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|
#! /bin/sh
#!perl -w # --*- Perl -*--
eval 'exec perl -x $0 ${1+"$@"}'
if 0;
#------------------------------------------------------------------------------
#$Author: andrius $
#$Revision: 5376 $
#$URL: svn://www.crystallography.net/cod-tools/tags/v2.3/scripts/cif_printout $
#$Date: 2017-05-30 14:51:03 +0300 (An, 30 geg. 2017) $
#$Id: cif_printout 5376 2017-05-30 11:51:03Z andrius $
#------------------------------------------------------------------------------
#*
#* Parse CIF file and print out the structure generated by CIF parser.
#*
#* USAGE:
#* $0 --options input1.cif input*.cif
#**
use strict;
use warnings;
use COD::CIF::JSON qw( cif2json json2cif );
use COD::CIF::Parser qw( parse_cif );
use COD::SOptions qw( getOptions );
use COD::SUsage qw( usage options );
use COD::ShowStruct qw( showRef );
use COD::ErrorHandler qw( process_errors
process_parser_messages
report_message );
use COD::ToolsVersion;
use Data::Dumper;
my $die_on_error_level = {
ERROR => 0,
WARNING => 0,
NOTE => 0
};
my $output_format = 'dump';
my $input_json = 0;
my %options = ( no_print => 1 );
#* OPTIONS:
#* --input-cif,
#* --input-json
#* Specify the format of input file(s). Default CIF.
#*
#* --output-dump
#* Output parsed CIF file in internal dump format (default).
#*
#* --output-json
#* Output generated structure in JSON.
#*
#* --output-struct
#* Output generated structure using COD::ShowStruct module.
#*
#* --json
#* Set both input and output formats to JSON.
#*
#* --use-perl-parser
#* Use Perl parser for CIF parsing.
#*
#* --use-c-parser
#* Use Perl & C parser for CIF parsing.
#*
#* --help, --usage
#* Output a short usage message (this message) and exit.
#* --version
#* Output version information and exit.
#**
@ARGV = getOptions(
"--do-not-unprefix-text" => sub{ $options{do_not_unprefix_text} = 1 },
"--do-not-unfold-text" => sub{ $options{do_not_unfold_text} = 1 },
"--fix-errors" => sub{ $options{fix_errors} = 1 },
"--fix-duplicate-tags-with-same-values" =>
sub{ $options{fix_duplicate_tags_with_same_values} = 1 },
"--fix-duplicate-tags-with-empty-values" =>
sub{ $options{fix_duplicate_tags_with_empty_values} = 1 },
"--fix-data-header" => sub{ $options{fix_data_header} = 1 },
"--fix-datablock-names" => sub{ $options{fix_datablock_names} = 1 },
"--fix-string-quotes" => sub{ $options{fix_string_quotes} = 1 },
"--fix-missing-closing-double-quote" =>
sub{ $options{fix_missing_closing_double_quote} = 1 },
"--fix-missing-closing-single-quote" =>
sub{ $options{fix_missing_closing_single_quote} = 1 },
"--fix-ctrl-z" => sub{ $options{fix_ctrl_z} = 1 },
"--allow-uqstring-brackets" => sub{ $options{allow_uqstring_brackets} = 1 },
# Bison parser is default:
"--input-cif" => sub { $options{parser} = 'c' },
"--input-json" => sub { $options{parser} = 'json' },
"--output-dump" => sub { $output_format = 'dump' },
"--output-json" => sub { $output_format = 'json' },
"--output-struct" => sub { $output_format = 'struct' },
"--json" => sub { $options{parser} = 'json'; $output_format = 'json' },
"--use-perl-parser" => sub { $options{parser} = 'perl' },
"--use-c-parser" => sub { $options{parser} = 'c' },
"--options" => sub { options; exit },
"--help,--usage" => sub { usage; exit },
'--version' => sub { print 'cod-tools version ',
$COD::ToolsVersion::Version, "\n";
exit }
);
@ARGV = ( "-" ) unless @ARGV;
binmode STDOUT, ':encoding(UTF-8)';
binmode STDERR, ':encoding(UTF-8)';
foreach( @ARGV ) {
my( $data, $err_count, $messages );
if( $input_json ) {
eval {
open my $inp, '<' . $_ or die 'ERROR, '
. 'could not open bibliography file for reading -- '
. lcfirst($!) . "\n";
$data = json2cif( join( "\n", <$inp> ) );
close $inp or die 'ERROR, '
. 'error while closing file after reading -- '
. lcfirst($!) . "\n";
$err_count = 0;
};
if ($@) {
process_errors( {
'program' => $0,
'filename' => $_,
'message' => $@
}, 1 );
}
} else {
$options{no_print} = 1;
($data, $err_count, $messages) = parse_cif( $_, \%options );
process_parser_messages( $messages, $die_on_error_level );
}
foreach my $datablock ( @$data ) {
if( $output_format eq 'json' ) {
print cif2json( $datablock );
} elsif( $output_format eq 'struct' ) {
showRef( $datablock );
} else {
local $Data::Dumper::Varname = 'datablock';
local $Data::Dumper::Sortkeys = 1;
print Dumper( $datablock );
}
}
report_message( {
'program' => $0,
'filename' => $_,
'err_level' => 'NOTE',
'message' => "$err_count error(s) encountered while processing the file"
}, $die_on_error_level->{'NOTE'} );
}
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