Adapted NMR related data to new pdb format.

[alexxy/gromacs.git] / scripts / xplor2gmx.pl

diff --git a/scripts/xplor2gmx.pl b/scripts/xplor2gmx.pl
index 7769e030445521e43b7d618a83b84be84665b97c..7422551d40f9de34a1f6c07e1b9b58ef83e1d2df 100755 (executable)
--- a/scripts/xplor2gmx.pl
+++ b/scripts/xplor2gmx.pl
@@ -18,30 +18,31 @@ $debug = 1;
 # 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++;
@@ -53,7 +54,7 @@ printf "; I found $nres residues in the pdb file $pdb\n";
 if ($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]);
     }
 }
 
@@ -68,11 +69,11 @@ $ntbl=0;
 while ($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++;
     }
 }
@@ -108,12 +109,12 @@ printf "; Read $ntbl entries from $tbl\n";
 $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];
@@ -123,33 +124,34 @@ sub transl_aname {
     }
     $nuntransltd++;
     if ($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 " $aa";
@@ -203,12 +205,12 @@ while ($line = <STDIN>) {
        $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++) { ; }