Synthesis R Group Molecule

I have a molecule with R1 and R2 in it, like to synthesis new molecules from a R group decomposition ligand table. Essentially I know what the real functional groups R1 and R2 represent. How to do that with JChem API? Please provide java code. Thanks!

Dear Hong,

the topic was moved to the "Storage & search: Markush search & enumeration" forum, my colleagues will answer you soon.

Best regards,

Zsuzsa

Dear Hong,

I am a little confused. Let me clarify it: you want to enumerate (have returned) all the possible explicit structures that are produced by substituting the R1, R2 groups with their definitions in all possible combination. Is that right?

Thank you,

Norbert.

Actually, I just need the code for substituting R1 with one ligand molecule and R2 with another ligand molecule. The ligand molecules are obtained from a R-group decomposition, which has attachment points on them already. No need to go through all the combinations.

Dear Hong,

 

Sorry for the delay, but it takes some time, to get a developer to provide you the appropriate code fragment. So I am still asking for some patience.

Thank you,

Norbert

Dear Hong,

You can find the code in the attached file.

Best regards,
Tamás

Dear Tamas,

     Thank you for the code, I will give it a try in the next few days and let you know how it works. Looking at the code, I couldn't have figured it out by myself. I am wondering if you could put in next version an API for substituting molAtom for molecule.

    Best Regards,

-Hong

The code works for single R replacement, Thanks! However, I do have some molecule that had R1, R2 and R3 in it, and R2 and R3 are attached to a half ring molecule. In other word, the same ligand is attached to two R attachment points. How do you handle that situation?

I close this topic with respect to the e-mail conversation with Mr. Guo.

this is good .

Hi Luigi,

 

Thanks for the compliment! Does this mean that the code works for you?

 

Best regards,

Norbert