Re: [Rdkit-discuss] identify anti-aromatic bonds

2015-08-28 Thread Yingfeng Wang 
Greg,

Thanks.

Yingfeng

On Fri, Aug 28, 2015 at 6:13 AM, Greg Landrum greg.land...@gmail.com
wrote:

 Well, here's a way to find the rings where all of the bonds are conjugated:

 In [1]: from rdkit import Chem

 In [2]: m = Chem.MolFromSmiles('C1CC1CC(=O)c1nnc2cc(-c3ccc(OC)cc3)nn2c1CC')

 In [3]: ri = m.GetRingInfo()

 In [4]: brs = ri.BondRings()

 In [5]: conjugatedRings = []

 In [6]: for i,br in enumerate(brs):
 conj=True
 for b in br:
 if not m.GetBondWithIdx(b).GetIsConjugated():
 conj=False
 break
 if conj:
 conjugatedRings.append(i)
...:


 Then, using those indices, you can find the lists of atoms that are in
 each of those conjugated rings:

 In [7]: ars = ri.AtomRings()
 In [8]: conjugatedAtomRings = [ars[x] for x in conjugatedRings]

 In [9]: len(ars)
 Out[9]: 4

 In [10]: len(conjugatedAtomRings)
 Out[10]: 3

 In [11]: conjugatedAtomRings
 Out[11]: [(7, 8, 9, 21, 22, 6), (10, 9, 21, 20, 11), (13, 14, 15, 18, 19,
 12)]


 From this point it's a matter of deciding how you want to count electrons
 from each atom. The approach used in the RDKit C++ code is described, more
 or less accurately, here:
 http://rdkit.org/docs/RDKit_Book.html#aromaticity

 -greg


 On Thu, Aug 27, 2015 at 5:36 PM, Yingfeng Wang ywang...@gmail.com wrote:

 Greg,

 Thanks. I believe identifying anti-aromatic bonds even just with simple
 rings will be very helpful to my project. Could you please give me some
 links or sample codes about identifying all the conjugated simple rings and
 do an electron count? Would you also like to share me some relevant rules
 you think could be reasonable?

 By the way, if there is a hard way to identify all anti-aromatic bonds,
 could you also please give me some hints? If fortunately I can implement
 it, I will share it by posting my code in this mailing list.


 Thanks.

 Yingfeng

 On Thu, Aug 27, 2015 at 10:08 AM, Greg Landrum greg.land...@gmail.com
 wrote:

 Hi Yingfeng,

 Non-aromatic is not a problem, but there's no easy way I can think of
 off the top of my head for identifying anti-aromatic systems without making
 C++ code changes.

 If you were willing to limit yourself to simple rings, you could write
 some python code to identify all the conjugated simple rings and do an
 electron count according to whatever rules you think are relevant.

 -greg


 On Thu, Aug 27, 2015 at 1:52 PM, Yingfeng Wang ywang...@gmail.com
 wrote:

 Could anyone please share your experience with identifying non-aromatic
 bonds using RDKit? I would greatly appreciate your help.

 Yingfeng


 On Mon, Aug 24, 2015 at 9:42 PM, Yingfeng Wang ywang...@gmail.com
 wrote:

 Sorry, my previous email has a typo.

 According to the following link,

 http://www.rdkit.org/docs/RDKit_Book.html

 I get sample code for identifying aromatic bonds like

  from rdkit import Chem
  m=Chem.MolFromSmiles('O=C1C=CC(=O)C2=C1OC=CO2')
  m.GetBondBetweenAtoms(6,7).GetIsAromatic()

 Is there a way to identify anti-aromatic bonds using Rdkit?

 Thanks.

 Yingfeng

 On Mon, Aug 24, 2015 at 9:38 PM, Yingfeng Wang ywang...@gmail.com
 wrote:

 According to the following link,

 http://www.rdkit.org/docs/RDKit_Book.html

 I get sample code for identifying identify anti-aromatic bonds like

  from rdkit import Chem
  m=Chem.MolFromSmiles('O=C1C=CC(=O)C2=C1OC=CO2')
  m.GetBondBetweenAtoms(6,7).GetIsAromatic()

 Is there a way to identify anti-aromatic bonds using Rdkit?

 Thanks.

 Yingfeng





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Re: [Rdkit-discuss] identify anti-aromatic bonds

2015-08-27 Thread Greg Landrum 
Hi Yingfeng,

Non-aromatic is not a problem, but there's no easy way I can think of off
the top of my head for identifying anti-aromatic systems without making C++
code changes.

If you were willing to limit yourself to simple rings, you could write some
python code to identify all the conjugated simple rings and do an electron
count according to whatever rules you think are relevant.

-greg


On Thu, Aug 27, 2015 at 1:52 PM, Yingfeng Wang ywang...@gmail.com wrote:

 Could anyone please share your experience with identifying non-aromatic
 bonds using RDKit? I would greatly appreciate your help.

 Yingfeng


 On Mon, Aug 24, 2015 at 9:42 PM, Yingfeng Wang ywang...@gmail.com wrote:

 Sorry, my previous email has a typo.

 According to the following link,

 http://www.rdkit.org/docs/RDKit_Book.html

 I get sample code for identifying aromatic bonds like

  from rdkit import Chem
  m=Chem.MolFromSmiles('O=C1C=CC(=O)C2=C1OC=CO2')
  m.GetBondBetweenAtoms(6,7).GetIsAromatic()

 Is there a way to identify anti-aromatic bonds using Rdkit?

 Thanks.

 Yingfeng

 On Mon, Aug 24, 2015 at 9:38 PM, Yingfeng Wang ywang...@gmail.com
 wrote:

 According to the following link,

 http://www.rdkit.org/docs/RDKit_Book.html

 I get sample code for identifying identify anti-aromatic bonds like

  from rdkit import Chem
  m=Chem.MolFromSmiles('O=C1C=CC(=O)C2=C1OC=CO2')
  m.GetBondBetweenAtoms(6,7).GetIsAromatic()

 Is there a way to identify anti-aromatic bonds using Rdkit?

 Thanks.

 Yingfeng





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 ___
 Rdkit-discuss mailing list
 Rdkit-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/rdkit-discuss


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Re: [Rdkit-discuss] identify anti-aromatic bonds

2015-08-27 Thread Yingfeng Wang 
Could anyone please share your experience with identifying non-aromatic
bonds using RDKit? I would greatly appreciate your help.

Yingfeng

On Mon, Aug 24, 2015 at 9:42 PM, Yingfeng Wang ywang...@gmail.com wrote:

 Sorry, my previous email has a typo.

 According to the following link,

 http://www.rdkit.org/docs/RDKit_Book.html

 I get sample code for identifying aromatic bonds like

  from rdkit import Chem
  m=Chem.MolFromSmiles('O=C1C=CC(=O)C2=C1OC=CO2')
  m.GetBondBetweenAtoms(6,7).GetIsAromatic()

 Is there a way to identify anti-aromatic bonds using Rdkit?

 Thanks.

 Yingfeng

 On Mon, Aug 24, 2015 at 9:38 PM, Yingfeng Wang ywang...@gmail.com wrote:

 According to the following link,

 http://www.rdkit.org/docs/RDKit_Book.html

 I get sample code for identifying identify anti-aromatic bonds like

  from rdkit import Chem
  m=Chem.MolFromSmiles('O=C1C=CC(=O)C2=C1OC=CO2')
  m.GetBondBetweenAtoms(6,7).GetIsAromatic()

 Is there a way to identify anti-aromatic bonds using Rdkit?

 Thanks.

 Yingfeng



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[Rdkit-discuss] identify anti-aromatic bonds

2015-08-24 Thread Yingfeng Wang 
According to the following link,

http://www.rdkit.org/docs/RDKit_Book.html

I get sample code for identifying identify anti-aromatic bonds like

 from rdkit import Chem
 m=Chem.MolFromSmiles('O=C1C=CC(=O)C2=C1OC=CO2')
 m.GetBondBetweenAtoms(6,7).GetIsAromatic()

Is there a way to identify anti-aromatic bonds using Rdkit?

Thanks.

Yingfeng
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Re: [Rdkit-discuss] identify anti-aromatic bonds

2015-08-24 Thread Yingfeng Wang 
Sorry, my previous email has a typo.

According to the following link,

http://www.rdkit.org/docs/RDKit_Book.html

I get sample code for identifying aromatic bonds like

 from rdkit import Chem
 m=Chem.MolFromSmiles('O=C1C=CC(=O)C2=C1OC=CO2')
 m.GetBondBetweenAtoms(6,7).GetIsAromatic()

Is there a way to identify anti-aromatic bonds using Rdkit?

Thanks.

Yingfeng

On Mon, Aug 24, 2015 at 9:38 PM, Yingfeng Wang ywang...@gmail.com wrote:

 According to the following link,

 http://www.rdkit.org/docs/RDKit_Book.html

 I get sample code for identifying identify anti-aromatic bonds like

  from rdkit import Chem
  m=Chem.MolFromSmiles('O=C1C=CC(=O)C2=C1OC=CO2')
  m.GetBondBetweenAtoms(6,7).GetIsAromatic()

 Is there a way to identify anti-aromatic bonds using Rdkit?

 Thanks.

 Yingfeng

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