Re: [Rdkit-discuss] About the original order algorithm of GetMorganFingerprintAsBitVect function

2022-07-25 Thread Nils Weskamp 

Dear Yuzhi,

a high-level discussion of the various fingerprints in the RDKit can be 
found at


https://www.rdkit.org/UGM/2012/Landrum_RDKit_UGM.Fingerprints.Final.pptx.pdf

If you want to know more, I would suggest to take a look at

Rogers, D.; Hahn, M. Extended-Connectivity Fingerprints. J. Chem. Inf. 
Model. 2010, 50(5): 742-754.


Morgan, H. L. The Generation of a Unique Machine Description for 
Chemical Structures - A Technique Developed at Chemical Abstracts 
Service. J. Chem. Doc. 1965, 5: 107-112.


Hope this helps.

Nils

Am 25.07.2022 um 12:01 schrieb Yuzhi Xu:



On Mon, Jul 25, 2022 at 6:00 PM Yuzhi Xu > wrote:


Dear Sir or Madam

Many thanks for your reading. I am a student who is using the rdkit
as a vital tool in my work. I wonder if I could know how the
GetMorganFingerprintAsBitVect function works. I noticed that there
will be a rigid order of various smiles. And I wonder in this
function how the order formed？Because I cannot find the detail in
the website.

For example, as to O=Cc1ccc(F)c([N+](=O)[O-])c1， the function fp =
AllChem.GetMorganFingerprintAsBitVect(mol,radius=1, nBits=1024,
bitInfo=info will show {39: ((6, 1),), 171: ((1, 1),), 356: ((0, 0),
(5, 0), (10, 0)), 650: ((2, 0), (7, 0)), 694: ((6, 0),), 699: ((11,
1),), 715: ((3, 0),), 716: ((0, 1),), 726: ((8, 1), (9, 1)), 753:
((2, 1),), 816: ((10, 1),), 838: ((3, 1),), 849: ((4, 0), (8, 0),
(9, 0)), 875: ((4, 1),), 904: ((11, 0),), 939: ((1, 0),), 1004: ((7,
1),), 1009: ((5, 1),)}， the （6，1）means the atom 6 and radius 1，
I wonder how the order made and if there is another function can
make the same order such as Chem.MolToSmiles（root=x）

Best,
Yuzhi



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Re: [Rdkit-discuss] About the original order algorithm of GetMorganFingerprintAsBitVect function

2022-07-25 Thread Yuzhi Xu 
On Mon, Jul 25, 2022 at 6:00 PM Yuzhi Xu  wrote:

> Dear Sir or Madam
>
> Many thanks for your reading. I am a student who is using the rdkit as a
> vital tool in my work. I wonder if I could know how the
> GetMorganFingerprintAsBitVect function works. I noticed that there will be
> a rigid order of various smiles. And I wonder in this function how the
> order formed？Because I cannot find the detail in the website.
>
> For example, as to O=Cc1ccc(F)c([N+](=O)[O-])c1， the function fp =
> AllChem.GetMorganFingerprintAsBitVect(mol,radius=1, nBits=1024,
> bitInfo=info will show {39: ((6, 1),), 171: ((1, 1),), 356: ((0, 0), (5,
> 0), (10, 0)), 650: ((2, 0), (7, 0)), 694: ((6, 0),), 699: ((11, 1),), 715:
> ((3, 0),), 716: ((0, 1),), 726: ((8, 1), (9, 1)), 753: ((2, 1),), 816:
> ((10, 1),), 838: ((3, 1),), 849: ((4, 0), (8, 0), (9, 0)), 875: ((4, 1),),
> 904: ((11, 0),), 939: ((1, 0),), 1004: ((7, 1),), 1009: ((5, 1),)}， the
> （6，1）means the atom 6 and radius 1，I wonder how the order made and if there
> is another function can make the same order such as Chem.MolToSmiles（root=x）
>
> Best,
> Yuzhi
>
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