Converting Wiggly (wavy) bonds to straight bonds

I am using the Standardizer to clean up some sets of structures and am having issues when trying to convert wiggly (wavy) bonds to straight bonds.

[1] In one set of compounds, I would like to convert all wiggly bonds to straight bonds.  While the Clear Stereo action can transform wiggly bonds and tetrahedral centers to straight bonds, there is no option to transform wiggly bonds at other (non-tetrahedral) atoms.   Is there a simple general solution to this problem?

[2] In a second set of compounds, I would like to convert the wiggly bonds to straight bonds only in specific instances.  I have attempted to write transforms to do this conversion without success.  I have tried with the match option set to check bond type, and this did no seem to help.  Should these transforms work, or is there something inherent in the tranform process that will prevent it from just converting a bond type? 

Here is a simple example:  Some of the input structures contain R-CH2-NH-Aryl, where the N-Aryl bond is a wiggly bond.  I would like to transform only those wiggly bonds to straight bonds, leaving all other wiggly bonds untouched.  Can this be done?  Any advice on how to accomplish this would be much appreciated.

tparrott wrote:

I am using the Standardizer to clean up some sets of structures and am having issues when trying to convert wiggly (wavy) bonds to straight bonds. [1] In one set of compounds, I would like to convert all wiggly bonds to straight bonds.  While the Clear Stereo action can transform wiggly bonds and tetrahedral centers to straight bonds, there is no option to transform wiggly bonds at other (non-tetrahedral) atoms.   Is there a simple general solution to this problem?

Cleaning cis-trans stereo generates wiggly bonds. Wiggly bond at the end of a double bond is a notation for double bond with unspecified cis-trans stereo. If you do not want wiggly bonds, then do not clean the double bond stereo info.

If you have already wiggly bond attached to a double bond, then you can use "Convert Double Bonds" action to convert them to crossed bonds. Converting wiggly bonds (attached to a double bond) to single bonds in a standardization process is not recommended, because it adds double bond stereo information to molecule (unspecified double bond becomes cis or trans).

tparrott wrote:

[2] In a second set of compounds, I would like to convert the wiggly bonds to straight bonds only in specific instances.  I have attempted to write transforms to do this conversion without success.  I have tried with the match option set to check bond type, and this did no seem to help.  Should these transforms work, or is there something inherent in the tranform process that will prevent it from just converting a bond type?  Here is a simple example:  Some of the input structures contain R-CH2-NH-Aryl, where the N-Aryl bond is a wiggly bond.  I would like to transform only those wiggly bonds to straight bonds, leaving all other wiggly bonds untouched.  Can this be done?  Any advice on how to accomplish this would be much appreciated.

Standardizer can change only the stereo configuration of a chiral center or double bond. Arranging the wedges (up, down, wiggly, etc.) is performed by 2D clean.

Please attach an example (input files, standardizer configuration XML, output file, expected output), so we can give more advice.

Regards,

Zsolt

We also have WedgeClean and ConvertWedgeInterpretation actions in Standardizer, maybe these can help. To be able to tell more we need specific examples.

Zsolt

In this example, I would like to convert all the wavy bonds in the molecule to straight bonds.  Is there a simple way to accomplish this?  For this data set, my goal is to have no wavy bonds and no crossed double bonds.

In another set of compounds, I like to standardize the structures in such a way to only allow some wiggly bonds, but not others.  Under these rules, wiggly bonds are not allowed to the nitrogens in azo compounds, but are otherwise tolerated.  Crossed double bonds are not allowed.  Clean 2D, WedgeClean, and ConvertWedgeInterpretation don't help.  How can I accomplish the desired tranformation?

I attached two standardizer config files.

1. removeWigglyConfig1.xml: it will remove all wiggly bonds from the molecule. It contains the following actions:

• 
  Clear Stereo with "Convert tetrahedral up or down bonds (wiggly) to single bonds" option


• Convert Double Bonds ("N=N" unspecified double bond should be converted to crossed representation)


• "N=N unspecified double bond stereo to trans" transform, Note: it adds stereo information to the molecule. An unspecified stereo double bond is transformed to trans.

 

2. removeWigglyConfig2.xml: it will remove the wiggly only from "N=N" unspecified double bond. The tetrahedral wiggly bonds will not be modified, so it's not exactly what you wanted. It does not contain the 1st action from removeWigglyConfig1.xml, the 2nd and 3rd actions are the same.

Zsolt