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---
title: Chemical JSON
---
## Specification
@Note [Reference](https://github.com/OpenChemistry/avogadrolibs/blob/master/avogadro/io/cjsonformat.cpp)
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.
## Example
Caffeine molecule in ``qcschema_molecule`` format.
```json
{
"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
]
}
}
```
## Missing features
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.
|
