On Thu, Jun 6, 2013 at 10:50 PM, Dimitri Maziuk <dmaz...@bmrb.wisc.edu>wrote:
> On 06/06/2013 03:13 PM, Tim Vandermeersch wrote:
> > Hi,
> >
> > The OpenChemsitry project also uses JSON (
> > http://wiki.openchemistry.org/Chemical_JSON).
>
> Not criticizing your effort, specifically, as this is common to most
> "life sciences" formats, but,
>
I was not involved with this effort but thought it might be good to make
others aware of this. The OpenChemistry project was started by Kitware and
I know Marcus Hanwell is working on this (I included him in the recipients).
> I'm afraid to a programmer this has about 0 information content:
>
> elements": {
> "number": [ 1, 6, 1, 1, 6, 1, 1, 1 ]
> },
> "coords": {
> "3d": [ 1.185080, -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 ]
> }
> },
> "bonds": {
> "connections": {
> "index": [ 0, 1,
> 1, 2,
> 1, 3,
> 1, 4,
> 4, 5,
> 4, 6,
> 4, 7 ]
> },
> "order": [ 1, 1, 1, 1, 1, 1, 1 ]
>
>
> Where does it say which one's "C1" and which one's "H7"? All I can tell
> from this is all atoms are linked with the same type of bond ("1" stands
> for "aromatic" perhaps?) What do you draw if the "-0.932892" is missing
> from the json the client sent you?
>
The molecule above contains al you need. The elements.number list contains
the chemical element number (i.e. 1 = H, 6 = C) for the atoms in the order
that will be adhered to in the rest of the JSON string (i.e. the list
indices are the atom indices). Ths bond.connections.index list contains
pairs that specify a start and end atom for a bond. The orders are the
orders of the bonds as they are listed in the conncections.index list. 1
simply means a single bond. The described molecule is therefore ethane with
explicit hydrogens.
I'm not sure what you mean by the "-0.932892" is missing, do you mean a
single value from the list is missing? If so, the code that produced the
JSON is wrong but this is not something the format tries to handle. Also
the 3d coordinates may well be left out. AFAIK, this format was meant as a
simple format to exchange molecules between different software modules
using a JSON to ensure no handwritten parser code is needed.
Marcus, could you elaborate on this?
> If you want it machine-usable, you need at least the table of elements,
> the table of bond "numbers" (might as well use names), and atoms encoded
> as (element, index) pairs. Connections as (atom1, atom2, bond) tuples
> and 3d coordinates as (x, y, z) tuples.
>
> One of the particularly annoying things about pubchem is nowhere in
> their ASN.1, XML, or SDF you will find compound name that is shown on
> the webpage.
>
> (Apologies for the mini-rant, I've been working for biochemists for too
> long.)
>
No problem, any feedback is welcome :)
Tim
> --
> Dimitri Maziuk
> Programmer/sysadmin
> BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
>
>
>
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