Hi all,
I have two lists of molecules. The first list contains testing molecules
(test.sdf) and the second contains training molecules (train.sdf).
I would like to compare each test molecule to all the training molecule and
calculate a corresponding Tanimoto similarity score. (I implemented it in my
code and it is super slow as it is O(n^2) ). I use GetFingerprint() and
Tanimoto() functions for such purpose. After the comparison, I picked up the
kth most similar molecules to the test molecule and predict something for
the test molecule. I am trying to make things a bit faster.
So I tried the following babel command:
babel test_mol.smi train_mols.sdf -ofpt
But the problem is that I have to manually replace each testing molecule
smile information for every time I run the command. In other words, the
script will only compare the first molecule in the 'test_mol.smi" to all the
molecules in 'train_mols.sdf'. So even if I have a list of testing molecules
in the 'test_mol.smi', the script will not compare them to the training
molecules except the first one in the list.
Is there a way or trick I can use so that I can compare all my testing
molecules to the training molecules and get a list of Tc scores?
Thanks so much for your help!
Rob
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