Straight alkyl or alkenyl chains with template based clean

Hi,

I try to straighten alkyl and alkenyl chains with template based cleaning, however I never seem to get the results I expect. The Standardizer help file says "template atom coordinates are copied to the corresponding target atoms and the remaining atoms are cleaned with partial clean. " So is there a way to turn of the partial clean, but just do template clean. For example in my case I want all the alkyl chains straight, pointed to the left, Marvin prefers to maximize the structural space and all three alkyl chains are pointed in maximum direction from each other. The alkyl chains can have a length from 2-30 carbon atoms, of course with double bonds and of  all possible length combinations.

 

My templates below seem to work to a certain chain length but then its wildly all over the place. I could imagine to do a step wise cleaning or multiple step cleaning process. TO avoid that I shortened and lengthened the alkyl chains (with generic "A" query atoms and bonds "any" but to no effect. I tried many possible length combinations for all three side chains.

<?xml version="1.0" encoding="UTF-8"?>



<StandardizerConfiguration>

    <Actions>

	<Aromatize ID="aromatize"/>

	<Clean ID="tbclean" Type="TemplateBased" TemplateFile="TAG-example-clean-p.sdf"/>

    </Actions>

</StandardizerConfiguration>

standardize -c tagtbclean.xml tag-example-smiles.smi -f sdf -o TAG-EXAMPLE-CLEANED-SDF.sdf

Thanks

Tobias

No, partial clean cannot be turned off in template based clean.

It seems you rather require a clean which generates more compact structures and leaves the alkil chains straight. We will consider this feature request.

Thanks.

Tobias