Re: [Rdkit-discuss] Molecules alignment broken in rdkit 2016 ?

[Fabrice Carles]

Perfect !
I apologies I have forgotten that list() is required in python 3 version.
It work well in python 3 now. Thanks


Le 24 mars 2017 16:11, "Greg Landrum"  a écrit :

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 
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
>
>
>
> 
> --
> 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
>
>
--
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

Re: [Rdkit-discuss] Molecules alignment broken in rdkit 2016 ?

[Greg Landrum]

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 
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
>
>
>
> 
> --
> 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
>
>
--
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

[Rdkit-discuss] Molecules alignment broken in rdkit 2016 ?

[Fabrice Carles]

Dear rdkit users,

I suspect a bug in AllChem.AlignMol() for some rdkit version.
Try to run this notebook http://nbviewer.jupyter.org/
gist/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
--
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