Q: Easy way to remove valence inf (v4) (v5) from molecule?

Hi,

is there an easy way to remove the atom valence info (v4) (v5) from molecules in MVIEW?

Possibly a switch similar to implicit hydrogens?

The only way I know is to open the molecule in MSKETCH and remove the valence info.

Is there a way to do it in Standardizer (clear valence info) I could not find it.

Sometimes SDf files have those v infos attached but I want to get rid of them.

 

Thank you

Tobias

TobiasKind wrote:

Is there a way to do it in Standardizer (clear valence info) I could not find it.

Yes, Standardizer can do this. Transform actions should be defined to remove valence info; see the attached standardizer config file, it removes v4 and v5 valences from any atom.

This feature works with Standardizer 5.3.0.1 or newer.

Zsolt

Hi,

very interesting, so looking at the task I could write an A (any) atom in MSKECTH,

attach a valence info to it, draw an reaction arrow and another A atom (Any) and remove the valence info there, safe as a reaction and put into standardizer. Neat.

 

Thanks

Tobias

TobiasKind wrote:

very interesting, so looking at the task I could write an A (any) atom in MSKECTH, ...

Hi,

You can use Standardizer (GUI) application to define such  transform. It contains an msketch, and saves the transform to a Standardizer configuration file.

Zsolt