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babel-1.6
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Makefile,
README.1ST,
addh.c,
addh2.c,
aromatic.c,
assbnd.c,
asstypes.c,
babel.h,
bblmacs.h,
bblmast.h,
bbltyp.h,
block.c,
bndord.c,
bo.c,
buildct.c,
combine.c,
convert.c,
delatms.c,
delh2o.c,
element.lis,
filesrch.c,
fileutil.c,
gastchg.c,
gauss.hdr,
htoend.c,
int2cart.c,
intcart.c,
menus.c,
miniums.c,
molwt.c,
new.lis,
nodummy.c,
orient.c,
precip.c,
printbad.c,
progress.c,
psgvb.hdr,
quanta.lis,
rdalch.c,
rdampout.c,
rdbalst.c,
rdbgf.c,
rdboogie.c,
rdc3d.c,
rdcacao.c,
rdcadpac.c,
rdcharmm.c,
rdcsd.c,
rddock.c,
rddpdb.c,
rdelmnts.c,
rdfdat.c,
rdfeat.c,
rdfract.c,
rdg96.c,
rdgamout.c,
rdgauout.c,
rdgzmat.c,
rdhin.c,
rdinsite.c,
rdint.c,
rdirc.c,
rdisis.c,
rdm3d.c,
rdmacmod.c,
rdmacmol.c,
rdmdl.c,
rdmicro.c,
rdmm2.c,
rdmm2in.c,
rdmm3.c,
rdmolen.c,
rdmopac.c,
rdmopcrt.c,
rdpcmod.c,
rdpdb.c,
rdprep.c,
rdpsgout.c,
rdpsgvin.c,
rdquanta.c,
rdschak.c,
rdshelx.c,
rdsmiles.c,
rdspart.c,
rdspmm.c,
rdspsemi.c,
rdsybmol.c,
rdsybyl.c,
rdtypes.c,
rdunichm.c,
rdwiz.c,
rdxed.c,
rdxyz.c,
renum.c,
report.c,
rings.c,
ringutil.c,
sets.c,
smilesto.c,
spline.c,
strngutl.c,
tokenst.c,
tosmiles.c,
tree.c,
typbybo.c,
types.lis,
umslist.c,
utils.c,
vectors.c,
wralch.c,
wrbalst.c,
wrbgf.c,
wrbmin.c,
wrbox.c,
wrc3d.c,
wrcacao.c,
wrcache.c,
wrcacint.c,
wrchdrw.c,
wrcontmp.c,
wrcsr.c,
wrcssr.c,
wrdock.c,
wrdpdb.c,
wrfeat.c,
wrfh.c,
wrg96.c,
wrgamess.c,
wrgau.c,
wrgaucrt.c,
wrhin.c,
wricon.c,
wrint.c,
wrisis.c,
wrm3d.c,
wrmaccs.c,
wrmacmod.c,
wrmcmol.c,
wrmdl.c,
wrmicro.c,
wrmimic.c,
wrmiv.c,
wrmm2.c,
wrmm3.c,
wrmopac.c,
wrpcmod.c,
wrpdb.c,
wrpsgv.c,
wrpsgvz.c,
wrsmiles.c,
wrspart.c,
wrsybmol.c,
wrsybyl.c,
wrtinker.c,
wrtorlst.c,
wrunichm.c,
wrwiz.c,
wrxed.c,
wrxyz.c
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/*****
This file is part of the Babel Program
Copyright (C) 1992-96 W. Patrick Walters and Matthew T. Stahl
All Rights Reserved
All Rights Reserved
All Rights Reserved
All Rights Reserved
For more information please contact :
babel@mercury.aichem.arizona.edu
--------------------------------------------------------------------------------
FILE : rdpsvbin.c
AUTHOR(S) : Pat Walters
DATE : 12-93
PURPOSE : routines to read a Gaussian Z-matrix
******/
#include "bbltyp.h"
#define PSGVB_DELIMS "\t\n, =@#*"
#define Sym(x) the_syms[x].sym
#define Val(x) the_syms[x].val
int
read_psgvb_input(FILE *file1, ums_type *mol)
{
char the_line[BUFF_SIZE];
int i = 0, j;
int sym_count = 0;
int result;
zsymbol *the_syms;
char lab1[10],lab2[10],lab3[10];
char sym1[30],sym2[30],sym3[30];
int blank_lines = 0;
int stop = FALSE;
long int atom_start = -1;
long int variable_start = -1;
char first_token[BUFF_SIZE];
int tokens;
double factor;
int itok;
int zmat_style = 0;
#ifdef DEBUG
int iline = 0;
#endif
Atoms = 0;
/* Next section */
while (fgets(the_line,sizeof(the_line), file1) != NULL)
{
#ifdef DEBUG
printf("%d -> %s\n",++iline,the_line);
#endif
if (count_tokens(the_line,PSGVB_DELIMS) == 0)
continue;
strcpy(first_token,gettoken(the_line,PSGVB_DELIMS,1));
lowercase(first_token);
if (EQ(first_token,"$zmat") || EQ(first_token,"&zmat"))
{
atom_start = ftell(file1);
#ifdef DEBUG
printf("(atom_start)\n");
#endif
i = 0;
while ( fgets(the_line,sizeof(the_line), file1) != NULL)
{
#ifdef DEBUG
printf("%d (Atom %d) -> %s\n",++iline,i+1,the_line);
#endif
if (the_line[0] == '$' || the_line[0] == '&')
break;
i++;
Atoms++;
if (i == 1 && count_tokens(the_line,PSGVB_DELIMS) == 1)
zmat_style=1;
}
}
if (EQ(first_token,"$zvar") || EQ(first_token,"&zvar"))
{
variable_start = ftell(file1);
#ifdef DEBUG
printf("(variable_start)\n");
#endif
}
}
initialize_ums(&mol);
initialize_internal(&mol);
/* Read zvars */
the_syms = (zsymbol *)malloc(3 * Atoms * sizeof(zsymbol));
sym_count = 0;
fseek(file1,variable_start,0);
while (fgets(the_line,sizeof(the_line), file1) != NULL)
{
#ifdef DEBUG
printf("%d -> %s",sym_count,the_line);
#endif
if (the_line[0] == '$' || the_line[0] == '&')
break;
tokens = count_tokens(the_line,PSGVB_DELIMS);
itok = 0;
while ( tokens >= 2 )
{
strcpy(Sym(sym_count),gettoken(the_line,PSGVB_DELIMS,++itok));
Val(sym_count) = (double)atof(gettoken(the_line,PSGVB_DELIMS,++itok));
#ifdef DEBUG
printf(" %d %s = %f\n",sym_count,Sym(sym_count),Val(sym_count));
#endif
tokens -= 2;
sym_count++;
}
}
/* Read zmat */
ShowProgress(Atoms,"Reading Atoms");
fseek(file1,atom_start,0);
for (j = 1; j <= Atoms; j++)
{
UpdateProgress();
fgets(the_line,sizeof(the_line), file1);
tokens = count_tokens(the_line,PSGVB_DELIMS);
if (zmat_style == 1)
{
switch(j)
{
case 1 :
strcpy(Type(j),gettoken(the_line,PSGVB_DELIMS,1));
break;
case 2 :
strcpy(Type(j),gettoken(the_line,PSGVB_DELIMS,1));
strcpy(lab1,gettoken(the_line,PSGVB_DELIMS,2));
strcpy(sym1,gettoken(the_line,PSGVB_DELIMS,3));
NA(j) = xlate_label(mol,lab1,j);
R(j) = xlate_ps_symbol(the_syms,sym1,sym_count);
break;
case 3 :
sscanf(the_line,"%s,%s,%s,%s,%s",Type(j),lab1,sym1,lab2,sym2);
strcpy(Type(j),gettoken(the_line,PSGVB_DELIMS,1));
strcpy(lab1,gettoken(the_line,PSGVB_DELIMS,2));
strcpy(sym1,gettoken(the_line,PSGVB_DELIMS,3));
strcpy(lab2,gettoken(the_line,PSGVB_DELIMS,4));
strcpy(sym2,gettoken(the_line,PSGVB_DELIMS,5));
NA(j) = xlate_label(mol,lab1,j);
NB(j) = xlate_label(mol,lab2,j);
R(j) = xlate_ps_symbol(the_syms,sym1,sym_count);
W(j) = xlate_ps_symbol(the_syms,sym2,sym_count);
break;
default :
strcpy(Type(j),gettoken(the_line,PSGVB_DELIMS,1));
strcpy(lab1,gettoken(the_line,PSGVB_DELIMS,2));
strcpy(sym1,gettoken(the_line,PSGVB_DELIMS,3));
strcpy(lab2,gettoken(the_line,PSGVB_DELIMS,4));
strcpy(sym2,gettoken(the_line,PSGVB_DELIMS,5));
strcpy(lab3,gettoken(the_line,PSGVB_DELIMS,6));
strcpy(sym3,gettoken(the_line,PSGVB_DELIMS,7));
NA(j) = xlate_label(mol,lab1,j);
NB(j) = xlate_label(mol,lab2,j);
NC(j) = xlate_label(mol,lab3,j);
R(j) = xlate_ps_symbol(the_syms,sym1,sym_count);
W(j) = xlate_ps_symbol(the_syms,sym2,sym_count);
T(j) = xlate_ps_symbol(the_syms,sym3,sym_count);
break;
}
}
else
{
strcpy(Type(j),gettoken(the_line,PSGVB_DELIMS,1));
strcpy(sym1,gettoken(the_line,PSGVB_DELIMS,2));
strcpy(sym2,gettoken(the_line,PSGVB_DELIMS,3));
strcpy(sym3,gettoken(the_line,PSGVB_DELIMS,4));
X(j) = xlate_ps_symbol(the_syms,sym1,sym_count);
Y(j) = xlate_ps_symbol(the_syms,sym2,sym_count);
Z(j) = xlate_ps_symbol(the_syms,sym3,sym_count);
}
}
for (i = 1; i <= Atoms; i++)
clean_atom_type(Type(i));
if (Atoms > 0)
{
if (zmat_style == 1)
{
result = int_to_cart(mol);
}
result = assign_radii(mol);
result = assign_bonds(mol);
result = assign_types(mol);
result = build_connection_table(mol);
assign_bond_order(mol);
}
free(the_syms);
read_to_eof(file1);
return(TRUE);
}
double xlate_ps_symbol(zsymbol *the_syms, char *sym, int max)
{
int i;
int is_neg = FALSE;
char the_str[100];
char numeric[] = "0123456789.+";
if (strchr(numeric,sym[0]) != NULL ||
(sym[0] == '-' && strchr(numeric,sym[1]) != NULL))
return(atof(sym));
if (sym[0] == '-')
{
is_neg = TRUE;
sym++;
}
for (i = 0; i < max; i++)
if (EQ(the_syms[i].sym,sym))
{
if (is_neg == TRUE)
return(the_syms[i].val * (-1));
else
return(the_syms[i].val);
}
sprintf(the_str,"cant translate symbol %s\n",sym);
show_warning(the_str);
return(0.0);
}
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