On Fri, Mar 12, 2021 at 7:48 AM Wendong Wang <wendong.w...@sjtu.edu.cn>
wrote:
> PS. By the way, how did you index all the atoms when you draw the
> molecule?
>
MolDraw2D has a drawing option to add atom indices.
If you're using the RDKit in Jupyer with IPythonConsole, you can do:
IPythonConsole.drawOptions.addAtomIndices=True
[image: image.png]
-greg
On Fri, Mar 12, 2021 at 2:28 PM Wendong Wang <wendong.w...@sjtu.edu.cn>
> wrote:
>
>> Hi Greg,
>> Thanks for the explanation and the references.
>>
>> Best wishes,
>> Wendong
>>
>> On Fri, Mar 12, 2021 at 1:58 PM Greg Landrum <greg.land...@gmail.com>
>> wrote:
>>
>>> Hi Wendong,
>>>
>>> The morgan fingerprint algorithm removes redundant atom environments
>>> (environments which contain exactly the same atoms/bonds).
>>> For example, when looking at valine:
>>> [image: image.png]
>>> The environments with radius 2 which are centered on atoms 5 and 6 are
>>> redundant with the environment of radius 1 which is centered on atom 4, so
>>> those environments are not reported in the output.
>>>
>>> This is described in more detail in the ECFP paper: Rogers, D.; Hahn, M.
>>> “Extended-Connectivity Fingerprints.” *J. Chem. Inf. and Model.*
>>> **50**:742-54 (2010).
>>>
>>> Best,
>>> -greg
>>>
>>> On Fri, Mar 12, 2021 at 4:16 AM Wendong Wang <wendong.w...@sjtu.edu.cn>
>>> wrote:
>>>
>>>> Greetings,
>>>> I have a question about morgan fingerprints. The code is pasted at the
>>>> end of the email, and please see the attached images for the results.
>>>>
>>>> For valine molecule, the radius is set to be 2. The dictionary (atom
>>>> index, radius) shows all the substructures of all atoms with radius 0 as
>>>> fingerprints, and all the substructures of all the atoms with radius 1 as
>>>> fingerprints. But there are only a few substructures with radius 2 as
>>>> fingerprints. Why so few?
>>>>
>>>> Thanks.
>>>>
>>>> Best wishes,
>>>> Wendong
>>>>
>>>> PS. The code is below:
>>>> m1 = Chem.MolFromSmiles('CC(C)[C@@H](C(=O)O)N')
>>>> di1 = {}
>>>> fp1 = AllChem.GetMorganFingerprintAsBitVect(m1, radius = 2, nBits =
>>>> 2048, bitInfo = di1)
>>>> tu1 = [(m1, x, di1) for x in fp1.GetOnBits()]
>>>> Draw.DrawMorganBits(tu1, molsPerRow = 4, legends=[str(x) for x in
>>>> fp1.GetOnBits()])
>>>>
>>>> _______________________________________________
>>>> Rdkit-discuss mailing list
>>>> Rdkit-discuss@lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>>
>>>
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