memset((void *)rrtp, 0, sizeof(t_restp));
}
+/* print all the ebtsNR type numbers */
+void print_resall_header(FILE *out, t_restp rtp[])
+{
+ fprintf(out,"[ bondedtypes ]\n");
+ fprintf(out,"; bonds angles dihedrals impropers all_dihedrals nr_exclusions HH14 remove_dih\n");
+ fprintf(out," %5d %6d %9d %9d %14d %14d %14d %14d\n\n",
+ rtp[0].rb[0].type,
+ rtp[0].rb[1].type,
+ rtp[0].rb[2].type,
+ rtp[0].rb[3].type,
+ rtp[0].bKeepAllGeneratedDihedrals,
+ rtp[0].nrexcl,
+ rtp[0].bGenerateHH14Interactions,
+ rtp[0].bRemoveDihedralIfWithImproper);
+}
+
+void print_resall(FILE *out, int nrtp, t_restp rtp[],
+ gpp_atomtype_t atype)
+{
+ int i,bt;
+
+ if (nrtp == 0) {
+ return;
+ }
+
+ print_resall_header(out, rtp);
+
+ for(i=0; i<nrtp; i++) {
+ if (rtp[i].natom > 0) {
+ print_resatoms(out,atype,&rtp[i]);
+ for(bt=0; bt<ebtsNR; bt++)
+ print_resbondeds(out,bt,&rtp[i]);
+ }
+ }
+}
+
void read_resall(char *rrdb, int *nrtpptr, t_restp **rtp,
gpp_atomtype_t atype, t_symtab *tab,
gmx_bool bAllowOverrideRTP)
char filebase[STRLEN],*ptr,line[STRLEN],header[STRLEN];
int i,nrtp,maxrtp,bt,nparam;
int dum1,dum2,dum3;
- t_restp *rrtp;
+ t_restp *rrtp, *header_settings;
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);
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 */
- 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;
+ 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: 1 means generate all dihedrals, 0 not.
+ * 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.
- * Coulmn 7: Generate 1,4 interactions between pairs of hydrogens
- * Column 8: Remove impropers over the same bond as a proper dihedral
+ * 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",
- &bts[ebtsBONDS],&bts[ebtsANGLES],
- &bts[ebtsPDIHS],&bts[ebtsIDIHS],
- &dum1,&nrexcl,&dum2,&dum3)) < 4 )
+ &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 at least 4 (up to 8) parameters in .rtp file at line:\n%s\n",line);
+ gmx_fatal(FARGS,"need 4 to 8 parameters in the header of .rtp file %s at line:\n%s\n", rrdb, line);
}
- bAlldih = (dum1 != 0);
- HH14 = (dum2 != 0);
- bRemoveDih = (dum3 != 0);
+ 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");
- bAlldih = FALSE;
+ header_settings->bKeepAllGeneratedDihedrals = FALSE;
}
if(nparam<6) {
fprintf(stderr,"Using default: excluding 3 bonded neighbors\n");
- nrexcl = 3;
+ header_settings->nrexcl = 3;
}
if(nparam<7) {
fprintf(stderr,"Using default: generating 1,4 H--H interactions\n");
- HH14 = TRUE;
+ header_settings->bGenerateHH14Interactions = TRUE;
}
if(nparam<8) {
- fprintf(stderr,"Using default: removing impropers on same bond as a proper\n");
- bRemoveDih = TRUE;
+ 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\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);
+ "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;
maxrtp+=100;
srenew(rrtp,maxrtp);
}
- clear_t_restp(&rrtp[nrtp]);
+
+ /* 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 = 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;
*rtp = rrtp;
}
-void print_resall(FILE *out, int nrtp, t_restp rtp[],
- gpp_atomtype_t atype)
-{
- int i,bt;
-
- if (nrtp == 0) {
- return;
- }
-
- /* print all the ebtsNR type numbers */
- fprintf(out,"[ bondedtypes ]\n");
- fprintf(out,"; bonds angles dihedrals impropers all_dihedrals nr_exclusions HH14 remove_dih\n");
- fprintf(out," %5d %6d %9d %9d %14d %14d %14d %14d\n\n",
- rtp[0].rb[0].type,
- rtp[0].rb[1].type,
- rtp[0].rb[2].type,
- rtp[0].rb[3].type,
- rtp[0].bAlldih,rtp[0].nrexcl,rtp[0].HH14,rtp[0].bRemoveDih);
-
- for(i=0; i<nrtp; i++) {
- if (rtp[i].natom > 0) {
- print_resatoms(out,atype,&rtp[i]);
- for(bt=0; bt<ebtsNR; bt++)
- print_resbondeds(out,bt,&rtp[i]);
- }
- }
-}
-
/************************************************************
*
* SEARCH ROUTINES
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