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 <greg.land...@gmail.com> 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 <serit...@gmail.com> 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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------------------------------------------------------------------------------
Dive into the World of Parallel Programming The Go Parallel Website, sponsored
by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
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