1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
|
#! /bin/sh
#!perl -w # --*- Perl -*--
eval 'exec perl -x $0 ${1+"$@"}'
if 0;
#------------------------------------------------------------------------------
#$Author: saulius $
#$Date: 2023-05-10 16:18:52 +0300 (Wed, 10 May 2023) $
#$Revision: 9576 $
#$URL: svn+ssh://www.crystallography.net/home/coder/svn-repositories/cod-tools/tags/v3.11.0/scripts/cif_estimate_Z $
#------------------------------------------------------------------------------
#*
#* Calculate Z value (i.e. the number of "chemical formula units" in
#* the unit cell) using the provided cell volume, crystal density
#* and molecular weight.
#*
#* USAGE:
#* $0 --options input1.cif input*.cif
#**
use strict;
use warnings;
use COD::CIF::Parser qw( parse_cif );
use COD::CIF::Data::EstimateZ qw(
cif_estimate_z
cif_estimate_z_from_formula
);
use COD::SOptions qw( getOptions );
use COD::SUsage qw( usage options );
use COD::ErrorHandler qw( process_warnings
process_errors
process_parser_messages );
use COD::ToolsVersion qw( get_version_string );
my $die_on_error_level = {
ERROR => 1,
WARNING => 0,
NOTE => 0
};
my $use_parser = 'c';
my $print_header = 0;
my $print_data_block_name = 0;
my $allow_fractional_Z = 0;
#* OPTIONS:
#* --use-perl-parser
#* Use development CIF parser written in Perl.
#* --use-c-parser
#* Use faster C/Yacc CIF parser. Default.
#*
#* --allow-fractional-z
#* Output also fractional Z values. They most probably
#* indicate errors, but might be needed for data checks.
#*
#* --disallow-fractional-z
#* Treat fractional Z values as errors. Default.
#*
#* -c, --always-continue
#* Continue processing and return successful return status
#* even if errors are diagnosed.
#*
#* -c-, --always-die
#* Stop and return error status if errors are diagnosed.
#*
#* --continue-on-errors
#* Do not terminate script if errors are raised.
#*
#* --die-on-errors
#* Terminate script immediately if errors are raised.
#* Default.
#*
#* --print-header
#* Print TSV stream header (column names).
#*
#* --no-header
#* Do not print TSV header. Default.
#*
#* --print-datablock-name
#* --print-data-block-name
#* Print the name of the data block and the file name.
#*
#* --no-datablock-name
#* --no-data-block-name
#* Do not print data block name. 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" },
"--allow-fractional-z" => sub { $allow_fractional_Z = 1 },
"--disallow-fractional-z" => sub { $allow_fractional_Z = 0 },
"-c,--always-continue" => sub {
$die_on_error_level->{ERROR} = 0;
$die_on_error_level->{WARNING} = 0;
$die_on_error_level->{NOTE} = 0;
},
"-c-,--always-die" => sub {
$die_on_error_level->{ERROR} = 1;
$die_on_error_level->{WARNING} = 1;
$die_on_error_level->{NOTE} = 1;
},
"--continue-on-errors" => sub { $die_on_error_level->{ERROR} = 0 },
"--die-on-errors" => sub { $die_on_error_level->{ERROR} = 1 },
"--print-header" => sub { $print_header = 1 },
"--no-header" => sub { $print_header = 0 },
"--print-data-block-name" => sub { $print_data_block_name = 1 },
"--print-datablock-name" => sub { $print_data_block_name = 1 },
"--no-data-block-name" => sub { $print_data_block_name = 0 },
"--no-datablock-name" => sub { $print_data_block_name = 0 },
'--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)';
if( $print_header ) {
print 'Z';
if( $print_data_block_name ) {
print "\tdatablock\tfilename";
}
print "\n";
}
for my $filename (@ARGV) {
my $options = { parser => $use_parser, no_print => 1, fix_errors => 1 };
my ( $data, $err_count, $messages ) = parse_cif( $filename, $options );
process_parser_messages( $messages, $die_on_error_level );
for my $dataset (@$data) {
my $dataname = 'data_' . $dataset->{'name'};
local $SIG{__WARN__} = sub {
process_warnings( {
'message' => @_,
'program' => $0,
'add_pos' => $dataname,
'filename' => $filename
}, $die_on_error_level )
};
my $Z = '';
eval {
eval {
# Try to estimate Z from crystal density:
$Z = cif_estimate_z( $dataset );
};
if($@) {
my $exception_message = $@;
# Try to estimate Z from the provided formula:
eval {
$Z = cif_estimate_z_from_formula( $dataset );
};
if($@) {
my $second_message = $@;
$second_message =~ s/\s*ERROR, \s*//g;
$exception_message =~ s/\s*\n$//;
die $exception_message . "; " . $second_message;
}
}
if( int($Z) != $Z && ! $allow_fractional_Z ) {
die "fractional value Z = $Z detected\n";
}
};
if ($@) {
process_errors( {
'message' => $@,
'program' => $0,
'filename' => $filename,
'add_pos' => $dataname
}, $die_on_error_level->{'ERROR'} );
};
print $Z;
if( $print_data_block_name ) {
print "\t", $dataset->{name}, "\t", $filename;
}
print "\n";
}
}
|
