Evaluation Ruleset for SCOP 1.65 Benchmarks

sub Criteria{
#1.65 version
#Takes as an input two SCOP classifications, and returns a flag. 
#1 if they're the same, 0 if it's ambiguous, and -1 if they're different
my $flag=-1;
my $one=$_[1];
my $two=$_[2];
my $cf1;
my $cf2;
my $sf1;
my $sf2;
my $fa1;
my $fa2;
my %rossmann=('c.2',0,'c.3',0,'c.4',0,'c.5',0,'c.27',0,'c.28',0,'c.30',0,'c.31',0);
#these all have notes in SCOP

if ($one =~ /^(\w\.\d+)(\.\d+)(\.\d+)/){
$fa1="$1$2$3";
$sf1="$1$2";
$cf1="$1";
}
else{
print STDERR "Error parsing classification: $one\n";
}
if ($two =~ /^(\w\.\d+)(\.\d+)(\.\d+)/){
$fa2="$1$2$3";
$sf2="$1$2";
$cf2="$1";
}
else{
print STDERR "Error parsing classification: $two\n";
}

#Same fold ambiguous
if ($cf1 eq $cf2){
$flag=0;
}
#plain right
if ($sf1 eq $sf2){
$flag=1;
}

#Fixed as of SCOP 1.63!
##Unless Membrane all-alpha
#if (($sf1 eq 'f.2.1' or $sf2 eq 'f.2.1') and $fa1 ne $fa2){
#$flag=-1;
#}

#TIM barrels
#first 7 similar -note in SCOP-
if (($sf1 eq 'c.1.1' or $sf1 eq 'c.1.2' or $sf1 eq 'c.1.3' or $sf1 eq 'c.1.4' or $sf1 eq 'c.1.5' or $sf1 eq 'c.1.6' or $sf1 eq 'c.1.7') and ($sf2 eq 'c.1.1' or $sf2 eq 'c.1.2' or $sf2 eq 'c.1.3' or $sf2 eq 'c.1.4' or $sf2 eq 'c.1.5' or $sf2 eq 'c.1.6' or $sf2 eq 'c.1.7')){
$flag=1;
}
elsif (($cf1 eq 'c.1' and $cf2 eq 'c.1')){
$flag=0;
}

#Rossmann-like
if (exists($rossmann{$cf1}) and exists($rossmann{$cf2})){
if ($cf1 eq $cf2){
$flag=1;
}
else{
$flag=0;
}
}
#Nah! Julian thinks now it's a grower, since 1.63
##as of 1.57  c.23.12 looks like superposes OK
#if ((exists($rossmann{$cf1}) and $sf2 eq 'c.23.12') or (exists($rossmann{$cf2}) and $sf1 eq 'c.23.12')){
#$flag=1;
#}
#Old note -correspondance checked-
#1ykf, residues 151-314 superpose with 1eiz: 2.26382 ANGSTROMS/ATOM over 98 residues
if ((exists($rossmann{$cf1}) and $cf2 eq 'c.66') or (exists($rossmann{$cf2}) and $cf1 eq 'c.66')){
$flag=0;
}
#1lvh superposes with 1ek6 to 2.19488 ANGSTROMS/ATOM over 88 residues(same topology), BUT is VERY different
if ((exists($rossmann{$cf1}) and $cf2 eq 'c.108') or (exists($rossmann{$cf2}) and $cf1 eq 'c.108')){
$flag=0;
}
#Can't find it and there are no cross-hits anyway.
##Old note -correspondance checked-
#if ((exists($rossmann{$cf1}) and $cf2 eq 'c.32') or (exists($rossmann{$cf2}) and $cf1 eq 'c.32')){
#$flag=0;
#}
#note: the ATP nucleotide-binding site is similar to that of the NAD-binding Rossmann-folds
if ((exists($rossmann{$cf1}) and $sf2 eq 'c.111.1') or (exists($rossmann{$cf2}) and $sf1 eq 'c.111.1')){
$flag=0;
}

#Other rules
#beta propellors 4-8 blades
if (($cf1 eq 'b.66' or $cf1 eq 'b.67' or $cf1 eq 'b.68' or $cf1 eq 'b.69' or $cf1 eq 'b.70') and ($cf2 eq 'b.66' or $cf2 eq 'b.67' or $cf2 eq 'b.68' or $cf2 eq 'b.69' or $cf2 eq 'b.70')){
if ($cf1 eq $cf2){
$flag=1;
}
else{
$flag=0;
}
}
#Note in SCOP, Similar in architecture but partly differs in topology
if (($cf1 eq 'c.94' and $cf2 eq 'c.93') or( $cf2 eq 'c.94' and $cf1 eq 'c.93')){
$flag=0;
}
#Cutinase-like
if (($sf1 eq 'c.23.9' and $sf2 eq 'c.69.1') or ($sf2 eq 'c.23.9' and $sf1 eq 'c.69.1')){
$flag=0;
}
#This re-classified in 1.63
#if (($fa1 eq 'f.2.1.10' and $sf2 eq 'c.108.1') or ($fa2 eq 'f.2.1.10' and $sf1 eq 'c.108.1')){
#$flag=1;
#}
#Very similar alpha super-helix
if (($sf1 eq 'a.118.8' and $sf2 eq 'a.118.6') or ($sf2 eq 'a.118.8' and $sf1 eq 'a.118.6')){
$flag=0;
}
#Similar motif sulphur binding
if (($sf1 eq 'd.58.1' and $sf2 eq 'a.1.2') or ($sf2 eq 'd.58.1' and $sf1 eq 'a.1.2')){
$flag=0;
}
#OK note in SCOP one of the previous cases
if (($sf1 eq 'a.137.4' and $sf2 eq 'c.96.1') or ($sf2 eq 'a.137.4' and $sf1 eq 'c.96.1')){
$flag=0;
}
#OK same fold and general look
if (($sf1 eq 'b.42.5' and $sf2 eq 'b.42.1') or ($sf2 eq 'b.42.5' and $sf1 eq 'b.42.1')){
$flag=0;
}
#Leucine rich repeats both of them,  structures look the same OK
if (($sf1 eq 'c.10.1' and $sf2 eq 'c.10.2') or ($sf2 eq 'c.10.1' and $sf1 eq 'c.10.2')){
$flag=0;
}
#Obvious sequence homology with blast,  one is beta-beta-alpha superhelix,  and one is beta-alpha togethor in PFAM
if (($sf1 eq 'c.11.1' and $sf2 eq 'c.10.2') or ($sf2 eq 'c.11.1' and $sf1 eq 'c.10.2')){
$flag=0;
}
#Obvious sequence homology with blast,  one is beta-beta-alpha superhelix,  and one is beta-alpha togethor in PFAM
if (($sf1 eq 'c.11.1' and $sf2 eq 'c.10.1') or( $sf2 eq 'c.11.1' and $sf1 eq 'c.10.1')){
$flag=0;
}
#Note in SCOP, contains P-loop
if (($sf1 eq 'c.91.1' and $sf2 eq 'c.37.1') or( $sf2 eq 'c.91.1' and $sf1 eq 'c.37.1')){
$flag=0;
}
#Note in SCOP, shared motif
if (($sf1 eq 'd.51.1' and $sf2 eq 'd.52.3') or( $sf2 eq 'd.51.1' and $sf1 eq 'd.52.3')){
$flag=0;
}
#Note in SCOP: variant of beta/alpha barrel
if (($cf1 eq 'c.6' and $cf2 eq 'c.1') or( $cf2 eq 'c.6' and $cf1 eq 'c.1')){
$flag=0;
}
#Note in SCOP, possible link
if (($sf1 eq 'a.24.1' and $sf2 eq 'a.63.1') or( $sf2 eq 'a.24.1' and $sf1 eq 'a.63.1')){
$flag=0;
}
#-----------------------------------

return ($flag);
}