NAME¶

cif_distances - calculate minimal distance between atoms read from a CIF file.

SYNOPSIS¶

cif_distances --options input1.cif input*.cif

DESCRIPTION¶

Calculate minimal distance between atoms read from a CIF file.

OPTIONS¶

-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.

REPORTING BUGS¶

Report cif_distances bugs using e-mail: cod-bugs@ibt.lt