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