ARGH Forgot to post to the group.
On 9 May 2012 10:23, JP <[email protected]> wrote:
>
> On 9 May 2012 05:12, Greg Landrum <[email protected]> wrote:
>
>> one last question:
>>
>>
>> Could this be due to the problem discussed on this thread?
>>
>> http://www.mail-archive.com/[email protected]/msg02100.html
>>
>> -greg
>>
>
>
> This is something related to format - because if I load this
> somewhat-truncated smaller mol2 file (
> http://dl.dropbox.com/u/13990555/rec.mol2) using rdkit I get the can't
> kekulize error. Note that this original mol2 file is created using open
> babel.
>
> Having been through the pains of incorrect file formats before - I load
> this file in MOE and save it again as a mol2 file (
> http://dl.dropbox.com/u/13990555/rec-moe.mol2) and this works fine and is
> read correctly by RDKit.
>
> Interesting, Sherlock.
>
> There is a difference in spacing between the two files - and data types on
> column 7 (using 0-based indexing). Also column 6 seems to be always 1 in
> the MOE version (which I do not think makes a difference -- as that is the
> substructure id - http://tripos.com/data/support/mol2.pdf). I haven't
> dug deeper in this yet... but I hope this offers a start.
>
>
>
>
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