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 (i.e. -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. For example,
more than one enumeration value could be defined
for a single element. Any number of data items can be
specified in the following way:
ddlm_validate --treat-as-set _tag_1 --treat-as-set _tag_2
The default consists of the '_atom_site_refinement_flags'
and '_atom_site.refinement_flags' data items.

--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).

--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