Re: [Rdkit-discuss] CalcNumAtoms import error

[Chris Swain via Rdkit-discuss]

Hi Ivan and Axel,

Thanks upgrading to the last version works,

Cheers

Chris

> On 14 Jul 2022, at 13:37, Ivan Tubert-Brohman 
>  wrote:
> 
> Hi Chris,
> 
> Please try a more recent version of RDKit. I believe this function was added 
> in the 2021.09 release.
> 
> Hope this helps,
> Ivan
> 
> 
> On Thu, Jul 14, 2022 at 7:04 AM Chris Swain via Rdkit-discuss 
>  > wrote:
> Hi,
> 
> If I try
> 
> from rdkit.Chem.rdMolDescriptors import CalcNumAtoms
> 
> I get
> 
> cannot import name 'CalcNumAtoms' from 'rdkit.Chem.rdMolDescriptors' 
> 
> I can import a range of other descriptors fine
> 
> Using Python 3.7.6 and RDKit 2020.09.1
> 
> Cheers
> 
> Chris
> 
> 
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Re: [Rdkit-discuss] CalcNumAtoms import error

[Axel Pahl]

Hi Chris,
this might not be a great help, but it works for me on Ubuntu 22.04 with
RDKit 2021.09.5:

import rdkit
print(rdkit.__version__)
from rdkit import Chem
from rdkit.Chem.rdMolDescriptors import CalcNumAtoms
m = Chem.MolFromSmiles("c1c1C(=O)NC")
print(CalcNumAtoms(m))

Output:
2021.09.5
19

According to Github, it was only added to the C++ MolDescriptors module
in June 2021:
https://github.com/rdkit/rdkit/commit/53523a4a1106e4e3b1a69ff26d0510225019e35c

KR Axel

On 14.07.22 12:46, Chris Swain via Rdkit-discuss wrote:

Hi,

If I try

from rdkit.Chem.rdMolDescriptors import CalcNumAtoms

I get

cannot import name 'CalcNumAtoms' from 'rdkit.Chem.rdMolDescriptors'

I can import a range of other descriptors fine

Using Python 3.7.6 and RDKit 2020.09.1

Cheers

Chris


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Re: [Rdkit-discuss] CalcNumAtoms import error

[Ivan Tubert-Brohman]

Hi Chris,

Please try a more recent version of RDKit. I believe this function was
added in the 2021.09 release.

Hope this helps,
Ivan


On Thu, Jul 14, 2022 at 7:04 AM Chris Swain via Rdkit-discuss <
rdkit-discuss@lists.sourceforge.net> wrote:

> Hi,
>
> If I try
>
> from rdkit.Chem.rdMolDescriptors import CalcNumAtoms
>
> I get
>
> cannot import name 'CalcNumAtoms' from 'rdkit.Chem.rdMolDescriptors'
>
> I can import a range of other descriptors fine
>
> Using Python 3.7.6 and RDKit 2020.09.1
>
> Cheers
>
> Chris
>
>
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Re: [Rdkit-discuss] fragment 3D molecules with BRICS

[Rafael L via Rdkit-discuss]

Renato, it seems that FragmentOnBRICSBonds and BRICS.BRICSDecompose work
differently. The first returns a mol object from which you can get the
fragments using GetMolFrags (as you did), while the second returns a list
of strings containing the fragments. I'm not sure if you can recover 3D
info from these strings.
If you want to get the fragments from BRICS.BRICSDecompose, use:

l = BRICS.BRICSDecompose(m2,minFragmentSize=9)
fr2 = [Chem.MolFromSmiles(x) for x in l]
Draw.MolsToGridImage(fr2,molsPerRow=4)


Alternatively, if you want to remove the small fragments obtained from
FragmentOnBRICSBonds, you can filter by using the atom count:

newmol2=Chem.FragmentOnBRICSBonds(m2)
frags=Chem.GetMolFrags(newmol2,asMols=True,sanitizeFrags=True)
frags = [x for x in frags if len(x.GetAtoms()) > 3]
Draw.MolsToGridImage(frags,molsPerRow=4)


On Wed, Jul 13, 2022 at 8:01 PM Renato Freitas  wrote:

> Dear Rdkit team,
>
> I want to fragment a ligand from PDB and keep the 3D coordinates of the
> resulting fragments. I was able to do that using the code below
>
> ###
> import rdkit
> import py3Dmol
> from rdkit import Chem
> from rdkit.Chem import rdmolops
> from rdkit import RDLogger
> from rdkit.Chem import BRICS
> from rdkit.Chem import Recap
> from rdkit.Chem import Draw
> from rdkit.Chem import AllChem
> from rdkit.Chem.Draw import IPythonConsole
> from rdkit import Chem, RDConfig
> from rdkit.Chem import AllChem, rdMolAlign
>
> mol ="""rot-1A5H-A
>  RDKit  3D
>
>  28 30  0  0  1  0  0  0  0  0999 V2000
> 0.5600   -9.3330  -12.4470 C   0  0  0  0  0  0  0  0  0  0  0  0
>-0.5220  -11.6860  -13.9640 C   0  0  2  0  0  0  0  0  0  0  0  0
>-1.3890  -10.8900  -13.0130 C   0  0  0  0  0  0  0  0  0  0  0  0
>-0.9370   -9.5080  -12.5700 C   0  0  0  0  0  0  0  0  0  0  0  0
> 1.3380   -9.3820  -13.7780 C   0  0  0  0  0  0  0  0  0  0  0  0
> 0.5150   -9.5890  -15.0480 C   0  0  2  0  0  0  0  0  0  0  0  0
> 0.0420  -10.9860  -15.1910 C   0  0  0  0  0  0  0  0  0  0  0  0
> 0.2540  -11.5680  -16.2200 O   0  0  0  0  0  0  0  0  0  0  0  0
>-0.9330  -12.9740  -14.0030 C   0  0  0  0  0  0  0  0  0  0  0  0
>-1.2340  -13.7900  -15.1940 C   0  0  0  0  0  0  0  0  0  0  0  0
>-0.7960  -15.1430  -15.2380 C   0  0  0  0  0  0  0  0  0  0  0  0
>-1.0610  -15.9350  -16.4000 C   0  0  0  0  0  0  0  0  0  0  0  0
>-1.7450  -15.3930  -17.5400 C   0  0  0  0  0  0  0  0  0  0  0  0
>-2.1670  -14.0630  -17.4730 C   0  0  0  0  0  0  0  0  0  0  0  0
>-1.9260  -13.2750  -16.3360 C   0  0  0  0  0  0  0  0  0  0  0  0
>-2.0200  -16.1830  -18.7390 C   0  0  0  0  0  0  0  0  0  0  0  0
>-1.3190  -17.2890  -19.0360 N   0  0  0  0  0  0  0  0  0  0  0  0
>-2.9740  -15.7940  -19.5590 N   0  0  0  0  0  0  0  0  0  0  0  0
> 0.8600   -8.8970  -16.1880 C   0  0  0  0  0  0  0  0  0  0  0  0
> 2.1700   -8.8390  -16.9320 C   0  0  0  0  0  0  0  0  0  0  0  0
> 2.1750   -8.5140  -18.3280 C   0  0  0  0  0  0  0  0  0  0  0  0
> 3.3880   -8.4510  -19.0560 C   0  0  0  0  0  0  0  0  0  0  0  0
> 4.6500   -8.7150  -18.4280 C   0  0  0  0  0  0  0  0  0  0  0  0
> 4.6430   -9.0360  -17.0580 C   0  0  0  0  0  0  0  0  0  0  0  0
> 3.4350   -9.0920  -16.3220 C   0  0  0  0  0  0  0  0  0  0  0  0
> 5.9450   -8.6500  -19.1820 C   0  0  0  0  0  0  0  0  0  0  0  0
> 6.9230   -9.5390  -18.9420 N   0  0  0  0  0  0  0  0  0  0  0  0
> 6.1630   -7.7040  -20.1250 N   0  0  0  0  0  0  0  0  0  0  0  0
>   1  4  1  0
>   1  5  1  0
>   2  3  1  0
>   2  7  1  0
>   2  9  1  6
>   3  4  1  0
>   5  6  1  0
>   6  7  1  0
>   6 19  1  6
>   7  8  2  0
>   9 10  1  0
>  10 11  2  0
>  10 15  1  0
>  11 12  1  0
>  12 13  2  0
>  13 14  1  0
>  13 16  1  0
>  14 15  2  0
>  16 17  2  0
>  16 18  1  0
>  19 20  1  0
>  20 21  2  0
>  20 25  1  0
>  21 22  1  0
>  22 23  2  0
>  23 24  1  0
>  23 26  1  0
>  24 25  2  0
>  26 27  2  0
>  26 28  1  0
> M  END
> """
>
> m2 = Chem.MolFromMolBlock(mol)
>
> newmol2=Chem.FragmentOnBRICSBonds(m2)
> frags=Chem.GetMolFrags(newmol2,asMols=True,sanitizeFrags=True)
> Draw.MolsToGridImage(frags,molsPerRow=4)
> ##
>
> However, some of the fragments are very small. I found that using
> "BRICS.BRICSDecompose" I can set the minimum size of the fragments with
> "minFragmentSize". So I tried the following code
>
> frag = [Chem.GetMolFrags(x) for x in sorted
> (BRICS.BRICSDecompose(m2,minFragmentSize=9))]
>
>
> which didn't work, and I got the following error:
>
>
> ###
>
> ArgumentError Traceback (most recent call last)
>
>   in ()
> > 1 frag = [Chem.GetMolFrags(x) for x in 
> sorted(BRICS.BRICSDecompose(m2,minFragmentSize=9))]
>
>
>   in (.0)
> > 1 frag = [Chem.GetMolFrags(x) for x in 
> 

[Rdkit-discuss] CalcNumAtoms import error

[Chris Swain via Rdkit-discuss]

Hi,

If I try

from rdkit.Chem.rdMolDescriptors import CalcNumAtoms

I get

cannot import name 'CalcNumAtoms' from 'rdkit.Chem.rdMolDescriptors' 

I can import a range of other descriptors fine

Using Python 3.7.6 and RDKit 2020.09.1

Cheers

Chris


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