Naeem,
On Sun, Mar 6, 2016 at 12:02 PM, Naeem Attari <[email protected]> wrote: > > 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 > ) > There must be something strange with your install. That functionality is available in that release: In [6]: rdBase.rdkitVersion Out[6]: '2015.09.2' In [8]: m = Chem.MolFromSmiles('c1cc(CC)ccn1') In [10]: Chem.MolFragmentToSmiles(m,atomsToUse=(1,2,3,4,5),rootedAtAtom=1) Out[10]: 'cc(c)CC' In [11]: m.GetProp('_smilesAtomOutputOrder') Out[11]: '[1,2,5,3,4,]' > 2> how to get the graphical *Structure *for mol fragment (as shown in > image in my previous mail) ? > The closest you can currently get to that in a straightforward way (that I'm aware of) is to use something like the code that's at the bottom of that blog post I referenced. I'm sure it's possible to write code to generate visualization like in your example, but I'm not aware of anyone having done that. -greg
------------------------------------------------------------------------------
_______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
