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;
}
