Further discussion in the office, the objection is more to the double
headed equilibrium arrows look like everything coming from nothing. For a
reversible metabolic reaction it's probably more accurate to split the
arrow (as we do for normal reversible reaction) and duplicate the side
components.
[image: Inline images 1]
Regards,
John W May
john.wilkinson...@gmail.com
On 12 May 2016 at 16:54, John M <john.wilkinson...@gmail.com> wrote:
> Hey all,
>
> I've been doing a fair bit on reaction depictions recently. It's tended to
> focus on organic chemistry but was wondering how much interest there would
> be in specialised metabolic reaction depictions.
>
> We do much better with the introduction of abbreviations:
>
> SMILES:
>
> C(C)(C)[C@@H]([C@H](C(=O)[O-])O)C(=O)[O-].C1=CC(=C[N+](=C1)[C@H]2[C@
>> @H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OC[C@@H]3[C@H]([C@H]([C@
>> @H](O3)N4C=NC5=C4N=CN=C5N)O)O)O)O)C(=O)N>>CC(CC(C(=O)[O-])=O)C.C=1N=C(C2=C(N1)N(C=N2)[C@H
>> ]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N.C(=O)=O
>> |SgD::cdk:ReactionConditions:1.1.1.85|
>
>
> CDK Depict
> <http://cdkdepict-openchem.rhcloud.com/depict/bow/svg?smi=C(C)(C)[C@@H]([C@H](C(=O)[O-])O)C(=O)[O-].C1=CC(=C[N%2B](=C1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)N4C=NC5=C4N=CN=C5N)O)O)O)O)C(=O)N%3E%3ECC(CC(C(=O)[O-])=O)C.C=1N=C(C2=C(N1)N(C=N2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N.C(=O)=O%20%7CSgD%3A%3Acdk%26%2358%3BReactionConditions%3A1.1.1.85%7C&abbr=on&suppressh=true&showtitle=false&zoom=1.3&annotate=none>
>
> [image: Inline images 1]
> Excluding the group abbreviations:
> [image: Inline images 3]
>
> But putting the NAD+,NADH,CO2 as side components with an arc may be more
> intuitive to some.
>
> See here: http://www.genome.jp/dbget-bin/www_bget?rn:R10052
>
> [image: Inline images 2]
>
>
> I did show this to a colleague with a background in Chemistry this morning
> though and he said he couldn't tell what was going on here.
>
> It's a moderate amount of work and I'm kind of under the impression the
> current depiction is pretty good at conveying what's going on. If there is
> significant demand for it though it could be something to add.
>
> Thoughts?
>
> John
>
> P.S. we can display a reversible arrow and individual molecule titles (in
> the reaction) but no way to put that in SMILES.
>
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