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|
#! /bin/sh
#!perl -w # --*- Perl -*--
eval 'exec perl -x $0 ${1+"$@"}'
if 0;
#------------------------------------------------------------------------------
#$Author: antanas $
#$Date: 2022-07-31 09:41:50 +0300 (Sun, 31 Jul 2022) $
#$Revision: 9352 $
#$URL: svn+ssh://www.crystallography.net/home/coder/svn-repositories/cod-tools/tags/v3.7.0/scripts/cif_classify $
#------------------------------------------------------------------------------
#*
#* Classify a CIF structure -- find out if it is organic compound,
#* inorganic, mineral, etc.
#*
#* USAGE:
#* $0 --options input1.cif input*.cif
#**
use strict;
use warnings;
use COD::CIF::Parser qw( parse_cif );
use COD::CIF::Data::Classifier qw( cif_class_flags );
use COD::AtomProperties;
use COD::SOptions qw( getOptions );
use COD::SUsage qw( usage options );
use COD::ErrorHandler qw( process_warnings
process_parser_messages
report_message );
use COD::ToolsVersion qw( get_version_string );
my $die_on_error_level = {
ERROR => 0,
WARNING => 0,
NOTE => 0
};
my $use_parser = "c";
#* OPTIONS:
#* --use-perl-parser
#* Use development CIF parser written in Perl.
#* --use-c-parser
#* Use faster C/Yacc CIF parser (default).
#*
#* --help, --usage
#* Output a short usage message (this message) and exit.
#* --version
#* Output version information and exit.
#**
@ARGV = getOptions(
"--use-perl-parser" => sub{ $use_parser = "perl" },
"--use-c-parser" => sub{ $use_parser = "c" },
'--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 ( $err_count > 0 );
if( !@$data || !defined $data->[0] || !defined $data->[0]{name} ) {
report_message( {
'program' => $0,
'filename' => $filename,
'err_level' => 'WARNING',
'message' => 'file seems to be empty'
}, $die_on_error_level->{WARNING} );
next;
}
my $bond_safety_margin = 0.2; # Angstroems
for my $datablock (@$data) {
my $dataname = 'data_' . $datablock->{'name'};
local $SIG{__WARN__} = sub {
process_warnings( {
'message' => @_,
'program' => $0,
'filename' => $filename,
'add_pos' => $dataname
}, $die_on_error_level )
};
eval {
my $flags = cif_class_flags( $datablock,
\%COD::AtomProperties::atoms,
$bond_safety_margin );
if( $flags ) {
print $datablock->{name}, "\t", $flags, "\n";
} else {
print $datablock->{name}, "\t", 0, "\n";
}
};
if( $@ ) {
$@ =~ s/^ERROR,/WARNING,/;
process_warnings( {
'message' => $@,
'program' => $0,
'filename' => $filename,
'add_pos' => $dataname,
}, $die_on_error_level )
}
}
}
|
