Dear Greg and Niko.
Thank you for your quick repry.
>To Greg, thanks for your recommendation.
I tried PCA with matplotlib and it worked with no problem. Thanks.
But Matplotlib returned view that was different from R.
>To Niko.
I using RDKit, version RDKit_2012_06_1.
And, when I tried PCA with the code, no response was returned.
KeyboardInterrupt, following message was returned.
Traceback (most recent call last):
File "mol_pca.py", line 33, in <module>
res=Stats.PrincipalComponents(matrix)
File "C:\RDKit_2012_06_1\rdkit\ML\Data\Stats.py", line 82, in
PrincipalComponents
covMat = FormCorrelationMatrix(mat)
File "C:\RDKit_2012_06_1\rdkit\ML\Data\Stats.py", line 66, in
FormCorrelationMatrix
sumY = sum(y)
So, what version of RDKit are you using?
And if you don't care, could you show me some results ?
Thanks.
Takayuki
2013/1/18 Nikolas Fechner <m...@fechner.cc>
> Hi Takayuki,
> I was able to run your code snippet without any errors (with different
> example molecules of course). Could possible explain in more detail what is
> not working for you? What version of RDKit are you using (from rdkit import
> rdBase;print rdBase.rdkitVersion) ?
>
> Niko
>
> On Jan 17, 2013, at 11:08 AM, Taka Seri <serit...@gmail.com> wrote:
>
> 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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