Sorry again...
for Torsion and Morgan I'm getting different values:
rdMolDescriptors.GetMorganFingerprint(molec[0])
rdMolDescriptors.GetHashedTopologicalTorsionFingerprint(molec[0])
and when I'm using on both .ToBitString() and use my "own" tanimoto
function: im getting defferent values
rdMolDescriptors.GetMorganFingerprint(molec[0]).ToBitString()
rdMolDescriptors.GetHashedTopologicalTorsionFingerprint(molec[0]).ToBitString()
torsion
0.0645161290323 #own
4 #size of c
0.0133333333333 #RDKIT
morgan
0.148648648649 #own
11 #size of c
0.173076923077 #RDKIT
For the fingerprints topological and maccs keys Im getting the same values
0.462686567164
31
0.462686567164
sorry again for spamin you
On 9 January 2016 at 05:56, A neuman <[email protected]> wrote:
> Oh, sorry.
>
> I think, I found my mistake
>
>
> FP1 and FP2 should be the count fomr ALL 1's in the FP and not the whole
> FP length.
>
>
>
> On 9 January 2016 at 05:46, A neuman <[email protected]> wrote:
>
>> Hello everyone,
>>
>> i want to calculate the tanimoto similarity from a bitstring of 1's und
>> 0's.
>>
>>
>> Im getting deffierent resulst for example:
>>
>>
>> for the RDKIT tanimoto I'm reading:
>> fingerprint= GenMACCSKeys(molec[0])
>>
>>
>> for the "own" tanimoto function im reading the key like:
>> fingerprint= GenMACCSKeys(molec[0])*.ToBitString() * so, a
>> ToBitString is added on the line
>>
>> If im comparing them im using:
>>
>> RDKIT function:
>>
>> DataStructs.TanimotoSimilarity(FP1,FP2)
>>
>> "own"n function :
>>
>> for i in range(len(FP1)):
>> if FP1[i]==1.0 and FP2[i]==1.0:
>> c+=1
>>
>> print float(c)/(len(FP1) + len(FP2) - c)
>>
>> So I'm just count al 1 Bits at the same position und FP1 und FP 2 to get
>> the c
>> and then im calculating: c / (a+b-c)
>>
>>
>> and I#m Getting these values:
>>
>> 0.00602409638554 From "own" function
>> 2 # counts of c
>> 0.0333333333333 from RDKit
>>
>> Somebody knows what I'm doing wrong?
>>
>> best,
>>
>> alex
>>
>>
>
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