FMCS(1) 							   User Commands							   FMCS(1)

NAME

       fmcs - fmcs

DESCRIPTION

       usage: fmcs [-h] [--maximize {atoms,bonds}] [--min-num-atoms INT]

	      [--compare  {topology,elements,types}]  [--atom-compare  {any,elements,isotopes}] [--bond-compare {any,bondtypes}] [--atom-class-tag
	      TAG] [--ring-matches-ring-only] [--complete-rings-only] [--select SELECT] [--timeout SECONDS] [--output  FILENAME]  [--output-format
	      {smarts,fragment-smiles,fragment-sdf,complete-sdf}]    [--output-all]    [--save-atom-class-tag	 TAG]	 [--save-counts-tag   TAG]
	      [--save-atom-indices-tag TAG] [--save-smarts-tag TAG] [--save-smiles-tag TAG] [--times] [-v] [--version] filename

       Find the maximum common substructure of a set of structures

   positional arguments:
       filename
	      SDF or SMILES file

   optional arguments:
       -h, --help
	      show this help message and exit

       --maximize {atoms,bonds}
	      Maximize the number of 'atoms' or 'bonds' in the MCS.  (Default: bonds)

       --min-num-atoms INT
	      Minimimum number of atoms in the MCS (Default: 2)

       --compare {topology,elements,types}
	      Use 'topology' as a shorthand for '--atom-compare any --bond-compare any', 'elements'  is  '--atom-compare  elements  --bond-compare
	      any', and 'types' is '--atomcompare elements --bond-compare bondtypes' (Default: types)

       --atom-compare {any,elements,isotopes}
	      Specify  the atom comparison method. With 'any', every atom matches every other atom. With 'elements', atoms match only if they con-
	      tain the same element. With 'isotopes', atoms match only if they have the same isotope number; element  information  is  ignored	so
	      [5C] and [5P] are identical. This can be used to implement user-defined atom typing. (Default: elements)

       --bond-compare {any,bondtypes}
	      Specify  the  bond  comparison method. With 'any', every bond matches every other bond. With 'bondtypes', bonds are the same only if
	      their bond types are the same.  (Default: bondtypes)

       --atom-class-tag TAG
	      Use atom class assignments from the field 'TAG'. The tag data must contain a space separated list of integers in the range  1-10000,
	      one  for	each  atom.  Atoms are identical if and only if their corresponding atom classes are the same. Note that '003' and '3' are
	      treated as identical values. (Not used by default)

       --ring-matches-ring-only
	      Modify the bond comparison so that ring bonds only match ring bonds and chain bonds only match chain bonds. (Ring  atoms	can  still
	      match non-ring atoms.)

       --complete-rings-only
	      If a bond is a ring bond in the input structures and a bond is in the MCS then the bond must also be in a ring in the MCS. Selecting
	      this option also enables --ring-matches-ring-only.

       --select SELECT
	      Select a subset of the input records to process.	Example: 1-10,13,20,50- (Default: '1-', which selects all structures)

       --timeout SECONDS
	      Report the best solution after running for at most 'timeout' seconds. Use 'none' for no timeout.	(Default: none)

       --output FILENAME, -o FILENAME
	      Write the results to FILENAME (Default: use stdout)

       --output-format {smarts,fragment-smiles,fragment-sdf,complete-sdf}
	      'smarts' writes the SMARTS pattern including the atom and bond criteria. 'fragment-smiles' writes a matching fragment  as  a  SMILES
	      string.  'fragment-sdf'  writes a matching fragment as a SD file; see --save-atom-class for details on how atom class information is
	      saved.  'complete-sdf' writes the entire SD file with  the  fragment  information  stored  in  the  tag  specified  by  --save-frag-
	      ment-indices-tag. (Default: smarts)

       --output-all
	      By  default  the	structure output formats only show an MCS for the first input structure. If this option is enabled then an MCS for
	      all of the structures are shown.

       --save-atom-class-tag TAG
	      If atom classes are specified (via --class-tag) and the output format is 'fragment-sdf' then save the substructure atom  classes	to
	      the tag TAG, in fragment atom order. By default this is the value of --atomclass-tag.

       --save-counts-tag TAG
	      Save the fragment count, atom count, and bond count to the specified SD tag as space separated integers, like '1 9 8'. (The fragment
	      count will not be larger than 1 until fmcs supports disconnected MCSes.)

       --save-atom-indices-tag TAG
	      If atom classes are specified and the output format is 'complete-sdf' then save the MCS fragment atom indices to the tag TAG, in MCS
	      order. (Default: mcs-atomindices)

       --save-smarts-tag TAG
	      Save the MCS SMARTS to the specified SD tag. Uses '-' if there is no MCS

       --save-smiles-tag TAG
	      Save the fragment SMILES to the specified SD tag. Uses '-' if there is no MCS

       --times
	      Print timing information to stderr

       -v, --verbose
	      Print progress statistics to stderr. Use twice for higher verbosity.

       --version

       For more details on these options, see https://bitbucket.org/dalke/fmcs/

fmcs 1.0							     June 2012								   FMCS(1)