Multi-step reaction SMILES?

[schymane]

Not sure if this is feasible ... but wanted to ask ;-)

The reaction SMILES functionality is awesome ... any chance we can deal with more steps?
The top three of these work ... the bottom one is invalid ... but would represent the flow of the top three.
Top two: individual steps. Third: a "two step" reaction that works ... Fourth: nice to have but invalid.
If it's already possible and I just got the syntax wrong, I'm all ears!

C(=O)(C(C(C(C(C(C(F)(F)F)(F)F)(F)F)(F)F)(F)F)(F)F)O>[CF2 loss]>C(=O)(C(C(C(C(C(F)(F)F)(F)F)(F)F)(F)F)(F)F)O PFHpA to PFHxA
C(=O)(C(C(C(C(C(F)(F)F)(F)F)(F)F)(F)F)(F)F)O>[CF2 loss]>C(=O)(C(C(C(C(F)(F)F)(F)F)(F)F)(F)F)O PFHxA to PFPeA
C(=O)(C(C(C(C(C(C(F)(F)F)(F)F)(F)F)(F)F)(F)F)(F)F)O>[CF2 loss (x2)]>C(=O)(C(C(C(C(F)(F)F)(F)F)(F)F)(F)F)O PFHpA to PFPeA
C(=O)(C(C(C(C(C(C(F)(F)F)(F)F)(F)F)(F)F)(F)F)(F)F)O>[CF2 loss]>C(=O)(C(C(C(C(C(F)(F)F)(F)F)(F)F)(F)F)(F)F)O>[CF2 loss]>C(=O)(C(C(C(C(F)(F)F)(F)F)(F)F)(F)F)O PFHpA to PFHxA to PFPeA

[johnmay]

Would be nice but a bespoke format/extension which I'm not really a fan off. Fundamentally CDK data structures make this tricky (more structures needed) and it would be always be limited by the URL length....

Maybe one day but beyond something quick and dirty fix it's challenging

[schymane]

Thanks! Hmm yes I suspected it may involve something beyond a quick fix ...

[johnmay]

Check it out :-)

[schymane]

This looks awesome! It hasn't filtered through yet to CDK Depict tho, right?
(I still get invalid SMILES if I try either my example above or your examples in cdk/cdk#986)

We're using CDK Depict to curate Emma P's ShinyTPs work and multistep reactions are in our future perspectives for sure, this is very cool to see!

[johnmay]

No I submitted the PR yesterday, which examples don't work.

This examples works fine on the branch:

C(=O)(C(C(C(C(C(C(F)(F)F)(F)F)(F)F)(F)F)(F)F)(F)F)O>[CF2 loss]>C(=O)(C(C(C(C(C(F)(F)F)(F)F)(F)F)(F)F)(F)F)O>[CF2 loss]>C(=O)(C(C(C(C(F)(F)F)(F)F)(F)F)(F)F)O PFHpA to PFHxA to PFPeA

The "CF2 Loss" is probably better as a title/condition. Space is not normally allowed in atom symbols :-).

for (IReaction reaction : reactionSet.reactions()) {
    reaction.setProperty(CDKConstants.REACTION_CONDITIONS, "CF2 Loss");
}

[johnmay]

Ignore the I-1, I-2, I-3 I was just playing around with compound naming.

[schymane]

I just tried it directly on the website copy pasting the SMILES from your issues cos I was curious...

[johnmay]

Yes as I said, it's not merged into CDK yet so won't be on the production website for sometime. Was just letting you know this was in the works.

[schymane]

Was very happy to see that it's in the works! ;-)