Building a molecule ( with SMILES) along a given vector

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Building a molecule ( with SMILES) along a given vector

raindeath
Hi all,

I'm trying to build ( by using SMILES) a molecule along a given vector.
I need to grow a polymeric chain (for example) along well-determined vectors, It is possible by using openbabel python module ? Do you have any suggestion from which I could start?

Thank you in advance,

Best Regards,
Frederick
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Re: Building a molecule ( with SMILES) along a given vector

Geoff Hutchison
> I'm trying to build ( by using SMILES) a molecule along a given vector.
> I need to grow a polymeric chain (for example) along well-determined

It's possible, although it might be easier to build the molecule, then translate and align the resulting 3D geometry.

For example, you could take atom 1, translate the whole molecule such that atom 1 is at the origin, and then rotate the molecular coordinates such that atom X is along the Z-axis (or your other preferred vector).

This is certainly something we do (in C++). Example code is here:
https://github.com/cryos/avogadro/blob/master/libavogadro/src/tools/aligntool.cpp#L212

Hope that helps,
-Geoff


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Re: Building a molecule ( with SMILES) along a given vector

raindeath
Hi,

Sorry for the late answer!
Thank you very much for your suggestion.
I used python and It's works!

Thank you again!

:)
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