I'm a bit confused by all this. The RDKit has Tanimoto (and a bunch of
other similarity measures) built in:
In [6]: from rdkit import DataStructs
In [7]: fp1 =
rdMolDescriptors.GetMorganFingerprintAsBitVect(theobromine,2,2048)
In [8]: fp2 =
rdMolDescriptors.GetMorganFingerprintAsBitVect(caffeine,2,2048)
In [9]: DataStructs.TanimotoSimilarity(fp1,fp2)
Out[9]: 0.5294117647058824
Is there a reason that you're interested in using something else?
-greg
On Thu, Mar 16, 2017 at 9:42 PM, matthew <msedd...@sheffield.ac.uk> wrote:
> I don't think you even need to cast them to numpy arrays if you use scipy.
> It should be able to take bit arrays. Also, jaccard distance is another
> name for tanimoto distance. This simplifies the code above:
>
> *from __future__ import print_function from rdkit import Chem*
> *from rdkit.Chem import AllChem*
>
>
> *from scipy.spatial import distance *
>
> *mol1 = Chem.MolFromSmiles('CCO')*
> *mol2 = Chem.MolFromSmiles('CCC')*
>
>
> *fp1 = AllChem.GetMorganFingerprintAsBitVect(mol1, 8) *
> *fp2 = AllChem.GetMorganFingerprintAsBitVect(mol2, 8)*
>
>
>
>
> * # jaccard distance is the same as tanimoto distance # 1 - distance =
> similarity print(1 - distance.jaccard(fp1, fp2)) *
>
> # 0.4285714285714286
>
> Matt
> PhD Student
> Chemoinformatics Research Group
> University of Sheffield
>
>
> On 16/03/2017 17:38, Curt Fischer wrote:
>
> If you are looking for something quick and dirty, you could stay in numpy
> to calculate Tanimoto.
>
> *from rdkit import Chem*
> *from rdkit.Chem import AllChem*
>
> *import numpy as np*
> *from __future__ import division*
>
> *mol1 = Chem.MolFromSmiles('CCO')*
> *mol2 = Chem.MolFromSmiles('CCC')*
>
> *fp1 = np.array(AllChem.GetMorganFingerprintAsBitVect(mol1, 8),
> dtype='bool')*
> *fp2 = np.array(AllChem.GetMorganFingerprintAsBitVect(mol2, 8),
> dtype='bool')*
>
> *def tanimoto(v1, v2):*
> * """*
> * Calculates tanimoto similarity for two bit vectors*
> * """*
> * return(np.bitwise_and(v1, v2).sum() / np.bitwise_or(v1, v2).sum())*
>
> *tanimoto(fp1, fp2)*
>
> *Out[4]:0.42857142857142855*
>
>
> On Thu, Mar 16, 2017 at 7:28 AM, Thomas Evangelidis <teva...@gmail.com>
> wrote:
>
>> Hello,
>>
>> I created a numpyarray from a molecule using the following function:
>>
>> AllChem.GetMorganFingerprintAsBitVect()
>>
>>
>> Now I would like to convert back to bit vector the numpy array, in order
>> to calculate the Tanimoto similarity of two compounds. Is this possible?
>>
>> thanks
>> Thomas
>>
>>
>>
>> --
>>
>> ======================================================================
>>
>> Thomas Evangelidis
>>
>> Research Specialist
>> CEITEC - Central European Institute of Technology
>> Masaryk University
>> Kamenice 5/A35/1S081,
>> 62500 Brno, Czech Republic
>>
>> email: tev...@pharm.uoa.gr
>>
>> teva...@gmail.com
>>
>>
>> website: https://sites.google.com/site/thomasevangelidishomepage/
>>
>>
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>
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