Note
Chemical JSON files are identified by the extension cjson
and parsed following the format implemented in Avogadro 2.
The entries name, atoms.elements.number, atoms.coords.3d, atoms.coords.3d fractional, unit cell, atoms.formalCharges, bonds.connections.index, and bonds.order are recognized by the reader.
Caffeine molecule in qcschema_molecule
format.
{
"chemicalJson": 1,
"atoms": {
"elements": {
"number": [
6, 7, 6, 7, 6, 6, 6, 8, 7, 6, 8, 7, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
]
},
"coords": {
"3d": [
1.0731997649702911E+00, 4.8899989290949721E-02, -7.5699983421776973E-02,
2.5136994495022558E+00, 1.2599997240612813E-02, -7.5799983399877077E-02,
3.3519992659154081E+00, 1.0958997599990143E+00, -7.5299983509376570E-02,
4.6189989884436962E+00, 7.3029984006504256E-01, -7.5499983465576764E-02,
4.5790989971817559E+00, -6.3139986172404194E-01, -7.5299983509376570E-02,
3.3012992770186567E+00, -1.1025997585317211E+00, -7.5199983531276451E-02,
2.9806993472297307E+00, -2.4868994553714288E+00, -7.3799983837875047E-02,
1.8252996002611557E+00, -2.9003993648153492E+00, -7.5799983399877077E-02,
4.1143990989505834E+00, -3.3042992763616597E+00, -6.9399984801470568E-02,
5.4516988060832432E+00, -2.8561993744951040E+00, -7.2399984144473614E-02,
6.3892986007497967E+00, -3.6596991985294207E+00, -7.2299984166373524E-02,
5.6623987599401575E+00, -1.4767996765823013E+00, -7.4899983596976152E-02,
7.0094984649266268E+00, -9.3649979490745228E-01, -7.5199983531276451E-02,
3.9205991413925863E+00, -4.7408989617477202E+00, -6.1599986509662634E-02,
7.3399983925474632E-01, 1.0878997617510062E+00, -7.4999983575076257E-02,
7.1239984398512435E-01, -4.5699989991746470E-01, 8.2339981967623732E-01,
7.1239984398512435E-01, -4.5579990018026340E-01, -9.7549978636649193E-01,
2.9929993445360430E+00, 2.1175995362477531E+00, -7.4799983618876062E-02,
7.7652982994071955E+00, -1.7262996219420552E+00, -7.5899983377977168E-02,
7.1485984344638682E+00, -3.2179992952612718E-01, 8.1969982048653345E-01,
7.1479984345952676E+00, -3.2079992974512617E-01, -9.6949978768048573E-01,
2.8649993725679135E+00, -5.0231988999243073E+00, -5.8299987232359275E-02,
4.4022990359007768E+00, -5.1591988701404459E+00, 8.2839981858124223E-01,
4.4001990363606742E+00, -5.1692988679285561E+00, -9.4779979243276369E-01
]
}
},
"bonds": {
"connections": {
"index": [
0, 1,
1, 2,
2, 3,
3, 4,
1, 5,
4, 5,
5, 6,
6, 7,
6, 8,
8, 9,
9, 10,
4, 11,
9, 11,
11, 12,
8, 13,
0, 14,
0, 15,
0, 16,
2, 17,
12, 18,
12, 19,
12, 20,
13, 21,
13, 22,
13, 23
]
},
"order": [
1, 4, 4, 4, 1, 4, 1, 2, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
]
}
}
The schema is not verified on completeness and not all data is stored in the final structure type.
Note
Feel free to contribute support for missing features or bring missing features to our attention by opening an issue.