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lib/Chemistry/File/SLN.pm  view on Meta::CPAN

        if ($node->{type} eq ':') { 
            $_->aromatic(1) for ($atom1, $atom2, $bond);
        }
    }
}

sub read_coords {
    my ($self, $mol, $coords_str) = @_;
    $coords_str =~ s/[()]//g;
    my (@coords) = split /,/, $coords_str;
    my $fh = $mol->formula_hash;
    my $n = sum(values %$fh);
    my $sprout = (@coords == 3*$n);
    for my $atom ($mol->atoms) {
        $atom->coords(splice @coords, 0, 3);
        if ($sprout) {
            for (1 .. $atom->implicit_hydrogens) {
                my $H = $mol->new_atom(symbol => 'H', 
                    coords => [splice @coords, 0, 3]);
                $mol->new_bond(atoms => [$atom, $H]);
            }