# Turn atom name translation on and off
$trans = 1;
-$res0 = shift;# || die "I need the residue offset\n";
+#$res0 = shift;# || die "I need the residue offset\n";
$pdb = shift || die "I need the name of the pdb file with correct atom numbers\n";
$core = shift || "core.ndx";
-$tbl = "/home/spoel/gmxdev/share/top/atom_nom.tbl";
+$tbl = "$ENV{GMXDATA}/gromacs/top/atom_nom.tbl";
printf "[ distance_restraints ]\n";
printf "; Read an xplor distance restraint file, and output GROMACS distance restraints.\n";
printf "; This also needs a pdb file with correct GROMACS atom numbering.\n";
printf "; I used $pdb for the atom numbers\n";
printf "; This also needs the offset in residues.\n";
-printf "; I used $res0 for the residue offset\n";
+#printf "; I used $res0 for the residue offset\n";
# Read the pdb file
# If things go wrong, check whether your pdb file is read correctly.
$natom = 0;
$nres = 0;
+@resname = ();
open(PDB,$pdb) || die "Can not open file $pdb\n";
while ($line = <PDB>) {
if (index($line,"ATOM") >= 0) {
@tmp = split(' ',$line);
$aname[$natom] = $tmp[2];
$resnr[$natom] = $tmp[4];
- if ($resnr[$natom] > $nres) {
- $rname[$nres] = $tmp[3];
+ if (!defined $resname[$tmp[4]]) {
+ $resname[$tmp[4]] = $tmp[3];
$nres++;
}
$natom++;
if ($debug > 1) {
for ($i = 0; ($i < $natom); $i ++) {
printf("; %5d %5s %5s %5d\n",$i+1,$aname[$i],
- $rname[$resnr[$i]-1],$resnr[$i]);
+ $resname[$resnr[$i]],$resnr[$i]);
}
}
while ($line = <TBL>) {
@ttt = split('#',$line);
@tmp = split(' ',$ttt[0]);
- if ($#tmp == 2) {
+ if ($#tmp == 3) {
# New table entry
$tblres[$ntbl] = $tmp[0];
$tblxplor[$ntbl] = $tmp[1];
- $tblgmx[$ntbl] = $tmp[2];
+ $tblgmx[$ntbl] = $tmp[3];
$ntbl++;
}
}
$ntranslated = 0;
$nuntransltd = 0;
sub transl_aname {
- my $atom = shift(@_);
- my $resnr = shift(@_);
+ my $resnm = shift;
+ my $atom = shift;
if ( $trans == 1 ) {
for(my $i = 0; ($i < $ntbl); $i ++) {
- if ($tblres[$i] eq $rname[$resnr]) {
+ if ($tblres[$i] eq $resnm) {
if ($tblxplor[$i] eq $atom) {
$ntranslated++;
return $tblgmx[$i];
}
$nuntransltd++;
if ($debug > 1) {
- printf "; No name change for $rname[$resnr] $atom\n";
+ printf "; No name change for $resname[$resnr] $atom\n";
}
return $atom;
}
sub expand_template {
my $atom = shift(@_);
- my $rnum = shift(@_)-1;
+ my $rnum = shift(@_);
my $bdone = 0;
my @atoms;
my $jj = 0;
+ die("No residue name for residue $rnum") if (!defined ($resname[$rnum]));
for (my $tt=0; (($tt <= $#templates) && ($bdone == 0)); $tt++) {
$templ = $templates[$tt];
if ($atom eq $templ->[0]) {
for ($jj = 1; ($jj <= $#{$templ}); $jj++) {
- push @atoms, transl_aname($templ->[$jj],$rnum);
+ push @atoms, transl_aname($resname[$rnum],$templ->[$jj]);
}
$bdone = 1;
}
}
if ($bdone == 0) {
- push @atoms, transl_aname($atom,$rnum);
+ push @atoms, transl_aname($resname[$rnum],$atom);
}
if ($debug > 0) {
my $natom = $#atoms+1;
- printf("; Found $natom elements for atom $rname[$rnum] %d $atom:",
+ printf("; Found $natom elements for atom $resname[$rnum] %d $atom:",
$rnum+1);
for $aa ( @atoms ) {
printf " $aa";
$bCore = 1;
foreach $a1 ( @at1 ) {
@info1 = split(' ',$a1);
- $r1 = $info1[1] - $res0;
+ $r1 = $info1[1];
@atoms1 = expand_template($info1[4],$r1);
foreach $a2 ( @at2 ) {
@info2 = split(' ',$a2);
- $r2 = $info2[1] - $res0;
+ $r2 = $info2[1];
@atoms2 = expand_template($info2[4],$r2);
for ($i = 0; ($i < $natom) && ($resnr[$i] < $r1); $i++) { ; }
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff