Thank you, Greg!
Very nice explanation and I think this issue has confused people before me
as well. I am going to have to keep reminding myself about it as the
subject comes up every now and then.
Igor
On Jan 29, 2014 10:59 PM, "Greg Landrum" <[email protected]> wrote:
> Hi Igor,
>
> On Wed, Jan 29, 2014 at 2:04 PM, Igor Filippov
> <[email protected]>wrote:
>
>> Greg et al,
>>
>> Here is a little script that demonstrates a problem with fingerprints
>> after the roundtrip through InChI.
>> My input mol file is also attached.
>> As you can see the similarity between "before" and "after" is not 1 in 45
>> out of 100 cases.
>> In one case it is as low as 0.29. Could someone take a look and tell me
>> what I'm doing wrong?
>>
>
> Ah! Now I see what you're doing and understand the problem.
>
> It's really important when using InChI to remember that InChI is designed
> to be an identifier, not an interchange format. The InChI algorithm
> modifies the molecule as part of its canonicalization step. This
> modification includes standardizing tautomers.
>
> Here's an example of the type of substructure modification that happens in
> your molecules:
> input smiles c1ccccc1C(=O)Nc1ccccc1 on begin converted to InChI and back
> yields: OC(=Nc1ccccc1)c1ccccc1
>
> Basically: If you think you know what your molecules are, you probably
> should be building them from SMILES or CTAB, not InChI.
>
> Apologies that I didn't think of this before; I was just focusing on the
> stereochemistry.
>
> -greg
>
------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends. Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
_______________________________________________
Rdkit-discuss mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
