Software for compound database creation\enumeration

Question

The only program I have found is Plexus Suite from chemaxon. (I asked for trial, but no answer to me yet).

The task is: create variation of compounds, where is scaffold and different substituents:

And I need to create dataset/database of all possible variations.

How to deal with this problem? Or I need to use some scripting to make the database?

UPD1: best option - creation of SMILES (Simplified molecular-input line-entry system), 3d structure is automated and easy step if there is correct SMILES/connectivity of molecule (which is the same, as smiles) Using XYZ - it means, you should make substituent database in correct position for adding. I am asking for software with functionality

https://www.youtube.com/watch?v=s4CgtUgGuzk

Vega ZZ has the module for database enumeration, but it is working as Python script.

Answer 1

This is typically called library (or scaffold) enumeration. Doing it in SMILES is usually pretty easy by script, but there are a few other options:

• KNIME
• SMILIB

But it's very easy to write a script like this, e.g. (in python)

r1 = [ "", "C", "N" ]
r2 = [ "H", "C", "c3ccccc3", "C(=O)O" ]
r3 = [ "", "C", "C#N", "O" ]
scaffold = "Xc(cc1c2)ccc1c(Y)cc2-C(C=C1)C=C1Z"


for x in r1:
    for y in r2:
        for z in r3:
            print scaffold.replace('X', x).replace('Y', y).replace('Z', z)

You can then process the resulting SMILES strings with your program of choice (e.g., Open Babel).

Answer 2

There are no doubt many software tools out there to do this kind of scaffold enumeration, however the problem is surely simple enough to do by scripting - or even by hand!

eg:

• Compound 1 = {R1=H, R2=H, R3=H}
• Compound 2 = {R1=H, R2=H, R3=Me}
• Compound 3 = {R1=H, R2=H, R3=CN}
• ...
• Compound N = {R1=NH2, R2=Ac, R3=OH}

So just the cartesian-product : R1 x R2 x R3 except with unordered output ... not sure what this is called. There is this math stackexchange question about this.

Oh, and this stackoverflow python code to do this.