User login

Chirality flags

Tue, 11/29/2011 - 10:00 — 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

‹ Molecular Formula Search and Molecular Weight Search node Atom Replacer Feature Request ›
Tue, 11/29/2011 - 11:48 — mikhail.rybalkin

Hello Lionel, Could you

Hello Lionel,

Could you attach your molecule?

Best regards,
Mikhail

Tue, 11/29/2011 - 12:16 — lcollia

Hi, Thanks for your rapid

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

AttachmentSize
chiral-notchiral.zip 571 bytes
Wed, 11/30/2011 - 09:17 — mikhail.rybalkin

Hi Lionel, The next version

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 - 14:01 — lcollia

Hi Mikhail,   Thanks for

Hi Mikhail,

 

Thanks for your help!

 

Best regards,

Lionel

Fri, 01/20/2012 - 08:40 — mikhail.rybalkin

Hi Lionel, An updated Indigo

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 - 13:28 — lcollia

Many thanks!

Many thanks!