Combining Steve's and Chris' answer gets to how I would do it with
reactions:
In [17]: core = Chem.MolFromSmiles('*c1c(C)1(O)')
In [18]: chain = Chem.MolFromSmiles('CN*')
In [19]: rxn =
AllChem.ReactionFromSmarts('[c:1][#0].[#0][*:2]>>[c:1]-[*:2]')
In [20]: ps = rxn.RunReactants((core,chain
I'm a bit confused by all this. The RDKit has Tanimoto (and a bunch of
other similarity measures) built in:
In [6]: from rdkit import DataStructs
In [7]: fp1 =
rdMolDescriptors.GetMorganFingerprintAsBitVect(theobromine,2,2048)
In [8]: fp2 =
rdMolDescriptors.GetMorganFingerprintAsBitVect(caffeine
I don't think you even need to cast them to numpy arrays if you use
scipy. It should be able to take bit arrays. Also, jaccard distance is
another name for tanimoto distance. This simplifies the code above:
*from __future__ import print_function
from rdkit import Chem*
*from rdkit.Chem import A
If you are looking for something quick and dirty, you could stay in numpy
to calculate Tanimoto.
*from rdkit import Chem*
*from rdkit.Chem import AllChem*
*import numpy as np*
*from __future__ import division*
*mol1 = Chem.MolFromSmiles('CCO')*
*mol2 = Chem.MolFromSmiles('CCC')*
*fp1 = np.array
You can match a dummy atom (*) with the SMARTS [#0]
Steve
On 16 Mar 2017 16:43, "Chris Earnshaw" wrote:
> Hi Brian
>
> I'm by no means an expert in RDKit with Python, but until someone else
> comes along, here are a few thoughts.
>
> Your reaction SMARTS specifically defines aromatic carbons jo
Hi,
Here is a Python script that was created with the help of some
rdkit wizards:
https://github.com/UnixJunkie/mol2ecfp4
It works with unfolded ECFP4 fingerprints, so not exactly
what you are looking for.
There would be more modifications needed in order to fold
the fingerprint to the desired nu
I'll send a Python script.
It works for .smi files.
If anyone can adapt it to work on sdf files, that would be wonderful.
Just give me 5mn to put it on github.
On 03/16/2017 09:28 AM, Thomas Evangelidis wrote:
> Hello,
>
> I created a numpyarray from a molecule using the following function:
>
> A
Hi Brian
I'm by no means an expert in RDKit with Python, but until someone else
comes along, here are a few thoughts.
Your reaction SMARTS specifically defines aromatic carbons joined by single
bonds which won't match an incoming benzene ring, and it's a bit redundant
to specify that aromatic car
Hello,
I created a numpyarray from a molecule using the following function:
AllChem.GetMorganFingerprintAsBitVect()
Now I would like to convert back to bit vector the numpy array, in order to
calculate the Tanimoto similarity of two compounds. Is this possible?
thanks
Thomas
--
==
9 matches
Mail list logo