[Openchemistry-developers] cjson: nested lists instead of 1D lists for multidimensional data?

[Ian Daniher]

Any thoughts on this?

I'm going to try and convert the PyChEBI database (
https://github.com/itdaniher/PyChEBI) to something akin to chemjson
shortly.

Definitely leaning towards the nested list solution unless someone has a
compelling reason not to do so.

Best,
--
Ian

On Wed, Jun 13, 2012 at 4:11 PM, Ian Daniher <ian at nonolithlabs.com> wrote:

> Hi All,
>
> Right now, Chemical JSON uses a 1D list for all of the multidimensional
> information including 3d coordinates for atoms and bonds.
>
> When parsing the format, this results in the following:
>
> ethane["atoms"]["coords"]["3d"]
>>
>
>
>> [1.18508, -0.003838, 0.987524, 0.751621, -0.022441, -0.020839, 1.166929,
>> 0.833015, -0.569312, 1.115519, -0.932892, -0.514525, -0.751587, 0.022496,
>> 0.020891, -1.166882, -0.833372, 0.568699, -1.115691, 0.932608, 0.515082,
>> -1.184988, 0.004424, -0.987522]
>
>
> Getting the x, y, z coordinates of the first atom is overcomplicated in
> both javascript and python. A reasonable use case might be looping through
> ethane["atoms"] and drawing based on the location of each.
>
> In python, this would look like:
>
> for i in range(len(ethane["atoms"]["elements"]["number"])):
>     start = 0+i
>     end = 3*(1+i)
>     x, y, z = ethane["atoms"]["coords"]["3d"][start:end]
>     draw(x,y,z)
>
> If the list was nested, it would look like the following:
>
> for i in range(len(ethane["atoms"]["elements"]["number"])):
>     x, y, z = ethane["atoms"]["coords"]["3d"][i]
>    draw(x, y, z)
>
> Fewer things to keep track of, fewer places to screw up, more implicit
> information. Everyone wins.
>
> Not sure what sort of performance hit you get with nested array
> serialization, but this might let you remove the "3d" subobject as
> dimensionality of coordinates would be explicit.
>
> The same argument applies to the "bonds" subobject.
>
> Best!
> --
> Ian
>
>
>
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