int add_atomtype(gpp_atomtype_t ga, t_symtab *tab,
t_atom *a, const char *name, t_param *nb,
int bondatomtype,
real radius, real vol, real surftens, int atomnumber,
real gb_radius, real S_hct)
{
int i;
for (i = 0; (i < ga->nr); i++)
{
if (strcmp(*ga->atomname[i], name) == 0)
{
if (NULL != debug)
{
fprintf(debug, "Trying to add atomtype %s again. Skipping it.\n", name);
}
break;
}
}
if (i == ga->nr)
{
ga->nr++;
srenew(ga->atom, ga->nr);
srenew(ga->atomname, ga->nr);
srenew(ga->nb, ga->nr);
srenew(ga->bondatomtype, ga->nr);
srenew(ga->radius, ga->nr);
srenew(ga->vol, ga->nr);
srenew(ga->surftens, ga->nr);
srenew(ga->atomnumber, ga->nr);
srenew(ga->gb_radius, ga->nr);
srenew(ga->S_hct, ga->nr);
return set_atomtype(ga->nr-1, ga, tab, a, name, nb, bondatomtype, radius,
vol, surftens, atomnumber, gb_radius, S_hct);
}
else
{
return i;
}
}
void pcmfin(int nth,int isubred)
{
unsigned int substrismin;
int newatom, i, ibondcount, ibonded, ibondorder,
icoord, imetcount, ioffset, ispin, iprint,
isubmap[MAXSS], j, numbonds, niatom;
int newat, newtype, ifile, isMetal, biotype, itype;
long int mask;
char ianame[3];
float ddcount, xtmp, ytmp, ztmp;
FILE *pcminfile;
imetcount = 0;
isMetal = FALSE;
ddcount = 0;
substrismin = False;
fxtor.nfxtor = 0;
pcmfile.nocaps = False;
numbonds = 0;
ibondcount = 0;
newatom = 0;
newtype = 0;
for (i = 0; i < MAXSS; i++)
{
isubmap[i] = 0;
}
ioffset = 0;
pcminfile = fopen_path(Openbox.path,Openbox.fname,"r");
if (pcminfile == NULL)
{
message_alert("Error Opening PCM file","PCM Setup");
fprintf(pcmoutfile,"PCMFIN error opening file %d %s\n",nth,Openbox.fname);
return;
}
if (default_intype != MMX)
read_atomtypes(default_intype);
ifile = 0;
if (nth != 1)
{
while ( FetchRecord(pcminfile,pcmfile.string) )
{
if (strncasecmp(pcmfile.string,"{PCM",4) == 0)
{
ifile++;
if (ifile == nth)
break;
}
}
}else
{
FetchRecord(pcminfile,pcmfile.string);
}
/* finished scaning to starting structure now read file */
if (isubred == 0)
{
sscanf(pcmfile.string, "{PCM %60c", Struct_Title);
clean_string(Struct_Title);
} else
{
if (natom < 1 )
{
sscanf(pcmfile.string, "{PCM %60c", Struct_Title);
clean_string(Struct_Title);
}
}
L_30:
FetchRecord(pcminfile,pcmfile.string);
*(pcmfile.string + strlen(pcmfile.string) ) = '\0';
if (feof(pcminfile))
goto L_170;
pcmfile.head = 1;
NL;
L_40:
if (strcmp(pcmfile.token, "NA") == 0)
{
gettoken();
if (pcmfile.head == 1000)
goto L_30;
niatom = atoi(pcmfile.token);
if (niatom + ioffset > MAXATOM)
{
natom = ioffset;
fclose(pcminfile);
message_alert(" Maximum number of atoms exceeded in PCMFIN","PCM Setup");
fprintf(pcmoutfile," unable to continue reading, more than Max atoms %d\n",MAXATOM);
return;
}
niatom += ioffset;
NL;
goto L_30;
} else if (strcmp(pcmfile.token,"ATOMTYPES") == 0)
{
gettoken();
if (pcmfile.head == 1000)
goto L_30;
default_intype = atoi(pcmfile.token);
read_atomtypes(default_intype);
NL;
goto L_30;
} else if (strcmp(pcmfile.token, "NT") == 0) /* This is for Amino Acids */
{
NL;
i = atoi(pcmfile.token); /* i is atom number of N terminus */
mask = 1L << NTERM; /* use bit 0 of substr 1 for N terminus*/
atom[i+ioffset].flags |= mask;
NL;
if (strcmp(pcmfile.token, "CT") == 0)
{
NL;
i = atoi(pcmfile.token); /* i is atom number of C terminus */
mask = 1L << CNTERM; /* use bit 1 of substr 1 for C terminus */
atom[i+ioffset].flags |= mask;
}
} else if (strcmp(pcmfile.token, "5PRIME") == 0) /* This is for Nucleic Acids */
{
NL;
i = atoi(pcmfile.token); /* i is atom number of 5prime terminus */
mask = 1L << P5;
atom[i+ioffset].flags |= mask;
}else if (strcmp(pcmfile.token, "3PRIME") == 0) /* This is for Nucleic Acids */
{
NL;
i = atoi(pcmfile.token); /* i is atom number of C terminus */
mask = 1L << P3; /* use bit 1 of substr 1 for C terminus */
atom[i+ioffset].flags |= mask;
} else if (strcmp(pcmfile.token, "FG") == 0) /* This is for functional groups */
{
NL;
i = atoi(pcmfile.token); /* i is atom number of connect point */
mask = 1L << DUMMY; /* use bit 0 of substr 1 for connect*/
atom[i+ioffset].flags |= mask;
} else if (strcmp(pcmfile.token, "OT") == 0) /* This is for Sugars */
{
NL;
i = atoi(pcmfile.token); /* i is atom number of O terminus */
mask = 1L << NTERM; /* use bit 0 of substr 1 for O terminus*/
atom[i+ioffset].flags |= mask;
NL;
if (strcmp(pcmfile.token, "CT") == 0)
{
NL;
i = atoi(pcmfile.token); /* i is atom number of H terminus */
mask = 1L << CNTERM; /* use bit 1 of substr 1 for H terminus */
atom[i+ioffset].flags |= mask;
}
NL;
if (strcmp(pcmfile.token, "OTWO") == 0)
{
NL;
i = atoi(pcmfile.token); /* i is atom number of H terminus */
oh2 = i+ioffset;
}
NL;
if (strcmp(pcmfile.token, "OTHR") == 0)
{
NL;
i = atoi(pcmfile.token); /* i is atom number of H terminus */
oh3 = i+ioffset;
}
NL;
if (strcmp(pcmfile.token, "OSIX") == 0)
{
NL;
i = atoi(pcmfile.token); /* i is atom number of H terminus */
oh6 = i+ioffset;
}
} else if (strcmp(pcmfile.token,"START") == 0) /* flag for polybuild */
{
NL;
i = atoi(pcmfile.token);
mask = 1L << DUMMY;
atom[i+ioffset].flags |= mask;
NL; // END
NL;
i = atoi(pcmfile.token);
mask = 1L << DUMMY;
atom[i+ioffset].flags |= mask;
} else if (strcmp(pcmfile.token,"NMOL") == 0)
{
NL;
NL;
NL;
NL;
NL;
NL;
NL;
goto L_30;
} else if (strcmp(pcmfile.token, "OPT") == 0)
{
NL; // para
NL;
optimize_data.param_avail = atoi(pcmfile.token);
NL; // conv
NL;
optimize_data.converge = atoi(pcmfile.token);
NL; // ie
NL;
optimize_data.initial_energy = atof(pcmfile.token);
NL; // fe
NL;
optimize_data.final_energy = atof(pcmfile.token);
NL; // iH
NL;
optimize_data.initial_heat = atof(pcmfile.token);
NL; // fH
NL;
optimize_data.final_heat = atof(pcmfile.token);
goto L_30;
} else if (strcmp(pcmfile.token, "SS") == 0)
{
goto L_30;
} else if (strcmp(pcmfile.token, "AT") == 0)
{
NL;
newat = atoi(pcmfile.token); // atom serial number
if (newat + ioffset > MAXATOM)
{
message_alert(" Maximum number of atoms exceeded in PCMFIN at atom read","PCM Setup");
fprintf(pcmoutfile,"atom read %d %d %d\n",newat,ioffset,natom);
natom = ioffset + newat - 1;
fclose(pcminfile);
exit(0);
}
newat += ioffset;
NL;
if (isdigit(*pcmfile.token))
{
newtype = atoi(pcmfile.token);
} else // character string for metal atom
{
strcpy(ianame,pcmfile.token);
isMetal = TRUE;
i = strlen(ianame);
if ( i == 2)
ianame[1] = tolower(ianame[1]);
}
NL;
xtmp = atof(pcmfile.token);
NL;
ytmp = (atof(pcmfile.token));
NL;
ztmp = atof(pcmfile.token);
NL;
if (isMetal == FALSE)
{
itype = newtype;
get_atomname(newtype,ianame);
if (default_intype == MM3)
itype = mm3_mmxtype(newtype);
else if (default_intype == MMFF94)
itype = mmff_mmxtype(newtype);
newatom = make_atom(newtype, xtmp, ytmp, ztmp,ianame);
if (default_intype == MM3)
set_atomtype(newatom, itype,newtype,0,0,0);
else if (default_intype == MMFF94)
set_atomtype(newatom, itype,0,newtype,0,0);
}else if (isMetal == TRUE)
{
newatom = make_atom(0, xtmp, ytmp, ztmp,ianame);
isMetal = FALSE;
}
L_90:
if (strcmp(pcmfile.token, "B") == 0)
{
/* Reading bonds now */
NL;
j = 0;
L_100:
j += 1;
if (pcmfile.state == NUMERIC)
{
ibonded = atoi(pcmfile.token);
ibonded += ioffset;
} else
{
goto L_90;
}
NL;
if (pcmfile.state == NUMERIC)
{
ibondorder = atoi(pcmfile.token);
} else
{
fprintf(stdout, "missing a bondorder, assuming 1\n");
goto L_40;
}
if (newatom < ibonded)
make_bond(newatom, ibonded, ibondorder);
if (ibondorder == 9)
{
atom[newatom].flags |= (1L << METCOORD_MASK);
atom[ibonded].flags |= (1L << METCOORD_MASK);
}
NL;
goto L_100;
}else if ( strcmp(pcmfile.token, "P")== 0)
{
atom[newatom].flags |= (1L << PI_MASK);
NL;
goto L_90;
}else if (strcmp(pcmfile.token, "D") == 0) // biomolecule marking
{
NL;
biotype = atoi(pcmfile.token);
atom[newatom].biotype = biotype;
NL;
goto L_90;
}else if (strcmp(pcmfile.token,"M")==0)
{
NL;
icoord = atoi(pcmfile.token);
if (icoord == 0)
{
atom[newatom].flags |= (1L << SATMET_MASK);
} else if (icoord == 2)
{
atom[newatom].flags |= (1L << GT18e_MASK);
} else{
atom[newatom].flags |= (1L << GT18e_MASK);
atom[newatom].flags |= (1L << SATMET_MASK);
}
NL;
if (pcmfile.state != 1)
goto L_90;
ispin = atoi(pcmfile.token);
if (ispin == 0)
{
atom[newatom].flags |= (1L << LOWSPIN_MASK);
} else if (ispin == 1)
{
atom[newatom].flags |= (1L << SQPLAN_MASK);
} else
{
atom[newatom].flags |= (1L << LOWSPIN_MASK);
atom[newatom].flags |= (1L << SQPLAN_MASK);
}
NL;
goto L_90;
}else if (strcmp(pcmfile.token,"S")== 0)
{
NL;
if (pcmfile.state == NUMERIC)
{
j = atoi(pcmfile.token);
mask = (1L << j);
NL;
goto L_90;
} else
{
goto L_90;
}
}else if (strcmp(pcmfile.token,"H")== 0)
{
atom[newatom].flags |= (1L << HBOND_MASK);
NL;
goto L_90;
}else if (strcmp(pcmfile.token,"C")==0)
{
NL;
atom[newatom].charge = atof(pcmfile.token);
NL;
goto L_90;
} else if (strcmp(pcmfile.token,"ML") == 0)
{
NL;
j = atoi(pcmfile.token);
atom[newatom].molecule = j;
goto L_90;
}else if (strcmp(pcmfile.token,"R")== 0)
{
NL;
atom[newatom].radius = atof(pcmfile.token);
NL;
goto L_90;
}
} else if (strncasecmp(pcmfile.token, "}",1) == 0)
{
goto L_170; /* end of structure */
} else if (strcmp(pcmfile.token, "FL") == 0)
{
NL;
L_120: if (strcmp(pcmfile.token, "PRINT") == 0)
{
iprint = 1;
NL;
if (pcmfile.state == ALPHABETIC)
goto L_120;
iprint = atoi(pcmfile.token);
NL;
goto L_120;
} else if (strcmp(pcmfile.token, "DIELC") == 0)
{
NL;
if (pcmfile.state != 1)
goto L_120;
// units.dielec = atof(pcmfile.token);
NL;
goto L_120;
} else if (strcmp(pcmfile.token, "UV") == 0)
{
NL;
if (pcmfile.state != 1)
goto L_120;
pistuf.iuv = atoi(pcmfile.token);
NL;
goto L_120;
} else if (strcmp(pcmfile.token, "PIPR") == 0)
{
NL;
if (pcmfile.state != 1)
goto L_120;
pistuf.jprint = atoi(pcmfile.token);
NL;
goto L_120;
} else if (strcmp(pcmfile.token, "PIPL") == 0)
{
NL;
if (pcmfile.state != 1)
goto L_120;
pistuf.nplane = atoi(pcmfile.token);
NL;
goto L_120;
} else if (strcmp(pcmfile.token, "EINT") == 0)
{
NL;
if (pcmfile.state != 1)
goto L_120;
minim_values.ndc = atoi(pcmfile.token);
NL;
goto L_120;
}
} else if (strcmp(pcmfile.token, "CO") == 0)
{
} else if (strcmp(pcmfile.token, "FBND") == 0)
{
NL;
ts_bondorder.fbnd[0] = atof(pcmfile.token);
NL;
ts_bondorder.fbnd[1] = atof(pcmfile.token);
NL;
ts_bondorder.fbnd[2] = atof(pcmfile.token);
NL;
ts_bondorder.fbnd[3] = atof(pcmfile.token);
NL;
ts_bondorder.fbnd[4] = atof(pcmfile.token);
NL;
ts_bondorder.fbnd[5] = atof(pcmfile.token);
NL;
ts_bondorder.fbnd[6] = atof(pcmfile.token);
NL;
ts_bondorder.fbnd[7] = atof(pcmfile.token);
NL;
ts_bondorder.fbnd[8] = atof(pcmfile.token);
NL;
ts_bondorder.fbnd[9] = atof(pcmfile.token);
NL;
ts_bondorder.fbnd[10] = atof(pcmfile.token);
NL;
ts_bondorder.fbnd[11] = atof(pcmfile.token);
NL;
ts_bondorder.fbnd[12] = atof(pcmfile.token);
NL;
ts_bondorder.fbnd[13] = atof(pcmfile.token);
NL;
ts_bondorder.fbnd[14] = atof(pcmfile.token);
} else if (strcmp(pcmfile.token, "FIX") == 0)
{
NL;
if (strcmp(pcmfile.token, "DIS") == 0)
{
NL;
fixdis.ifxstr[fixdis.nfxstr][0] = atoi(pcmfile.token);
NL;
fixdis.ifxstr[fixdis.nfxstr][1] = atoi(pcmfile.token);
NL;
L_1223: if (strcmp(pcmfile.token, "R") == 0)
{
NL;
fixdis.fxstrd[fixdis.nfxstr] = atof(pcmfile.token);
NL;
goto L_1223;
} else if (strcmp(pcmfile.token, "K") == 0)
{
NL;
fixdis.fxstrc[fixdis.nfxstr] = atof(pcmfile.token);
fixdis.nfxstr +=1;
NL;
goto L_1223;
}
}
} else if (strcmp(pcmfile.token, "DD") == 0)
{
if (isubred == 1)
goto L_30;
NL;
if (pcmfile.state == NUMERIC)
{
fxtor.iatom[fxtor.nfxtor][0] = atoi(pcmfile.token);
NL;
fxtor.iatom[fxtor.nfxtor][1] = atoi(pcmfile.token);
NL;
fxtor.iatom[fxtor.nfxtor][2] = atoi(pcmfile.token);
NL;
fxtor.iatom[fxtor.nfxtor][3] = atoi(pcmfile.token);
NL;
L_150: if (strcmp(pcmfile.token, "FROM") == 0)
{
NL;
fxtor.start_ang[fxtor.nfxtor] = atoi(pcmfile.token);
fxtor.curr_ang[fxtor.nfxtor] = fxtor.start_ang[fxtor.nfxtor];
NL;
goto L_150;
} else if (strcmp(pcmfile.token, "TO") == 0)
{
NL;
fxtor.final_ang[fxtor.nfxtor] = atoi(pcmfile.token);
NL;
goto L_150;
} else if (strcmp(pcmfile.token, "BY") == 0)
{
NL;
fxtor.step[fxtor.nfxtor] = atoi(pcmfile.token);
fxtor.nfxtor++;
NL;
goto L_150;
}
}
}
goto L_30;
L_170:
fclose(pcminfile);
for (i=1; i <= natom; i++)
{
if (atom[i].mmx_type == 5)
{
flags.noh = True;
break;
}
}
if (default_intype != MMX)
read_atomtypes(MMX);
return;
}
