Call rdkit from Ruby

Recently I use web app made with ruby.
The app is very useful for me, but there is not chemoinformatics library in ruby.
So, I want to find way to use rdkit from ruby.
I found some web page that described how to run shell script from ruby. The simplest way is using back quotation.
It is means call “python xxx.py” from ruby.
I tested it.
At first, I wrote sample script named test.py. Just load SDF and print molecules as smiles.

 from rdkit import Chem
 sdf = Chem.SDMolSupplier( 'cdk2.sdf' )
  
 for mol in sdf:
     smi = Chem.MolToSmiles( mol )
     print( smi )
                               

Then, I wrote ruby script.
It just call test.py. That’s all. ;-)

callpy.rb

         
res = `python test.py`
  print res

Run callpy.rb.

         
iwatobipen$ ruby callpy.rb 
...........
Cn1cnc2c(NCc3ccccc3)nc(NCCO)nc21
CCC(CO)Nc1nc(NCc2ccccc2)c2ncn(C(C)C)c2n1
COc1ccc(CNc2nc(N(CCO)CCO)nc3c2ncn3C(C)C)cc1
Nc1nc(N)c(N=O)c(OCC2CCCCC2)n1
COc1ccc2c(c1)C(=Cc1cnc[nH]1)C(=O)N2
COc1cc[nH]c1C=C1C(=O)Nc2ccc([N+](=O)[O-])cc21
CCc1cnc(CSc2cnc(NC(=O)C(C)C)s2)o1
CCCCOc1c(C(=O)c2nccs2)cnc2[nH]ncc12
COc1cc(-c2ccc[nH]2)c2c3c(ccc(F)c13)NC2=O
[NH3+]CCSc1cc(-c2ccc[nH]2)c2c3c(ccc(F)c13)NC2=O
NC(=O)Nc1cccc2c1C(=O)c1c-2n[nH]c1-c1cccs1
COc1ccc2c(c1)C(=Cc1[nH]cc3c1CCOC3=O)C(=O)N2
CNS(=O)(=O)c1ccc2c(c1)C(=Cc1[nH]cc3c1CCNC3=O)C(=O)N2
CC(=O)Nc1cccc2c1C(=O)c1c-2n[nH]c1-c1ccncc1
....

It worked. ;-)

There are some ways to call shell script from ruby. I will try another method soon.

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