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JSON Structure format (Principles)
AlexanderSavelyev edited this page Jan 26, 2021
·
1 revision
Everything is a graph. Nodes and Edges which can have types
{
id: '/Graph',
type: 'object',
required: ['root'],
properties: {
root: { $ref: '#/root' }
},
patternProperties: {
'^mol': { $ref: '/Molecule' },
'^rg': { $ref: '/RGroup' }
},
root: rootSchema
}
const rootSchema = {
id: '/Root',
required: ['nodes'],
properties: {
nodes: {
type: 'array',
items: {
oneOf: [
{ $ref: '/RxnPlus' },
{ $ref: '/RxnArrow' },
{
type: 'object',
required: ['$ref'],
properties: {
$ref: {
type: 'string'
}
}
}
]
}
},
edges: {
type: 'array',
items: {
oneOf: [
{
properties: {
$refs: {
type: 'array',
maxItems: 2,
items: {
type: 'string'
}
}
}
}
// ...
]
}
}
}
};
{
id: '/Molecule',
type: 'object',
allOf: [
{ $ref: '#/header' },
{
properties: {
atoms: {
title: 'Atoms',
type: 'array',
items: {
oneOf: [
{ $ref: '#/atom' },
{ $ref: '#/rgatom' },
{ $ref: '#/atomlist' }
]
}
},
bonds: {
title: 'Bonds',
type: 'array',
items: { $ref: '#/bond' }
},
sgroups: {
title: 'SGroups',
type: 'array',
items: { $ref: '#/sgroup' }
}
}
}
],
header,
atom,
atomlist,
rgatom,
bond,
sgroup
}
{
id: '/RGroup',
type: 'object',
allOf: [
{
properties: {
rlogic: { $ref: '#/logic' }
}
},
{ $ref: '/Molecule' }
],
logic: rgroupLogic
}
const rgroupLogic = {
title: "RGroupLogic",
type: "object",
required: ['number'],
properties: {
number: {
type: 'number'
},
range: {
title: 'Occurrence',
type: 'string',
maxLength: 50,
default: ''
},
resth: {
title: 'RestH',
type: 'boolean',
default: false
},
ifthen: {
title: 'Condition',
type: 'integer',
minimum: 0,
default: 0
}
}
};
{
"root" : {
"id" : "",
"type" : "molecule",
"atoms" : [
{"id": "a1", "label" : "C", "location": [ -0.762160, 1.168557, 0.022754 ]},
{"id": "a2", "label" : "C", "location": [ 0.631044, 1.242862, -0.013022 ]},
{"id": "a3", "label" : "N", "location": [ 0.631044, 1.242862, -0.013022 ]}
],
"bonds" : [
{ "atoms" : ["a1", "a2"], "order" : 1 },
{ "atoms" : ["a2", "a3"], "order" : 2 }
]
}
}
{
"root" : {
"id" : "",
"type" : "graph",
"nodes" : [
{
"$ref": "mol1"
},
{
"$ref":"mol2"
}
],
"edges" : [
{
"refs" : ["mol1", "mol2"]
}
]
},
// All graphs, types "graph", "atom", "bond". Will use the molecule instead of graph, but keep it here
"mol1" : {
"type" : "graph",
"nodes" : [
{"id": "a1", "type": "atom", "label" : "C", "location": [ -0.762160, 1.168557, 0.022754 ]},
{"id": "a2", "type": "atom", "label" : "C", "location": [ 0.631044, 1.242862, -0.013022 ]}
],
"edges" : [
{ "type": "bond", "refs" : ["a1", "a2"], "order" : 1 }
]
}
// Just a sugar for the first variant
"mol2" : {
"type" : "molecule",
"atoms" : [
{ "id": "a1", "label" : "C", "location": [ -0.762160, 1.168557, 0.022754 ] },
{ "id": "a2", "label" : "C", "location": [ 0.631044, 1.242862, -0.013022 ] }
{ "type": "rg-label", "location": [ 1, 1, 1 ], "$refs": ["r1", ...], "rgroups": [{ /RGroup }, ...] } // refs to RGroups in root OR inline RGroups
],
"bonds" : [
{ "refs" : ["a1", "a2"], "order" : 1 }
]
}
"r1" : {
"type" : "rgroup",
"rlogic": {
"ifthen":"r5"
"number":4
"range":">0"
}
"atoms" : [
{"id": "a1", "label" : "C", "location": [ -0.762160, 1.168557, 0.022754 ]},
}
}
{
"root" : {
"id" : "",
"type" : "graph",
"nodes" : [
{
"id" : "mol1",
"type" : "molecule",
"atoms" : [
{"id": "a1", "label" : "C", "location": [ -0.762160, 1.168557, 0.022754 ]},
{"id": "a2", "label" : "C", "location": [ 0.631044, 1.242862, -0.013022 ]},
{"id": "a3", "label" : "N", "location": [ 0.631044, 1.242862, -0.013022 ]}
],
"bonds" : [
{ "refs" : ["a1", "a2"], "order" : 1 },
{ "refs" : ["a2", "a3"], "order" : 2 }
]
},
{
"id": "prop1",
"type": "map",
"properties": [
{
"key": "name",
"value": "benzene"
},
{
"key": "mass",
"value": 200
}
]
},
{
"id" : "mol2",
"type" : "molecule",
"atoms" : [
{"id": "a1", "label" : "C", "location": [ -0.762160, 1.168557, 0.022754 ]},
{"id": "a2", "label" : "C", "location": [ 0.631044, 1.242862, -0.013022 ]},
{"id": "a3", "label" : "N", "location": [ 0.631044, 1.242862, -0.013022 ]}
],
"bonds" : [
{ "refs" : ["a1", "a2"], "order" : 1 },
{ "refs" : ["a2", "a3"], "order" : 2 }
]
},
{
"id": "prop2",
"type": "map",
"properties": [
{
"key": "name",
"value": "benzene"
},
{
"key": "mass",
"value": 200
}
]
}
],
"edges" : [
{ "refs" : ["mol1", "prop1"] },
{ "refs" : ["mol2", "prop2"]}
]
}
}
// Reaction
{
"root": {
"nodes": [
{
"$ref": "mol0"
},
{
"type": "plus",
"location": [ 4.4201487709352, 10.724237873791509, 0 ],
"prop": {}
},
{
"$ref": "mol1"
},
{
"$ref": "mol2"
},
{
"type": "plus",
"location": [ 9.925, 9.675, 0 ],
"prop": {}
},
{
"type": "arrow",
"location": [ 12.103548353650336, 9.895950639370875, 0 ],
"prop": {}
},
{
"$ref": "mol3"
},
{
"type": "plus",
"location": [ 18.13344958231073, 8.317663404950244, 0 ],
"prop": {}
},
{
"$ref": "mol4"
}
]
},
"mol0": {
"type": "molecule",
"atoms": [
{
"label": "C",
"alias": "Hello",
"location": [ 1.9424188114308452, 11.698729991857089, 0 ],
"explicitValence": 4,
"radical": 2
},
{
"label": "Fe",
"location": [ 2.6495130922765844, 10.991635711011353, 0 ],
"ringBondCount": -1,
"substitutionCount": 5,
"unsaturatedAtom": true,
"hCount": 3,
"invRet": 2,
"exactChangeFlag": true
}
],
"bonds": [
{
"type": 1,
"atoms": [ 0, 1 ]
}
]
},
"mol1": {
"type": "molecule",
"atoms": [
{
"label": "P",
"location": [ 5.940784449593817, 10.556840036571668, 0 ],
"isotope": 1
},
{
"type": "rg-label",
"location": [ 6.647878730439557, 9.849745755725928, 0 ],
"attachmentPoints": 1,
"$refs": [ "rg-3" ]
}
],
"bonds": [
{
"type": 3,
"atoms": [ 0, 1 ],
"topology": 1
}
]
},
"mol2": {
"type": "molecule",
"atoms": [
{
"label": "O",
"location": [ 7.841987298107781, 10.125, 0 ]
},
{
"label": "O",
"location": [ 8.708012701892219, 9.625, 0 ]
}
],
"bonds": [
{
"type": 1,
"atoms": [ 0, 1 ]
}
]
},
"mol3": {
"type": "molecule",
"atoms": [
{
"label": "C",
"location": [ 15.859217976861114, 9.13405680175757, 0 ]
},
{
"label": "C",
"location": [ 16.566412256898033, 8.426962520911832, 0 ]
}
],
"bonds": [
{
"type": 1,
"atoms": [ 0, 1 ]
}
],
"sgroups": [
{
"type": "SUP",
"atoms": [ 0, 1 ],
"name": "NameAtom"
}
]
},
"mol4": {
"type": "molecule",
"atoms": [
{
"label": "N",
"location": [ 19.70048690772342, 8.208364288988655, 0 ]
},
{
"type": "atom-list",
"location": [ 20.407581188569157, 7.501270008142915, 0 ],
"elements": [ "Sg", "Tl", "Er", "Ru", "Cm" ]
}
],
"bonds": [
{
"type": 1,
"atoms": [ 0, 1 ]
}
]
}
}
// RGroups
{
"root": {
"nodes": [
{
"$ref": "rg4"
},
{
"$ref": "mol0"
},
{
"$ref": "rg5"
},
{
"$ref": "mol1"
}
]
},
"rg4": {
"type": "rgroup",
"rlogic": {
"number": 4,
"range": ">3",
"resth": true,
"ifthen": 5
},
"atoms": [
{
"label": "O",
"location": [ 16.674999999999997, 9.775, 0 ]
},
{
"label": "O",
"location": [ 17.540999999999993, 10.275, 0 ]
},
{
"label": "O",
"location": [ 18.407099999999996, 9.775, 0 ]
}
],
"bonds": [
{
"type": 1,
"atoms": [ 0, 1 ]
},
{
"type": 1,
"atoms": [ 1, 2 ]
}
]
},
"rg5": {
"type": "rgroup",
"rlogic": {
"number": 5
},
"atoms": [
{
"label": "C",
"location": [ 21.44198729810778, 10.300000000000002, 0 ]
},
{
"label": "C",
"location": [ 22.30801270189222, 9.800000000000002, 0 ]
}
],
"bonds": [
{
"type": 1,
"atoms": [ 0, 1 ]
}
]
},
"mol0": {
"type": "molecule",
"atoms": [
{
"label": "Na",
"location": [ 15.884, 7.025, 0 ],
"ringBondCount": -2,
"substitutionCount": 2,
"unsaturatedAtom": true,
"hCount": 3
},
{
"label": "Fe",
"alias": "Hello",
"location": [ 17.216, 7.575, 0 ],
"explicitValence": 7
},
{
"type": "atom-list",
"location": [ 5.125, 2.55, 0 ],
"elements": [ "Hs", "Mt", "Ds", "Rg" ]
},
{
"type": "rg-label",
"location": [ 18.475, 6.35, 0 ],
"attachmentPoints": 1,
"$refs": [ "rg-4", "rg-5", "rg-32" ]
}
],
"bonds": [
{
"type": 2,
"atoms": [ 2, 0 ]
},
{
"type": 6,
"atoms": [ 0, 1 ],
"topology": 2
},
{
"type": 1,
"atoms": [ 1, 3 ],
"topology": 1,
"center": -1
}
]
},
"mol1": {
"type": "molecule",
"atoms": [
{
"label": "C",
"location": [ 21.1, 6.5, 0 ]
},
{
"label": "C",
"location": [ 21.96602540378444, 7, 0 ]
}
],
"bonds": [
{
"type": 1,
"atoms": [ 0, 1 ]
}
],
"sgroups": [
{
"type": "DAT",
"atoms": [ 0, 1 ],
"context": "Bond",
"fieldName": "MDLBG_STEREO_KEY",
"fieldData": "endo"
},
{
"type": "DAT",
"atoms": [ 0, 1 ],
"context": "Bond",
"fieldName": "MDLBG_STEREO_KEY",
"fieldData": "alpha"
}
]
}
}