The AC NMR Document format¶

For the storage in the database and for an exchange file format the AC-NMR DB uses a JSON file format. This format encodes the structure formula and the literature reference.

The atom and bonds objects in this file format are modeled as closely as possible to the CML XML format in terms of label names and options.

The NMR Document Object JSON Format¶

The ‘*‘ signifies a required Field.

Data format for molecules and NMR data.

Type:	object
Contains:	_rev, _id, docid, owner, date, molecule, NMRDatasets, sdf, Litref, Annotations, Error
Required:	True
JSON Path:	#

Example JSON:

{
  "NMRDatasets": [],
  "molecule": {
    "Mol_ID": "",
    "bonds": [],
    "atoms": []
  }
}

_rev¶

Revision ID as used by the document store.

Type:	string
Required:	False
JSON Path:	# [‘_rev‘]

Example JSON:

{"_rev": ""}

_id¶

Document ID GUID as used by the document store.

Type:	string
Required:	False
JSON Path:	# [‘_id‘]

Example JSON:

{"_id": ""}

docid¶

Unique document ID. This is used as ID throughout the application.

Type:	string
Required:	False
JSON Path:	# [‘docid‘]

Example JSON:

{"docid": ""}

owner¶

User who did last edit.

Type:	string
Required:	False
JSON Path:	# [‘owner‘]

Example JSON:

{"owner": ""}

date¶

UTC Time of last edit as Unix time stamp. (seconds since epoc)

Type:	number
Required:	False
JSON Path:	# [‘date‘]

Example JSON:

{"date": 0}

molecule¶

Contains molecule data. Data, like atoms, bonds and color coding.

Type:	object
Contains:	InChI, InChIKey, Mol_ID, MolLinked, Mol_Name, CAS_RN, SMILES, Stereoinformation, BoilingPoint, MSPeakListPeaks, MSPeakListSourceID, MeltingPoint, FORMULA, Comment, atoms, bonds*
Required:	True
JSON Path:	# [‘molecule‘]

Example JSON:

{"molecule": {"Mol_ID": "","bonds": [],"atoms": []}}

InChI¶

International chemical identifier.

Type:	string
Required:	False
JSON Path:	# [‘molecule‘][‘InChI‘]

Example JSON:

{"InChI": ""}

InChIKey¶

International chemical identifier hashed. If available, it will be used for finding data sets with the same chemical structure.

Type:	string
Required:	False
JSON Path:	# [‘molecule‘][‘InChIKey‘]

Example JSON:

{"InChIKey": ""}

Mol_ID¶

Arbitrary ID for molecule. This is used if InChI is not available.

Type:	string
Required:	True
JSON Path:	# [‘molecule‘][‘Mol_ID‘]

Example JSON:

{"Mol_ID": ""}

MolLinked¶

Flag for deciding if changes on this molecule structure should affect the others with the same ID

Type:	boolean
Required:	False
Default:	False
JSON Path:	# [‘molecule‘][‘MolLinked‘]

Example JSON:

{"MolLinked": false}

Mol_Name¶

Compound name.

Type:	string
Required:	False
JSON Path:	# [‘molecule‘][‘Mol_Name‘]

Example JSON:

{"Mol_Name": ""}

CAS_RN¶

Compound number from the American Chemical Society.

Type:	string
Required:	False
JSON Path:	# [‘molecule‘][‘CAS_RN‘]

Example JSON:

{"CAS_RN": ""}

SMILES¶

SMILES Code. This represents the connection graph of the molecule and is used for substructure and similarity search.

Type:	string
Required:	False
JSON Path:	# [‘molecule‘][‘SMILES‘]

Example JSON:

{"SMILES": ""}

Stereoinformation¶

Marker for molecules containing chiral structure.

Type:	boolean
Required:	False
JSON Path:	# [‘molecule‘][‘Stereoinformation‘]

Example JSON:

{"Stereoinformation": true}

BoilingPoint¶

Boiling point [°C].

Type:	string
Required:	False
JSON Path:	# [‘molecule‘][‘BoilingPoint‘]

Example JSON:

{"BoilingPoint": ""}

MSPeakListPeaks¶

Type:	string
Required:	False
JSON Path:	# [‘molecule‘][‘MSPeakListPeaks‘]

Example JSON:

{"MSPeakListPeaks": ""}

MSPeakListSourceID¶

Type:	string
Required:	False
JSON Path:	# [‘molecule‘][‘MSPeakListSourceID‘]

Example JSON:

{"MSPeakListSourceID": ""}

MeltingPoint¶

Melting point [°C].

Type:	string
Required:	False
JSON Path:	# [‘molecule‘][‘MeltingPoint‘]

Example JSON:

{"MeltingPoint": ""}

FORMULA¶

Sum formula.

Type:	string
Required:	False
JSON Path:	# [‘molecule‘][‘FORMULA‘]

Example JSON:

{"FORMULA": ""}

Comment¶

Arbitrary comment.

Type:	string
Required:	False
JSON Path:	# [‘molecule‘][‘Comment‘]

Example JSON:

{"Comment": ""}

atoms¶

Type:	array() items: {2d, 3d, elementType, hydrogenCount, formalCharge, role, properties}
Required:	True
JSON Path:	# [‘molecule‘][‘atoms‘]

Example JSON:

{"atoms": []}

2d¶

2D atom coordinates for structure diagrams. [a.u]

Type:	array(2) items: number
Required:	True
JSON Path:	# [‘molecule‘][‘atoms‘][0][‘2d‘]

Example JSON:

{"2d": []}

3d¶

3D atom coordinates for 3d structure (crystal-structure). [a.u]

Type:	array(3) items: number
Required:	False
JSON Path:	# [‘molecule‘][‘atoms‘][0][‘3d‘]

Example JSON:

{"3d": []}

elementType¶

Symbol of chemical Element. Allowed are the symbols as defined in CML.

Type:	string
values:	[H, He, Li, Be, B, C, N, O, F, Ne, Na, Mg, Al, Si, P, S, Cl, Ar, K, Ca, Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Ga, Ge, As, Se, Br, Kr, Rb, Sr, Y, Zr, Nb, Mo, Tc, Ru, Rh, Pd, Ag, Cd, In, Sn, Sb, Te, I, Xe, Cs, Ba, La, Ce, Pr, Nd, Pm, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu, Hf, Ta, W, Re, Os, Ir, Pt, Au, Hg, Tl, Pb, Bi, Po, At, Rn, Fr, Ra, Ac, Th, Pa, U, Np, Pu, Am, Cm, Bk, Cf, Es, Fm, Md, No, Lr, Rf, Db, Sg, Bh, Hs, Mt, Ds, Rg, Cn, Uuq, Uuh, Du, R]
Required:	True
JSON Path:	# [‘molecule‘][‘atoms‘][0][‘elementType‘]

Example JSON:

{"elementType": "H"}

hydrogenCount¶

Hydrocen-count as defined in CML.

Type:	number
Required:	False
JSON Path:	# [‘molecule‘][‘atoms‘][0][‘hydrogenCount‘]

Example JSON:

{"hydrogenCount": 0}

formalCharge¶

Formal charge as defined in CML.

Type:	number
Required:	False
JSON Path:	# [‘molecule‘][‘atoms‘][0][‘formalCharge‘]

Example JSON:

{"formalCharge": 0}

role¶

The role is used to further describe ‘R’ or ‘Du’ pseudo Atoms. May be used to describe polymeres by using ‘*’

Type:	string
Required:	False
JSON Path:	# [‘molecule‘][‘atoms‘][0][‘role‘]

Example JSON:

{"role": ""}

properties¶

Properties of the atom that are not directly related to the molecular structure, such as coloring, and other annotations.

Type:	object
Contains:	color
Required:	False
JSON Path:	# [‘molecule‘][‘atoms‘][0][‘properties‘]

Example JSON:

{"properties": {}}

color¶

Color code of atom to hilight or mark atom or set of atoms.

Type:	string or null
Required:	False
JSON Path:	# [‘molecule‘][‘atoms‘][0][‘properties‘][‘color‘]

Example JSON:

{"color": null}

bonds¶

Array of bonds.

Type:	array() items: {id, bond, order, stereoType}
Required:	True
JSON Path:	# [‘molecule‘][‘bonds‘]

Example JSON:

{"bonds": []}

id¶

type:	object
Required:	False
JSON Path:	# [‘molecule‘][‘bonds‘][0][‘id‘]

Example JSON:

{"id": {}}

bond¶

Indices of atoms which are connected via this bond. Index starts with 1.

Type:	array(2) items: number
Required:	True
JSON Path:	# [‘molecule‘][‘bonds‘][0][‘bond‘]

Example JSON:

{"bond": []}

order¶

The type or ‘order’ of this bond. The bond order values are as defined in CML.

Type:	string
values:	[1, hbond, partial01, partial12, 2, partial23, 3, A]
Required:	True
JSON Path:	# [‘molecule‘][‘bonds‘][0][‘order‘]

Example JSON:

{"order": "1"}

stereoType¶

Stereo-type as defined in CML.

Type:	string
values:	[C, T, W, H]
Required:	False
JSON Path:	# [‘molecule‘][‘bonds‘][0][‘stereoType‘]

Example JSON:

{"stereoType": "C"}

NMRDatasets¶

Chemical shifts and couplings.

Type:	array() items: {Shifts, Nucleus, Solvent, Standard, Method, Temp}
Required:	True
JSON Path:	# [‘NMRDatasets‘]

Example JSON:

{"NMRDatasets": []}

Shifts¶

List of shifts for from one nucleus, standard, solvent, temperature ... -combination.

Type:	array() items: {Shift, ColorRef, Comment, J}
Required:	False
JSON Path:	# [‘NMRDatasets‘][0][‘Shifts‘]

Example JSON:

{"Shifts": []}

Shift¶

Numerical value of chemical shift in [ppm].

Type:	number or object
Contains:	from, to
Required:	False
JSON Path:	# [‘NMRDatasets‘][0][‘Shifts‘][0][‘Shift‘]

Example JSON:

{"Shift": null}

from¶

Type:	number
Required:	False
JSON Path:	# [‘NMRDatasets‘][0][‘Shifts‘][0][‘Shift‘][‘from‘]

Example JSON:

{"from": 0}

to¶

Type:	number
Required:	False
JSON Path:	# [‘NMRDatasets‘][0][‘Shifts‘][0][‘Shift‘][‘to‘]

Example JSON:

{"to": 0}

ColorRef¶

Colour label to match the colors in molecular structure.

Type:	string
Required:	False
JSON Path:	# [‘NMRDatasets‘][0][‘Shifts‘][0][‘ColorRef‘]

Example JSON:

{"ColorRef": ""}

Comment¶

Comment for shift.

Type:	string
Required:	False
JSON Path:	# [‘NMRDatasets‘][0][‘Shifts‘][0][‘Comment‘]

Example JSON:

{"Comment": ""}

J¶

List of coupling constants for this shift.

Type:	array() items: {ftype, textval, type, unit, value}
Required:	False
JSON Path:	# [‘NMRDatasets‘][0][‘Shifts‘][0][‘J‘]

Example JSON:

{"J": []}

ftype¶

Coupling type including text formatting information.

Type:	string
Required:	True
Default:	J()
JSON Path:	# [‘NMRDatasets‘][0][‘Shifts‘][0][‘J‘][0][‘ftype‘]

Example JSON:

{"ftype": "J()"}

textval¶

Unparsed text value if availabe.

Type:	string
Required:	True
JSON Path:	# [‘NMRDatasets‘][0][‘Shifts‘][0][‘J‘][0][‘textval‘]

Example JSON:

{"textval": ""}

type¶

Coupling type whithout text formatting information.

Type:	string
Required:	True
JSON Path:	# [‘NMRDatasets‘][0][‘Shifts‘][0][‘J‘][0][‘type‘]

Example JSON:

{"type": ""}

unit¶

Unit of numeric value.

Type:	string
Required:	False
Default:	Hz
JSON Path:	# [‘NMRDatasets‘][0][‘Shifts‘][0][‘J‘][0][‘unit‘]

Example JSON:

{"unit": "Hz"}

value¶

Numeric value of coupling constant.[Hz]

Type:	number
Required:	True
JSON Path:	# [‘NMRDatasets‘][0][‘Shifts‘][0][‘J‘][0][‘value‘]

Example JSON:

{"value": 0}

Nucleus¶

Type of nucleus used in NMR, ‘29Si’, for example.

Type:	string
Required:	False
JSON Path:	# [‘NMRDatasets‘][0][‘Nucleus‘]

Example JSON:

{"Nucleus": ""}

Solvent¶

Solvent in which NMR measurement took place.

Type:	string
Required:	False
JSON Path:	# [‘NMRDatasets‘][0][‘Solvent‘]

Example JSON:

{"Solvent": ""}

Standard¶

Reference compount for shift.

Type:	string
Required:	False
JSON Path:	# [‘NMRDatasets‘][0][‘Standard‘]

Example JSON:

{"Standard": ""}

Method¶

NMR Method.

Type:	string
Required:	False
JSON Path:	# [‘NMRDatasets‘][0][‘Method‘]

Example JSON:

{"Method": ""}

Temp¶

Sample teperature. [°C]

Type:	string
Required:	False
JSON Path:	# [‘NMRDatasets‘][0][‘Temp‘]

Example JSON:

{"Temp": ""}

sdf¶

Field to store legacy sdf source if available.

Type:	string
Required:	False
JSON Path:	# [‘sdf‘]

Example JSON:

{"sdf": ""}

Litref¶

Literature reference. Each data document may be associated with one literature reference.

Type:	object
Contains:	LitrefLinked, Author, YEAR, Title, DOCTYPE, Page, REFNO*, Source, Volume, Keyword, Editor, CASAN, DOI
Required:	False
JSON Path:	# [‘Litref‘]

Example JSON:

{"Litref": {"REFNO": ""}}

LitrefLinked¶

Flag for deciding if changes on this literature reference should be changed in all documents.

Type:	boolean
Required:	False
Default:	True
JSON Path:	# [‘Litref‘][‘LitrefLinked‘]

Example JSON:

{"LitrefLinked": true}

Author¶

Author.

Type:	string
Required:	False
Default:
JSON Path:	# [‘Litref‘][‘Author‘]

Example JSON:

{"Author": ""}

YEAR¶

Year of publication.

Type:	number
Required:	False
JSON Path:	# [‘Litref‘][‘YEAR‘]

Example JSON:

{"YEAR": 0}

Title¶

Title.

Type:	string
Required:	False
JSON Path:	# [‘Litref‘][‘Title‘]

Example JSON:

{"Title": ""}

DOCTYPE¶

Journal, book, thesis ...

Type:	string
Required:	False
JSON Path:	# [‘Litref‘][‘DOCTYPE‘]

Example JSON:

{"DOCTYPE": ""}

Page¶

Page number.

Type:	string
Required:	False
JSON Path:	# [‘Litref‘][‘Page‘]

Example JSON:

{"Page": ""}

REFNO¶

This is an ID for the reference. Many documents may come from the same Literature reference.

Type:	string
Required:	True
JSON Path:	# [‘Litref‘][‘REFNO‘]

Example JSON:

{"REFNO": ""}

Source¶

Journal name, for example.

Type:	string
Required:	False
JSON Path:	# [‘Litref‘][‘Source‘]

Example JSON:

{"Source": ""}

Volume¶

Journal or book volume.

Type:	string
Required:	False
JSON Path:	# [‘Litref‘][‘Volume‘]

Example JSON:

{"Volume": ""}

Keyword¶

List of keywords seperated by ‘ ‘ or ‘,’.

Type:	string
Required:	False
JSON Path:	# [‘Litref‘][‘Keyword‘]

Example JSON:

{"Keyword": ""}

Editor¶

Publication Editor

Type:	string
Required:	False
JSON Path:	# [‘Litref‘][‘Editor‘]

Example JSON:

{"Editor": ""}

CASAN¶

Chemical Abstract Service reference id of the American Chemical Society.

Type:	string
Required:	False
JSON Path:	# [‘Litref‘][‘CASAN‘]

Example JSON:

{"CASAN": ""}

DOI¶

Digital Object Identifier for the literature reference.

Type:	string
Required:	False
Default:
JSON Path:	# [‘Litref‘][‘DOI‘]

Example JSON:

{"DOI": ""}

Annotations¶

This may contain arbitrary data and comments.

Type:

object

Contains:

Required:

False

JSON Path:

# [‘Annotations‘]

Example JSON:

{"Annotations": {}}

Error¶

Processing errors.

Type:	string
Required:	False
JSON Path:	# [‘Error‘]

Example JSON:

{"Error": ""}