.TH CIF_MOLECULE 1 .SH NAME cif_molecule \- restore molecules from a CIF file. .SH SYNOPSIS cif_molecule \-\-options input1.cif input*.cif .SH DESCRIPTION Restore molecules from a CIF file. .SH 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 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. \-\-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. .SH "REPORTING BUGS" Report cif_molecule bugs using e\-mail: cod\-bugs@ibt.lt