Re: [Rdkit-discuss] RDkit Molecule Fragmenter

[Jan Halborg Jensen]

I was also searching for this functionality earlier

For what it’s worth here’s some *very* simple code I hacked together to do 
fragmentation.  The focus is aromatic heterocycles, but it could be more 
general by, for example '[c,n]-[*]’ -> ‘[R]-[*]’  and ring = 
Chem.MolFromSmarts(‘[R]’) instead of '[n]'

Not pretty, but it worked for me

Bet regards, Jan


import sys, os, re
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import Draw
from rdkit.Chem.Draw import IPythonConsole

rings_mol = []
rings_smiles = []

substituent_mol = []
substituent_smiles = []

smiles_file_name = "/Users/jan/Dropbox/Lundbeck/big.smiles"

smiles_file = open(smiles_file_name, "r")

for line in smiles_file:
words = line.split()
name = words[0]
smiles = words[1]

mol =  Chem.MolFromSmiles(smiles)

bis = mol.GetSubstructMatches(Chem.MolFromSmarts('[c,n]-[*]'))
bs = [mol.GetBondBetweenAtoms(x,y).GetIdx() for x,y in bis]

if len(bs) == 0:
if smiles not in rings_smiles:
rings_smiles.append(smiles)
rings_mol.append(Chem.MolFromSmiles(smiles))
continue

fragments_mol = Chem.FragmentOnBonds(mol,bs,addDummies=True)

big_fragment = Chem.MolToSmiles(fragments_mol,True)

big_fragment = re.sub(r'\[\d+\*\]',r'[*]',big_fragment)

fragments = big_fragment.split(".")

ring = Chem.MolFromSmarts('[n]')

for fragment in fragments:
if Chem.MolFromSmiles(fragment).HasSubstructMatch(ring):
if fragment not in rings_smiles:
rings_mol.append(Chem.MolFromSmiles(fragment))
rings_smiles.append(fragment)
else:
if fragment not in substituent_smiles:
substituent_mol.append(Chem.MolFromSmiles(fragment))
substituent_smiles.append(fragment)

img = 
Draw.MolsToGridImage(rings_mol,molsPerRow=4,subImgSize=(200,200),useSVG=True)

svg_file_name = "/Users/jan/Dropbox/Lundbeck/rings.svg"
svg_file = open(svg_file_name, 'w')
svg_file.write(img.data)
svg_file.close()
os.system('sed -i "" "s/xmlns:svg/xmlns/" '+svg_file_name)

img


On 06 Jun 2017, at 13:43, Popov, Maxim (Ext) 
> wrote:

Dear All,

I have discovered a very usefule tool in Knime, Molecule Fragmenter by RDKit, 
but can’t find a corresponding class or function outside of Knime. Can I use 
the Fragmenter without Knime?

Thanks!

Maxim
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Re: [Rdkit-discuss] RDkit Molecule Fragmenter

[Greg Landrum]

On Tue, Jun 6, 2017 at 1:43 PM, Popov, Maxim (Ext)  wrote:

>
>
> I have discovered a very usefule tool in Knime, Molecule Fragmenter by
> RDKit, but can’t find a corresponding class or function outside of Knime.
> Can I use the Fragmenter without Knime?
>
>
>
Yep:
http://www.rdkit.org/docs/GettingStartedInPython.html#molecular-fragments

There's also:
http://www.rdkit.org/docs/GettingStartedInPython.html#brics-implementation
and
http://www.rdkit.org/docs/GettingStartedInPython.html#recap-implementation
which use different strategies.

-greg
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[Rdkit-discuss] RDkit Molecule Fragmenter

[Popov, Maxim (Ext)]

Dear All,

I have discovered a very usefule tool in Knime, Molecule Fragmenter by RDKit, 
but can't find a corresponding class or function outside of Knime. Can I use 
the Fragmenter without Knime?

Thanks!

Maxim
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss