Section 5.3.5.2.2. Invocation of the program

cif2cif is another application of the CIFtbx library by the same author, and so has a similar user interface to that of CYCLOPS (Section 5.3.4.1.2). Under a Unix-like operating system, the program is typically called with a command such as

cif2cif -i infile -o outfile [ -q reqfile]

where infile is the name of the input file, outfile is the output file and reqfile is an optional file containing a request list for a subset of the original contents.

A more complete set of options available in a Unix-like operating environment is

cif2cif [ -i infile] [ -o outfile] [ -d dictfile] [ -q reqfile] [ -f cmndfile] [ -c catck] [ -a alias] [ -t tab] [ -e sulim] [ -p prefix]

where the options are as follows:

-i specifies the name of the input file, infile.

-o specifies the name of the output file, outfile.

-d specifies the name of a dictionary file, dictfile, against which the existence, type and category of data names are checked. The dictionary file may be either a CIF dictionary or a list of file names. That is, it may contain dictionary definitions in DDL format or (if the file begins with the characters #DICT) it may contain a list of dictionary file names to be entered. Thus, multiple dictionaries may be specified to the program.

-q specifies the name of the request file, reqfile, containing a list of data names (with associated data-block directives) that should be extracted as a subset of the contents of the original file.

-f specifies the name of a command file cmndfile that contains additional directives to the program.

-c is a flag indicating whether an error message should be raised if a data name has been assigned a category different from the leading portion of the data name itself. The Boolean variable catck may take the values `t', `1' or `y' for true, `f', `0' or `n' for false.

-a is a flag indicating whether data-name aliases in the validating dictionary should be used to replace user-supplied names by their canonical forms. The Boolean variable alias may take the same values for true or false as above.

-t is a flag indicating whether the output should be reformatted with tabs to produce a regular table layout within looped lists. The Boolean variable tab takes the same values as above. If true, text is reformatted; if false, the original formatting is retained.

For the flags expecting Boolean values, the default is `f' (false).

-e specifies the precision to retain in rounding standard uncertainty values. The permitted integer values are 9, 19 (the default) and 29.

-p takes a string value which is prefixed to every line of output. Every occurrence of the underscore character ` _' in the prefix is changed to a space on output.

If no input or output file names are specified, the program will read from the standard input channel or write to standard output, respectively. The special character hyphen (` -') may also be supplied as an argument in place of a file name to indicate standard input or standard output as appropriate.

Finally, if the operating system supports the passing of environment variables to a program, the name of the input file may be passed as the value of $cif2cif_INPUT_CIF, and likewise the output file, $cif2cif_OUTPUT_CIF, dictionary file, $cif2cif_CHECK_DICTIONARY, and request file, $cif2cif_REQUEST_LIST, may be specified.