Cleaning Options in Marvin

Both 2D and 3D options can be divided into two groups: Base and Extra. Base contains the typically used options which are also accessible via "Structure/Clean 2D" or "Structure/Clean 3D" menu in Marvin. You can use them in each case. Extra includes further options which are accepted only by the MolConvert application and the clean method of MoleculeGraph in the Marvin Beans API.

2D options

• Base: (none available)
• Extra:

  e Keep verbose either flag
  

  If the 'e' parameter is given and it is not possible to decide whether the double bond is CIS or TRANS, the double bond either flag (crossed double bond) is kept.
  Otherwise, it the 'e' option is not given the double bond either flag is removed and converted to double bond with a wiggly bond.

  E Error output:

  0 - no output (default)
  1 - error output to standard error

  d show debugging info

  2 try to keep actual 2D alignment

  p ignore parity setting

  do not set wedges, the parity information is lost.

  H add Hydrogens

  Add Hydrogen atoms to chiral centers
  having no terminal atoms, and not being part of an Sgroup.

  w wedge clean

  Do not try to keep the actual wedge arrangement,
  but rearrange the wedges also.

  W stereo clean

  Only rearrange the wedges of the molecule, but keep the original coordinates untouched.

  s shorten explicit H bond lengths

  Use 1.0 Angstrom explicit Hydrogen bond length. All other bonds will remain 1.54 Angstrom long.

  tX set time limit to X ms

  maximum time spent in the cleaning
  default value: 20000ms
  if X<1, no time limit used

  T{filename} ring system template file name
  

  Use the template file during ring system cleaning together with the system template file definition (chemaxon/marvin/templates/bicycles.t, chemaxon/marvin/templates/crown_ethers.t, chemaxon/marvin/templates/heterocycles.t, chemaxon/marvin/templates/cleantemplate.cxsmi, chemaxon/marvin/templates/fullerenes.t, chemaxon/marvin/templates/bridged_polycycles.t, chemaxon/marvin/templates/cleancage.cxsmi) and the local template file definition (which is located at the users home directory .chemaxon/cleantemplates.t).

  Toff
  

  Turn off system template file definition usage during template based cleaning (only local template file definition is used).

  Tf
  

  Force template based cleaning during clean process. Try to use templates for ring system which contains only on ring.

3D options

• Base:

  S{fine} Find low energy conformer. Leave failed fragments intact.

  S{fast} Fast clean, if failed, perform fine clean, accept any generated structure (default)

  Notes: null always specifies the default value. O0 and OD are deprecated. They use the default value.

• Extra:

  ? Print the complete list of options to System.err. The same list can be printed by invoking the MolConverter with the -H3D option.
  

  S{nofaulty} Same as S{fast}, but leave failed fragments intact.

  S{conformers} Generate conformers, store the calculated conformer coordinates and energies in PropertyObjects.

  E Store calculated Dreiding energy in SDF property string. The Dreiding energy for each fragment will be calculated in the last step.  Their sum will be stored in the sdf property called "Energy".