.TH CIF_COD_NUMBERS 1
.SH NAME
cif_cod_numbers \- find COD numbers for the CIF files in given directories of file lists.

.SH SYNOPSIS
cif_cod_numbers \-\-options input1.cif input*.cif

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

.SH 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.

.SH "REPORTING BUGS"
Report cif_cod_numbers bugs using e\-mail: cod\-bugs@ibt.lt