Great. Thanks, Greg.
Best wishes,
Wendong
On Fri, Mar 12, 2021 at 2:55 PM Greg Landrum <greg.land...@gmail.com> wrote:
>
> 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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