cif_filter
--authors
--journal
--volume
--issue
--page
--start-page
--end-page
--year
--doi
Specify bibliographic data to be included into the output.
--bibliography
Provide a bibliography file with the bibliographic information to be included into the output. The bibliography information can be provided in CIF format or in a XML-like .mrk file with data items between <authors>, <journal>, <volume>, <issue>, <year>, <pages>123-132</pages> tags.
--leave-title
Do not delete the publication title obtained from the source of lower precedence, even if the '--discard-bibliography' option is enabled.
--add-cif-header
Prepend each of the output files with the comments from the beginning of the specified file.
--placeholder-tag-list
A comma-separated list of data items that should be checked for placeholder values. Default: '_chemical_name_common,_chemical_name_systematic'.
--extra-tag-list
Add additional tags to the list of recognised CIF tags. These extra tags are presented in a separate file, one tag per line.
--original-filename
Use the provided string as the name of the original file. (see --record-original-filename).
--clear-original-filename
Do not use any previously provided strings as the name of the original file.
--start-data-block-number
Use the provided number as the start number when renaming data blocks. Default: '7000001'. Setting this option enables the '-R' option.
--datablock-format
Use the provided format to determine new data block names from the provided data block numbers. Default: '%07d'.
--original-filename-tag
--original-data-block-tag
Use the provided tags to record original filename/data block name. Default: '_cod_data_source_file' and '_cod_data_source_block'.
--database-code-tag
Use the provided tag while adding or updating the database code upon renaming the data blocks. Default: '_cod_database_code'.
--folding-width
Specify the length of the longest unfolded line. Default: 76.
--help
Output a short usage message (this message) and exit.
--version
Output version information and exit.
--leave-bibliography
Combine bibliographies from various sources. Values of lower precedence are overwritten, but never deleted. List of bibliography sources in order of increasing precedence: 1) the bibliography tags of the original CIF file; 2) the optional bibliography file; 3) the user specified command line options.
--discard-bibliography
Only retain the bibliography tags from the bibliography source of highest precedence (see '--leave-bibliography' option). Default.
--global-priority
Assume bibliography found in 'data_global' data block has precedence over bibliographies found in all the other data blocks.
--no-global-priority
Assume bibliography found in 'data_global' data block does not have precedence over bibliographies found in all the other data blocks. Only missing bibliographic information will be copied from the 'data_global' data block. Default.
--exclude-publication-details
Exclude potentially copyrighted and irrelevant tags.
--no-exclude-publication-details
Do not exclude potentially copyrighted and irrelevant tags.
--estimate-space-group
Estimate space group symbols from the symmetry operators in the input.
--no-estimate-space-group
Do not estimate space group symbols from the symmetry operators in the input. Default.
--keep-unrecognised-space-groups
This option is a modifier for the '--estimate-space-group' option. Leave tags with unrecognised space group information as they are.
--no-keep-unrecognised-space-groups
This option is a modifier for the '--estimate-space-group' option. Replace the values of tags with unrecognised space group information with unknown values (represented as '?') and store the unrecognised space group information in '_cod_original_sg_*' tags. Default.
--reformat-space-group
Correct the formatting of Hermann-Mauguin symmetry space group symbol.
--dont-reformat-spacegroup
Leave the Hermann-Mauguin symmetry space group symbol as is. Default.
--dont-reformat-space-group
--reformat-space-group
Correct the formatting of Hermann-Mauguin symmetry space group symbol.
--exclude-empty-tags
Remove data items that contain only empty values. A value is considered empty if it is equal to a single question mark ('?') or a single period ('.').
--no-exclude-empty-tags
Disable the '--exclude-empty-tags' option. Default.
--exclude-placeholder-tags
Remove data items that contain common placeholder values (i.e. multiline value consisting only of white spaces and question marks. Only data items specified using the --placeholder-tag-list are affected by this option.
--no-exclude-placeholder-tags
Disable the '--exclude-placeholder-tags' option. Default.
--exclude-redundant-chemical-names
Remove data items related to various chemical names (systematic, common, mineral) if the stored values match the chemical formula.
--no-exclude-redundant-chemical-names
Disable the '--exclude-redundant-chemical-names' option. Default.
--exclude-empty-non-loop-tags
Remove tags that contain empty values and are not contained within the CIF loop_ structure. For the definition of empty values, see '--exclude-empty-tags' option. This option does not override the '--exclude-empty-tags' option.
--no-exclude-non-loop-empty-tags
Disable the '--exclude-empty-non-loop-tags' option. Default.
--exclude-unknown-tags
Remove tags that contain only unknown values. A value is considered unknown if it is equal to a single question mark ('?').
--no-exclude-unknown-tags
Disable the '--exclude-unknown-tags' option. Default.
--exclude-unknown-non-loop-tags
Remove tags that contain unknown values and are not contained within the CIF loop_ structure. For the definition of unknown values, see '--exclude-unknown-tags' option. This option does not override the '--exclude-unknown-tags' option.
--no-exclude-non-loop-unknown-tags
Disable the '--exclude-unknown-non-loop-tags' option. Default.
--exclude-misspelled-tags
Remove tags that were not present in the recognised tag list.
--no-exclude-misspelled-tags
Disable the '--exclude-misspelled-tags' option. Default.
--parse-formula-sum
Parse '_chemical_formula_sum' tag value and reformat it according to the Hill system ordering. If the original and reformatted formulae differ, replace the original value with the reformatted one and store the original value as the '_cod_original_formula_sum' tag value. Default.
--no-parse-formula-sum
Do not parse '_chemical_formula_sum' tag value.
--fix-syntax-errors
Try to fix syntax errors in the input CIF files that can be corrected unambiguously.
--no-fix-syntax-errors
Do not try to fix syntax errors in input CIF files. Default.
--retain-tag-order
Print tags in the same order they appeared in the original file.
--dont-retain-tag-order
Disregard original tag order while printing the tags. Default.
--preserve-loop-order
Print loops in the same order they appeared in the original file.
--use-internal-loop-order
Disregard original loop order while printing the tags. Default.
--calculate-cell-volume
Calculate the unit cell volume from the cell constants. If the calculated value differs from the one already present in the CIF, replace the original value with the calculated one and store the original value as the '_cod_original_cell_volume' tag value.
--dont-calculate-cell-volume
Do not calculate unit cell volume from the cell constants. Default.
--record-original-filename
Record the original filename and the original data block name for each data block as the '_cod_data_source_*' tag values.
--dont-record-original-filename
Do not record the original filename and the original data block name. Default.
--renumber-data-blocks
Rename all data blocks. The new names are constructed by taking a start number (specified by the '-S' option), applying the string format (specified by the '-d' option) and then incrementing the start number for each sequential data block.
--dont-renumber-data-blocks
Do not rename data blocks. Default. Enabling this option sets the '-S' option to default value.
--update-database-code
Update the database code tag value upon renaming the data blocks. Default.
--dont-update-database-code
Do not update the database code tag value upon renaming the data blocks.
--use-datablocks-without-coordinates
Do not remove data blocks without coordinates.
--no-use-datablocks-without-coordinates
Remove data blocks without coordinates. Default.
--use-datablocks-with-structure-factors
Do not remove data blocks with structure factors (Fobs).
--no-use-datablocks-with-structure-factors
Filter out data blocks with structure factors (Fobs). Default.
--fold-title
Folds the title, if longer than folding width.
--dont-fold-title
Do not fold the title. Default.
--fold-long-fields
Fold fields, longer than folding width.
--dont-fold-long-fields
Do not fold fields. Default.
--use-perl-parser
Use Perl parser for CIF parsing.
--use-c-parser
Use Perl & C parser for CIF parsing. Default.
--cif-input
Use CIF format for input. Default.
--json-input
Use JSON format for input.
--cif-output
Use CIF format for output. Default.
--json-output
Use JSON format for output.
--cif
Use CIF format for both input and output. Default.
--json
Use JSON format for both input and output.
Pass the output to the next command:
chemonomatopist
cif-perceive-chemistry
cif-to-chemname
cif-to-utf8
cif_cod_check
cif_filter
cif_fix_values