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package SmilesScripts::MolecularTransformations;
use strict;
use warnings;
use Chemistry::OpenSMILES qw(
is_double_bond
is_single_bond
valence
);
use List::Util qw( first );
use parent Exporter::;
our @EXPORT_OK = qw(
canonicalise_nitro_groups
);
sub canonicalise_nitro_groups
{
my( $moiety ) = @_;
my @N = grep { $_->{symbol} eq 'N' &&
$_->{charge} &&
$_->{charge} == 1 &&
$moiety->degree( $_ ) == 3 &&
valence( $moiety, $_ ) == 4 } $moiety->vertices;
for my $N (@N) {
my @O = sort { $a->{number} <=> $b->{number} }
grep { $_->{symbol} eq 'O' && $moiety->degree( $_ ) == 1 }
$moiety->neighbours( $N );
next unless @O >= 2;
my $ketone = first { is_double_bond( $moiety, $N, $_ ) } @O;
my $O = first { is_single_bond( $moiety, $N, $_ ) &&
$_->{charge} &&
$_->{charge} == -1 } @O;
next unless $ketone && $O;
delete $N->{charge};
delete $O->{charge};
$moiety->set_edge_attribute( $N, $O, 'bond', '=' );
}
}
1;
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