Re: [Rdkit-discuss] Molecule Editting in RDKit

[Malitha Kabir]

To Gerg Landrum,
Dear sir,
Your script worked as expected and I have got idea on what to do. Many
thanks for the tutorial.
Sincerely,
Malitha


On Jul 5, 2017 12:07 AM, "Greg Landrum"  wrote:

> Hi Malitha,
>
> Here's a gist that provides, I think, a sketch of a solution for what you
> want to do.
>
> https://gist.github.com/greglandrum/da88ead12b396ada4e1b3258fab771a7
>
> Best,
> -greg
>
>
> On Tue, Jul 4, 2017 at 5:18 PM, Malitha Kabir 
> wrote:
>
>> Hi,
>>
>> I want to create RDKit Mol object manually. I can create RWMol object
>> with appropriate (I guess) atoms and bonds. The required atoms and bond
>> information are taken from another Mol object. It is indeed a tedious
>> coding gymnastic you can say. Unfortunately, the end molecule lacks the 3D
>> geometry information (xyz).
>>
>> However, my question is:
>>
>> Is it possible to set custom coordinates (xyz) to any kinds of RDKit
>> object that represents a molecule class?
>>
>> *** it would be great if you kindly manage time to provide me a complete
>> molecule building tutorial. I'm very very confused about the events that
>> happen behind the seen when we typically create molecules from SD file
>> through Python API.
>>
>> *** I am travelling right now. So, I will be able to respond against your
>> queries/suggestions after 10/15 hours.
>>
>> Many thanks for kindly looking into it.
>>
>> Best regards,
>> -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] Molecule Editting in RDKit

[Greg Landrum]

Hi Malitha,

Here's a gist that provides, I think, a sketch of a solution for what you
want to do.

https://gist.github.com/greglandrum/da88ead12b396ada4e1b3258fab771a7

Best,
-greg


On Tue, Jul 4, 2017 at 5:18 PM, Malitha Kabir 
wrote:

> Hi,
>
> I want to create RDKit Mol object manually. I can create RWMol object with
> appropriate (I guess) atoms and bonds. The required atoms and bond
> information are taken from another Mol object. It is indeed a tedious
> coding gymnastic you can say. Unfortunately, the end molecule lacks the 3D
> geometry information (xyz).
>
> However, my question is:
>
> Is it possible to set custom coordinates (xyz) to any kinds of RDKit
> object that represents a molecule class?
>
> *** it would be great if you kindly manage time to provide me a complete
> molecule building tutorial. I'm very very confused about the events that
> happen behind the seen when we typically create molecules from SD file
> through Python API.
>
> *** I am travelling right now. So, I will be able to respond against your
> queries/suggestions after 10/15 hours.
>
> Many thanks for kindly looking into it.
>
> Best regards,
> -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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[Rdkit-discuss] Molecule Editting in RDKit

[Malitha Kabir]

Hi,

I want to create RDKit Mol object manually. I can create RWMol object with
appropriate (I guess) atoms and bonds. The required atoms and bond
information are taken from another Mol object. It is indeed a tedious
coding gymnastic you can say. Unfortunately, the end molecule lacks the 3D
geometry information (xyz).

However, my question is:

Is it possible to set custom coordinates (xyz) to any kinds of RDKit object
that represents a molecule class?

*** it would be great if you kindly manage time to provide me a complete
molecule building tutorial. I'm very very confused about the events that
happen behind the seen when we typically create molecules from SD file
through Python API.

*** I am travelling right now. So, I will be able to respond against your
queries/suggestions after 10/15 hours.

Many thanks for kindly looking into it.

Best regards,
-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