Hello there,
Hope you are doing very well.
I would like to compute tanimoto similarity using obspectrophore
fingerprint. I have found a formula on the net for the tanimoto similarity:
def tanimoto(list1, list2):
#list1 and list2 #spectrophore fingerprint
intersection = [common_item for common_
Distance between two compounds is obtained using the euclidean distance
between the two fingerprint vectors of the two compounds.
https://jcheminf.biomedcentral.com/articles/10.1186/s13321-018-0268-9
On Sat, 14 Mar 2020 at 16:24, Chris Swain via OpenBabel-discuss <
openbabel-discuss@lists.sourcefo
If you working in python this should help you.
I wrote these scripts when using obspectrophores. "get_spectrophore.py"
will get you a compound spectrophore (tested with sdf but should work with
other obabel supported format).The second one will compute their euclidean
distances.
def get_spectrophor
e from a reference ligand spectrophore and N spectrophores from N
> different ligands?
>
> -- Rudy
>
>
> On Mon, Mar 16, 2020 at 1:46 PM Bakary N'tji Diallo <
> diallobaka...@gmail.com> wrote:
>
>>
>> If you working in python this should help you.
>>
print(obspectrophores_euclidean(test_ligand, test_ligand)) #should
>> return zero
>> File "obspectrophores_euclidean.py", line 9, in
>> obspectrophores_euclidean
>> ligand1_spectrophore = get_spectrophore(ligand1)
>> NameError: name 'get_spectrophore&
Dear all,
I have the following depiction for a structure file. As you can see the
first compound is scaled up.
[image: image.png]
Is there way to maintain a uniform structure size.
I am using the following command: "obabel structure.smi -O out.svg -xC -xe
-d"
Thanks
Best regards
--
Bakary N’tj
