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|
#! /bin/sh
#!perl -w # --*- Perl -*--
eval 'exec perl -x $0 ${1+"$@"}'
if 0;
#------------------------------------------------------------------------------
#$Author: antanas $
#$Date: 2020-09-29 10:54:47 +0300 (Tue, 29 Sep 2020) $
#$Revision: 8533 $
#$URL: svn+ssh://www.crystallography.net/home/coder/svn-repositories/cod-tools/tags/v3.7.0/scripts/cif_cod_numbers $
#------------------------------------------------------------------------------
#*
#* Find COD numbers for the CIF files in given directories of file lists.
#*
#* USAGE:
#* $0 --options input1.cif input*.cif
#**
use strict;
use warnings;
use COD::CIF::Parser qw( parse_cif );
use COD::CIF::Data::CODNumbers qw( cif_fill_data fetch_duplicates );
use COD::CIF::Tags::CanonicalNames qw( canonicalize_all_names );
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 %database = (
host => 'www.crystallography.net',
user => 'cod_reader',
name => 'cod',
table => 'data',
password => '',
platform => 'mysql',
);
my $use_parser = 'c';
my $input_format = 'cif';
my $die_on_error_level = {
ERROR => 1,
WARNING => 0,
NOTE => 0
};
my $print_datablock_name = 0;
my %options = (
'check_bibliography' => 1,
'check_compound_source' => 0,
'check_sample_history' => 0,
'use_su' => 1,
'max_cell_length_diff' => 0.5, # angstrom
'max_cell_angle_diff' => 1.2, # degree of arc
);
my %cif_fill_data_options = (
'use_attached_hydrogens' => 1,
);
#* OPTIONS:
#* --platform 'SQLite'
#* Use the SQL database platform 'SQLite' to query structures
#* (default: 'mysql').
#*
#* -d, --database cod
#* Use database "cod" to query for structures.
#*
#* -h, --host www.crystallography.net
#* -s, --server www.crystallography.net
#* Query COD database on the host 'www.crystallography.net'.
#*
#* -l, --localhost
#* Use database server on the localhost to query the
#* COD database.
#*
#* -p, --port 3306
#* Use use the specified port to query structures
#* (default: 3306).
#*
#* -t, --table data
#* Use SQL table "data" to query for structures.
#*
#* -u, --user cod_reader
#* Use user name "cod_reader" to access COD database;
#* this reader should be granted SELECT privilege, i.e.
#* should be able to read the COD database without
#* supplying a password.
#*
#* --password
#* Use the specified password to connect (default: '').
#*
#* -P, --print-datablock-name
#* Print data block name as the fifth column.
#* -P-, --no-print-datablock-name, --dont-print-datablock-name
#* Do not print data block names (default).
#*
#* -S, --series 9
#* Check only COD entries starting with 9 (so called 9* series).
#* Default: check the whole COD database. Set series to
#* "" (empty string) to restore the default behaviour.
#*
#* --max-cell-length-difference 0.5
#* Maximum difference of unit cell lengths allowed
#* for entries regarded as the same, in angstroms
#* (default: 0.5).
#*
#* --max-cell-angle-difference 1.2
#* Maximum difference of unit cell angles allowed for
#* entries regarded as the same, in angstroms
#* (default: 1.2).
#*
#* --check-bibliography
#* Only CIFs that have different bibliography data are
#* declared different if all other parameters match
#* CIFs with missing bibliographies are assumed to
#* have matching bibliographies (default).
#* --no-check-bibliography, --dont-check-bibliography
#* Ignore bibliographic data of all CIFs; thus even files
#* with different bibliographies will be regarded the same
#* if their cells, chemical formulae and measurement
#* conditions match.
#*
#* --use-sigma, --no-ignore-sigma, --dont-ignore-sigma
#* Use standard deviations (sigmas) when comparing unit
#* cell constants (default).
#* --no-use-sigma, --dont-use-sigma, --ignore-sigma
#* Ignore standard deviations (sigmas) when comparing unit
#* cell constants.
#*
#* --check-sample-history
#* Only CIFs that have different sample history data
#* (as recorded in the _exptl_crystal_thermal_history
#* and _exptl_crystal_pressure_history tags) are declared
#* different if all other parameters match.
#* --no-check-sample-history,
#* --dont-check-sample-history,
#* --disregard-sample-history
#* Ignore sample history of all CIFs; thus even files
#* with different sample histories will be regarded the
#* same if their cells, chemical formulae and measurement
#* conditions match (default).
#*
#* --check-compound-source
#* Only CIFs that have different compound source
#* (as recorded in the _chemical_compound_source)
#* are declared different if all other parameters
#* match.
#* --no-check-compound-source,
#* --dont-check-compound-source,
#* --disregard-compound-source
#* Ignore compound source of all CIFs; thus even files
#* with different compound sources will be regarded the
#* same if other conditions match (default).
#*
#* --use-attached-hydrogens
#* Include number of implicit hydrogens, specified using
#* _atom_site_attached_hydrogens tag, into the formula
#* sum (default).
#* --no-use-attached-hydrogens,
#* --dont-use-attached-hydrogens,
#* --ignore-attached-hydrogens
#* Ignore number of implicit hydrogens, specified using
#* _atom_site_attached_hydrogens tag, in calculation of
#* the formula sum.
#*
#* --use-perl-parser
#* Use the Perl-only CIF parser.
#* --use-c-parser
#* Use the speed-optimised C/Perl parser (default).
#*
#* --cif-input
#* Use CIF format for input (default).
#* --json-input
#* Use JSON format for input.
#*
#* --help, --usage
#* Output a short usage message (this message) and exit.
#* --version
#* Output version information and exit.
#**
@ARGV = getOptions(
'-d,--database' => \$database{'name'},
'-l,--localhost' => sub { $database{'host'} = 'localhost' },
'-h,--host' => \$database{'host'},
'-p,--port' => \$database{'port'},
'-s,--server' => \$database{'host'},
'-t,--table' => \$database{'table'},
'-u,--user' => \$database{'user'},
'--password' => \$database{'password'},
'--platform' => \$database{'platform'},
'-P,--print-datablock-name' => sub{ $print_datablock_name = 1 },
'-P-,--no-print-datablock-name' => sub{ $print_datablock_name = 0 },
'--dont-print-datablock-name' => sub{ $print_datablock_name = 0 },
'-S,--series' => \$options{'cod_series_prefix'},
'--max-cell-length-difference' => \$options{'max_cell_length_diff'},
'--max-cell-angle-difference' => \$options{'max_cell_angle_diff'},
'--check-bibliography' => sub { $options{'check_bibliography'} = 1 },
'--dont-check-bibliography' => sub { $options{'check_bibliography'} = 0 },
'--no-check-bibliography' => sub { $options{'check_bibliography'} = 0 },
'--check-sample-history'
=> sub { $options{'check_sample_history'} = 1 },
'--dont-check-sample-history'
=> sub { $options{'check_sample_history'} = 0 },
'--no-check-sample-history'
=> sub { $options{'check_sample_history'} = 0 },
'--disregard-sample-history'
=> sub { $options{'check_sample_history'} = 0 },
'--check-compound-source'
=> sub { $options{'check_compound_source'} = 1 },
'--dont-check-compound-source'
=> sub { $options{'check_compound_source'} = 0 },
'--no-check-compound-source'
=> sub { $options{'check_compound_source'} = 0 },
'--disregard-compound-source'
=> sub { $options{'check_compound_source'} = 0 },
'--ignore-sigma' => sub{ $options{'use_su'} = 0 },
'--dont-ignore-sigma' => sub{ $options{'use_su'} = 1 },
'--no-ignore-sigma' => sub{ $options{'use_su'} = 1 },
'--use-sigma' => sub{ $options{'use_su'} = 1 },
'--dont-use-sigma' => sub{ $options{'use_su'} = 0 },
'--no-use-sigma' => sub{ $options{'use_su'} = 0 },
'--use-attached-hydrogens' =>
sub { $cif_fill_data_options{'use_attached_hydrogens'} = 1 },
'--dont-use-attached-hydrogens' =>
sub { $cif_fill_data_options{'use_attached_hydrogens'} = 0 },
'--no-use-attached-hydrogens' =>
sub { $cif_fill_data_options{'use_attached_hydrogens'} = 0 },
'--ignore-attached-hydrogens' =>
sub { $cif_fill_data_options{'use_attached_hydrogens'} = 0 },
'--use-perl-parser' => sub{ $use_parser = 'perl' },
'--use-c-parser' => sub{ $use_parser = 'c' },
'--cif-input' => sub { $input_format = 'cif' },
'--json-input' => sub { $input_format = 'json' },
'--options' => sub { options; exit },
'--help,--usage' => sub { usage; exit },
'--version' => sub { print get_version_string(), "\n"; exit }
);
if( $input_format eq 'json' ) {
$use_parser = 'json';
}
@ARGV = ('-') unless @ARGV;
binmode STDOUT, ':encoding(UTF-8)';
binmode STDERR, ':encoding(UTF-8)';
for my $filename (@ARGV) {
my $parser_options = { 'parser' => $use_parser, 'no_print' => 1 };
my ( $data, $err_count, $messages ) = parse_cif( $filename, $parser_options );
process_parser_messages( $messages, $die_on_error_level );
canonicalize_all_names( $data );
local $SIG{__WARN__} = sub { process_warnings( {
'message' => @_,
'program' => $0,
'filename' => $filename
}, $die_on_error_level ) };
if( !defined $data->[0] || !defined $data->[0]{name} ) {
warn "WARNING, file seems to be empty\n";
next;
}
my %structures = ();
my $index = 0;
foreach 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 {
my $structure = cif_fill_data( $dataset,
$filename,
$index,
\%cif_fill_data_options );
if ( defined $structure ) {
$structures{$structure->{id}} = $structure;
$index++;
}
};
if ($@) {
process_errors( {
'message' => $@,
'program' => $0,
'filename' => $filename,
'add_pos' => $dataname
}, $die_on_error_level->{'ERROR'} );
};
}
my $duplicates;
eval {
$duplicates = fetch_duplicates( \%structures, \%database, \%options );
};
if ($@) {
process_errors( {
'message' => $@,
'program' => $0,
'filename' => $filename,
}, $die_on_error_level->{'ERROR'} );
};
for my $datablock ( @{$duplicates} ) {
if( keys %{ $datablock->{duplicates} } > 0 ) {
for my $key (sort keys %{ $datablock->{duplicates} } ) {
my $cod_entry = $datablock->{duplicates}{$key};
printf
'%-35s %15s %3d %s',
$datablock->{formula},
$cod_entry->{filename},
scalar keys %{ $datablock->{duplicates} },
$filename;
if( $print_datablock_name ) {
printf ' %s', $datablock->{datablock}{id};
}
print "\n"
}
} else {
printf
'%-35s %15s %3d %s',
$datablock->{formula}, '?', 0,
$filename;
if( $print_datablock_name ) {
printf ' %s', $datablock->{datablock}{id};
}
print "\n"
}
}
}
|
