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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_bounding_box $
#------------------------------------------------------------------------------
#*
#* Transform non-crystal CIF file (missing cell parameters and symmetry
#* information, Cartesian coordinates are given instead of fractional)
#* into a crystal description.
#*
#* USAGE:
#* $0 --options input1.cif input*.cif
#**
use strict;
use warnings;
use COD::CIF::Data qw( get_symmetry_operators );
use COD::CIF::Parser qw( parse_cif );
use COD::CIF::Tags::CanonicalNames qw( canonicalize_all_names );
use COD::CIF::Tags::Manage qw( exclude_tag set_loop_tag set_tag );
use COD::CIF::Tags::Print qw( print_cif );
use COD::ErrorHandler qw( process_parser_messages
report_message );
use COD::SOptions qw( getOptions );
use COD::SUsage qw( usage options );
use COD::ToolsVersion qw( get_version_string );
use List::Util qw( reduce );
my @margin = ( 5, 5, 5 );
my $use_parser = 'c';
my $die_on_error_level = {
ERROR => 0,
WARNING => 0,
NOTE => 0,
};
#* OPTIONS:
#* --margin-x, --margin-y, --margin-z 6
#* Set margins in x, y and z directions
#* (default: 5 angstroms).
#*
#* --use-perl-parser
#* Use Perl parser for CIF parsing.
#* --use-c-parser
#* Use Perl & C parser for CIF parsing (default).
#*
#* --help, --usage
#* Output a short usage message (this message) and exit.
#* --version
#* Output version information and exit.
#**
@ARGV = getOptions(
'--margin-x' => \$margin[0],
'--margin-y' => \$margin[1],
'--margin-z' => \$margin[2],
'--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, $die_on_error_level );
if( !@{$data} || !defined $data->[0] || !defined $data->[0]{name} ) {
report_message( {
'program' => $0,
'filename' => $filename,
'err_level' => 'WARNING',
'message' => 'file seems to be empty'
}, 0 );
next;
}
canonicalize_all_names( $data );
for my $dataset (@$data) {
my $values = $dataset->{values};
my @bounding_box;
if( exists $values->{'_atom_site_Cartn_x'} &&
exists $values->{'_atom_site_Cartn_y'} &&
exists $values->{'_atom_site_Cartn_z'} &&
!exists $values->{'_atom_site_fract_x'} &&
!exists $values->{'_atom_site_fract_y'} &&
!exists $values->{'_atom_site_fract_z'} ) {
my @bounding_box = get_bounding_box( $values );
my @cell = ( $bounding_box[1] - $bounding_box[0] + $margin[0],
$bounding_box[3] - $bounding_box[2] + $margin[1],
$bounding_box[5] - $bounding_box[4] + $margin[2],
90, 90, 90 );
set_tag( $dataset, '_cell_length_a', $cell[0] );
set_tag( $dataset, '_cell_length_b', $cell[1] );
set_tag( $dataset, '_cell_length_c', $cell[2] );
set_tag( $dataset, '_cell_angle_alpha', $cell[3] );
set_tag( $dataset, '_cell_angle_beta', $cell[4] );
set_tag( $dataset, '_cell_angle_gamma', $cell[5] );
my @Cartn_x_now = map { $_ - $bounding_box[0] + $margin[0] / 2 }
@{$values->{'_atom_site_Cartn_x'}};
my @Cartn_y_now = map { $_ - $bounding_box[2] + $margin[1] / 2 }
@{$values->{'_atom_site_Cartn_y'}};
my @Cartn_z_now = map { $_ - $bounding_box[4] + $margin[2] / 2 }
@{$values->{'_atom_site_Cartn_z'}};
my @fract_x = map { $_ / $cell[0] } @Cartn_x_now;
my @fract_y = map { $_ / $cell[1] } @Cartn_y_now;
my @fract_z = map { $_ / $cell[2] } @Cartn_z_now;
set_loop_tag( $dataset,
'_atom_site_fract_x',
'_atom_site_label',
\@fract_x );
set_loop_tag( $dataset,
'_atom_site_fract_y',
'_atom_site_label',
\@fract_y );
set_loop_tag( $dataset,
'_atom_site_fract_z',
'_atom_site_label',
\@fract_z );
exclude_tag( $dataset, '_atom_site_Cartn_x' );
exclude_tag( $dataset, '_atom_site_Cartn_y' );
exclude_tag( $dataset, '_atom_site_Cartn_z' );
}
eval {
get_symmetry_operators( $dataset );
};
if( $@ ) {
# structure probably does not contain symmetry information
set_tag( $dataset, '_space_group_name_Hall', 'P 1' );
}
print_cif( $dataset,
{
preserve_loop_order => 1,
keep_tag_order => 1
} );
}
}
# Returns x_min, x_max, y_min, y_max, z_min, z_max
sub get_bounding_box
{
my( $values ) = @_;
return
(reduce { $b ne '.' && $b ne '?' && $b < $a ? $b : $a }
@{$values->{'_atom_site_Cartn_x'}}),
(reduce { $b ne '.' && $b ne '?' && $b > $a ? $b : $a }
@{$values->{'_atom_site_Cartn_x'}}),
(reduce { $b ne '.' && $b ne '?' && $b < $a ? $b : $a }
@{$values->{'_atom_site_Cartn_y'}}),
(reduce { $b ne '.' && $b ne '?' && $b > $a ? $b : $a }
@{$values->{'_atom_site_Cartn_y'}}),
(reduce { $b ne '.' && $b ne '?' && $b < $a ? $b : $a }
@{$values->{'_atom_site_Cartn_z'}}),
(reduce { $b ne '.' && $b ne '?' && $b > $a ? $b : $a }
@{$values->{'_atom_site_Cartn_z'}});
}
|
