MongoChem Schema

This page describes the schema for the mongo database used by MongoChem.

Molecules Collection

The data is stored in a format similar to Chemical JSON.

{ 
  "name" : "phenol"
  "smiles": "C1=CC=C(C=C1)O",
  "atomCount" : 13,
  "heavyAtomCount" : 7,
  "formula" : "C6H6O",
  "inchi" : "1S/C6H6O/c7-6-4-2-1-3-5-6/h1-5,7H",
  "inchikey" : "ISWSIDIOOBJBQZ-UHFFFAOYSA-N",
  "descriptors" : {
    "tpsa" : 20.2,
    "xlogp3" : 0,
    "mass" : 94.11,
    "rotatable-bonds" : 0,
    "vabc" : 89.95
  },
  "annotations" : {
      ["john", Date(), "ran test #4 on phenol"]
  },
  "diagram" : {
      "png" : BinData(0, "..."),
      "svg": "<?xml version=\"1.0\"?>\n<svg vers ... >" 
  },
  "3dStructure" :  {
      "$ref" : "quantum",
      "$id" : ObjectId("5126bc054aed4daf9e2ab772")
  }
}

The data is indexed by inchikey (unique) and heavyAtomCount (non-unique).

Quantum Collection

{ 
  "molecule" : {
    "$ref" : "molecules",
    "$id" : ObjectId("5126bc054aed4daf9e2ab772")
  },
  "name" : "C15H6N1S.39.86.sp.upbe10.tv.n.s",
  "calculation" : {
    "guess" : { ... },
    "theory" : "B3LYP",
    "basis" : "TZVP" 
  },
  "energy" : {
    "total" : -1923.12,
    "alpha" : {
      "homo" : -0.3,
      "lumo" : -0.1,
      "gap" : 0.2 
    },
    "beta" : : {
      "homo" : -0.3,
      "lumo" : -0.1,
      "gap" : 0.2 
    },
  },
  "totalDipoleMoment" : 3.3101,
  "files" : {
    "log" : [  ],
    "binary" : [ ]
  }
  "atoms": { ... } 
}