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|
#! /bin/sh
#!perl -w # --*- Perl -*--
eval 'exec perl -x $0 ${1+"$@"}'
if 0;
#------------------------------------------------------------------------------
#$Author: antanas $
#$Date: 2018-06-28 02:54:33 +0300 (Kt, 28 birž. 2018) $
#$Revision: 6252 $
#$URL: svn://www.crystallography.net/cod-tools/tags/v2.3/scripts/find_numbers $
#------------------------------------------------------------------------------
#*
#* Find COD numbers for the .cif files in given directories of file lists.
#*
#* USAGE:
#* $0 my-cif-dir1/ my-cif-dir2/files*.cif COD-cif-dir/
#* USAGE:
#* $0 input1.cif input1_alt.cif
#**
use strict;
use warnings;
use COD::CIF::Data::CODNumbers qw( cif_fill_data
entries_are_the_same );
use COD::CIF::Parser qw( parse_cif );
use COD::CIF::Tags::CanonicalNames qw( canonicalize_all_names );
use COD::ErrorHandler qw( process_warnings
process_errors
process_parser_messages
report_message );
use COD::SOptions qw( getOptions );
use COD::SUsage qw( usage );
use COD::ToolsVersion;
my $die_on_error_level = {
'ERROR' => 1,
'WARNING' => 0,
'NOTE' => 0
};
#* OPTIONS:
#* --help, --usage
#* Output a short usage message (this message) and exit.
#* --version
#* Output version information and exit.
#**
@ARGV = getOptions(
'--help,--usage' => sub { usage; exit },
'--version' => sub { print 'cod-tools version ',
$COD::ToolsVersion::Version, "\n";
exit }
);
my $check_bibliography = 1;
my $max_cell_length_diff = 0.5; # Angstroems
my $max_cell_angle_diff = 1.2; # degrees
my %has_numeric_value = (
'_journal_year' => 1,
'_journal_volume' => 1,
'_journal_issue' => 1,
);
my %skip_tag = (
'_journal_name_full' => 0,
);
my %COD = ();
if( @ARGV < 2 ) {
report_message( {
'program' => $0,
'err_level' => 'ERROR',
'message' => 'please supply at least two directory names on the '
. 'command line -- names of directories with the '
. 'analysed CIF files come first and the name of the '
. 'directory with COD CIF files comes last'
}, 1 );
}
my $COD_cif_dir = pop @ARGV;
my @COD_cif_files = `find $COD_cif_dir -name "*.cif" -o -name "*.CIF"`;
do {
print int @COD_cif_files . "\n";
print "@COD_cif_files";
} if 0;
for my $file (sort @COD_cif_files) {
local $SIG{__WARN__} = sub {
process_warnings( {
'message' => @_,
'program' => $0,
'filename' => $file,
}, $die_on_error_level )
};
chomp $file;
my %structures = ();
eval {
my $structures = structures_from_cif_file( $file );
%structures = %$structures;
}; # end of eval
if ($@) {
process_errors( {
'program' => $0,
'filename' => $file,
'message' => $@,
}, $die_on_error_level->{'ERROR'} )
};
for my $id (sort keys %structures) {
my $formula = $structures{$id}{chemical_formula_sum};
$formula = '?' unless defined $formula;
push( @{$COD{$formula}}, $structures{$id} );
}
}
do {
use COD::Serialise qw( serialiseRef );
serialiseRef( \%COD );
} if 0;
#------------------------------------------------------------------------------
my @cif_files = `find @ARGV -name "*.cif" -o -name "*.CIF"`;
for my $file (sort @cif_files) {
local $SIG{__WARN__} = sub {
process_warnings( {
'message' => @_,
'program' => $0,
'filename' => $file,
}, $die_on_error_level )
};
chomp $file;
my %structures = ();
eval {
my $structures = structures_from_cif_file( $file );
%structures = %$structures;
}; # end of eval
if ($@) {
process_errors( {
'program' => $0,
'filename' => $file,
'message' => $@,
}, $die_on_error_level->{'ERROR'} )
};
for my $id (sort keys %structures) {
my $formula = $structures{$id}{chemical_formula_sum};
$formula = '?' unless defined $formula;
my $final_formula = $formula;
$final_formula =~ s/\s/_/g;
my $n = 0;
if( defined $COD{$formula} ) {
for my $COD_entry (@{$COD{$formula}}) {
if( entries_are_the_same( $structures{$id},
$COD_entry,
{ check_bibliography =>
$check_bibliography } ) ) {
$n++;
}
}
}
if( $n > 0 ) {
for my $COD_entry (@{$COD{$formula}}) {
if( entries_are_the_same( $structures{$id},
$COD_entry,
{ check_bibliography =>
$check_bibliography } ) ) {
printf
"%-35s %15s %3d %s\n",
$final_formula,
$COD_entry->{filename}, $n, $file;
}
}
} else {
printf "%-35s %15s %3d %s\n", $final_formula, '?', 0, $file;
}
}
}
#------------------------------------------------------------------------------
sub structures_from_cif_file
{
my( $filename ) = @_;
my $options = { 'no_print' => 1 };
my ( $data, $err_count, $messages ) = parse_cif( $filename, $options );
process_parser_messages( $messages, $die_on_error_level );
return {} if $err_count > 0;
canonicalize_all_names( $data );
my %structures;
for my $datablock (@$data) {
my $structure = cif_fill_data( $datablock, $filename );
$structures{$datablock->{name}} = $structure;
}
return \%structures;
}
|
