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|
#! /bin/sh
#!perl -w # --*- Perl -*--
eval 'exec perl -x $0 ${1+"$@"}'
if 0;
#------------------------------------------------------------------------------
#$Author: antanas $
#$Date: 2021-07-30 20:10:23 +0300 (Fri, 30 Jul 2021) $
#$Revision: 8841 $
#$URL: svn+ssh://www.crystallography.net/home/coder/svn-repositories/cod-tools/tags/v3.7.0/scripts/cif_automorphism $
#------------------------------------------------------------------------------
#*
#* Find automorphism orbits in CIF files.
#*
#* USAGE:
#* $0 --options input1.cif input*.cif
#**
use strict;
use warnings;
use COD::AtomNeighbours qw( neighbour_list_from_cif
neighbour_list_to_graph );
use COD::CIF::Parser qw( parse_cif );
use COD::CIF::Tags::CanonicalNames qw( canonicalize_all_names );
use COD::CIF::Tags::Manage qw( contains_data_item exclude_tag set_loop_tag );
use COD::CIF::Tags::Print qw( print_cif );
use COD::ErrorHandler qw( process_errors process_parser_messages process_warnings );
use COD::SOptions qw( getOptions );
use COD::SUsage qw( options usage );
use COD::ToolsVersion qw( get_version_string );
use Graph::Nauty qw( orbits );
my $neighbour_list_options = {};
my $print_atom_site_type_symbol = 0;
my $use_parser = 'c';
my $die_on_error_level = {
ERROR => 1,
WARNING => 0,
NOTE => 0,
};
#* OPTIONS:
#* --ignore-hydrogens
#* Do not consider hydrogen atoms in automorphism
#* detection.
#* --no-ignore-hydrogens
#* Take hydrogen atoms into consideration when searching
#* for automorphisms (default).
#*
#* --print-atom-site-type-symbol
#* Output assumed atom chemical types as values of
#* '_atom_site_type_symbol', if this data item is not
#* used.
#* --no-print-atom-site-type-symbol
#* Do not output assumed atom chemical types as values
#* of '_atom_site_type_symbol' (default).
#*
#* --use-c-parser
#* Use Perl & C parser for CIF parsing (default).
#* --use-perl-parser
#* Use Perl parser for CIF parsing.
#*
#* --help, --usage
#* Output a short usage message (this message) and exit.
#* --version
#* Output version information and exit.
#**
@ARGV = getOptions(
"--ignore-hydrogens" =>
sub { $neighbour_list_options->{exclude_hydrogens} = 1 },
"--no-ignore-hydrogens" =>
sub { $neighbour_list_options->{exclude_hydrogens} = 0 },
"--print-atom-site-type-symbol" => sub { $print_atom_site_type_symbol = 1 },
"--no-print-atom-site-type-symbol" => sub { $print_atom_site_type_symbol = 0 },
"--use-c-parser" => sub { $use_parser = "c" },
"--use-perl-parser" => sub { $use_parser = "perl" },
'--options' => sub { options; exit },
'--help,--usage' => sub { usage; exit },
'--version' => sub { print get_version_string(), "\n"; exit }
);
@ARGV = ("-") unless @ARGV;
binmode STDOUT, ':encoding(UTF-8)';
binmode STDERR, ':encoding(UTF-8)';
for my $filename (@ARGV) {
my $options = { 'parser' => $use_parser, 'no_print' => 1 };
my ( $data, $err_count, $messages ) = parse_cif( $filename, $options );
process_parser_messages( $messages, $die_on_error_level );
next if $err_count > 0;
canonicalize_all_names( $data );
for my $dataset (@$data) {
my $dataname = 'data_' . $dataset->{name};
local $SIG{__WARN__} = sub {
process_warnings( {
'message' => @_,
'program' => $0,
'filename' => $filename,
'add_pos' => $dataname
}, $die_on_error_level )
};
eval {
my $neighbour_list =
neighbour_list_from_cif( $dataset,
$neighbour_list_options );
my $graph = neighbour_list_to_graph( $neighbour_list );
my @orbits = orbits( $graph,
sub { return $_[0]->{chemical_type} },
sub { return $_[0]->{index} } );
for my $orbit (0..$#orbits) {
for (@{$orbits[$orbit]}) {
$_->{orbit} = $orbit;
}
}
my %labels;
for my $i (0..$#{$dataset->{values}{_atom_site_label}}) {
my $label = $dataset->{values}{_atom_site_label}[$i];
if( exists $labels{$label} ) {
# TODO: warn
next;
}
$labels{$label} = $i;
}
if( $print_atom_site_type_symbol ) {
if( contains_data_item( $dataset, '_atom_site_type_symbol' ) ) {
warn 'output assumed chemical types requested, but data ' .
'item \'_atom_site_type_symbol\' is already present, ' .
'overwriting' . "\n";
exclude_tag( $dataset, '_atom_site_type_symbol' );
}
my @atom_site_type_symbol =
( 'H' ) x scalar @{$dataset->{values}{_atom_site_label}};
for my $atom (@{$neighbour_list->{atoms}}) {
$atom_site_type_symbol[$labels{$atom->{site_label}}] =
$atom->{chemical_type};
}
set_loop_tag( $dataset,
'_atom_site_type_symbol',
'_atom_site_label',
\@atom_site_type_symbol );
}
my @orbit_number =
( '.' ) x scalar @{$dataset->{values}{_atom_site_label}};
for my $atom (@{$neighbour_list->{atoms}}) {
$orbit_number[$labels{$atom->{site_label}}] = $atom->{orbit};
}
set_loop_tag( $dataset,
'_[local]_cod_molecule_automorphism_orbit_number',
'_atom_site_label',
\@orbit_number );
print_cif( $dataset,
{
preserve_loop_order => 1,
keep_tag_order => 1,
}
);
};
if ( $@ ) {
process_errors( {
'message' => $@,
'program' => $0,
'filename' => $filename,
'add_pos' => $dataname
}, $die_on_error_level )
}
}
}
|
