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 contain 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-fragment-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/