There is a new KNIME forum. You can still browse and read content from our old forum but if you want to create new posts or join ongoing discussions, please visit our new KNIME forum: https://forum.knime.com

Chirality flags

Member for

7 years lcollia

Hi,

 

I have some trouble with chirality flags and the indigo nodes.

In a SDF there are 3 locations to say that the molecule has chirality: in the count line (just to say the molecule is chiral), in the atom block (to say this atom is chiral with this chirality [1=odd, 2=even, 3=either]), and in the bond block (to say in 2D the bond is up or down).

With the following protocol: SDF reader -> MoltoIndigo -> IndigoToMol -> SDFwiter; when I read a SDF with a chiral molecule the chiral flag on the chiral atom (1, 2 or 3) is changed to 0.

Is it possible to conserve this flag inchanged?

 

thanks for all and for your work with Indigo,

 

Lionel

Comments
Tue, 11/29/2011 - 11:48

Member for

7 years 4 months

mikhail.rybalkin

Hello Lionel,

Could you attach your molecule?

Best regards,
Mikhail

Tue, 11/29/2011 - 12:16

Member for

7 years

lcollia

Hi,

Thanks for your rapid response. Here one exemple of molecule:

chiral.sdf: the molecule has chiral flag;

notchiral.sdf: the same molecule without chiral flag.

 

Thanks for your help,

 

Lionel

Files
Wed, 11/30/2011 - 09:17

Member for

7 years 4 months

mikhail.rybalkin

Hi Lionel,

The next version of Indigo nodes will be saving chirality flag for atoms too. It will be released soon, after being tested.

Thank you for your suggestions!

Best regards,
Mikhail

Wed, 11/30/2011 - 02:01

Member for

7 years

lcollia

Hi Mikhail,

 

Thanks for your help!

 

Best regards,

Lionel

Fri, 01/20/2012 - 08:40

Member for

7 years 4 months

mikhail.rybalkin

Hi Lionel,

An updated Indigo nodes version from the nightly builds is saving this flag correctly. Thank you for your comment again!

Best regards,
Mikhail

Tue, 01/31/2012 - 01:28

Member for

7 years

lcollia

Many thanks!