Thanks for the detailed reply
>
> The fact that this isn't happening for you indicates that you are reading
> the molecules in without sanitizing them - the mol file parser calls
> assignStereochemistry() by default if you sanitize. Are you sure that you
> should be disabling sanitization?
>
>
I did turn it off, but then afterwards I call sanitize, but with a
user-specified option for whether to perform the
Kekulization/setAromaticity steps. I'm not certain what we want to set as
the default behavior, but I want the user to have the option of having the
molecule stay in the particular kekulized state that they input. I will go
through the molfile parser to see what else I'm missing out on by doing the
sanitization step afterward.
Would it break functionality to add a sanitizeOps optional argument to some
of the XXXToMol functions (defaulting to SANITIZE_ALL of course)?
Looking at the bonds block I pasted in, I do see that the bond directions
were specified therein. Will have to ruminate on what to do with them -
when they were written out the intention was obviously to convey the 3D
geometry, but it clearly clashes with the convention of using wedges and
dashes to indicate chirality.
> -greg
>
>
>
>>
>> The mol file for the second question is pasted below, and here is the
>> generated depiction,
>>
>> [image: Inline image 2]
>>
>>
>> aspirin.mol
>>
>> 21 21 0 0 0
>> -2.2240 -1.4442 -0.4577 C 0 0 0 0 0
>> -2.1657 -0.0545 -0.5349 C 0 0 0 0 0
>> -0.9916 0.6085 -0.1694 C 0 0 0 0 0
>> 0.1471 -0.0738 0.2764 C 0 0 0 0 0
>> 0.0751 -1.4832 0.3390 C 0 0 0 0 0
>> -1.1052 -2.1532 -0.0188 C 0 0 0 0 0
>> 1.2412 -2.2934 0.7925 C 0 0 0 0 0
>> 2.4223 -1.7619 1.1727 O 0 0 0 0 0
>> 1.1650 -3.5162 0.8364 O 0 0 0 0 0
>> 1.2795 0.6233 0.5954 O 0 0 0 0 0
>> 1.1005 1.7577 1.3258 C 0 0 0 0 0
>> 2.4429 2.3635 1.6825 C 0 0 0 0 0
>> 0.0255 2.2041 1.6578 O 0 0 0 0 0
>> -3.1430 -1.9775 -0.7500 H 0 0 0 0 0
>> -3.0382 0.5167 -0.8915 H 0 0 0 0 0
>> -0.9608 1.7083 -0.2479 H 0 0 0 0 0
>> -1.1740 -3.2520 0.0315 H 0 0 0 0 0
>> 2.9869 -2.5132 1.4166 H 0 0 0 0 0
>> 2.3142 3.3967 2.0773 H 0 0 0 0 0
>> 3.1051 2.4141 0.7884 H 0 0 0 0 0
>> 2.9391 1.7459 2.4657 H 0 0 0 0 0
>> 1 2 2 0 0 0
>> 1 6 1 0 0 0
>> 1 14 1 0 0 0
>> 2 3 1 0 0 0
>> 2 15 1 0 0 0
>> 3 4 2 0 0 0
>> 3 16 1 0 0 0
>> 4 5 1 0 0 0
>> 4 10 1 0 0 0
>> 5 6 2 0 0 0
>> 5 7 1 0 0 0
>> 6 17 1 0 0 0
>> 7 8 1 0 0 0
>> 7 9 2 0 0 0
>> 8 18 1 0 0 0
>> 10 11 1 1 0 0
>> 11 12 1 0 0 0
>> 11 13 2 0 0 0
>> 12 19 1 0 0 0
>> 12 20 1 6 0 0
>> 12 21 1 1 0 0
>> M END
>>
>>
>> Thanks,
>>
>> Jason
>>
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>
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