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|
#! /bin/sh
#!perl -w # --*- Perl -*--
eval 'exec perl -x $0 ${1+"$@"}'
if 0;
#------------------------------------------------------------------------------
#$Author: andrius $
#$Date: 2020-09-08 10:56:51 +0300 (Tue, 08 Sep 2020) $
#$Revision: 8471 $
#$URL: svn+ssh://www.crystallography.net/home/coder/svn-repositories/cod-tools/tags/v3.1.0/scripts/cif2xyz $
#------------------------------------------------------------------------------
#*
#* Read CIF files and print atom coordinates in XYZ format.
#*
#* USAGE:
#* $0 --options input.cif
#**
use strict;
use warnings;
use COD::AtomProperties;
use COD::CIF::Data qw( get_cell );
use COD::CIF::Data::AtomList qw( get_atom_chemical_type );
use COD::CIF::Parser qw( parse_cif );
use COD::ErrorHandler qw( process_warnings
process_errors
process_parser_messages
report_message );
use COD::Fractional qw( symop_ortho_from_fract );
use COD::Spacegroups::Symop::Algebra qw( symop_vector_mul );
use COD::SOptions qw( getOptions );
use COD::SUsage qw( usage options );
use COD::ToolsVersion;
my $die_on_error_level = {
ERROR => 1,
WARNING => 0,
NOTE => 0
};
my $print_radii = 0;
my $add_xyz_header = 1;
my $use_parser = "c"; # Used CIF parser
#* OPTIONS:
#* --print-radii
#* Append covalent radii to the atom coordinates.
#* --no-print-radii, --dont-print-radii, --xyz-only
#* Print only Cartesian XYZ coordinates for input atoms
#* (default).
#*
#* --add-xyz-header
#* Add the total number of atoms on the first line of
#* the output, followed by an empty line (default).
#*
#* --do-not-add-xyz-header,
#* --dont-add-xyz-header,
#* --no-add-xyz-header
#* Do not add the total number of atoms on the first line.
#*
#* --use-perl-parser
#* --use-c-parser
#* Specify parser to parse CIF files (default: C parser).
#*
#* --help, --usage
#* Output a short usage message (this message) and exit.
#* --version
#* Output version information and exit.
#**
@ARGV = getOptions(
"--print-radii" => sub { $print_radii = 1 },
"--no-print-radii,--dont-print-radii" => sub { $print_radii = 0 },
"--xyz-only" => sub { $print_radii = 0 },
"--add-xyz-header" => sub { $add_xyz_header = 1 },
"--do-not-add-xyz-header,--dont-add-xyz-header,--no-add-xyz-header" =>
sub { $add_xyz_header = 0 },
"--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)';
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 $dataset (@$data) {
my $dataname = 'data_' . $dataset->{'name'};
local $SIG{__WARN__} = sub {
process_warnings( {
'message' => @_,
'program' => $0,
'filename' => $filename,
'add_pos' => $dataname
}, $die_on_error_level )
};
eval {
local $, = ' ';
local $\ = "\n";
my $values = $dataset->{values};
my @cell = get_cell( $values );
my $f2o = symop_ortho_from_fract(@cell);
my $atom_site_tag;
if( exists $values->{_atom_site_label} ) {
$atom_site_tag = '_atom_site_label';
} elsif( exists $values->{_atom_site_type_symbol} ) {
$atom_site_tag = '_atom_site_type_symbol';
} else {
die 'ERROR, neither \'_atom_site_label\' nor ' .
"'_atom_site_type_symbol' data items were found\n";
}
my $atom_labels = $values->{$atom_site_tag};
if( $add_xyz_header ) {
print scalar @$atom_labels;
print '';
}
for (my $i = 0; $i < @$atom_labels; $i++) {
my $options = { allow_unknown_chemical_types => 1 };
delete $options->{allow_unknown_chemical_types} if $print_radii;
my $atom_type = get_atom_chemical_type( $dataset, $i, $options );
my $covalent_radius =
$COD::AtomProperties::atoms{$atom_type}->{covalent_radius};
my @atom_xyz = map { s/\([0-9]+\)$//; $_ }
map { $values->{"_atom_site_fract_$_"}[$i] }
qw( x y z );
my $coordinates_ortho = symop_vector_mul( $f2o, \@atom_xyz );
print $atom_type,
@{$coordinates_ortho},
($print_radii ? $covalent_radius : ());
}
};
if ($@) {
process_errors( {
'message' => $@,
'program' => $0,
'filename' => $filename,
'add_pos' => $dataname
}, $die_on_error_level->{'ERROR'} );
}
}
}
|
