Dear All.
I want to do PCA with molecular fingerprint .
So, I wrote following code.
But, this code did not work .
Does anyone have a suggestion?
Thanks.
Takayuki
1 from rdkit import Chem
2 from rdkit.Chem import AllChem
3 from rdkit.ML.Data import Stats
4 import numpy
5 import sys
6
7
8 mols = [mol for mol in Chem.SDMolSupplier(sys.argv[1])]
9 fps = [AllChem.GetMorganFingerprintAsBitVect(mol,2) for mol in mols]
10
11 mat = []
12 for fp in fps:
13 bits = fp.ToBitString()
14 bitsvec = [int(bit) for bit in bits]
15 mat.append(bitsvec)
16
17 mat=numpy.array(mat)
18 res = Stats.PrincpalComponents(mat)
19 print res[1]
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