void gmx_atomprop_destroy(gmx_atomprop_t aps)
{
gmx_atomprop *ap = (gmx_atomprop*) aps;
int p;
if (aps == NULL) {
printf("\nWARNING: gmx_atomprop_destroy called with a NULL pointer\n\n");
return;
}
for(p=0; p<epropNR; p++) {
destroy_prop(&ap->prop[p]);
}
gmx_residuetype_destroy(ap->restype);
sfree(ap);
}
void analyse(t_atoms *atoms,t_blocka *gb,char ***gn,gmx_bool bASK,gmx_bool bVerb)
{
gmx_residuetype_t rt;
char *resnm;
atom_id *aid;
const char ** restype;
int nra;
int i,k;
size_t j;
int ntypes;
char * p;
const char ** p_typename;
int iwater,iion;
int nwater,nion;
int found;
if (bVerb)
{
printf("Analysing residue names:\n");
}
/* Create system group, every single atom */
snew(aid,atoms->nr);
for(i=0;i<atoms->nr;i++)
{
aid[i]=i;
}
add_grp(gb,gn,atoms->nr,aid,"System");
sfree(aid);
/* For every residue, get a pointer to the residue type name */
gmx_residuetype_init(&rt);
snew(restype,atoms->nres);
ntypes = 0;
p_typename = NULL;
for(i=0;i<atoms->nres;i++)
{
resnm = *atoms->resinfo[i].name;
gmx_residuetype_get_type(rt,resnm,&(restype[i]));
/* Note that this does not lead to a N*N loop, but N*K, where
* K is the number of residue _types_, which is small and independent of N.
*/
found = 0;
for(k=0;k<ntypes && !found;k++)
{
found = !strcmp(restype[i],p_typename[k]);
}
if(!found)
{
srenew(p_typename,ntypes+1);
p_typename[ntypes++] = strdup(restype[i]);
}
}
if (bVerb)
{
p_status(restype,atoms->nres,p_typename,ntypes);
}
for(k=0;k<ntypes;k++)
{
aid=mk_aid(atoms,restype,p_typename[k],&nra,TRUE);
/* Check for special types to do fancy stuff with */
if(!gmx_strcasecmp(p_typename[k],"Protein") && nra>0)
{
sfree(aid);
/* PROTEIN */
analyse_prot(restype,atoms,gb,gn,bASK,bVerb);
/* Create a Non-Protein group */
aid=mk_aid(atoms,restype,"Protein",&nra,FALSE);
if ((nra > 0) && (nra < atoms->nr))
{
add_grp(gb,gn,nra,aid,"non-Protein");
}
sfree(aid);
}
else if(!gmx_strcasecmp(p_typename[k],"Water") && nra>0)
{
add_grp(gb,gn,nra,aid,p_typename[k]);
/* Add this group as 'SOL' too, for backward compatibility with older gromacs versions */
add_grp(gb,gn,nra,aid,"SOL");
sfree(aid);
/* Solvent, create a negated group too */
aid=mk_aid(atoms,restype,"Water",&nra,FALSE);
if ((nra > 0) && (nra < atoms->nr))
{
add_grp(gb,gn,nra,aid,"non-Water");
}
sfree(aid);
}
else if(nra>0)
{
/* Other groups */
add_grp(gb,gn,nra,aid,p_typename[k]);
sfree(aid);
analyse_other(restype,atoms,gb,gn,bASK,bVerb);
}
}
sfree(p_typename);
sfree(restype);
gmx_residuetype_destroy(rt);
/* Create a merged water_and_ions group */
iwater = -1;
iion = -1;
nwater = 0;
nion = 0;
for(i=0;i<gb->nr;i++)
{
if(!gmx_strcasecmp((*gn)[i],"Water"))
{
iwater = i;
nwater = gb->index[i+1]-gb->index[i];
}
else if(!gmx_strcasecmp((*gn)[i],"Ion"))
{
iion = i;
nion = gb->index[i+1]-gb->index[i];
}
}
if(nwater>0 && nion>0)
{
srenew(gb->index,gb->nr+2);
srenew(*gn,gb->nr+1);
(*gn)[gb->nr] = strdup("Water_and_ions");
srenew(gb->a,gb->nra+nwater+nion);
if(nwater>0)
{
for(i=gb->index[iwater];i<gb->index[iwater+1];i++)
{
gb->a[gb->nra++] = gb->a[i];
}
}
if(nion>0)
{
for(i=gb->index[iion];i<gb->index[iion+1];i++)
{
gb->a[gb->nra++] = gb->a[i];
}
}
gb->nr++;
gb->index[gb->nr]=gb->nra;
}
}
static int name2type(t_atoms *at, int **cgnr, gpp_atomtype_t atype,
t_restp restp[])
{
int i,j,prevresind,resind,i0,prevcg,cg,curcg;
char *name;
gmx_bool bProt, bNterm;
double qt;
int nmissat;
gmx_residuetype_t rt;
nmissat = 0;
resind=-1;
bProt=FALSE;
bNterm=FALSE;
i0=0;
snew(*cgnr,at->nr);
qt=0;
prevcg=NOTSET;
curcg=0;
cg=-1;
j=NOTSET;
gmx_residuetype_init(&rt);
for(i=0; (i<at->nr); i++) {
prevresind=resind;
if (at->atom[i].resind != resind) {
resind = at->atom[i].resind;
bProt = gmx_residuetype_is_protein(rt,*(at->resinfo[resind].name));
bNterm=bProt && (resind == 0);
if (resind > 0) {
nmissat += missing_atoms(&restp[prevresind],prevresind,at,i0,i);
}
i0=i;
}
if (at->atom[i].m == 0) {
if (debug)
fprintf(debug,"atom %d%s: curcg=%d, prevcg=%d, cg=%d\n",
i+1,*(at->atomname[i]),curcg,prevcg,
j==NOTSET ? NOTSET : restp[resind].cgnr[j]);
qt=0;
prevcg=cg;
name=*(at->atomname[i]);
j=search_jtype(&restp[resind],name,bNterm);
at->atom[i].type = restp[resind].atom[j].type;
at->atom[i].q = restp[resind].atom[j].q;
at->atom[i].m = get_atomtype_massA(restp[resind].atom[j].type,
atype);
cg = restp[resind].cgnr[j];
/* A charge group number -1 signals a separate charge group
* for this atom.
*/
if ( (cg == -1) || (cg != prevcg) || (resind != prevresind) ) {
curcg++;
}
} else {
if (debug)
fprintf(debug,"atom %d%s: curcg=%d, qt=%g, is_int=%d\n",
i+1,*(at->atomname[i]),curcg,qt,is_int(qt));
cg=-1;
if (is_int(qt)) {
qt=0;
curcg++;
}
qt+=at->atom[i].q;
}
(*cgnr)[i]=curcg;
at->atom[i].typeB = at->atom[i].type;
at->atom[i].qB = at->atom[i].q;
at->atom[i].mB = at->atom[i].m;
}
nmissat += missing_atoms(&restp[resind],resind,at,i0,i);
gmx_residuetype_destroy(rt);
return nmissat;
}
int gmx_chi(int argc,char *argv[])
{
const char *desc[] = {
"[TT]g_chi[tt] computes [GRK]phi[grk], [GRK]psi[grk], [GRK]omega[grk], and [GRK]chi[grk] dihedrals for all your ",
"amino acid backbone and sidechains.",
"It can compute dihedral angle as a function of time, and as",
"histogram distributions.",
"The distributions [TT](histo-(dihedral)(RESIDUE).xvg[tt]) are cumulative over all residues of each type.[PAR]",
"If option [TT]-corr[tt] is given, the program will",
"calculate dihedral autocorrelation functions. The function used",
"is C(t) = < cos([GRK]chi[grk]([GRK]tau[grk])) cos([GRK]chi[grk]([GRK]tau[grk]+t)) >. The use of cosines",
"rather than angles themselves, resolves the problem of periodicity.",
"(Van der Spoel & Berendsen (1997), Biophys. J. 72, 2032-2041).",
"Separate files for each dihedral of each residue",
"[TT](corr(dihedral)(RESIDUE)(nresnr).xvg[tt]) are output, as well as a",
"file containing the information for all residues (argument of [TT]-corr[tt]).[PAR]",
"With option [TT]-all[tt], the angles themselves as a function of time for",
"each residue are printed to separate files [TT](dihedral)(RESIDUE)(nresnr).xvg[tt].",
"These can be in radians or degrees.[PAR]",
"A log file (argument [TT]-g[tt]) is also written. This contains [BR]",
"(a) information about the number of residues of each type.[BR]",
"(b) The NMR ^3J coupling constants from the Karplus equation.[BR]",
"(c) a table for each residue of the number of transitions between ",
"rotamers per nanosecond, and the order parameter S^2 of each dihedral.[BR]",
"(d) a table for each residue of the rotamer occupancy.[PAR]",
"All rotamers are taken as 3-fold, except for [GRK]omega[grk] and [GRK]chi[grk] dihedrals",
"to planar groups (i.e. [GRK]chi[grk]2 of aromatics, Asp and Asn; [GRK]chi[grk]3 of Glu",
"and Gln; and [GRK]chi[grk]4 of Arg), which are 2-fold. \"rotamer 0\" means ",
"that the dihedral was not in the core region of each rotamer. ",
"The width of the core region can be set with [TT]-core_rotamer[tt][PAR]",
"The S^2 order parameters are also output to an [TT].xvg[tt] file",
"(argument [TT]-o[tt] ) and optionally as a [TT].pdb[tt] file with",
"the S^2 values as B-factor (argument [TT]-p[tt]). ",
"The total number of rotamer transitions per timestep",
"(argument [TT]-ot[tt]), the number of transitions per rotamer",
"(argument [TT]-rt[tt]), and the ^3J couplings (argument [TT]-jc[tt]), ",
"can also be written to [TT].xvg[tt] files.[PAR]",
"If [TT]-chi_prod[tt] is set (and [TT]-maxchi[tt] > 0), cumulative rotamers, e.g.",
"1+9([GRK]chi[grk]1-1)+3([GRK]chi[grk]2-1)+([GRK]chi[grk]3-1) (if the residue has three 3-fold ",
"dihedrals and [TT]-maxchi[tt] >= 3)",
"are calculated. As before, if any dihedral is not in the core region,",
"the rotamer is taken to be 0. The occupancies of these cumulative ",
"rotamers (starting with rotamer 0) are written to the file",
"that is the argument of [TT]-cp[tt], and if the [TT]-all[tt] flag",
"is given, the rotamers as functions of time",
"are written to [TT]chiproduct(RESIDUE)(nresnr).xvg[tt] ",
"and their occupancies to [TT]histo-chiproduct(RESIDUE)(nresnr).xvg[tt].[PAR]",
"The option [TT]-r[tt] generates a contour plot of the average [GRK]omega[grk] angle",
"as a function of the [GRK]phi[grk] and [GRK]psi[grk] angles, that is, in a Ramachandran plot",
"the average [GRK]omega[grk] angle is plotted using color coding.",
};
const char *bugs[] = {
"Produces MANY output files (up to about 4 times the number of residues in the protein, twice that if autocorrelation functions are calculated). Typically several hundred files are output.",
"[GRK]phi[grk] and [GRK]psi[grk] dihedrals are calculated in a non-standard way, using H-N-CA-C for [GRK]phi[grk] instead of C(-)-N-CA-C, and N-CA-C-O for [GRK]psi[grk] instead of N-CA-C-N(+). This causes (usually small) discrepancies with the output of other tools like [TT]g_rama[tt].",
"[TT]-r0[tt] option does not work properly",
"Rotamers with multiplicity 2 are printed in [TT]chi.log[tt] as if they had multiplicity 3, with the 3rd (g(+)) always having probability 0"
};
/* defaults */
static int r0=1,ndeg=1,maxchi=2;
static gmx_bool bAll=FALSE;
static gmx_bool bPhi=FALSE,bPsi=FALSE,bOmega=FALSE;
static real bfac_init=-1.0,bfac_max=0;
static const char *maxchistr[] = { NULL, "0", "1", "2", "3", "4", "5", "6", NULL };
static gmx_bool bRama=FALSE,bShift=FALSE,bViol=FALSE,bRamOmega=FALSE;
static gmx_bool bNormHisto=TRUE,bChiProduct=FALSE,bHChi=FALSE,bRAD=FALSE,bPBC=TRUE;
static real core_frac=0.5 ;
t_pargs pa[] = {
{ "-r0", FALSE, etINT, {&r0},
"starting residue" },
{ "-phi", FALSE, etBOOL, {&bPhi},
"Output for [GRK]phi[grk] dihedral angles" },
{ "-psi", FALSE, etBOOL, {&bPsi},
"Output for [GRK]psi[grk] dihedral angles" },
{ "-omega",FALSE, etBOOL, {&bOmega},
"Output for [GRK]omega[grk] dihedrals (peptide bonds)" },
{ "-rama", FALSE, etBOOL, {&bRama},
"Generate [GRK]phi[grk]/[GRK]psi[grk] and [GRK]chi[grk]1/[GRK]chi[grk]2 Ramachandran plots" },
{ "-viol", FALSE, etBOOL, {&bViol},
"Write a file that gives 0 or 1 for violated Ramachandran angles" },
{ "-periodic", FALSE, etBOOL, {&bPBC},
"Print dihedral angles modulo 360 degrees" },
{ "-all", FALSE, etBOOL, {&bAll},
"Output separate files for every dihedral." },
{ "-rad", FALSE, etBOOL, {&bRAD},
"in angle vs time files, use radians rather than degrees."},
{ "-shift", FALSE, etBOOL, {&bShift},
"Compute chemical shifts from [GRK]phi[grk]/[GRK]psi[grk] angles" },
{ "-binwidth", FALSE, etINT, {&ndeg},
"bin width for histograms (degrees)" },
{ "-core_rotamer", FALSE, etREAL, {&core_frac},
"only the central [TT]-core_rotamer[tt]*(360/multiplicity) belongs to each rotamer (the rest is assigned to rotamer 0)" },
{ "-maxchi", FALSE, etENUM, {maxchistr},
"calculate first ndih [GRK]chi[grk] dihedrals" },
{ "-normhisto", FALSE, etBOOL, {&bNormHisto},
"Normalize histograms" },
{ "-ramomega",FALSE,etBOOL, {&bRamOmega},
"compute average omega as a function of phi/psi and plot it in an [TT].xpm[tt] plot" },
{ "-bfact", FALSE, etREAL, {&bfac_init},
"B-factor value for [TT].pdb[tt] file for atoms with no calculated dihedral order parameter"},
{ "-chi_prod",FALSE,etBOOL, {&bChiProduct},
"compute a single cumulative rotamer for each residue"},
{ "-HChi",FALSE,etBOOL, {&bHChi},
"Include dihedrals to sidechain hydrogens"},
{ "-bmax", FALSE, etREAL, {&bfac_max},
"Maximum B-factor on any of the atoms that make up a dihedral, for the dihedral angle to be considere in the statistics. Applies to database work where a number of X-Ray structures is analyzed. [TT]-bmax[tt] <= 0 means no limit." }
};
FILE *log;
int natoms,nlist,idum,nbin;
t_atoms atoms;
rvec *x;
int ePBC;
matrix box;
char title[256],grpname[256];
t_dlist *dlist;
gmx_bool bChi,bCorr,bSSHisto;
gmx_bool bDo_rt, bDo_oh, bDo_ot, bDo_jc ;
real dt=0, traj_t_ns;
output_env_t oenv;
gmx_residuetype_t rt;
atom_id isize,*index;
int ndih,nactdih,nf;
real **dih,*trans_frac,*aver_angle,*time;
int i,j,**chi_lookup,*xity;
t_filenm fnm[] = {
{ efSTX, "-s", NULL, ffREAD },
{ efTRX, "-f", NULL, ffREAD },
{ efXVG, "-o", "order", ffWRITE },
{ efPDB, "-p", "order", ffOPTWR },
{ efDAT, "-ss", "ssdump", ffOPTRD },
{ efXVG, "-jc", "Jcoupling", ffWRITE },
{ efXVG, "-corr", "dihcorr",ffOPTWR },
{ efLOG, "-g", "chi", ffWRITE },
/* add two more arguments copying from g_angle */
{ efXVG, "-ot", "dihtrans", ffOPTWR },
{ efXVG, "-oh", "trhisto", ffOPTWR },
{ efXVG, "-rt", "restrans", ffOPTWR },
{ efXVG, "-cp", "chiprodhisto", ffOPTWR }
};
#define NFILE asize(fnm)
int npargs;
t_pargs *ppa;
CopyRight(stderr,argv[0]);
npargs = asize(pa);
ppa = add_acf_pargs(&npargs,pa);
parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,npargs,ppa,asize(desc),desc,asize(bugs),bugs,
&oenv);
/* Handle result from enumerated type */
sscanf(maxchistr[0],"%d",&maxchi);
bChi = (maxchi > 0);
log=ffopen(ftp2fn(efLOG,NFILE,fnm),"w");
if (bRamOmega) {
bOmega = TRUE;
bPhi = TRUE;
bPsi = TRUE;
}
/* set some options */
bDo_rt=(opt2bSet("-rt",NFILE,fnm));
bDo_oh=(opt2bSet("-oh",NFILE,fnm));
bDo_ot=(opt2bSet("-ot",NFILE,fnm));
bDo_jc=(opt2bSet("-jc",NFILE,fnm));
bCorr=(opt2bSet("-corr",NFILE,fnm));
if (bCorr)
fprintf(stderr,"Will calculate autocorrelation\n");
if (core_frac > 1.0 ) {
fprintf(stderr, "core_rotamer fraction > 1.0 ; will use 1.0\n");
core_frac=1.0 ;
}
if (core_frac < 0.0 ) {
fprintf(stderr, "core_rotamer fraction < 0.0 ; will use 0.0\n");
core_frac=0.0 ;
}
if (maxchi > MAXCHI) {
fprintf(stderr,
"Will only calculate first %d Chi dihedrals in stead of %d.\n",
MAXCHI, maxchi);
maxchi=MAXCHI;
}
bSSHisto = ftp2bSet(efDAT,NFILE,fnm);
nbin = 360/ndeg ;
/* Find the chi angles using atoms struct and a list of amino acids */
get_stx_coordnum(ftp2fn(efSTX,NFILE,fnm),&natoms);
init_t_atoms(&atoms,natoms,TRUE);
snew(x,natoms);
read_stx_conf(ftp2fn(efSTX,NFILE,fnm),title,&atoms,x,NULL,&ePBC,box);
fprintf(log,"Title: %s\n",title);
gmx_residuetype_init(&rt);
dlist=mk_dlist(log,&atoms,&nlist,bPhi,bPsi,bChi,bHChi,maxchi,r0,rt);
fprintf(stderr,"%d residues with dihedrals found\n", nlist);
if (nlist == 0)
gmx_fatal(FARGS,"No dihedrals in your structure!\n");
/* Make a linear index for reading all. */
index=make_chi_ind(nlist,dlist,&ndih);
isize=4*ndih;
fprintf(stderr,"%d dihedrals found\n", ndih);
snew(dih,ndih);
/* COMPUTE ALL DIHEDRALS! */
read_ang_dih(ftp2fn(efTRX,NFILE,fnm),FALSE,TRUE,FALSE,bPBC,1,&idum,
&nf,&time,isize,index,&trans_frac,&aver_angle,dih,oenv);
dt=(time[nf-1]-time[0])/(nf-1); /* might want this for corr or n. transit*/
if (bCorr)
{
if (nf < 2)
{
gmx_fatal(FARGS,"Need at least 2 frames for correlation");
}
}
/* put angles in -M_PI to M_PI ! and correct phase factor for phi and psi
* pass nactdih instead of ndih to low_ana_dih_trans and get_chi_product_traj
* to prevent accessing off end of arrays when maxchi < 5 or 6. */
nactdih = reset_em_all(nlist,dlist,nf,dih,maxchi);
if (bAll)
dump_em_all(nlist,dlist,nf,time,dih,maxchi,bPhi,bPsi,bChi,bOmega,bRAD,oenv);
/* Histogramming & J coupling constants & calc of S2 order params */
histogramming(log,nbin,rt,nf,maxchi,dih,nlist,dlist,index,
bPhi,bPsi,bOmega,bChi,
bNormHisto,bSSHisto,ftp2fn(efDAT,NFILE,fnm),bfac_max,&atoms,
bDo_jc,opt2fn("-jc",NFILE,fnm),oenv);
/* transitions
*
* added multiplicity */
snew(xity,ndih) ;
mk_multiplicity_lookup(xity, maxchi, dih, nlist, dlist,ndih);
strcpy(grpname, "All residues, ");
if(bPhi)
strcat(grpname, "Phi ");
if(bPsi)
strcat(grpname, "Psi ");
if(bOmega)
strcat(grpname, "Omega ");
if(bChi){
strcat(grpname, "Chi 1-") ;
sprintf(grpname + strlen(grpname), "%i", maxchi);
}
low_ana_dih_trans(bDo_ot, opt2fn("-ot",NFILE,fnm),
bDo_oh, opt2fn("-oh",NFILE,fnm),maxchi,
dih, nlist, dlist, nf, nactdih, grpname, xity,
*time, dt, FALSE, core_frac,oenv) ;
/* Order parameters */
order_params(log,opt2fn("-o",NFILE,fnm),maxchi,nlist,dlist,
ftp2fn_null(efPDB,NFILE,fnm),bfac_init,
&atoms,x,ePBC,box,bPhi,bPsi,bChi,oenv);
/* Print ramachandran maps! */
if (bRama)
do_rama(nf,nlist,dlist,dih,bViol,bRamOmega,oenv);
if (bShift)
do_pp2shifts(log,nf,nlist,dlist,dih);
/* rprint S^2, transitions, and rotamer occupancies to log */
traj_t_ns = 0.001 * (time[nf-1]-time[0]) ;
pr_dlist(log,nlist,dlist,traj_t_ns,edPrintST,bPhi,bPsi,bChi,bOmega,maxchi);
pr_dlist(log,nlist,dlist,traj_t_ns,edPrintRO,bPhi,bPsi,bChi,bOmega,maxchi);
ffclose(log);
/* transitions to xvg */
if (bDo_rt)
print_transitions(opt2fn("-rt",NFILE,fnm),maxchi,nlist,dlist,
&atoms,x,box,bPhi,bPsi,bChi,traj_t_ns,oenv);
/* chi_product trajectories (ie one "rotamer number" for each residue) */
if (bChiProduct && bChi ) {
snew(chi_lookup,nlist) ;
for (i=0;i<nlist;i++)
snew(chi_lookup[i], maxchi) ;
mk_chi_lookup(chi_lookup, maxchi, dih, nlist, dlist);
get_chi_product_traj(dih,nf,nactdih,nlist,
maxchi,dlist,time,chi_lookup,xity,
FALSE,bNormHisto, core_frac,bAll,
opt2fn("-cp",NFILE,fnm),oenv);
for (i=0;i<nlist;i++)
sfree(chi_lookup[i]);
}
/* Correlation comes last because it f***s up the angles */
if (bCorr)
do_dihcorr(opt2fn("-corr",NFILE,fnm),nf,ndih,dih,dt,nlist,dlist,time,
maxchi,bPhi,bPsi,bChi,bOmega,oenv);
do_view(oenv,opt2fn("-o",NFILE,fnm),"-nxy");
do_view(oenv,opt2fn("-jc",NFILE,fnm),"-nxy");
if (bCorr)
do_view(oenv,opt2fn("-corr",NFILE,fnm),"-nxy");
gmx_residuetype_destroy(rt);
thanx(stderr);
return 0;
}
void write_pdbfile_indexed(FILE *out, const char *title,
t_atoms *atoms, rvec x[],
int ePBC, matrix box, char chainid,
int model_nr, int nindex, const int index[],
gmx_conect conect, gmx_bool bTerSepChains)
{
gmx_conect_t *gc = (gmx_conect_t *)conect;
char resnm[6], nm[6];
int i, ii;
int resind, resnr;
enum PDB_record type;
unsigned char resic, ch;
char altloc;
real occup, bfac;
gmx_bool bOccup;
int chainnum, lastchainnum;
gmx_residuetype_t*rt;
const char *p_restype;
const char *p_lastrestype;
gmx_residuetype_init(&rt);
fprintf(out, "TITLE %s\n", (title && title[0]) ? title : gmx::bromacs().c_str());
if (box && ( norm2(box[XX]) || norm2(box[YY]) || norm2(box[ZZ]) ) )
{
gmx_write_pdb_box(out, ePBC, box);
}
if (atoms->pdbinfo)
{
/* Check whether any occupancies are set, in that case leave it as is,
* otherwise set them all to one
*/
bOccup = TRUE;
for (ii = 0; (ii < nindex) && bOccup; ii++)
{
i = index[ii];
bOccup = bOccup && (atoms->pdbinfo[i].occup == 0.0);
}
}
else
{
bOccup = FALSE;
}
fprintf(out, "MODEL %8d\n", model_nr > 0 ? model_nr : 1);
lastchainnum = -1;
p_restype = NULL;
for (ii = 0; ii < nindex; ii++)
{
i = index[ii];
resind = atoms->atom[i].resind;
chainnum = atoms->resinfo[resind].chainnum;
p_lastrestype = p_restype;
gmx_residuetype_get_type(rt, *atoms->resinfo[resind].name, &p_restype);
/* Add a TER record if we changed chain, and if either the previous or this chain is protein/DNA/RNA. */
if (bTerSepChains && ii > 0 && chainnum != lastchainnum)
{
/* Only add TER if the previous chain contained protein/DNA/RNA. */
if (gmx_residuetype_is_protein(rt, p_lastrestype) || gmx_residuetype_is_dna(rt, p_lastrestype) || gmx_residuetype_is_rna(rt, p_lastrestype))
{
fprintf(out, "TER\n");
}
lastchainnum = chainnum;
}
strncpy(resnm, *atoms->resinfo[resind].name, sizeof(resnm)-1);
resnm[sizeof(resnm)-1] = 0;
strncpy(nm, *atoms->atomname[i], sizeof(nm)-1);
nm[sizeof(nm)-1] = 0;
/* rename HG12 to 2HG1, etc. */
xlate_atomname_gmx2pdb(nm);
resnr = atoms->resinfo[resind].nr;
resic = atoms->resinfo[resind].ic;
if (chainid != ' ')
{
ch = chainid;
}
else
{
ch = atoms->resinfo[resind].chainid;
if (ch == 0)
{
ch = ' ';
}
}
if (resnr >= 10000)
{
resnr = resnr % 10000;
}
if (atoms->pdbinfo)
{
type = static_cast<enum PDB_record>(atoms->pdbinfo[i].type);
altloc = atoms->pdbinfo[i].altloc;
if (!isalnum(altloc))
{
altloc = ' ';
}
occup = bOccup ? 1.0 : atoms->pdbinfo[i].occup;
bfac = atoms->pdbinfo[i].bfac;
}
else
{
type = epdbATOM;
occup = 1.0;
bfac = 0.0;
altloc = ' ';
}
gmx_fprintf_pdb_atomline(out,
type,
i+1,
nm,
altloc,
resnm,
ch,
resnr,
resic,
10*x[i][XX], 10*x[i][YY], 10*x[i][ZZ],
occup,
bfac,
atoms->atom[i].elem);
if (atoms->pdbinfo && atoms->pdbinfo[i].bAnisotropic)
{
fprintf(out, "ANISOU%5d %-4.4s%4.4s%c%4d%c %7d%7d%7d%7d%7d%7d\n",
(i+1)%100000, nm, resnm, ch, resnr,
(resic == '\0') ? ' ' : resic,
atoms->pdbinfo[i].uij[0], atoms->pdbinfo[i].uij[1],
atoms->pdbinfo[i].uij[2], atoms->pdbinfo[i].uij[3],
atoms->pdbinfo[i].uij[4], atoms->pdbinfo[i].uij[5]);
}
}
fprintf(out, "TER\n");
fprintf(out, "ENDMDL\n");
if (NULL != gc)
{
/* Write conect records */
for (i = 0; (i < gc->nconect); i++)
{
fprintf(out, "CONECT%5d%5d\n", gc->conect[i].ai+1, gc->conect[i].aj+1);
}
}
gmx_residuetype_destroy(rt);
}
void write_pdbfile_indexed(FILE *out, const char *title,
t_atoms *atoms, rvec x[],
int ePBC, matrix box, char chainid,
int model_nr, atom_id nindex, atom_id index[],
gmx_conect conect, gmx_bool bTerSepChains)
{
gmx_conect_t *gc = (gmx_conect_t *)conect;
char resnm[6], nm[6], pdbform[128], pukestring[100];
atom_id i, ii;
int resind, resnr, type;
unsigned char resic, ch;
real occup, bfac;
gmx_bool bOccup;
int nlongname = 0;
int chainnum, lastchainnum;
int lastresind, lastchainresind;
gmx_residuetype_t rt;
const char *p_restype;
const char *p_lastrestype;
gmx_residuetype_init(&rt);
bromacs(pukestring, 99);
fprintf(out, "TITLE %s\n", (title && title[0]) ? title : pukestring);
if (bWideFormat)
{
fprintf(out, "REMARK This file does not adhere to the PDB standard\n");
fprintf(out, "REMARK As a result of, some programs may not like it\n");
}
if (box && ( norm2(box[XX]) || norm2(box[YY]) || norm2(box[ZZ]) ) )
{
gmx_write_pdb_box(out, ePBC, box);
}
if (atoms->pdbinfo)
{
/* Check whether any occupancies are set, in that case leave it as is,
* otherwise set them all to one
*/
bOccup = TRUE;
for (ii = 0; (ii < nindex) && bOccup; ii++)
{
i = index[ii];
bOccup = bOccup && (atoms->pdbinfo[i].occup == 0.0);
}
}
else
{
bOccup = FALSE;
}
fprintf(out, "MODEL %8d\n", model_nr > 0 ? model_nr : 1);
lastchainresind = -1;
lastchainnum = -1;
resind = -1;
p_restype = NULL;
for (ii = 0; ii < nindex; ii++)
{
i = index[ii];
lastresind = resind;
resind = atoms->atom[i].resind;
chainnum = atoms->resinfo[resind].chainnum;
p_lastrestype = p_restype;
gmx_residuetype_get_type(rt, *atoms->resinfo[resind].name, &p_restype);
/* Add a TER record if we changed chain, and if either the previous or this chain is protein/DNA/RNA. */
if (bTerSepChains && ii > 0 && chainnum != lastchainnum)
{
/* Only add TER if the previous chain contained protein/DNA/RNA. */
if (gmx_residuetype_is_protein(rt, p_lastrestype) || gmx_residuetype_is_dna(rt, p_lastrestype) || gmx_residuetype_is_rna(rt, p_lastrestype))
{
fprintf(out, "TER\n");
}
lastchainnum = chainnum;
lastchainresind = lastresind;
}
strncpy(resnm, *atoms->resinfo[resind].name, sizeof(resnm)-1);
strncpy(nm, *atoms->atomname[i], sizeof(nm)-1);
/* rename HG12 to 2HG1, etc. */
xlate_atomname_gmx2pdb(nm);
resnr = atoms->resinfo[resind].nr;
resic = atoms->resinfo[resind].ic;
if (chainid != ' ')
{
ch = chainid;
}
else
{
ch = atoms->resinfo[resind].chainid;
if (ch == 0)
{
ch = ' ';
}
}
if (resnr >= 10000)
{
resnr = resnr % 10000;
}
if (atoms->pdbinfo)
{
type = atoms->pdbinfo[i].type;
occup = bOccup ? 1.0 : atoms->pdbinfo[i].occup;
bfac = atoms->pdbinfo[i].bfac;
}
else
{
type = 0;
occup = 1.0;
bfac = 0.0;
}
if (bWideFormat)
{
strcpy(pdbform,
"%-6s%5u %-4.4s %3.3s %c%4d%c %10.5f%10.5f%10.5f%8.4f%8.4f %2s\n");
}
else
{
/* Check whether atomname is an element name */
if ((strlen(nm) < 4) && (gmx_strcasecmp(nm, atoms->atom[i].elem) != 0))
{
strcpy(pdbform, pdbformat);
}
else
{
strcpy(pdbform, pdbformat4);
if (strlen(nm) > 4)
{
int maxwln = 20;
if (nlongname < maxwln)
{
fprintf(stderr, "WARNING: Writing out atom name (%s) longer than 4 characters to .pdb file\n", nm);
}
else if (nlongname == maxwln)
{
fprintf(stderr, "WARNING: More than %d long atom names, will not write more warnings\n", maxwln);
}
nlongname++;
}
}
strcat(pdbform, "%6.2f%6.2f %2s\n");
}
fprintf(out, pdbform, pdbtp[type], (i+1)%100000, nm, resnm, ch, resnr,
(resic == '\0') ? ' ' : resic,
10*x[i][XX], 10*x[i][YY], 10*x[i][ZZ], occup, bfac, atoms->atom[i].elem);
if (atoms->pdbinfo && atoms->pdbinfo[i].bAnisotropic)
{
fprintf(out, "ANISOU%5u %-4.4s%3.3s %c%4d%c %7d%7d%7d%7d%7d%7d\n",
(i+1)%100000, nm, resnm, ch, resnr,
(resic == '\0') ? ' ' : resic,
atoms->pdbinfo[i].uij[0], atoms->pdbinfo[i].uij[1],
atoms->pdbinfo[i].uij[2], atoms->pdbinfo[i].uij[3],
atoms->pdbinfo[i].uij[4], atoms->pdbinfo[i].uij[5]);
}
}
fprintf(out, "TER\n");
fprintf(out, "ENDMDL\n");
if (NULL != gc)
{
/* Write conect records */
for (i = 0; (i < gc->nconect); i++)
{
fprintf(out, "CONECT%5d%5d\n", gc->conect[i].ai+1, gc->conect[i].aj+1);
}
}
gmx_residuetype_destroy(rt);
}
