Re: [Rdkit-discuss] aromatic ring that contain sulfur atom

[Taka S. <ser...@gm...>]

Dear Greg.
Thank you for your quick and kindful reply.
I'm interested in morph approach.
http://www.ncbi.nlm.nih.gov/pubmed/20481489
I want to test this approach in rdkit.
Based on your adivice, I wrote sample script get atoms in aromatic rings
that degree < 3.
And the script works.
Thank you!
Takayuki.
-----code snippet---
from rdkit import Chem
import copy

def replace_atom( mol ):
    res = []
    # get atoms , degree <3
    aro_idxs = [ atom.GetIdx() for atom in mol.GetAromaticAtoms() if
atom.GetDegree() < 3 ]
    # replace aromatic atoms to carbon, nitrogen, oxygen, sulfur
    for atm_num in [6, 7, 8, 16]:
        for idx in aro_idxs:
            cp_mol = copy.deepcopy( mol )
            cp_mol.GetAtomWithIdx(idx).SetAtomicNum( atm_num )
            try:
                Chem.SanitizeMol(cp_mol)
                res.append( cp_mol )
            except:
                pass
    return res

def recursive_replace(mols, res = [],  check = set([])):
    for mol in mols:
        replaced_mols = replace_atom( mol )
        res.extend(replaced_mols)
    for mol in res:
        check.add( Chem.MolToSmiles( mol ) )
    if len(res) <= len(check):
        recursive_replace( res, res=res, check=check )
    else:
        return [ Chem.MolFromSmiles(mol) for mol in check ]


On Sun, Mar 1, 2015 at 3:16 PM Greg Landrum <gre...@gm...> wrote:

> Hi Takayuki,
>
> When doing this, you have to be careful how you change the valence of the
> atom. The sanitization step is going to attempt to Kekulize the aromatic
> ring (i.e. convert all the aromatic bonds to either single or double) and
> this isn't possible for all atom patterns.
>
> When you change atom 2 to a nitrogen, you end up creating a three
> coordinate aromatic nitrogen. During kekulization, both aromatic bonds to
> this atom must be converted to single bonds; this leads to a pattern that
> does not allow the rest of the ring to be kekulized.
>
> There's a similar problem when you replace a two-coordinate carbon with a
> sulfur.
>
> Replacing the three-coordinate carbon with a sulfur, on the other hand, is
> different: the RDKit allows the three coordinate sulfur to have an
> additional double bond added. The result ring is ok, but it's not aromatic:
>
> In [13]: mol = Chem.MolFromSmiles('COc1ccccc1')
> In [14]: mol.GetAtomWithIdx(2).SetAtomicNum( 16 )
> In [15]: Chem.SanitizeMol(mol)
> Out[15]: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE
> In [16]: print Chem.MolToSmiles(mol,True)
> COS1=CC=CC=C1
>
> Does that make sense?
>
> -greg
>
>
> On Sat, Feb 28, 2015 at 3:11 PM, Taka Seri <ser...@gm...> wrote:
>
>> Dear rdkitter.
>> I have a question about aromatic rings.
>> So, I want to change atoms in aromatic ring.
>> For example code is following.
>> Convert aromatic carbon to nitrogen.
>> mol = Chem.MolFromSmiles('COc1ccccc1')
>> mol.GetAtomWithIdx(3).SetAtomicNum( 7 )
>> Chem.SanitizeMol(mol)
>> Work Fine.
>>
>> mol.GetAtomWithIdx(2).SetAtomicNum( 7 )
>> Chem.SanitizeMol(mol)
>> ValueError.
>>
>> mol = Chem.MolFromSmiles('COc1ccccc1')
>> mol.GetAtomWithIdx(2).SetAtomicNum( 7 )
>> Chem.SanitizeMol(mol)
>> ValueError.
>>
>> Next, I tried to convert aromatic carbon to sulfur.
>> mol = Chem.MolFromSmiles('COc1ccccc1')
>> mol.GetAtomWithIdx(3).SetAtomicNum( 16 )
>> Chem.SanitizeMol(mol)
>> ValueError. OK
>>
>> mol = Chem.MolFromSmiles('COc1ccccc1')
>> mol.GetAtomWithIdx(2).SetAtomicNum( 16 )
>> Chem.SanitizeMol(mol)
>> This case, work fine. ???
>> Why this case work ?
>> Any advice or information you could provide would be greatly appreciated.
>> Thanks.
>> Takayuki
>>
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>