NAME¶

cif_mark_disorder - mark disorder in CIF files judging by distance and occupancy.

SYNOPSIS¶

cif_mark_disorder --options input1.cif input*.cif

DESCRIPTION¶

Mark disorder in CIF files judging by distance and occupancy.

OPTIONS¶

-d, --distance-sensitivity 0.000001
Specify maximum distance between two atoms that should
be perceived as belonging to the same atom site.
Default: 0.000001.

--occupancy-sensitivity 0.01
Set maximum deviation for the sum of occupancies of
the atoms from the same atom site from 1.
Default: 0.01.

-h, --add-cif-header
Comments from the beginning of this file will be
prepended to the output.

--exclude-zero-occupancies
Ignore atoms with an occupancy of 0 in the calculations.
Default.

--no-exclude-zero-occupancies,

--dont-exclude-zero-occupancies
Use atoms with an occupancy of 0 in the calculations.

--ignore-occupancies
Do not require occupancies of atoms in the same
atom site to sum up to 1.

--no-ignore-occupancies,

--dont-ignore-occupancies
Require occupancies of atoms in the same atom site
to sum up to 1 to be recognised as a disordered site.
Default.

--reconstruct-symmetry
Reconstruct crystal symmetry before searching for
possible unmarked disorder.

--no-reconstruct-symmetry,

--dont-reconstruct-symmetry
Do not reconstruct symmetry, act on asymmetric unit
cell only. Default.

--output-dot-assemblies
Use dot ('.') assembly names. With this option on,
already existing dot assemblies in the input CIF
will be preserved. If no assemblies have existed in
the input file, but the script found a single new
assembly, it will be named '.'.

--no-output-dot-assemblies,

--dont-output-dot-assemblies
Rename dot ('.') assemblies in the input and do not
name new assemblies '.'. Default.

--report-marked-disorders
Print each of the marked disorder assemblies to
stderr, listing atom labels. Default.

--no-report-marked-disorders,

--dont-report-marked-disorders
Do not print marked disorder assemblies to stderr.

--add-depositor-comments
Append reports about newly marked disorder assemblies
together with the signature of this script to the
'_cod_depositor_comments' value. Default.

--no-add-depositor-comments,

--dont-add-depositor-comments
Do not append anything to the value of
'_cod_depositor_comments'.

--brick-size 1
Brick size parameter for the 'AtomBricks' algorithm.

--uniquify-atoms
Makes unique the labels of atoms.

--no-uniquify-atoms, --dont-uniquify-atoms
Do not makes unique labels for atoms,
exclude duplicates. Default.

--continue-on-errors
Do not terminate script if errors are raised.

--die-on-errors
Terminate script immediately if errors are raised.
Default.

--continue-on-warnings
Do not terminate script if warnings are raised. Default.

--die-on-warnings
Terminate script immediately if warnings are raised.

--continue-on-notes
Do not terminate script if notes are raised. Default.

--die-on-notes
Terminate script immediately if notes are raised.

--use-perl-parser
Use Perl parser for CIF parsing.

--use-c-parser
Use Perl & C parser for CIF parsing. Default.

--help, --usage
Output a short usage message (this message) and exit.

--version
Output version information and exit.

REPORTING BUGS¶

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