[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

[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

Post by 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).
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
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[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

Post by 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

Post by 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).
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
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss