Re: [Rdkit-discuss] Atoms with strange positions/bonds when drawer makes PNG

2016-02-18 Thread Paul Emsley 
Hi Greg,

I tried to investigate this further with github rdkit but I am as yet 
unable to configure/cmake it yet on this Mac (something related to boost 
python has changed) :-/ :-) - will keep poking at it and/or abstracting 
it...

Thanks,

Paul.

On 19/02/2016 09:19, Greg Landrum wrote:
>
>
> That is indeed very strange behavior and I can't think of what would 
> cause it. I'm not able to reproduce it with either the current github 
> master, the 2015_09_2, or the 2015_03_1 release. Can you please send 
> me a small test program that reproduces the problem?
>
>


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Re: [Rdkit-discuss] Atoms with strange positions/bonds when drawer makes PNG

2016-02-18 Thread Greg Landrum 
Hi Paul,

That is indeed very strange behavior and I can't think of what would cause
it. I'm not able to reproduce it with either the current github master, the
2015_09_2, or the 2015_03_1 release. Can you please send me a small test
program that reproduces the problem?

-greg


On Wed, Feb 17, 2016 at 1:10 AM, Paul Emsley 
wrote:

>
> Dear RDKitters,
>
> I have the following test code:
>
>std::string smiles="Clc1c1";
>RDKit::ROMol *m_local = RDKit::SmilesToMol(smiles);
>RDDepict::compute2DCoords(*m_local);
>RDKit::Conformer conf = m_local->getConformer();
>WedgeMolBonds(*m_local, );
>bool includeStereo = true;
>bool kekulize = false;
>std::string mol_file_name = "testmol.mol";
>RDKit::MolToMolFile(*m_local, mol_file_name, includeStereo, confId,
> kekulize);
>std::string png_file_name = "image-test.png";
>{
>   RDKit::MolDraw2DCairo drawer(200, 200);
>   drawer.drawMolecule(*m_local);
>   drawer.finishDrawing();
>   drawer.writeDrawingText(png_file_name.c_str());
>}
>
> The mol file seems sane (attached) but the png has strangely positioned
> atoms (the Cl in this case) (attached).
>
> What am I doing wrong?
>
> (Using RDKit-2015-03-01)
>
> Thanks,
>
> Paul.
>
>
>
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Re: [Rdkit-discuss] Suppress stdout and stderr in rdkit

2016-02-18 Thread Gaetano Calabro 
Hi Paolo,

Thanks a lot for your prompt reply. I ended up coding this:

from rdkit import Chem
from rdkit import RDLogger

smart = 
'[#6]1(:[#6]:[#6]:[#6]2:[#6](:[#6]:1):[#6]:[#6]:[#6]:[#6]:2)-[#8,#6]'

mol = Chem.MolFromSmarts(smart)

lg = RDLogger.logger()

lg.setLevel(RDLogger.CRITICAL)

try:
 Chem.SanitizeMol(mol)
except:
 print 'OK'


Ciao,

Gaetano


On 02/18/2016 01:09 AM, Paolo Tosco wrote:
> Dear Gaetano,
>
> you may try the following:
>
> from rdkit import rdBase
> rdBase.DisableLog('rdApp.error')
>
> You may check the logging levels you wish to disable/enable in 
> rdkit/RDLogger.py, or use a wildcard such as 'rdApp.*' to affect all 
> levels at once.
>
> Best,
> Paolo
>
> On 17/02/2016 23:54, Gaetano Calabro wrote:
>> from rdkit import Chem
>>
>> smart = 
>> '[#6]1(:[#6]:[#6]:[#6]2:[#6](:[#6]:1):[#6]:[#6]:[#6]:[#6]:2)-[#8,#6]'
>>
>> mol = Chem.MolFromSmarts(smart)
>>
>> Chem.SanitizeMol(mol)
>


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Re: [Rdkit-discuss] Suppress stdout and stderr in rdkit

2016-02-18 Thread Paolo Tosco 
Dear Gaetano,

you may try the following:

from rdkit import rdBase
rdBase.DisableLog('rdApp.error')

You may check the logging levels you wish to disable/enable in 
rdkit/RDLogger.py, or use a wildcard such as 'rdApp.*' to affect all 
levels at once.

Best,
Paolo

On 17/02/2016 23:54, Gaetano Calabro wrote:
> from rdkit import Chem
>
> smart = '[#6]1(:[#6]:[#6]:[#6]2:[#6](:[#6]:1):[#6]:[#6]:[#6]:[#6]:2)-[#8,#6]'
>
> mol = Chem.MolFromSmarts(smart)
>
> Chem.SanitizeMol(mol)


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