NAME

       cif_cod_numbers - find COD numbers for the CIF files in given directories of file lists.

SYNOPSIS

       cif_cod_numbers --options input1.cif input*.cif

DESCRIPTION

       Find COD numbers for the CIF files in given directories of file lists.

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.

REPORTING BUGS

       Report cif_cod_numbers bugs using e-mail: cod-bugs@ibt.lt

                                                                               CIF_COD_NUMBERS(1)