static void get_xlatoms(const char *fn,FILE *fp,
int *nptr,t_xlate_atom **xlptr)
{
char filebase[STRLEN];
char line[STRLEN];
char rbuf[1024],abuf[1024],repbuf[1024],dumbuf[1024];
char *_ptr;
int n,na,idum;
t_xlate_atom *xl;
fflib_filename_base(fn,filebase,STRLEN);
n = *nptr;
xl = *xlptr;
while (get_a_line(fp,line,STRLEN))
{
na = sscanf(line,"%s%s%s%s",rbuf,abuf,repbuf,dumbuf);
/* Check if we are reading an old format file with the number of items
* on the first line.
*/
if (na == 1 && n == *nptr && sscanf(rbuf,"%d",&idum) == 1)
{
continue;
}
if (na != 3)
{
gmx_fatal(FARGS,"Expected a residue name and two atom names in file '%s', not '%s'",fn,line);
}
srenew(xl,n+1);
xl[n].filebase = strdup(filebase);
/* Use wildcards... */
if (strcmp(rbuf,"*") != 0)
{
xl[n].res = strdup(rbuf);
}
else
{
xl[n].res = NULL;
}
/* Replace underscores in the string by spaces */
while ((_ptr = strchr(abuf,'_')) != 0)
{
*_ptr = ' ';
}
xl[n].atom = strdup(abuf);
xl[n].replace = strdup(repbuf);
n++;
}
*nptr = n;
*xlptr = xl;
}
void read_resall(char *rrdb, int *nrtpptr, t_restp **rtp,
gpp_atomtype_t atype, t_symtab *tab,
gmx_bool bAllowOverrideRTP)
{
FILE *in;
char filebase[STRLEN], line[STRLEN], header[STRLEN];
int i, nrtp, maxrtp, bt, nparam;
int dum1, dum2, dum3;
t_restp *rrtp, *header_settings;
gmx_bool bNextResidue, bError;
int firstrtp;
fflib_filename_base(rrdb, filebase, STRLEN);
in = fflib_open(rrdb);
if (debug)
{
fprintf(debug, "%9s %5s", "Residue", "atoms");
for (i = 0; i < ebtsNR; i++)
{
fprintf(debug, " %10s", btsNames[i]);
}
fprintf(debug, "\n");
}
snew(header_settings, 1);
/* these bonded parameters will overwritten be when *
* there is a [ bondedtypes ] entry in the .rtp file */
header_settings->rb[ebtsBONDS].type = 1; /* normal bonds */
header_settings->rb[ebtsANGLES].type = 1; /* normal angles */
header_settings->rb[ebtsPDIHS].type = 1; /* normal dihedrals */
header_settings->rb[ebtsIDIHS].type = 2; /* normal impropers */
header_settings->rb[ebtsEXCLS].type = 1; /* normal exclusions */
header_settings->rb[ebtsCMAP].type = 1; /* normal cmap torsions */
header_settings->bKeepAllGeneratedDihedrals = FALSE;
header_settings->nrexcl = 3;
header_settings->bGenerateHH14Interactions = TRUE;
header_settings->bRemoveDihedralIfWithImproper = TRUE;
/* Column 5 & 6 aren't really bonded types, but we include
* them here to avoid introducing a new section:
* Column 5 : This controls the generation of dihedrals from the bonding.
* All possible dihedrals are generated automatically. A value of
* 1 here means that all these are retained. A value of
* 0 here requires generated dihedrals be removed if
* * there are any dihedrals on the same central atoms
* specified in the residue topology, or
* * there are other identical generated dihedrals
* sharing the same central atoms, or
* * there are other generated dihedrals sharing the
* same central bond that have fewer hydrogen atoms
* Column 6: Number of bonded neighbors to exclude.
* Column 7: Generate 1,4 interactions between two hydrogen atoms
* Column 8: Remove proper dihedrals if centered on the same bond
* as an improper dihedral
*/
get_a_line(in, line, STRLEN);
if (!get_header(line, header))
{
gmx_fatal(FARGS, "in .rtp file at line:\n%s\n", line);
}
if (gmx_strncasecmp("bondedtypes", header, 5) == 0)
{
get_a_line(in, line, STRLEN);
if ((nparam = sscanf(line, "%d %d %d %d %d %d %d %d",
&header_settings->rb[ebtsBONDS].type, &header_settings->rb[ebtsANGLES].type,
&header_settings->rb[ebtsPDIHS].type, &header_settings->rb[ebtsIDIHS].type,
&dum1, &header_settings->nrexcl, &dum2, &dum3)) < 4)
{
gmx_fatal(FARGS, "need 4 to 8 parameters in the header of .rtp file %s at line:\n%s\n", rrdb, line);
}
header_settings->bKeepAllGeneratedDihedrals = (dum1 != 0);
header_settings->bGenerateHH14Interactions = (dum2 != 0);
header_settings->bRemoveDihedralIfWithImproper = (dum3 != 0);
get_a_line(in, line, STRLEN);
if (nparam < 5)
{
fprintf(stderr, "Using default: not generating all possible dihedrals\n");
header_settings->bKeepAllGeneratedDihedrals = FALSE;
}
if (nparam < 6)
{
fprintf(stderr, "Using default: excluding 3 bonded neighbors\n");
header_settings->nrexcl = 3;
}
if (nparam < 7)
{
fprintf(stderr, "Using default: generating 1,4 H--H interactions\n");
header_settings->bGenerateHH14Interactions = TRUE;
}
if (nparam < 8)
{
fprintf(stderr, "Using default: removing proper dihedrals found on the same bond as a proper dihedral\n");
header_settings->bRemoveDihedralIfWithImproper = TRUE;
}
}
else
{
fprintf(stderr,
"Reading .rtp file without '[ bondedtypes ]' directive,\n"
"Will proceed as if the entry was:\n");
print_resall_header(stderr, header_settings);
}
/* We don't know the current size of rrtp, but simply realloc immediately */
nrtp = *nrtpptr;
rrtp = *rtp;
maxrtp = nrtp;
while (!feof(in))
{
if (nrtp >= maxrtp)
{
maxrtp += 100;
srenew(rrtp, maxrtp);
}
/* Initialise rtp entry structure */
rrtp[nrtp] = *header_settings;
if (!get_header(line, header))
{
gmx_fatal(FARGS, "in .rtp file at line:\n%s\n", line);
}
rrtp[nrtp].resname = gmx_strdup(header);
rrtp[nrtp].filebase = gmx_strdup(filebase);
get_a_line(in, line, STRLEN);
bError = FALSE;
bNextResidue = FALSE;
do
{
if (!get_header(line, header))
{
bError = TRUE;
}
else
{
bt = get_bt(header);
if (bt != NOTSET)
{
/* header is an bonded directive */
bError = !read_bondeds(bt, in, line, &rrtp[nrtp]);
}
else if (gmx_strncasecmp("atoms", header, 5) == 0)
{
/* header is the atoms directive */
bError = !read_atoms(in, line, &(rrtp[nrtp]), tab, atype);
}
else
{
/* else header must be a residue name */
bNextResidue = TRUE;
}
}
if (bError)
{
gmx_fatal(FARGS, "in .rtp file in residue %s at line:\n%s\n",
rrtp[nrtp].resname, line);
}
}
while (!feof(in) && !bNextResidue);
if (rrtp[nrtp].natom == 0)
{
gmx_fatal(FARGS, "No atoms found in .rtp file in residue %s\n",
rrtp[nrtp].resname);
}
if (debug)
{
fprintf(debug, "%3d %5s %5d",
nrtp+1, rrtp[nrtp].resname, rrtp[nrtp].natom);
for (i = 0; i < ebtsNR; i++)
{
fprintf(debug, " %10d", rrtp[nrtp].rb[i].nb);
}
fprintf(debug, "\n");
}
firstrtp = -1;
for (i = 0; i < nrtp; i++)
{
if (gmx_strcasecmp(rrtp[i].resname, rrtp[nrtp].resname) == 0)
{
firstrtp = i;
}
}
if (firstrtp == -1)
{
nrtp++;
fprintf(stderr, "\rResidue %d", nrtp);
fflush(stderr);
}
else
{
if (firstrtp >= *nrtpptr)
{
gmx_fatal(FARGS, "Found a second entry for '%s' in '%s'",
rrtp[nrtp].resname, rrdb);
}
if (bAllowOverrideRTP)
{
fprintf(stderr, "\n");
fprintf(stderr, "Found another rtp entry for '%s' in '%s', ignoring this entry and keeping the one from '%s.rtp'\n",
rrtp[nrtp].resname, rrdb, rrtp[firstrtp].filebase);
/* We should free all the data for this entry.
* The current code gives a lot of dangling pointers.
*/
clear_t_restp(&rrtp[nrtp]);
}
else
{
gmx_fatal(FARGS, "Found rtp entries for '%s' in both '%s' and '%s'. If you want the first definition to override the second one, set the -rtpo option of pdb2gmx.", rrtp[nrtp].resname, rrtp[firstrtp].filebase, rrdb);
}
}
}
gmx_ffclose(in);
/* give back unused memory */
srenew(rrtp, nrtp);
fprintf(stderr, "\nSorting it all out...\n");
qsort(rrtp, nrtp, (size_t)sizeof(rrtp[0]), comprtp);
check_rtp(nrtp, rrtp, rrdb);
*nrtpptr = nrtp;
*rtp = rrtp;
}
void read_resall(char *rrdb, int *nrtpptr, t_restp **rtp,
gpp_atomtype_t atype, t_symtab *tab,
gmx_bool bAllowOverrideRTP)
{
FILE *in;
char filebase[STRLEN],*ptr,line[STRLEN],header[STRLEN];
int i,nrtp,maxrtp,bt,nparam;
int dum1,dum2,dum3;
t_restp *rrtp;
gmx_bool bNextResidue,bError;
int bts[ebtsNR];
gmx_bool bAlldih;
int nrexcl;
gmx_bool HH14;
gmx_bool bRemoveDih;
int firstrtp;
fflib_filename_base(rrdb,filebase,STRLEN);
in = fflib_open(rrdb);
if (debug) {
fprintf(debug,"%9s %5s", "Residue", "atoms");
for(i=0; i<ebtsNR; i++)
fprintf(debug," %10s",btsNames[i]);
fprintf(debug,"\n");
}
/* these bonded parameters will overwritten be when *
* there is a [ bondedtypes ] entry in the .rtp file */
bts[ebtsBONDS] = 1; /* normal bonds */
bts[ebtsANGLES] = 1; /* normal angles */
bts[ebtsPDIHS] = 1; /* normal dihedrals */
bts[ebtsIDIHS] = 2; /* normal impropers */
bts[ebtsEXCLS] = 1; /* normal exclusions */
bts[ebtsCMAP] = 1; /* normal cmap torsions */
bAlldih = FALSE;
nrexcl = 3;
HH14 = TRUE;
bRemoveDih = TRUE;
/* Column 5 & 6 aren't really bonded types, but we include
* them here to avoid introducing a new section:
* Column 5: 1 means generate all dihedrals, 0 not.
* Column 6: Number of bonded neighbors to exclude.
* Coulmn 7: Generate 1,4 interactions between pairs of hydrogens
* Column 8: Remove impropers over the same bond as a proper dihedral
*/
get_a_line(in,line,STRLEN);
if (!get_header(line,header))
gmx_fatal(FARGS,"in .rtp file at line:\n%s\n",line);
if (gmx_strncasecmp("bondedtypes",header,5)==0) {
get_a_line(in,line,STRLEN);
if ((nparam=sscanf(line,"%d %d %d %d %d %d %d %d",
&bts[ebtsBONDS],&bts[ebtsANGLES],
&bts[ebtsPDIHS],&bts[ebtsIDIHS],
&dum1,&nrexcl,&dum2,&dum3)) < 4 )
{
gmx_fatal(FARGS,"need at least 4 (up to 8) parameters in .rtp file at line:\n%s\n",line);
}
bAlldih = (dum1 != 0);
HH14 = (dum2 != 0);
bRemoveDih = (dum3 != 0);
get_a_line(in,line,STRLEN);
if(nparam<5) {
fprintf(stderr,"Using default: not generating all possible dihedrals\n");
bAlldih = FALSE;
}
if(nparam<6) {
fprintf(stderr,"Using default: excluding 3 bonded neighbors\n");
nrexcl = 3;
}
if(nparam<7) {
fprintf(stderr,"Using default: generating 1,4 H--H interactions\n");
HH14 = TRUE;
}
if(nparam<8) {
fprintf(stderr,"Using default: removing impropers on same bond as a proper\n");
bRemoveDih = TRUE;
}
} else {
fprintf(stderr,
"Reading .rtp file without '[ bondedtypes ]' directive,\n"
"Will proceed as if the entry\n"
"\n"
"\n[ bondedtypes ]"
"\n; bonds angles dihedrals impropers all_dihedrals nr_exclusions HH14 remove_dih"
"\n %3d %3d %3d %3d %3d %3d %3d %3d"
"\n"
"was present at the beginning of %s",
bts[0],bts[1],bts[2],bts[3], bAlldih ? 1 : 0,nrexcl,HH14,bRemoveDih,rrdb);
}
/* We don't know the current size of rrtp, but simply realloc immediately */
nrtp = *nrtpptr;
rrtp = *rtp;
maxrtp = nrtp;
while (!feof(in)) {
if (nrtp >= maxrtp) {
maxrtp+=100;
srenew(rrtp,maxrtp);
}
clear_t_restp(&rrtp[nrtp]);
if (!get_header(line,header))
gmx_fatal(FARGS,"in .rtp file at line:\n%s\n",line);
rrtp[nrtp].resname = strdup(header);
rrtp[nrtp].filebase = strdup(filebase);
/* Set the bonded types */
rrtp[nrtp].bAlldih = bAlldih;
rrtp[nrtp].nrexcl = nrexcl;
rrtp[nrtp].HH14 = HH14;
rrtp[nrtp].bRemoveDih = bRemoveDih;
for(i=0; i<ebtsNR; i++) {
rrtp[nrtp].rb[i].type = bts[i];
}
get_a_line(in,line,STRLEN);
bError=FALSE;
bNextResidue=FALSE;
do {
if (!get_header(line,header)) {
bError = TRUE;
} else {
bt = get_bt(header);
if (bt != NOTSET) {
/* header is an bonded directive */
bError = !read_bondeds(bt,in,line,&rrtp[nrtp]);
} else if (gmx_strncasecmp("atoms",header,5) == 0) {
/* header is the atoms directive */
bError = !read_atoms(in,line,&(rrtp[nrtp]),tab,atype);
} else {
/* else header must be a residue name */
bNextResidue = TRUE;
}
}
if (bError)
gmx_fatal(FARGS,"in .rtp file in residue %s at line:\n%s\n",
rrtp[nrtp].resname,line);
} while (!feof(in) && !bNextResidue);
if (rrtp[nrtp].natom == 0)
gmx_fatal(FARGS,"No atoms found in .rtp file in residue %s\n",
rrtp[nrtp].resname);
if (debug) {
fprintf(debug,"%3d %5s %5d",
nrtp+1,rrtp[nrtp].resname,rrtp[nrtp].natom);
for(i=0; i<ebtsNR; i++)
fprintf(debug," %10d",rrtp[nrtp].rb[i].nb);
fprintf(debug,"\n");
}
firstrtp = -1;
for(i=0; i<nrtp; i++) {
if (gmx_strcasecmp(rrtp[i].resname,rrtp[nrtp].resname) == 0) {
firstrtp = i;
}
}
if (firstrtp == -1) {
nrtp++;
fprintf(stderr,"\rResidue %d",nrtp);
} else {
if (firstrtp >= *nrtpptr)
{
gmx_fatal(FARGS,"Found a second entry for '%s' in '%s'",
rrtp[nrtp].resname,rrdb);
}
if (bAllowOverrideRTP)
{
fprintf(stderr,"\n");
fprintf(stderr,"Found another rtp entry for '%s' in '%s', ignoring this entry and keeping the one from '%s.rtp'\n",
rrtp[nrtp].resname,rrdb,rrtp[firstrtp].filebase);
/* We should free all the data for this entry.
* The current code gives a lot of dangling pointers.
*/
clear_t_restp(&rrtp[nrtp]);
}
else
{
gmx_fatal(FARGS,"Found rtp entries for '%s' in both '%s' and '%s'. If you want the first definition to override the second one, set the -rtpo option of pdb2gmx.",rrtp[nrtp].resname,rrtp[firstrtp].filebase,rrdb);
}
}
}
ffclose(in);
/* give back unused memory */
srenew(rrtp,nrtp);
fprintf(stderr,"\nSorting it all out...\n");
qsort(rrtp,nrtp,(size_t)sizeof(rrtp[0]),comprtp);
check_rtp(nrtp,rrtp,rrdb);
*nrtpptr = nrtp;
*rtp = rrtp;
}
static void read_h_db_file(const char *hfn,int *nahptr,t_hackblock **ah)
{
FILE *in;
char filebase[STRLEN],line[STRLEN], buf[STRLEN];
int i, n, nab, nah;
t_hackblock *aah;
if (debug) fprintf(debug,"Hydrogen Database (%s):\n",hfn);
fflib_filename_base(hfn,filebase,STRLEN);
/* Currently filebase is read and set, but not used.
* hdb entries from any hdb file and be applied to rtp entries
* in any rtp file.
*/
in = fflib_open(hfn);
nah = *nahptr;
aah = *ah;
while (fgets2(line,STRLEN-1,in)) {
if (sscanf(line,"%s%n",buf,&n) != 1) {
fprintf(stderr,"Error in hdb file: nah = %d\nline = '%s'\n",
nah,line);
break;
}
if (debug) fprintf(debug,"%s",buf);
srenew(aah,nah+1);
clear_t_hackblock(&aah[nah]);
aah[nah].name = strdup(buf);
aah[nah].filebase = strdup(filebase);
if (sscanf(line+n,"%d",&nab) == 1) {
if (debug) fprintf(debug," %d\n",nab);
snew(aah[nah].hack,nab);
aah[nah].nhack = nab;
for(i=0; (i<nab); i++) {
if (feof(in))
gmx_fatal(FARGS, "Expected %d lines of hydrogens, found only %d "
"while reading Hydrogen Database %s residue %s",
nab, i-1, aah[nah].name, hfn);
if(NULL==fgets(buf, STRLEN, in))
{
gmx_fatal(FARGS,"Error reading from file %s",hfn);
}
read_ab(buf,hfn,&(aah[nah].hack[i]));
}
}
nah++;
}
ffclose(in);
/* Sort the list (necessary to be able to use bsearch */
qsort(aah,nah,(size_t)sizeof(**ah),compaddh);
/*
if (debug)
dump_h_db(hfn,nah,aah);
*/
*nahptr = nah;
*ah = aah;
}
static void read_ter_db_file(const char *fn,
int *ntbptr, t_hackblock **tbptr,
gpp_atomtype_t atype)
{
char filebase[STRLEN], *ptr;
FILE *in;
char header[STRLEN], buf[STRLEN], line[STRLEN];
t_hackblock *tb;
int i, j, n, ni, kwnr, nb, maxnb, nh;
fflib_filename_base(fn, filebase, STRLEN);
/* Remove the C/N termini extension */
ptr = strrchr(filebase, '.');
if (ptr != nullptr)
{
ptr[0] = '\0';
}
in = fflib_open(fn);
tb = *tbptr;
nb = *ntbptr - 1;
maxnb = 0;
kwnr = NOTSET;
get_a_line(in, line, STRLEN);
while (!feof(in))
{
if (get_header(line, header))
{
/* this is a new block, or a new keyword */
kwnr = find_kw(header);
if (kwnr == NOTSET)
{
nb++;
/* here starts a new block */
if (nb >= maxnb)
{
maxnb = nb + 100;
srenew(tb, maxnb);
}
clear_t_hackblock(&tb[nb]);
tb[nb].name = gmx_strdup(header);
tb[nb].filebase = gmx_strdup(filebase);
}
}
else
{
if (nb < 0)
{
gmx_fatal(FARGS, "reading termini database: "
"directive expected before line:\n%s\n"
"This might be a file in an old format.", line);
}
/* this is not a header, so it must be data */
if (kwnr >= ebtsNR)
{
/* this is a hack: add/rename/delete atoms */
/* make space for hacks */
if (tb[nb].nhack >= tb[nb].maxhack)
{
tb[nb].maxhack += 10;
srenew(tb[nb].hack, tb[nb].maxhack);
}
nh = tb[nb].nhack;
clear_t_hack(&(tb[nb].hack[nh]));
for (i = 0; i < 4; i++)
{
tb[nb].hack[nh].a[i] = nullptr;
}
tb[nb].nhack++;
/* get data */
n = 0;
if (kwnr == ekwRepl || kwnr == ekwDel)
{
if (sscanf(line, "%s%n", buf, &n) != 1)
{
gmx_fatal(FARGS, "Reading Termini Database '%s': "
"expected atom name on line\n%s", fn, line);
}
tb[nb].hack[nh].oname = gmx_strdup(buf);
/* we only replace or delete one atom at a time */
tb[nb].hack[nh].nr = 1;
}
else if (kwnr == ekwAdd)
{
read_ab(line, fn, &(tb[nb].hack[nh]));
get_a_line(in, line, STRLEN);
}
else
{
gmx_fatal(FARGS, "unimplemented keyword number %d (%s:%d)",
kwnr, __FILE__, __LINE__);
}
if (kwnr == ekwRepl || kwnr == ekwAdd)
{
snew(tb[nb].hack[nh].atom, 1);
read_atom(line+n, kwnr == ekwAdd,
&tb[nb].hack[nh].nname, tb[nb].hack[nh].atom, atype,
&tb[nb].hack[nh].cgnr);
if (tb[nb].hack[nh].nname == nullptr)
{
if (tb[nb].hack[nh].oname != nullptr)
{
tb[nb].hack[nh].nname = gmx_strdup(tb[nb].hack[nh].oname);
}
else
{
gmx_fatal(FARGS, "Reading Termini Database '%s': don't know which name the new atom should have on line\n%s", fn, line);
}
}
}
}
else if (kwnr >= 0 && kwnr < ebtsNR)
{
/* this is bonded data: bonds, angles, dihedrals or impropers */
srenew(tb[nb].rb[kwnr].b, tb[nb].rb[kwnr].nb+1);
n = 0;
for (j = 0; j < btsNiatoms[kwnr]; j++)
{
if (sscanf(line+n, "%s%n", buf, &ni) == 1)
{
tb[nb].rb[kwnr].b[tb[nb].rb[kwnr].nb].a[j] = gmx_strdup(buf);
}
else
{
gmx_fatal(FARGS, "Reading Termini Database '%s': expected %d atom names (found %d) on line\n%s", fn, btsNiatoms[kwnr], j-1, line);
}
n += ni;
}
for (; j < MAXATOMLIST; j++)
{
tb[nb].rb[kwnr].b[tb[nb].rb[kwnr].nb].a[j] = nullptr;
}
strcpy(buf, "");
sscanf(line+n, "%s", buf);
tb[nb].rb[kwnr].b[tb[nb].rb[kwnr].nb].s = gmx_strdup(buf);
tb[nb].rb[kwnr].nb++;
}
else
{
gmx_fatal(FARGS, "Reading Termini Database: Expecting a header at line\n"
"%s", line);
}
}
get_a_line(in, line, STRLEN);
}
nb++;
srenew(tb, nb);
gmx_ffclose(in);
*ntbptr = nb;
*tbptr = tb;
}
