NAME¶

cif_validate - validate CIF files against CIF dictionaries (DDL1 or DDLm).

SYNOPSIS¶

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

DESCRIPTION¶

Validate CIF files against CIF dictionaries (DDL1 or DDLm).

OPTIONS¶

-d, --dictionaries 'cif_core.dic,cif_cod.dic'
A list of CIF dictionaries that the CIF files should
be validated against. May include DDL1 and DDLm
dictionaries. The order of DDL1 dictionaries
in the list is important (see --ddl1-dictionaries).
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 end of the list.

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

--ddl1-dictionaries 'cif_core.dic,cif_cod.dic'
A list of DDL1 dictionaries that the CIF files should
be validated against. The order of dictionaries in
the list is important as it determines the dictionary
merge order. The first DDL1 dictionary serves as the
base while the remaining ones are merged sequentially
using the OVERLAY mode. DDL1 dictionaries provided in
the generic dictionary list (see --dictionaries) are
appended to the end of this list.
List elements are separated either by ',' or by ' '.
To include dictionaries with filenames containing
these symbols, the --ddl1-add-dictionary option
should be used.

--ddl1-add-dictionary
Add an additional dictionary to the end of DDL1
dictionary list.

--ddl1-clear-dictionaries
Remove all dictionaries from the DDL1 dictionary list.

--merge-ddl1-dictionaries
Merge all DDL1 dictionaries into a single virtual
dictionary prior to validation. Default.

--no-merge-ddl1-dictionaries
Do not merge DDL1 dictionaries into a single virtual
dictionary prior to validation. Using this option
may result in incorrect validation results.

--ddlm-dictionaries
A list of DDLm dictionaries that the CIF files should
be validated against. DDLm dictionaries provided in
the generic dictionary list (see --dictionaries) are
appended to the end of this list.
List elements are separated either by ',' or by ' '.
To include dictionaries with filenames containing
these symbols, the --ddlm-add-dictionary option
should be used.

--ddlm-add-dictionary
Add an additional dictionary to the end of DDLm
dictionary list.

--ddlm-clear-dictionaries
Remove all dictionaries from the DDLm dictionary 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 provided in the following way:
cif_validate --treat-as-set _tag_1 --treat-as-set _tag_2
Default: '_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 other
data items.

--no-report-deprecated, --ignore-deprecated
Do not report 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.

--ignore-case
Ignore letter case while validating enumeration values.
For example, even though '_atom_site_adp_type' is
restricted to values ('Uani', 'Uiso', 'Uovl', ...),
value 'UANI' would still be treated as valid.
Applies only to DDL1 dictionaries.

--respect-case, --case-sensitive, --dont-ignore-case
Respect letter case while validating enumeration
values. Default.
Applies only to DDL1 dictionaries.

--allow-double-precision-notation
Treat numbers expressed using the double precision
notation (e.g. 0.42D+7) as proper numbers in a way
that is compatible with DDL1, but not the CIF_1.1
syntax.
Applies only to DDL1 dictionaries.

--no-allow-double-precision-notation
Treat numbers expressed using the double precision
notation (e.g. 0.42D+7) as character strings in a
way compatible with the CIF_1.1 syntax, but does not
cover the full extent of the DDL1 numbers variations.
Default.
Applies only to DDL1 dictionaries.

--report-missing-su
Report measurand data items that are not accompanied by
the mandatory standard uncertainty values.
Applies only to DDLm dictionaries.

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

--use-perl-parser
Use Perl parser to parse CIF files.

--use-c-parser
Use C parser to parse CIF files. Default.

-c, --always-continue
Continue processing and return successful return status
even if errors are diagnosed.

-c-, --always-die
Stop and return error status if errors are diagnosed.

--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.

-v, --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 cif_validate bugs using e-mail: cod-bugs@ibt.lt