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 <sushilbioi...@gmail.com>
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 <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
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>
>
>
>
> --
> ==================================================
> 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
> ==================================================
--
==================================================
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
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