2-thiouridine.json

{
  "Chemical JSON": 0,
  "name": ""2-thiouridine"",
  "formula": "C 9 N 2 O 5 S 1",
  "inchi": "InChI=1S/C9H12N2O5S/c12-3-4-6(14)7(15)8(16-4)11-2-1-5(13)10-9(11)17/h1-2,4,6-8,12,14-15H,3H2,(H,10,13,17)",
  "atoms": {
    "elements": [6, 7, 8, 6, 6, 6, 6, 6, 8, 7, 16, 6, 8, 6, 6, 8, 8],
    "coords": {
      "3d": [
        12.0825, 1.1289, 0,
        12.0825, 1.9539, 0,
        11.4151, 0.6439, 0,
        12.75, 0.6439, 0,
        12.797, 2.3664, 0,
        11.3681, 2.3664, 0,
        11.67, -0.1407, 0,
        12.495, -0.1407, 0,
        13.5346, 0.8989, 0,
        12.797, 3.1914, 0,
        13.5115, 1.9539, 0,
        11.3681, 3.1914, 0,
        12.98, -0.8081, 0,
        12.0825, 3.6039, 0,
        11.1851, -0.8081, 0,
        11.5207, -1.5618, 0,
        12.0825, 4.4289, 0
      ]
    }
  },
  "bonds": {
    "connections": [
      0, 1, 
      0, 2, 
      0, 3, 
      1, 4, 
      1, 5, 
      2, 6, 
      3, 7, 
      3, 8, 
      4, 9, 
      4, 10, 
      5, 11, 
      6, 14, 
      7, 12, 
      9, 13, 
      13, 16, 
      6, 7, 
      11, 13, 
      14, 15
    ],
    "order": [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 1, 1, 1]
  }
}

jsonFail.txt

Traceback (most recent call last):
  File "writerFail.py", line 9, in <module>
    json.loads(f.writeString())
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/json/__init__.py", line 326, in loads
    return _default_decoder.decode(s)
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/json/decoder.py", line 360, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/json/decoder.py", line 376, in raw_decode
    obj, end = self.scan_once(s, idx)
ValueError: Expecting , delimiter: line 3 column 13 (char 36)

writerFail.py

import urllib2
import chemkit
f = chemkit.MoleculeFile()
f.setFormat('sdf')
f.readString(urllib2.urlopen('http://www.ebi.ac.uk/chebi/saveStructure.do?defaultImage=true&chebiId=60731&imageId=0').read())
f.setFormat('cjson')

import json
json.loads(f.writeString())