Re: [Rdkit-discuss] How to get a list of available properties from SD file

2017-06-27 Thread Malitha Kabir 
Dear Paolo Tosco,
Thank you very much for offering a concrete coding lesson in your previous
email. This will help me a lot. I have got all the answers.
-Malitha


On Tue, Jun 27, 2017 at 3:58 PM, Malitha Kabir 
wrote:

> Dear Maciek Wójcikowski,
>
> list(m0.GetPropNames()) returned the object I need.
> Thank you very much.
>
> -Malitha
>
>
>
>
> On Tue, Jun 27, 2017 at 3:45 PM, Maciek Wójcikowski  > wrote:
>
>> Hi,
>>
>> There is a method GetPropsAsDict() or GetPropNames() for RDKit molecule.
>> http://www.rdkit.org/Python_Docs/rdkit.Chem.rdchem
>> .Mol-class.html#GetPropsAsDict which should do what you want.
>>
>> 
>> Pozdrawiam,  |  Best regards,
>> Maciek Wójcikowski
>> mac...@wojcikowski.pl
>>
>> 2017-06-27 11:26 GMT+02:00 Malitha Kabir :
>>
>>> Hi,
>>>
>>> Thank you very much in advance for kindly looking into this.
>>> My question is in short:
>>> Is there any method that can create a list of available properties from
>>> SD file?
>>>
>>> I am describing the scenario here:
>>> You can view a sample SD file from the following github link:
>>> https://github.com/rdkit/rdkit/blob/master/Docs/Book/data/cdk2.sdf
>>>
>>> That file contains previously calculated properties (eg: Cluster,
>>> MODEL.SOURCE etc.). I can read the file in RDKit using the following codes:
>>>
>>> from rdkit.Chem.rdmolfiles import SDMolSupplier
>>> file1='cdk2.sdf'
>>> data=SDMolSupplier(fileName=file1, sanitize=True, removeHs=False,
>>> strictParsing=True)
>>>
>>> I can access the first molecule by using the following code:
>>> m0=data[0]
>>>
>>> Now the object m0 (rdkit Mol object) contains all the necessary
>>> information about the molecule including properties.
>>>
>>> I need to create a list of previously calculated properties from that
>>> file without seeing the file visually.
>>>
>>> Any direction is warmly appreciated. Thank you very much. Have a great
>>> day!
>>>
>>> -Malitha
>>>
>>>
>>>
>>> 
>>> --
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> ___
>>> Rdkit-discuss mailing list
>>> Rdkit-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>
>>>
>>
>
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Re: [Rdkit-discuss] How to get a list of available properties from SD file

2017-06-27 Thread Malitha Kabir 
Dear Maciek Wójcikowski,

list(m0.GetPropNames()) returned the object I need.
Thank you very much.

-Malitha




On Tue, Jun 27, 2017 at 3:45 PM, Maciek Wójcikowski 
wrote:

> Hi,
>
> There is a method GetPropsAsDict() or GetPropNames() for RDKit molecule.
> http://www.rdkit.org/Python_Docs/rdkit.Chem.rdchem.Mol-class.html#
> GetPropsAsDict which should do what you want.
>
> 
> Pozdrawiam,  |  Best regards,
> Maciek Wójcikowski
> mac...@wojcikowski.pl
>
> 2017-06-27 11:26 GMT+02:00 Malitha Kabir :
>
>> Hi,
>>
>> Thank you very much in advance for kindly looking into this.
>> My question is in short:
>> Is there any method that can create a list of available properties from
>> SD file?
>>
>> I am describing the scenario here:
>> You can view a sample SD file from the following github link:
>> https://github.com/rdkit/rdkit/blob/master/Docs/Book/data/cdk2.sdf
>>
>> That file contains previously calculated properties (eg: Cluster,
>> MODEL.SOURCE etc.). I can read the file in RDKit using the following codes:
>>
>> from rdkit.Chem.rdmolfiles import SDMolSupplier
>> file1='cdk2.sdf'
>> data=SDMolSupplier(fileName=file1, sanitize=True, removeHs=False,
>> strictParsing=True)
>>
>> I can access the first molecule by using the following code:
>> m0=data[0]
>>
>> Now the object m0 (rdkit Mol object) contains all the necessary
>> information about the molecule including properties.
>>
>> I need to create a list of previously calculated properties from that
>> file without seeing the file visually.
>>
>> Any direction is warmly appreciated. Thank you very much. Have a great
>> day!
>>
>> -Malitha
>>
>>
>>
>> 
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> ___
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
>
--
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Re: [Rdkit-discuss] How to get a list of available properties from SD file

2017-06-27 Thread Maciek Wójcikowski 
Hi,

There is a method GetPropsAsDict() or GetPropNames() for RDKit molecule.
http://www.rdkit.org/Python_Docs/rdkit.Chem.rdchem.Mol-class.html#GetPropsAsDict
which should do what you want.


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

2017-06-27 11:26 GMT+02:00 Malitha Kabir :

> Hi,
>
> Thank you very much in advance for kindly looking into this.
> My question is in short:
> Is there any method that can create a list of available properties from SD
> file?
>
> I am describing the scenario here:
> You can view a sample SD file from the following github link:
> https://github.com/rdkit/rdkit/blob/master/Docs/Book/data/cdk2.sdf
>
> That file contains previously calculated properties (eg: Cluster,
> MODEL.SOURCE etc.). I can read the file in RDKit using the following codes:
>
> from rdkit.Chem.rdmolfiles import SDMolSupplier
> file1='cdk2.sdf'
> data=SDMolSupplier(fileName=file1, sanitize=True, removeHs=False,
> strictParsing=True)
>
> I can access the first molecule by using the following code:
> m0=data[0]
>
> Now the object m0 (rdkit Mol object) contains all the necessary
> information about the molecule including properties.
>
> I need to create a list of previously calculated properties from that file
> without seeing the file visually.
>
> Any direction is warmly appreciated. Thank you very much. Have a great day!
>
> -Malitha
>
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
--
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