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One can use cleaning options in various cases, for example:

  • Command line parameter in the MolConverter application
  • Parameter for Cleaner.clean(MoleculeGraph, int, String)
  • Marvin Beans and Marvin Applets parameters:  clean2dOpts clean3dOpts.

2D options

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).


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


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

3D options

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

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

? Print the complete list of options to System.err. The same list can be printed by invoking the MolConverter with the -H3Doption. 

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".

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

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