NAME¶

ddlm_validate - validate CIF files against DDLm-compliant CIF dictionaries.

SYNOPSIS¶

ddlm_validate --dictionaries 'cif_core.dic,cif_cod.dic' --options input1.cif input*.cif

DESCRIPTION¶

Validate CIF files against DDLm-compliant CIF dictionaries.

OPTIONS¶

-d, --dictionaries 'cif_core.dic,cif_cod.dic'
A list of DDLm-compliant CIF dictionary files
that the CIF files should be validated against.
List elements are separated either by ',' or by ' '.
To include dictionaries with filenames containing
these symbols, the --add-dictionary option should
be used.

-D, --add-dictionary 'cif new dictionary.dic'
Add an additional CIF dictionary to the list.

--clear-dictionaries
Remove all CIF dictionaries from the list.

-I, --add-ddlm-import-path './ddlm/cod/'
Prepend an additional directory to the dictionary
import path. The dictionary import path specifies
a list of directories in which to look for files
that are imported by DDLm-compliant CIF dictionaries.
Directories provided using this option are assigned
the highest priority and are searched prior to
the directories listed in the COD_TOOLS_DDLM_IMPORT_PATH
environment variable or the default import path
(directory of the importing dictionary).

--clear-ddlm-import-path
Remove all directories from the dictionary import path
that were added using the --add-ddlm-import-path option.
Neither COD_TOOLS_DDLM_IMPORT_PATH environment variable
nor the default import path is affected by this option.

--max-message-count 5
Maximum number of validation messages that are reported
for each unique combination of validation criteria and
validated data items. Provide a negative value (e.g. -1)
to output all of the generated validation messages
Default: -1.

--range-su-multiplier 3.5
Multiplier that should be applied to the standard
uncertainty (s.u.) when determining if a numeric
value resides in the specified range. For example,
a multiplier of 3.5 means that the value is treated
as valid if it falls in the interval of
[lower bound - 3.5 * s.u.; upper bound + 3.5 * s.u.].
Default: 3.

--treat-as-set _atom_site_refinement_flags
Treat values of given data items as a set. Due to
historical reasons data values of some data items
are sometimes formed by concatenating several of
the available enumeration values. Any number of data
items can be specified in the following way:
ddlm_validate --treat-as-set _tag_1 --treat-as-set _tag_2
Default: '_atom_site_refinement_flags' and
'_atom_site.refinement_flags'.

--no-treat-as-set
Do not treat values of any data items as sets.
(see --treat-as-set).

--report-deprecated
Report the presence of data items that are marked as
deprecated in the dictionaries. Data item deprecation
usually means that it has been replaced with an another
data item.

--ignore-deprecated
Do not report the presence of data items that are marked
as deprecated in the dictionaries. Default.

--report-local-tags
Report the presence of local data items.

--no-report-local-tags, --ignore-local-tags
Do not report the presence of local data items. Default.

--report-missing-su
Report measurand data items that are not accompanied by
the mandatory standard uncertainty values.

--no-report-missing-su, --ignore-missing-su
Do not report measurand data items that are not
accompanied by the mandatory standard uncertainty
values. Default.

--follow-iucr-style-guide
Do not report missing recommended attributes
if they fit the criteria defined in the IUCr
DDLm dictionary style guide version 1.1.0,
rule 3.1.6.

--no-follow-iucr-style-guide
Do not make any validation exceptions based
on the IUCr DDLm dictionary style guide. Default.

--continue-on-errors
Do not terminate script if errors are raised.

--die-on-errors
Terminate script immediately if errors are raised.
Default.

--continue-on-warnings
Do not terminate script if warnings are raised. Default.

--die-on-warnings
Terminate script immediately if warnings are raised.

--continue-on-notes
Do not terminate script if notes are raised. Default.

--die-on-notes
Terminate script immediately if notes are raised.

--help, --usage
Output a short usage message (this message) and exit.

--version
Output version information and exit.

ENVIRONMENT¶

COD_TOOLS_DDLM_IMPORT_PATH
A list of directories in which to look for the
DDLm-compliant CIF dictionaries that are imported
by other DDLm-compliant CIF dictionaries. List
elements are separated by the colon symbol (':').
Directories listed in COD_TOOLS_DDLM_IMPORT_PATH
have a lower priority than those provided using
the command line option (--add-dictionary-import-path),
but higher than the default import path directory
(directory of the importing dictionary).

REPORTING BUGS¶

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