---
name: "cif_cod_numbers"
section: "1"
platform: "linux"
package: "cod-tools"
version: "3.11.0+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/cif_cod_numbers"
---

# cif\_cod\_numbers(1)

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

## 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 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 the COD database.\
                   This user should have at least the 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