Thanks, John -
On the same vein: what is the appropriate way to handle these comparisons when
the source is an MDL V3000 with placeholder atoms/wildcards (nots, etc)? Is
there a CDK test that can handle this or would I have to implement a custom
comparison library?
John
> On Jul 7, 2015, at 13:50, John M <john.wilkinson...@gmail.com> wrote:
>
> > So is there a reasonable way to do that? can we just generate canonical
> > form for molecules (like SMILES, then compare the SMILES)? Is it reasonable
> > for this? Or other methods? Thanks.
>
> Yep Unique SMILES (canon,no stereo), Absolute SMILES (canon,with stereo) or
> InChI should do what you need.
>
> J
>
> Regards,
> John W May
> john.wilkinson...@gmail.com
>
>> On 6 July 2015 at 22:16, Zheng Shi <zs...@ualberta.ca> wrote:
>> The "compare" means to tell if two molecules are equal. Suppose I have a
>> molecule B, which is generated by molecule A during a reaction: A -> B, and
>> I get a molecule C, which is also generated by molecule A during a reaction:
>> A->C. I want to tell whether B and C are the same. Usually we can visualize
>> the structure of the two structures to see. But if the number of molecules
>> is too big, for example, two sdf files contain some molecules, then it's not
>> convenient to visualize manually. So is there a reasonable way to do that?
>> can we just generate canonical form for molecules (like SMILES, then compare
>> the SMILES)? Is it reasonable for this? Or other methods? Thanks.
>>
>>> On Mon, Jul 6, 2015 at 3:17 AM, John M <john.wilkinson...@gmail.com> wrote:
>>> Hit send too soon...
>>>
>>> b) Generate hash codes (CDK/InChIKey)
>>> c) Graph-Isomorphism check.
>>>
>>> Normally the best approach is (a) but this might not be the
>>> equality/comparison you want?
>>>
>>> John
>>>
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