Re: [Rdkit-discuss] kekulizing carbazole
On 31/10/10 14:18, Greg Landrum wrote:
Hi Paul,
On Sun, Oct 31, 2010 at 12:09 PM, Paul Emsley
paul.ems...@bioch.ox.ac.uk wrote:
I'm running into problems when I try to kekulize carbazole.
The description I start with is that all the bonds are marked as
Bond::AROMATIC and I do setIsAromatic(true) on all the atoms (which are
all non-hydrogens). The explicitValence() for the N is 3.
MolOps::Kekulize() fails in that case, Can't kekulize mol.
If I add single bonds to hydrogens (including a hydrogens on the N) then
MolOps::Kekulize() works.
So my question is, how should I adjust the molecule description in the
first case so that MolOps::Kekulize() works without hydrogens too?
The problem is probably the lack of an explicit H on the nitrogen
atom. It's easily demonstrated with pyrrole:
[2] m=Chem.MolFromSmiles('c1cccn1')
[15:10:05] Can't kekulize mol
You can fix this by letting the RDKit know that there's an H on the N atom:
[3] m=Chem.MolFromSmiles('c1ccc[nH]1')
[4]
Carbazole is the same story:
[4] m=Chem.MolFromSmiles('c1ccc2c(c1)[nH]c1c21')
[5]
Note that in either case if you provide the structure in its Kekule
form this doesn't happen, here's the illustration for pyrrole:
[5] m=Chem.MolFromSmiles('C1=CC=CN1')
[6] Chem.MolToSmiles(m)
Out[6] 'c1cc[nH]c1'
There's an argument to be made that the Kekulization code could be
made more robust with respect to this particular edge case, but to
this point the effort involved has not seem justified by the payoff:
most of the time the H is present in the SMILES, so this problem
doesn't occur.
Hi Greg,
Thanks for your informative and speedy reply.
For the record, I would like to describe how I proceeded in the light of
your reply.
My starting point to construct an RWMol is an mmCIF restraints file. As
well as containing description of the bonds and angles (etc.) this file
describes the atoms, part of the description of which is the
type_energy. Pyrrole and carbazole Ns (for example) have the type
NR15(energy types are listed in energy_lib.cif [1]) so now when I see
an atom of that type [2], I add an extra H bonded to the N and
everything is then peachy.
Thanks again,
Paul.
[1]
http://www.ccp4.ac.uk/ccp4bin/viewcvs/ccp4/lib/data/monomers/ener_lib.cif
[2] there are other cases that I need to handle
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Re: [Rdkit-discuss] kekulizing carbazole
Hi Paul,
On Mon, Nov 1, 2010 at 3:54 PM, Paul Emsley paul.ems...@bioch.ox.ac.uk wrote:
For the record, I would like to describe how I proceeded in the light of
your reply.
My starting point to construct an RWMol is an mmCIF restraints file. As
well as containing description of the bonds and angles (etc.) this file
describes the atoms, part of the description of which is the
type_energy. Pyrrole and carbazole Ns (for example) have the type
NR15(energy types are listed in energy_lib.cif [1]) so now when I see
an atom of that type [2], I add an extra H bonded to the N and
everything is then peachy.
What you are describing sounds correct. One possible, minor,
optimization if you are building the molecule atom by atom (as opposed
to reading it from a mol block): you don't actually need to put the H
in the graph. You can instead do something like the following:
[6] m = Chem.MolFromSmiles('c1cccn1',sanitize=False)
[7] m.GetAtomWithIdx(4).SetNumExplicitHs(1)
[8] Chem.SanitizeMol(m)
[9] print Chem.MolToSmiles(m)
- print(Chem.MolToSmiles(m))
c1cc[nH]c1
Thanks again,
you're welcome!
Best Regards,
-greg
--
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Create new apps games for the Nokia N8 for consumers in U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
http://p.sf.net/sfu/nokia-dev2dev
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[Rdkit-discuss] kekulizing carbazole
Hi, I'm running into problems when I try to kekulize carbazole. The description I start with is that all the bonds are marked as Bond::AROMATIC and I do setIsAromatic(true) on all the atoms (which are all non-hydrogens). The explicitValence() for the N is 3. MolOps::Kekulize() fails in that case, Can't kekulize mol. If I add single bonds to hydrogens (including a hydrogens on the N) then MolOps::Kekulize() works. So my question is, how should I adjust the molecule description in the first case so that MolOps::Kekulize() works without hydrogens too? Thanks, Paul. -- Nokia and ATT present the 2010 Calling All Innovators-North America contest Create new apps games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] kekulizing carbazole
Hi Paul,
On Sun, Oct 31, 2010 at 12:09 PM, Paul Emsley
paul.ems...@bioch.ox.ac.uk wrote:
I'm running into problems when I try to kekulize carbazole.
The description I start with is that all the bonds are marked as
Bond::AROMATIC and I do setIsAromatic(true) on all the atoms (which are
all non-hydrogens). The explicitValence() for the N is 3.
MolOps::Kekulize() fails in that case, Can't kekulize mol.
If I add single bonds to hydrogens (including a hydrogens on the N) then
MolOps::Kekulize() works.
So my question is, how should I adjust the molecule description in the
first case so that MolOps::Kekulize() works without hydrogens too?
The problem is probably the lack of an explicit H on the nitrogen
atom. It's easily demonstrated with pyrrole:
[2] m=Chem.MolFromSmiles('c1cccn1')
[15:10:05] Can't kekulize mol
You can fix this by letting the RDKit know that there's an H on the N atom:
[3] m=Chem.MolFromSmiles('c1ccc[nH]1')
[4]
Carbazole is the same story:
[4] m=Chem.MolFromSmiles('c1ccc2c(c1)[nH]c1c21')
[5]
Note that in either case if you provide the structure in its Kekule
form this doesn't happen, here's the illustration for pyrrole:
[5] m=Chem.MolFromSmiles('C1=CC=CN1')
[6] Chem.MolToSmiles(m)
Out[6] 'c1cc[nH]c1'
There's an argument to be made that the Kekulization code could be
made more robust with respect to this particular edge case, but to
this point the effort involved has not seem justified by the payoff:
most of the time the H is present in the SMILES, so this problem
doesn't occur.
Best Regards,
-greg
--
Nokia and ATT present the 2010 Calling All Innovators-North America contest
Create new apps games for the Nokia N8 for consumers in U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
http://p.sf.net/sfu/nokia-dev2dev
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