Hello,
I have found the way... using MolToImage
Thank you again!!
Best,
Andrés
from rdkit import Chem
from rdkit.Chem import Draw
def main():
#First we get the parameters
if len(sys.argv) != 4:
return 1
smile=sys.argv[1]
path=sys.argv[2]
image_format=sys.argv[3]
#We setup the image file
size = (240, 240)
#Create the molecule using SMILES as input
m = Chem.MolFromSmiles(smile)
#Draw the molecule and save in path
Draw.MolToImage(m, path, image_format, size=size)
El Jun 25, 2014, a las 10:38 AM, acanada escribió:
> Hi Greg,
>
> Thank you very much for your answer! I get what you mean, but still unclear
> to me. If for example, I want to draw molecules, in the documentation I need
> the sdf file as the input... But instead I have the SMILES.... How should I
> proceed? I thought to translate SMILES to sdf and then use the sdf as input.
>
> If it's as you say, I don't need the sdf file... So I think I can handle this
> by loading the sdf files of the molecules in my database (i.e using chebi web
> service to retrieve sdf and serializing to the database), then I can retrieve
> the sdf from the database and use
>
> suppl = Chem.SDMolSupplier('data/cdk2.sdf')
>
> to draw the molecule... But I should create a file with the data from the
> table and it seems to me not very efficient at all...
>
>
> Am I messing too much? Is there an standard way to do this?
>
>
> Bests regards,
> Andrés
>
>
> El Jun 25, 2014, a las 7:59 AM, Greg Landrum escribió:
>
>> [Andres: sorry you're getting two copies of this; I forgot to include the
>> mailing list on the first one]
>>
>> Hi Andres,
>>
>> On Tue, Jun 24, 2014 at 5:43 PM, acanada <[email protected]> wrote:
>>
>> I'm very new to RDKit and the RDKit database cartridge. I'm not chemist so
>> please my apologize for the simple question.
>> After reading the documentation it's clear to me how to create the
>> emolecules database with the raw_data table and populate with the
>> version.smi.gz file
>> (http://downloads.emolecules.com/free/2014-06-01/version.smi.gz). Then I
>> create the mols table that will have only the smiles accepted by RDKit.
>> Great!
>>
>> My question, if it has any sense: Is there a how-to to create a sdf table
>> populating it with the version.sdf.gz file
>> (http://downloads.emolecules.com/free/2014-06-01/version.sdf.gz)?? Can you
>> please point me where the instructions are?
>>
>> There is not currently an easy way to do this analogous to the way things
>> are built from the smiles file. The SMILES file is easier for postgresql to
>> manage on its own because it has one record per line. SDF files have
>> multi-line records, so you would need to use something that understands the
>> format (e.g. the RDKit python wrappers) to be able to load it.
>>
>> Or what is the version.sdf.gz file used for?
>>
>> It provides another format of more-or-less the same data. Unless you have a
>> concrete reason for wanting that version of the data, there is probably no
>> need to use the file at all.
>>
>> Best,
>> -greg
>>
>>
>> On Tue, Jun 24, 2014 at 5:43 PM, acanada <[email protected]> wrote:
>> Hello,
>>
>> I'm very new to RDKit and the RDKit database cartridge. I'm not chemist so
>> please my apologize for the simple question.
>> After reading the documentation it's clear to me how to create the
>> emolecules database with the raw_data table and populate with the
>> version.smi.gz file
>> (http://downloads.emolecules.com/free/2014-06-01/version.smi.gz). Then I
>> create the mols table that will have only the smiles accepted by RDKit.
>> Great!
>>
>> My question, if it has any sense: Is there a how-to to create a sdf table
>> populating it with the version.sdf.gz file
>> (http://downloads.emolecules.com/free/2014-06-01/version.sdf.gz)?? Can you
>> please point me where the instructions are?
>> Or what is the version.sdf.gz file used for?
>>
>> Sorry for this basic questions and thank you for your time...
>>
>> Andrés
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transmisiÿn por parte de otra persona que no sea el destinatario. Si usted
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mensaje recibido.
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designated recipient named above. Distribution, reproduction or any other use
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Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
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