| cif_cod_numbers() | cif_cod_numbers() |
cif_cod_numbers - Find COD numbers for the CIF files in given directories of file lists.
cif_cod_numbers --options input1.cif input*.cif
Find COD numbers for the CIF files in given directories of file lists.
--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 (default 3306) to query
structures.
-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 (default empty) to connect.
-P, --print-datablock-name
Print data block name as the fifth column.
-P-, --dont-print-datablock-name, --no-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.
--max-cell-angle-difference 1.2
Maximum difference of unit cell angles allowed for
entries regarded as the same, in angstroms.
--check-bibliography
Only CIFs that have different bibliography data are
declared different if all other parameters match
(default). CIFs with missing bibliographies are
assumed to have matching bibliographies.
--dont-check-bibliography, --no-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.
--ignore-sigma, --dont-use-sigma, --no-use-sigma
Ignore standard deviations (sigmas) when comparing unit
cell constants
--dont-ignore-sigma, --no-ignore-sigma, --use-sigma
Use 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.
--dont-check-sample-history, --no-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.
--dont-check-compound-source, --no-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-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.
Report cif_cod_numbers bugs using e-mail: cod-bugs@ibt.lt