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'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?
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.)
--
Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
signature.asc
Description: OpenPGP digital signature
------------------------------------------------------------------------------ How ServiceNow helps IT people transform IT departments: 1. A cloud service to automate IT design, transition and operations 2. Dashboards that offer high-level views of enterprise services 3. A single system of record for all IT processes http://p.sf.net/sfu/servicenow-d2d-j
_______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
