How to contract group when standardize the Structures?

Hi, when i want to standardize the Structures,the structure as the picture stocks.png,i want to get the result as the picture stocks1.png,how can i do it?Thanks!

Hi,

1./ If the nitro group in stocks.png structure is an expanded abbreviated group (sgroup), then use "Aromatize" and "Contract Group" actions.

2./ If the nitro in stocks.png structure is not an expanded abbreviated group, then perform the following actions:

 - Aromatize
 - Transform: convert nitro to NO2 pseudo atom
 - Alias to Group

We don't yet have a standardizer action which finds and converts a group of atoms to an abbreviated group (we are working on this), so a trick is needed. First the nitro has to be converted to an "NO2" pseudo atom, and then "Alias to Group" action should be used to convert the  "NO2" pseudo atom to abbreviated nitro group.

Example:

standardize -c standardizer_group_nitro_config.xml in.sdf -f sdf -o out.sdf

I attached the Standardizer config file.

Zsolt

Thank you for help. I can contract some usual abbreviated group now

But I wonder if the standardizer do automatically upgroup to all the structures. There are only "contract group", "Alias to group" and "clean2D" in my config file. But all the abbreviated group in original file were upgroup, please see the attached file. Could you tell me how to avoid this status? some big structures are unfit to ungroup.

Another question: I wanted to correct the wrong wedge bond by standardizer(please see the last three structures in the "original" file), but failed. Could you tell us how to set the config file?

Thanks

cd2002 wrote:

But I wonder if the standardizer do automatically upgroup to all the structures. There are only "contract group", "Alias to group" and "clean2D" in my config file. But all the abbreviated group in original file were upgroup, please see the attached file. Could you tell me how to avoid this status? some big structures are unfit to ungroup. Another question: I wanted to correct the wrong wedge bond by standardizer(please see the last three structures in the "original" file), but failed. Could you tell us how to set the config file?

The "Contract Group" action should be the last in the Standardzier config. Please attach your Standardzier config file, so we could check it.

What action did you use to correct the wedge bonds?

Zsolt

Hi,Zsolt,

I attached the config.file, please check it.

Appreciate your help。

cd2002 wrote:

But I wonder if the standardizer do automatically upgroup to all the structures. There are only "contract group", "Alias to group" and "clean2D" in my config file. But all the abbreviated group in original file were upgroup, please see the attached file. Could you tell me how to avoid this status? some big structures are unfit to ungroup.

It's a bug: "Remove Explicit Hydrogens" action ungroups the abbreviated groups. Until we fix it the "Remove Explicit Hydrogens" action should be removed from the configuration to avoid ungrouping of abbrev. groups.

cd2002 wrote:

Another question: I wanted to correct the wrong wedge bond by standardizer(please see the last three structures in the "original" file), but failed. Could you tell us how to set the config file?

15th structure: with the modified config file (attached) the wedge is placed between the chiral carbon atom and the nitrogen

16th and 17th structures: we will check  why the wedges are removed, and get back to you soon

In the attached config file I removed the "Remove Explicit Hydrogens" action, and moved the two "Clean2D" actions to the end.

$ standardize -c config_mod.xml original.sdf -f sdf -o standardized.sdf

Warning: Partial parity information is applied.

Zsolt