Chemical JSON

Specification

Note

Reference

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.

{
  "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.