dear all
i am trying to align molecules read from a *sdf file (list of conformers)
against another molecule (reference - a crystal structure), also read from
a *sdf file and make a nice 3d picture in jupyter notebook as shown in:
http://nbviewer.jupyter.org/github/greglandrum/rdkit_blog/
blob/master/notebooks/Trying%20py3Dmol.ipynb
i can reproduce all that happens in that notebook, but if i try to read
molecules from *sdf files, "AllChem.AlignMolConformers" fails
a simple example is here:
http://nbviewer.jupyter.org/github/gosiao/test_notebooks/blob/master/wrong_alignment.ipynb
<http://nbviewer.jupyter.org/github/gosiao/test_notebooks/blob/master/test_rdkit.ipynb>
the same thing happens if i generate a list of conformers with rdkit "on
the fly" (example in that notebook also),
in addition i found few difficulties:
- how to write "ConfToMolBlock" - like method - right now i'm writing all
conformers to sdf file and reading them in again as mol
- now i'm using a very small molecule fragment ("core") which i want to be
most-aligned among all molecules - from an example notebook (
http://nbviewer.jupyter.org/github/greglandrum/rdkit_blog/
blob/master/notebooks/Trying%20py3Dmol.ipynb) this works very well, but not
for my molecule. why is that and how can i fix that?
thank you for any tips!
best regards,
gosia
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