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|
#! /bin/sh
#!perl -w # --*- Perl -*--
eval 'exec perl -x $0 ${1+"$@"}'
if 0;
#------------------------------------------------------------------------------
#$Author: andrius $
#$Date: 2017-05-30 14:51:03 +0300 (An, 30 geg. 2017) $
#$Revision: 5376 $
#$URL: svn://www.crystallography.net/cod-tools/tags/v2.3/scripts/cif_symop_apply $
#------------------------------------------------------------------------------
#*
#* Apply symmetry operator(s) to all atoms in a CIF.
#*
#* USAGE:
#* $0 --options input1.cif input*.cif
#**
use strict;
use warnings;
use COD::CIF::Parser qw( parse_cif );
use COD::Spacegroups::Symop::Parse qw( symop_from_string );
use COD::Spacegroups::Symop::Algebra qw( symop_mul symop_vector_mul );
use COD::CIF::Tags::Print qw( print_cif );
use COD::SOptions qw( getOptions get_value );
use COD::SUsage qw( usage options );
use COD::ErrorHandler qw( process_parser_messages report_message );
use COD::ToolsVersion;
my $die_on_error_level = {
ERROR => 1,
WARNING => 0,
NOTE => 0
};
my $use_parser = "c";
my @symops = ();
#* OPTIONS:
#* -s, --symop, --symmetry-operator -x,-y,z
#* Apply the specified symmetry operator.
#*
#* -a, --add-symop, --add-symmetry-operator -x,-y,z
#* Add the specified symmetry operator to the applied
#* operator list.
#*
#* --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(
"-s,--symop,--symmetry-operator" => sub { @symops = (get_value()) },
"-a,--add-symop,--add-symmetry-operator" => \@symops,
"--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 'cod-tools version ',
$COD::ToolsVersion::Version, "\n";
exit }
);
@ARGV = ( "-" ) unless @ARGV;
binmode STDOUT, ':encoding(UTF-8)';
binmode STDERR, ':encoding(UTF-8)';
my $symop_matrix = symop_from_string( "x,y,z");
for my $symop (@symops) {
$symop_matrix = symop_mul
( $symop_matrix, symop_from_string( $symop ));
}
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, $die_on_error_level );
if( !@$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;
}
for my $datablock (@$data) {
my $values = $datablock->{values};
for( my $i = 0; $i <= $#{$values->{_atom_site_fract_x}}; $i ++ ) {
my @xyz = (
$values->{_atom_site_fract_x}[$i],
$values->{_atom_site_fract_y}[$i],
$values->{_atom_site_fract_z}[$i],
);
my $new_xyz = symop_vector_mul( $symop_matrix, \@xyz );
$values->{_atom_site_fract_x}[$i] = $new_xyz->[0];
$values->{_atom_site_fract_y}[$i] = $new_xyz->[1];
$values->{_atom_site_fract_z}[$i] = $new_xyz->[2];
}
do {
local $, = " ";
local $\ = "\n";
print @{$datablock->{tags}};
} if 0;
print_cif( $datablock, {
dictionary_tags => $datablock->{values},
dictionary_tag_list => $datablock->{tags},
});
}
}
|
