Recently I had to figure out if two residues are bonded together or not. This is not as straightforward as you might think. Here is a subroutine to do the job.

if ( ResiduesAreBonded(\$document, \$r1, \$r2) ) {
...
}

sub ResiduesAreBonded(\$\$\$) {
my \$debug = 0;
my (\$doc,\$res1,\$res2) = @_;
my \$regex1 = "^" . \$res1->Name . "[^0-9].*";
my \$regex2 = \$res2->Name . "[^0-9].*";
my \$filter = "Bond Name=\"" . \$regex1 . " - " . \$regex2 . "\"";
my \$bonds = \$doc->FilterByProperty(\$filter);
my \$bondcount = \$bonds->Count;
if (\$bondcount && \$debug) {
printf "FILTER:%s\n", \$filter;
printf "Bonds %d\n", \$bonds->Count;
foreach (@\$bonds) {
printf "Bond %s\n", \$_->Name;
}
}
my \$filter = "Bond Name=\"" . \$regex2 . " - " . \$regex1 . "\"";
my \$bonds = \$doc->FilterByProperty(\$filter);
if (\$bondcount && \$debug) {
printf "FILTER:%s\n", \$filter;
printf "Bonds %d\n", \$bonds->Count;
foreach (@\$bonds) {
printf "Bond %s\n", \$_->Name;
}
}
\$bondcount += \$bonds->Count;
return \$bondcount;
}