Re: [Rdkit-discuss] getting substructure for Morgan fingerprint bit
Naeem,
On Sun, Mar 6, 2016 at 12:02 PM, Naeem Attari 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
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Re: [Rdkit-discuss] getting substructure for Morgan fingerprint bit
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 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 > 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 >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >> > -- ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] getting substructure for Morgan fingerprint bit
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 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 > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > -- ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] getting substructure for Morgan fingerprint bit
He might want the hydrogen counts specified to block unwanted substitutions? Dave > On 6 Mar 2016, at 03:38, Peter S. Shenkin wrote: > > Just curious here > > Since every SMILES is a valid SMARTS, > How do you want the SMARTS to differ from the SMARTS the SMILES already is? > What would be the advantage if you could do so? > Thanks, > -P. > >> On Sat, Mar 5, 2016 at 8:40 PM, Naeem Attari 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 >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > -- > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] getting substructure for Morgan fingerprint bit
Just curious here Since every SMILES is a valid SMARTS, - How do you want the SMARTS to differ from the SMARTS the SMILES already is? - What would be the advantage if you could do so? Thanks, -P. On Sat, Mar 5, 2016 at 8:40 PM, Naeem Attari 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 > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > -- ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
