Provided by: cod-tools_3.6.0+dfsg-1_amd64 bug


       cif_molecule - restore molecules from a CIF file.


       cif_molecule --options input1.cif input*.cif


       Restore molecules from a CIF file.


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

                         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

       --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).

                         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 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 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).

                         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.

                         Do not use atoms with 0 occupancies in calculations

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

                         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.

                         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).

                         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,

                         Leave occupancies as they are (default).

                         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 AU atom, 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.

                         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.



                         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).


                         Specify parser to parse CIF files. C parser is default.

                         Print debug output for symmetry reconstruction.

                         Do not print any symmetry debug output (default).

                         Print some human-readable debug output.

                         Suppress any debug output (default).

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

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

                         Do not print audit information to the generated CIF file.

                         Print warning messages in long format.

                         Print warning messages in concise format (default).

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

                         Output version information and exit.


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