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|
#!/usr/bin/perl
use strict;
use warnings;
use Chemistry::OpenSMILES qw( is_cis_trans_bond );
use Chemistry::OpenSMILES::Aromaticity qw( aromatise kekulise );
use Chemistry::OpenSMILES::Parser;
use Chemistry::OpenSMILES::Stereo qw(
chirality_to_pseudograph
cis_trans_to_pseudoedges
mark_all_double_bonds
);
use Chemistry::OpenSMILES::Writer qw( write_SMILES );
use File::Basename qw( basename );
use Getopt::Long::Descriptive;
use Graph::Nauty qw( canonical_order );
use List::Util qw( shuffle );
sub represent_vertex
{
my( $vertex ) = @_;
return '' unless %$vertex;
my %atom = %$vertex;
delete $atom{chirality};
return write_SMILES( \%atom );
}
my %parser_options;
my $basename = basename $0;
my( $opt, $usage ) = describe_options( <<"END" . 'OPTIONS',
USAGE
$basename [<args>] [<files>]
DESCRIPTION
$basename reads in files with SMILES descriptors and outputs them
according to stable atom ordering established by Graph::Nauty.
Moieties, if more than one, are ordered in lexicographic order.
END
[ raw => hidden => {
one_of => [
[ 'infer-hydrogens' =>
'infer hydrogen atom counts according to valency rules [default]' ],
[ 'no-infer-hydrogens' =>
'do not infer hydrogen atom counts' ]
],
default => 'infer_hydrogens'
}
],
[ aroma => hidden => {
one_of => [
[ 'aromatise' => 'aromatise Kekule structures ' .
'(experimental)' ],
[ 'no-aromatise' => 'do not attempt to aromatise [default]' ]
],
default => 'no-aromatise'
}
],
[ kekul => hidden => {
one_of => [
[ 'kekulise' => 'kekulise simple aromatic structures ' .
'(experimental)' ],
[ 'no-kekulise' => 'do not attempt to kekulise [default]' ]
],
default => 'no-kekulise'
}
],
[],
[ 'random-order',
'instead of canonical, output SMILES in random order (useful for testing)' ],
[],
[ 'help', 'print usage message and exit', { shortcircuit => 1 } ],
);
if( $opt->help ) {
print $usage->text;
exit;
}
if( $opt->raw eq 'no_infer_hydrogens' ) {
$parser_options{raw} = 1;
}
my $errors = 0;
while (<>) {
chomp;
my $additional_position = '';
if( s/\t([^\t]*)$// ) {
$additional_position = ' ' . $1;
}
my $parser = Chemistry::OpenSMILES::Parser->new;
my @moieties;
eval {
@moieties = $parser->parse( $_, \%parser_options );
};
if( $@ ) {
$@ =~ s/^[^:]+:\s*// if !index( $@, $0 );
print STDERR "$0: $ARGV($.)$additional_position: $@";
$errors++;
}
my @smiles_parts;
for my $moiety (@moieties) {
aromatise( $moiety ) if $opt->aroma eq 'aromatise';
kekulise( $moiety ) if $opt->kekul eq 'kekulise';
my @order;
if( !$opt->random_order ) {
# copy() makes a shallow copy without edge attributes, thus they
# have to be added later:
my $copy = $moiety->copy;
for my $bond ($moiety->edges) {
next unless $moiety->has_edge_attribute( @$bond, 'bond' );
$copy->set_edge_attribute( @$bond,
'bond',
$moiety->get_edge_attribute( @$bond, 'bond' ) );
}
cis_trans_to_pseudoedges( $copy );
chirality_to_pseudograph( $copy );
@order = canonical_order( $copy, \&represent_vertex );
my %order;
for (0..$#order) {
$order{$order[$_]} = $_;
}
# Drop cis/trans markers from the input graph and mark them
# anew.
for my $bond ($moiety->edges) {
next unless is_cis_trans_bond( $moiety, @$bond );
$moiety->delete_edge_attribute( @$bond, 'bond' );
}
mark_all_double_bonds( $moiety,
sub {
if( $copy->has_edge( $_[0], $_[3] ) &&
$copy->has_edge_attribute( $_[0], $_[3], 'pseudo' ) ) {
return $copy->get_edge_attribute( $_[0], $_[3], 'pseudo' );
}
},
sub { return $order{$_[0]} } );
} else {
@order = shuffle $moiety->vertices;
}
my %order;
for (0..$#order) {
$order{$order[$_]} = $_;
}
eval {
my $part =
write_SMILES( $moiety,
sub {
my @sorted = sort { $order{$a} <=> $order{$b} }
keys %{$_[0]};
return $_[0]->{shift @sorted};
} );
# In a SMILES descriptor, one can substitute all '/' with '\'
# and vice versa, retaining correct cis/trans settings.
# Similar rule is explained in O'Boyle (2012), Rule H.
if( $part =~ /([\/\\])/ && $1 eq '\\' ) {
$part =~ tr/\/\\/\\\//;
}
push @smiles_parts, $part;
};
if( $@ ) {
print STDERR "$0: $ARGV($.)$additional_position: $@";
$errors++;
}
}
$additional_position =~ s/^ /\t/;
print join( '.', sort @smiles_parts ), $additional_position, "\n";
}
exit( $errors > 0 );
|
