>> I have identified at least the following limitations :
>> - the atomic mass can be specified in the SMILES string but is not used
>> for
>> the pattern matching (I didn't find the notion of atomic mass in Jmol)
>
>Q: Is there general value in adding a table of atomic masses to Jmol?
>
>Q: If we did add such a table, would it just create more problems ...
>becaue everyone would want to define their own masses?
I don't think we are talking about the same thing ;) By atomic mass, I was
refering to the number of protons + neutrons of an atom. It can be used for
example to select for U235 but not U238.
So, I don't think there is a need for a table. The only think that could be
added to Jmol is an "atomic mass" field to the atoms and then modify the
readers to put the correct value in this field.
>> - the chirality can not be specified in the SMILES string. I will probably
>> modify the parser to work when the chirality is specified, but, unless
>> someone really needs it, I don't plan to add it to the pattern matching
>> part.
>
>Q: Are you saying that there is no support for chirality in the SMILES
>specification?
SMILES specification supports chirality, but I didn't take the time to add the
code to parse it ;)
I will modify the parser so that if someone input a SMILES string with
chirality, there won't be a parsing error.
But I am not sure I will modify the pattern matching code to take advantage of
this information : it seems a lot of work.
>> - directional bonds can not be specified in the SMILES string. Same
>> comment as for chirality.
>
>Q: What is a 'directional bond' ?
For example,
H H
\ /
C=C
/ \
Cl Cl
can be distinguished from
Cl H
\ /
C=C
/ \
H Cl
>> - aromaticity is not handled correctly (I didn't test it) : the definition
>> of aromatic bonds (':') should work but not the symbol in lower case.
>
>Q: Are you having some specific problems handling aromaticity? Or is it
>the case that you simply have not had time to implement it yet?
I just gave aromaticity a quick look (and the notion of sp2 hibridization) and
it seemed a bit complex for a first version.
For the moment, let's say I didn't have time to implement it yet but maybe I
will find some problems ;)
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