solvt->resinfo,atoms_solvt->nr);
snew(atoms_solvt->atomname,atoms_solvt->nr);
snew(atoms_solvt->atom,atoms_solvt->nr);
atoms_solvt->pdbinfo = NULL;
fprintf(stderr,"Reading solvent configuration%s\n",
v_solvt?" and velocities":"");
read_stx_conf(filename,title_solvt,atoms_solvt,x_solvt,v_solvt,
&ePBC_solvt,box_solvt);
fprintf(stderr,"\"%s\"\n",title_solvt);
fprintf(stderr,"solvent configuration contains %d atoms in %d residues\n",
atoms_solvt->nr,atoms_solvt->nres);
fprintf(stderr,"\n");
/* apply pbc for solvent configuration for whole molecules */
rm_res_pbc(atoms_solvt,x_solvt,box_solvt);
/* initialise van der waals arrays of solvent configuration */
mk_vdw(atoms_solvt,r_solvt,aps,r_distance);
/* calculate the box multiplication factors n_box[0...DIM] */
nmol=1;
for (i=0; (i < DIM);i++) {
n_box[i] = 1;
while (n_box[i]*box_solvt[i][i] < box[i][i])
n_box[i]++;
nmol*=n_box[i];
}
fprintf(stderr,"Will generate new solvent configuration of %dx%dx%d boxes\n",
n_box[XX],n_box[YY],n_box[ZZ]);
/* realloc atoms_solvt for the new solvent configuration */
srenew(atoms_solvt->resinfo,atoms_solvt->nres*nmol);
srenew(atoms_solvt->atomname,atoms_solvt->nr*nmol);
srenew(atoms_solvt->atom,atoms_solvt->nr*nmol);
srenew(x_solvt,atoms_solvt->nr*nmol);
if (v_solvt) srenew(v_solvt,atoms_solvt->nr*nmol);
srenew(r_solvt,atoms_solvt->nr*nmol);
/* generate a new solvent configuration */
genconf(atoms_solvt,x_solvt,v_solvt,r_solvt,box_solvt,n_box);
#ifdef DEBUG
print_stat(x_solvt,atoms_solvt->nr,box_solvt);
#endif
#ifdef DEBUG
print_stat(x_solvt,atoms_solvt->nr,box_solvt);
#endif
/* Sort the solvent mixture, not the protein... */
sort_molecule(&atoms_solvt,x_solvt,v_solvt,r_solvt);
/* add the two configurations */
onr=atoms->nr;
onres=atoms->nres;
add_conf(atoms,x,v,r,TRUE,ePBC,box,FALSE,
atoms_solvt,x_solvt,v_solvt,r_solvt,TRUE,rshell,max_sol);
*atoms_added=atoms->nr-onr;
*residues_added=atoms->nres-onres;
sfree(x_solvt);
sfree(r_solvt);
fprintf(stderr,"Generated solvent containing %d atoms in %d residues\n",
*atoms_added,*residues_added);
}
