| CIF_DISTANCES(1) | General Commands Manual | CIF_DISTANCES(1) |
cif_distances - calculate minimal distance between atoms read from a CIF file.
cif_distances --options input1.cif input*.cif
Calculate minimal distance between atoms read from a CIF file.
-P, --pairwise-distance
Set pairwise distance output format (default).
-M, --distance-matrix
Set distance matrix output format.
--format "%8.6f"
Use the specified format for distance matrix
and pairwise printout format (default: "%-11.3f"
for matrix, "%-6.3f" for pairwise).
-l, --matrix-line-length "80"
Maximum length of an output line in distance
matrix format (default: 80).
-F, --add-filename
Add a filename field at the end of pairwise
distance format lines.
--no-add-filename, --do-not-add-filename
Do not add a filename field at the end of
pairwise distance format lines (default).
--process-disordered-structures,
--include-disordered-structures
Force processing of disordered structures (default).
--no-process-disordered-structures,
--exclude-disordered-structures,
--skip-disordered-structures
Skip disordered structures.
--process-duplicate-structures,
--include-duplicate-structures,
Force processing of structures, that are flagged
as duplicates with '_cod_duplicate_entry' or
'_[local]_cod_duplicate_entry' tags.
--no-process-duplicate-structures,
--exclude-duplicate-structures,
--skip-duplicate-structures
Skip duplicate structures (default).
--include-null-distances
Include entries of null distance relationship between
atoms from different disorder groups of the same
disorder assembly in pairwise distances output format.
--no-null-distances, --exclude-null-distances
Exclude entries of null distance relationship between
atoms from different disorder groups of the same
disorder assembly in pairwise distances output format
(default).
--include-self-distances
Include entries of distances between symmetry-related
instances of the same atom (default).
--no-self-distances, --exclude-self-distances
Exclude entries of distances between symmetry-related
instances of the same atom.
-U, --include-unknown-types
Include entries containing atoms of undetermined
chemical type. Atom type will be marked as 'UN'.
--no-unknown-types, --exclude-unknown-types
Exclude entries containing atoms of undetermined
chemical type (default).
--uniquify-atoms
Make atom labels unique (default).
--no-uniquify-atoms
Do not make atom labels unique.
--use-perl-parser
Use Perl parser to parse CIF files.
--use-c-parser
Use C parser to parse CIF files (default).
--help, --usage
Output a short usage message (this message) and exit.
--version
Output version information and exit.
Report cif_distances bugs using e-mail: cod-bugs@ibt.lt