Thank you all for replies, @Peter: I thought smarts could give additional information of substructure regarding its environment and bond order
I am actually interested in the structural fragment that depict the fingerprint bit. @Greg: I have seen that blog earlier. We learn a lot from your blogs. That code can get me the smiles with explicit bond order and hydrogens and aromaticity. however.. 1> i am unable to get _smilesAtomOutputOrder (i am using python 2015.09.2) 2> how to get the graphical *Structure *for mol fragment (as shown in image in my previous mail) ? Regards Naeem On 6 March 2016 at 14:56, Greg Landrum <[email protected]> wrote: > Hi, > > Useful code for generating the SMARTS for a Morgan bit (originally written > by Nadine Schneider) was part of a recent RDKit blog post. > Look at input [20] here: > http://rdkit.blogspot.ch/2016/02/morgan-fingerprint-bit-statistics.html > You can grab the notebook itself here: > https://github.com/greglandrum/rdkit_blog/blob/4a939401fe5a7f0842fa59f3061510f1a4d4aa4e/notebooks/Looking%20at%20Morgan%20bit%20counts.ipynb > > Best, > -greg > > > On Sun, Mar 6, 2016 at 2:40 AM, Naeem Attari <[email protected]> > wrote: > >> Hi, >> >> I was wondering if there is any way to get the substructure for the bits >> of Morgan fingerprint as follows >> [dx.doi.org/10.1021/ci2001583 |J. Chem. Inf. Model. 2011, 51, 1447–1456] >> >> though I am able to get the smiles for the bits by >> Chem.MolFragmentToSmiles, i think it would be more informative/specific to >> have smart for the bit >> >> >> Kind Regards >> Shaikh Naeem Attari >> Ph.D. Candidate, Department of Pharmacoinformatics >> National Institute of Pharmaceutical Education and Research (NIPER) >> S.A.S. Nagar, India. +91 7814727792 >> in.linkedin.com/in/naeemraza25/ >> >> >> >> ------------------------------------------------------------------------------ >> >> _______________________________________________ >> Rdkit-discuss mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >> >
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