> 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
[email protected]
On 6 July 2015 at 22:16, Zheng Shi <[email protected]> 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 <[email protected]>
> 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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