Hi,
I didn't follow this thread - but the smiles seem to be ok (actually, as
long as the rings are closed sensible the smiles don't need enumeration):
In [6]: mol =
Chem.MolFromSmiles('Fc1ccccc1N1N=C(CC1c1ccccc1Cl)c1ccc(Br)cc1')
In [7]: Chem.MolToSmiles(mol)
Out[7]: 'Fc1ccccc1N1N=C(c2ccc(Br)cc2)CC1c1c(Cl)cccc1'
and if I run the MolWt calculator I do get sensible results.
In [9]: AvailDescriptors.descDict['MolWt'](mol)
Out[9]: 429.72000000000008
Bouille - could you run the same as above for your database molecules and
highlight the outcome - maybe you could first assign the db call to a
string variable and use that - I guess there is still something wrong in
your strings ...
Cheers
nik
Adrian Schreyer <[email protected]>
11/19/2009 12:50 PM
To
[email protected]
cc
[email protected]
Subject
Re: [Rdkit-discuss] Thank you to clarify
The SMILES strings are not correct, rings should be enumerated. In the
first string for example, all four rings are labelled with '1' but it
should look like this: c1ccc(c(c1)C2CC(=NN2c3ccccc3F)c4ccc(cc4)Br)Cl. That
is why RDKit is throwing an error. Which software did you use to create
the SMILES strings?
Adrian
On Thu, Nov 19, 2009 at 11:48, bouille <[email protected]> wrote:
Dear Greg
Thank you Adrian Schreyer for his quick answer
now I have the following error on some structures
rdkit.Chem.rdMolDescriptors._CalcMolWt(NoneType)
did not match C++ signature:
_CalcMolWt(RDKit::ROMol mol, bool onlyHeavy=False)
I have written
AvailDescriptors.descDict['MolWt'](mol,onlyHeavy=False) to repair ???
Is it not clear ?
I read other alternative to handle heavy structure
print 'embed: ',i
AllChem.EmbedMolecule(mol)
print 'optimize: ',i
AllChem.UFFOptimizeMolecule(mol)
mols.append(mol)
As example 3 compounds with difficulties why ?
bad molecule Fc1ccccc1N1N=C(CC1c1ccccc1Cl)c1ccc(Br)cc1 |c:9|
bad molecule NC1=C(C#N)C2=CCCCC2C2(C(=O)Nc3ccccc23)C1(C#N)C#N |c:1,t:5|
bad molecule
CCOC(=O)C1=C(C)N(c2ccc(OC)cc2)C(C)=C(C1c1ccc(Cl)cc1)C(=O)OCC |c:5,19|
Thank you to clarify
Best Regards
Bouille
------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008
30-Day
trial. Simplify your report design, integration and deployment - and focus
on
what you do best, core application coding. Discover what's new with
Crystal Reports now. http://p.sf.net/sfu/bobj-july
_______________________________________________
Rdkit-discuss mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008
30-Day
trial. Simplify your report design, integration and deployment - and focus
on
what you do best, core application coding. Discover what's new with
Crystal Reports now. http://p.sf.net/sfu/bobj-july
_______________________________________________
Rdkit-discuss mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
_________________________
CONFIDENTIALITY NOTICE
The information contained in this e-mail message is intended only for the
exclusive use of the individual or entity named above and may contain
information that is privileged, confidential or exempt from disclosure
under applicable law. If the reader of this message is not the intended
recipient, or the employee or agent responsible for delivery of the
message to the intended recipient, you are hereby notified that any
dissemination, distribution or copying of this communication is strictly
prohibited. If you have received this communication in error, please
notify the sender immediately by e-mail and delete the material from any
computer. Thank you.
------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now. http://p.sf.net/sfu/bobj-july
_______________________________________________
Rdkit-discuss mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
