table of contents
| cif_distances() | cif_distances() |
NAME¶
cif_distances - Calculates minimal distance between atoms read from a CIF file.SYNOPSIS¶
cif_distances --options input1.cif input*.cifDESCRIPTION¶
Calculates minimal distance between atoms read from a CIF file.OPTIONS¶
-M, --distance-matrix Set distance matrix output format.-P, --pairwise-distance Set pairwise distance output format (default).
-l, --matrix-line-length "80" Maximum length of an output line in distance matrix format (default 80).
--format "%8.6f" Use the specified format for distance matrix and pairwise printout format (default "%-11.3f" for matrix, "%-6.3f" for pairwise).
-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 Makes unique the labels of atoms (default).
--no-uniquify-atoms Does not make unique labels for atoms.
--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.