molecules 2D clean

Hi all,





I try to clean some molecules (aureus_origine.sdf) using the following code:

Code:

String molecule = ... ;//retrieve a molfile from String m = (new MolImporter(new MolInputStream(new ByteArrayInputStream(molecule.getBytes())))).read(); m.hydrogenize(false); m.aromatize(false); b = m.stereoClean(); m.clean(2,null); return m.toFormat("mol");

the cleaning seems to give a bad renderer in some other viewer.


Do I need to specify the options in MoleculeGraph.clean(int, String)?


What are the format of the String to define the cleaning options.





How could I clean to change the H atoms written like [H;v1] into H (cf http://www.chemaxon.hu/forum/ftopic511.html)?

Hi!





I don't think the Clean options will help you.


However the following basic cleaning options can be used:


O0 No optimization


O1 Optimize if needed (default)


O2 Always optimize


for more option see:


http://www.chemaxon.com/marvin/doc/user/cleanoptions.html





We try to develop the clean module, but it is likely that template based cleaning will solve complex molecules like the big ring at the second molecule in the sdf file. (We should correct the cleaning of the first molecule at the sdf.)





You can change the [H;v1] into H using standardizer:

Code:

bin/standardize -c "[H;v1]>>[H]" <aureus_origine.sdf >aureus_converted.sdf

It will give you warning but you can ignore it as you just want to interpret [H;v1] as Hydrogen atom.





All the best


Andras

Hi,


thank you for your fast reply.





So for example, if I want to use cleaning in API, I will paramatrate options like

Code:

molecule.clean(2,"O2:t10:i7:r2");

?


or the separator ":" is not needed?





Thank you again, and I apologize for those dumb questions.


Kind Regards


Jacques

Hi!





The ':' is not needed. Just write:

Code:

mol.clean(2,"O2t10i7r2");

all the best


Andras

thank you very much


best regards.