Hi Andrew,
Thanks a lot for the suggestions. MCS search return I am getting is similar
what you have said:
'[#6](-!@[#6]-!@[#6]-@1(-!@[#6])-@[#6](-!@[#6]-!@[#6])(-!@[#6])-@[#6](-!@[#6]-!@[#6])(-!@[#6])-@[#6](-!@[#6]-!@[#6])(-!@[#6])-@[#6](-!@[#6](-!@[#6])(-!@[#6])-!@[#6])(-!@[#6])-@[#6]-@1)(-!@[#6])(-!@[#6])-!@[#6]'
Your idea of using atomCompare = 'isotopes' seem to be good and I will give
a try..
I am using this approach to prepare input structures from Free Energy
Perturbation calculations. Thus , if I have structure A and B I would like
to generate a starting structures for calculations which should contain MCS
atoms plus rest of the atoms of A ( only will be changed to dummy during
calculations) + rest of the atoms of B as dummy atoms (will be dummy in
input structure and changed to their respective atoms during calculations).
There can be another structure for perturbing B into A.
I will see if "isotopes" can solve the problem.
Thanks
Sushil
On Thu, May 8, 2014 at 1:04 PM, Andrew Dalke <da...@dalkescientific.com>wrote:
> Hi Sushil,
>
> On May 8, 2014, at 12:26 PM, Sushil Mishra wrote:
> > MCS algorithm seems to me unable to handle chiral carbons and it can not
> differentiate chiral changes in ligands.
>
> That's correct. The MCS algorithm in RDKit doesn't consider chirality.
> While in principle I think it would be possible to extend the current
> algorithm to support it, it would require some extensive changes.
>
> > Moreover, it also fails to differentiate between position of atoms in
> symmetrical positions.For example I have 6 atoms ring (C1, C2, C3, C4, C5,
> O5) with one -CH3 at C1 and another structure with -CH3 at C5. MCS can not
> differentiate such structures.
>
> The MCS search returns a SMARTS pattern, in this case something like:
>
> [#6]1~[#6]~[#6]~[#6]~[#6]~([~6])~[#8]1
>
> I don't think there's any way for a SMARTS, or a least a non-recursive
> SMARTS, to handle those other than symmetrically.
>
> It may be possible, through isotope labeling, for you to define your own
> atom classes, so that the C1 atom in one carbohydrate can only ever match
> the C1 atom in another.
>
> What would you like for it to return instead, in order to get the
> information you need?
>
> Cheers,
>
> Andrew
> da...@dalkescientific.com
>
>
>
> ------------------------------------------------------------------------------
> Is your legacy SCM system holding you back? Join Perforce May 7 to find
> out:
> • 3 signs your SCM is hindering your productivity
> • Requirements for releasing software faster
> • Expert tips and advice for migrating your SCM now
> http://p.sf.net/sfu/perforce
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
--
==================================================
Sushil Kumar Mishra, PhD
--------------------------------------------------
CEITEC- Central European Institute of Technology. MU
ILBIT, Building A4 - 2.12
Kamenice 5, Brno 625 00
Czech Republic
--------------------------------------------------
Email : sus...@chemi.muni.cz
Phone : +420-549 496 307
==================================================
------------------------------------------------------------------------------
Is your legacy SCM system holding you back? Join Perforce May 7 to find out:
• 3 signs your SCM is hindering your productivity
• Requirements for releasing software faster
• Expert tips and advice for migrating your SCM now
http://p.sf.net/sfu/perforce
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
