Re: [Rdkit-discuss] reaction fingerprint as bitstring

2017-03-24 Thread Greg Landrum
Hi Ambrish, Assuming that I understand correctly what you want to do, here's an example using built-in RDKit functionality that generates a reaction fingerprint (using default parameters, you can change these) and then converts it into a bit vector using a simple: "if the bit is set in the

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

2017-03-24 Thread 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

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

2017-03-24 Thread 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

Re: [Rdkit-discuss] reaction fingerprint as bitstring

2017-03-24 Thread Ambrish
Thanks Greg. I am trying to pre-calculate reaction fingerprints of all my database reactions and store it in database, so that for any new reaction I can run Tanimoto similarity or similar calculation and pick similar reactions. So I decided to convert it to a BitString of fixed length, but I get