Hi Sushil,
There is some information on using isotope information in MCS here:
http://rdkit.blogspot.ch/2014/01/an-interesting-mcs-use-case.html
-greg
On Thu, May 8, 2014 at 4:14 PM, Sushil Mishra <[email protected]>wrote:
> Hello again,
>
> Using isotopes seems to produce something that I am unable to understand.
> Sorry, I am new to python so may be I am not able to do it correctly. I
> have two mol2 structures stored in mol2str_1 and mol2str_2. These two have
> exactly same atom name of the MCS only. Rest of the names doesn't match
> with each other at all. What I am doing is:
>
> -------------------------------------------------------------------------------------------------
> mol1 = rdkit.Chem.MolFromMol2Block(mol2str_1, sanitize = False,
> removeHs = False)
>
> mol2 = rdkit.Chem.MolFromMol2Block(mol2str_2, sanitize = False,
> removeHs = False)
> mcs = rdkit.Chem.MCS.FindMCS( (mol1, mol2), maximize = 'atoms',
> atomCompare = 'isotopes', bondCompare =
> 'bondtypes',
> ringMatchesRingOnly = True,
> completeRingsOnly = True, timeout =
> maxtime)
> print mcs
>
> --------------------------------------------------------------------------------------------------------------
> Its is printing :
>
> '[0*](-!@[0*])(-!@[0*])(-!@[0*])-!@[0*]-!@[0*]-@1(-!@[0*])-@[0*]-@[0*](-!@[0*])(-@[0*](-@[0*](-@[0*]-@1(-!@[0*]-!@[0*])-!@[0*])(-!@[0*]-!@[0*])-!@[0*])(-!@[0*]-!@[0*])-!@[0*])-!@[0*](-!@[0*])(-!@[0*])-!@[0*]'
>
> Can someone suggest me if I am doing a mistake here ?
>
> /Sushil
>
>
>
> On Thu, May 8, 2014 at 1:57 PM, Sushil Mishra <[email protected]>
> wrote:
> >
> > 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 <[email protected]>
> 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
> >> [email protected]
> >>
> >>
> >>
> ------------------------------------------------------------------------------
> >> 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
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> >> 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 : [email protected]
> > Phone : +420-549 496 307
> > ==================================================
>
>
>
>
> --
> ==================================================
> Sushil Kumar Mishra, PhD
> --------------------------------------------------
> CEITEC- Central European Institute of Technology. MU
> ILBIT, Building A4 - 2.12
> Kamenice 5, Brno 625 00
> Czech Republic
> --------------------------------------------------
> Email : [email protected]
> 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
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
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