Simple way for making SMILES file #RDKit

To convert SDF to SMILES I write like a following code.

..snip..
sdf = Chem.SDMolSupplier( 'some.sdf' )
with open('smiles.smi', 'w') as f:
    for mol in sdf:
        smi = Chem.MolToSmiles(mol)
        f.write("{}\n".format(smi)

In this way, to write smiles strings with properties it is needed to get properties by using GetProp(“some prop”). If I need several properties my code tend to be long.
Greg who is developer of RDKit advised me to use SmilesMolWriter. ;)

I have never used this function so I used it and found it was very useful.
Let me show the example. (copy & paste from Jupyter notebook)

import pprint
from rdkit import rdBase
from rdkit import Chem
from rdkit.Chem.rdmolfiles import SmilesWriter
print(rdBase.rdkitVersion)
[OUT]
2017.09.2

mols = [mol for mol in Chem.SDMolSupplier('cdk2.sdf') if mol != None]
# make writer object with a file name.
writer = SmilesWriter('cdk2smi1.smi')
#Check prop names.
pprint.pprint(list(mols[0].GetPropNames()))
[OUT]
['id',
 'Cluster',
 'MODEL.SOURCE',
 'MODEL.CCRATIO',
 'r_mmffld_Potential_Energy-OPLS_2005',
 'r_mmffld_RMS_Derivative-OPLS_2005',
 'b_mmffld_Minimization_Converged-OPLS_2005']

#SetProps method can set properties that will be written to files with SMILES.
writer.SetProps(['Cluster'])
#The way of writing molecules can perform common way.
for mol in mols:
    writer.write( mol )
writer.close()

Then check the file.

!head -n 10 cdk2smi1.smi
[OUT]
SMILES Name Cluster
CC(C)C(=O)COc1nc(N)nc2[nH]cnc12 ZINC03814457 1
Nc1nc(OCC2CCCO2)c2nc[nH]c2n1 ZINC03814459 2
Nc1nc(OCC2CCC(=O)N2)c2nc[nH]c2n1 ZINC03814460 2

How about set all props ?

writer = SmilesWriter('cdk2smi2.smi')
writer.SetProps(list(mols[0].GetPropNames()))
for mol in mols:
    writer.write( mol )
writer.close()
!head -n 10 cdk2smi2.smi
[OUT]
SMILES Name id Cluster MODEL.SOURCE MODEL.CCRATIO r_mmffld_Potential_Energy-OPLS_2005 r_mmffld_RMS_Derivative-OPLS_2005 b_mmffld_Minimization_Converged-OPLS_2005
CC(C)C(=O)COc1nc(N)nc2[nH]cnc12 ZINC03814457 ZINC03814457 1 CORINA 3.44 0027  09.01.2008 1 -78.6454 0.000213629 1
Nc1nc(OCC2CCCO2)c2nc[nH]c2n1 ZINC03814459 ZINC03814459 2 CORINA 3.44 0027  09.01.2008 1 -67.4705 9.48919e-05 1
Nc1nc(OCC2CCC(=O)N2)c2nc[nH]c2n1 ZINC03814460 ZINC03814460 2 CORINA 3.44 0027  09.01.2008 1 -89.4303 5.17485e-05 1
Nc1nc(OCC2CCCCC2)c2nc[nH]c2n1 ZINC00023543 ZINC00023543 3 CORINA 3.44 0027  09.01.2008 1 -70.2463 6.35949e-05 1

Wow it works fine. This method is useful and easy to use.
Do most of the RDKiters use the function?
I’m totally out of fashion!!!

I pushed my Fast Clustering code to rdkit/Contrib repository. It was big news for me.