NAME¶

cif_molecule - restore molecules from a CIF file.

SYNOPSIS¶

cif_molecule --options input1.cif input*.cif

DESCRIPTION¶

Restore molecules from a CIF file.

OPTIONS¶

--use-optimised-spacegroup-builder
Use the space group builder algorithm optimised
for speed as implemented in the
COD::Spacegroups::Builder module (default).

--use-simple-spacegroup-builder
Use the simpler and slower space group builder
algorithm as implemented in the
COD::Spacegroups::SimpleBuilder module.

-1, --one-datablock-output
Output all moieties to a single output data block.

However, if the --split-disorder-groups option is
enabled all generated alternative conformations will
be put into separate data blocks starting with the
most likely one (disorder group occupancy wise) and
ending with the least likely one. In order to retrieve
only the most likely one, the --largest-molecule-only
option should be used in combination with the
--one-datablock-output option.

-1-, --multiple-datablocks-output
Separate each molecule and each example of an alternative
conformation into a separate data block (default).

-c, --covalent-sensitivity
Set a new covalent sensitivity value (default: 0.35).

-g, --geom-bond-output
Output _geom_bond_... data items (bond lengths,
valencies, etc.).

-g-, --no-geom-bond-output
Do not output _geom_bond_... information (default).

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

-i, --ignore-bumps
Detect and warn about close atom "bumps" but do not
stop processing.

--dont-ignore-bumps, --no-ignore-bumps
Stop processing immediately if bumps are
detected (default).

-s, --sort-molecules
Sort molecules in descending order by their atom count
and overall occupancy before outputting them. Atom count
takes precedence over overall occupancy (default).

--dont-sort-molecules, --no-sort-molecules
Do not sort molecules, print them out in the order they
are detected.

--expand-to-P1, --P1-expand, --p1-expand
Expand all atoms to the P1 unit cell, so that the
translation operators can be used to restore the whole
crystal.

--dont-expand-to-P1, --no-expand-to-P1

--dont-P1-expand, --no-p1-expand
Do not expand to P1, output only the minimal molecule
list (default).

--uniquify-atoms
Makes unique the labels of atoms (default).

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

--use-morgan-fingerprints
Use Morgan fingerprints to identify and skip
duplicated moieties.

--no-use-morgan-fingerprints, --dont-use-morgan-fingerprints
Use atom labels to identify and skip duplicated
moieties. This method is default, however under
certain circumstances it leaves duplicate moieties,
as asymmetric unit can initially contain more than
one copy of a single moiety (default).

--use-atom-classes
Use COD atom classes, generated by AtomClassifier
module from 'atomclasses' repository, for the
generation of Morgan fingerprints. Requires the
external AtomClassifier module (default).

--no-use-atom-classes, --dont-use-atom-classes
Use atom chemical types for generation of Morgan
fingerprints instead of COD atom classes.

--bump-distance-factor 0.75
A fraction of covalent bond radii sum used to
determine when atoms are too close and are
considered a bump (default: 0.75).

--vdw-distance-factor 1.2
A factor for the vdW radii sum used to
determine when atoms are too close and are
considered a vdW clash (default: 1.2).

--continue-on-errors
Do not stop if errors such as unrecognised atoms are
encountered; the output may be incorrect and missing
some atoms if this option is used!

--dont-continue-on-errors, --no-continue-on-errors
Stop immediately when an error is encountered.

--exclude-zero-occupancies
Do not use atoms with 0 occupancies in calculations
(default).

--dont-exclude-zero-occupancies, --no-exclude-zero-occupancies
Use atoms with 0 occupancies in calculations.

--exclude-dummy-atoms
Do not use dummy atoms (marked by the 'dum' calc flag)
in calculations (default).

--dont-exclude-dummy-atoms, --no-exclude-dummy-atoms
Use dummy atoms (marked by the 'dum' calc flag)
in calculations. Dummy atoms can be used to mark
interesting positions within the unit cell
(e.g. geometric centers of coordinated atom rings),
but they are not considered as part of the molecule.
As a result, the occupancies of all output dummy atoms
are set to '.'. It should also be noted that dummy atoms
with non-numeric coordinates will still be excluded.

--preserve-stoichiometry
Apply necessary symmetry operators to preserve molecular
stoichiometry (charges, etc.).

--dont-preserve-stoichiometry, --no-preserve-stoichiometry
Do not apply any more symmetry operators than needed to
reconstruct covalently connected networks; may
break stoichiometry of salts and complexes (default).

--force-unit-occupancies
Set occupancies of all output atoms to 1.0. Unit
occupancies are only set when outputting the atoms
and do not affect the flow of the algorithm
(disorder group processing, molecule sorting, etc.).
Dummy atoms are excluded from the effects of this option
and are always output with the '.' occupancy.

Some programs, notably Jumbo converter's cif2cml,
assume unresolved disorder and do not recognize
aromatic rings if occupancies are not unities.
Obviously, this flag has only sense in combination
with --split-disorder-groups.

--dont-force-unit-occupancies, --do-not-force-unit-occupancies,

--no-force-unit-occupancies
Leave occupancies as they are (default).

--dump-atoms
Dump atoms (including symmetry-equivalent) in CIF
format for inspection with some graphics program.

--dont-dump-atoms, --no-dump-atoms
Do not dump atoms (default).

--max-polymer-span 4
A span, in +/- unit cells, in which polymeric
molecules (repeating units) will be constructed.

--max-polymer-atoms 100
A maximum allowed count of polymer example atoms:
more than this amount of symmetry (translational)
equivalent atoms, for each atom of the asymmetric
unit, will not be written to the output:

Using --max-polymer-span=0 --max-polymer-atoms=1
essentially switches off the polymer detection.

--split-disorder-groups, --dont-merge-disorder-groups
Put examples of disorder group conformations into
separate data blocks (default).

--merge-disorder-groups, --dont-split-disorder-groups
Put all disorder groups into one data block.

--use-special-disorder-symmetry
Generate symmetry equivalents for disorder groups
with negative indices (default).

--random-seed 123456
Use the provided seed to initialise the random
number generator. Use "" (empty string) as a seed
to revert back to the default seed.

--special-disorder-operator-set 0

--special-disorder-operator-set random
Indicates which operator set to apply to atom groups
that are disordered around a special position. Can be
an integer (0, 1, 2, ...) or as special value "random",
in which case a random operator is selected for each
special position image.

--no-use-special-disorder-symmetry,

--dont-use-special-disorder-symmetry,

--do-not-use-special-disorder-symmetry,
Do not generate symmetry equivalents for disorder
groups with negative indices.

--largest, --largest-molecule-only
Output only the largest molecule. The largest molecule
is selected based on two criteria in the given order:
atom count and overall occupancy of the molecule.
When the combination of the --one-datablock-output and
--split-disorder-groups options is in effect the
molecule with the most likely disorder conformation
(occupancy wise) is returned.

NOTE: if there is more than one disorder assembly
and the --split-disorder-groups option is in effect,
the conformation with the highest atom count might not
be generated at all. In this case, a molecule that best
fits the previously defined criteria out of the generated
conformation subset will be returned.

--all, --all-molecules
Output all molecules (default).

--use-perl-parser

--use-c-parser
Specify parser to parse CIF files. C parser is default.

--symdebug
Print debug output for symmetry reconstruction.

--no-symdebug
Do not print any symmetry debug output (default).

--debug
Print some human-readable debug output.

--no-debug
Suppress any debug output (default).

--format "%8.6f"
Use the specified format for output coordinate printout.

--audit
Print audit information to the generated CIF file (default).

--no-audit
Do not print audit information to the generated CIF file.

--verbose
Print warning messages in long format.

--no-verbose
Print warning messages in concise format (default).

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

--version
Output version information and exit.

REPORTING BUGS¶

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