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 "Edit/Clean" 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:

  O0 No optimization
  O1 Optimize if needed (default)
  O2 Always optimize

  Note: null always specifies the default value.

• Extra:

  e Verbose either flag removal
  

  If it is not possible to decide whether
  the double bond is CIS or TRANS, the double
  bond either flag is removed

  d show debugging info

  tX set optimization time limit to X ms
  

  maximum time spent in the optimization
  default value: 5000ms
  if X<1, no time limit used

  iX set iteration limit to X step
  

  maximum iteration step in the optimization algorithm
  default value: 100

  rX set ring step limit to X step
  

  maximum number of steps when drawing a ring
  avoiding bond cross
  default value: no limit

  cX set branch step limit to X
  

  step limit for the recursively drawing
  a branch of a molecule avoiding bond cross
  default value: no limit

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".