This is just a guess but you could try doing:
AllChem.AlignMol(m2,m1,atomMap=list(zip(match2,match1)))
-greg
On Fri, Mar 24, 2017 at 3:34 PM, Fabrice Carles <carlesfabr...@gmail.com>
wrote:
> Dear rdkit users,
>
> I suspect a bug in AllChem.AlignMol() for some rdkit version.
> Try to run this notebook http://nbviewer.jupyter.org/gi
> st/greglandrum/4316435/Working%20in%203D.ipynb
> input [25] : AllChem.AlignMol(m2,m1,atomMap=zip(match2,match1)) seem to
> be broken for me in rdkit 2016.03 and 2016.09 python3.4/3.5 and raise
> "ValueError: sequence does not support length query"
> Note that it work well in rdkit 2015.09.2 python2.7
>
> Did you have a solution ?
>
> Thanks
>
> Fabrice Carles - PhD student
> Structural Bioinformatics & Chemoinformatics
> University of Orleans - France
>
>
>
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