Chemaxon Object Notation - CXON

Code: cxon

Chemaxon Object Notation (CXON [sɪksɒn]) is a Chemaxon specific JSON representation for chemical documents.

About the format

The CXON file format is primarily designed to support web based transfer of chemical documents. CXON files can store both chemical (explicit molelcules, Markush structures, chemical reactions) and graphical content (visual properties, graphical objects, formatted text boxes, etc.).

Main characteristics:

• A CXON document is a well formed JSON
• The applied standards were chosen to support the matching of the content to web-based technologies, e.g. HTML color-codes are used to represent colors or the standard SVG Path is used to store graphical paths
• A CXON document can be easily inserted in REST payloads as is
• CXON can be used with JSON.stringify and JSON.parse natively in JavaScript

Schema

The CXON format has a JSON Schema descriptor. The all-time latest CXON schema specification can be accessed here.

Document Structure

ChemicalDocument

Chemaxon specific JSON representation of a chemical document.

{warning} Please mind that this project is in beta phase, which means that currently no backward compatibility is guaranteed.

Fields

field	type	description
$schema	string	The url for the schema the CXON file is compliant with
$version	string	The version of the CXON schema (e.g.: 1.0.0-beta)
title	string	The title of the entire chemical document.
comment	string?	Comment for the chemical document.
molecules	Molecule[]	List of the simple Molecules in the document. Reaction and Markush components are handled separately.
reactions	Reaction[]	List of chemical Reactions in the document.
markushStructures	MarkushStructure[]	List of Markush structures in the document.
graphicalObjects	(Arrow | Bracket | Ellipse | Image | Line | Path | Rectangle | TextBox | PlusSign)[]?	List of graphical objects in the document.
displayProperties	DisplayProperties?	Object to hold all display related properties, such as visibility options, rendering hints, or graphical statuses.
properties	{ [k: string]: any; }?	Key-value pairs of additional custom properties.

Molecule

A simple chemical structure. Can be listed in the document as is, or defined as an entity in a Reaction or Markush structure.

Fields

field	type	description
id	string	Reference id of this object. Should be unique for the entire document.
nature	MoleculeNature	Logical property of the molecule, marking its type from cheminformatical point of view. PLAIN is for regular molecules, NO_STRUCTURE for placeholder molecule for search purposes.
atoms	Atom[]	The list of the Atoms in this molecule.
bonds	Bond[]	The list of the Bonds in this molecule.
groups	Group[]	The list of the Groups in this molecule.
properties	{ [k: string]: any; }?	Key-value pairs of additional custom properties.

Reaction

A chemical Reaction. Only single step reactions are supported.

Fields

field	type	description
id	string	Reference id of this object. Should be unique for the entire document
direction	ReactionDirection?	The direction of the reaction. If omitted, the reaction direction is FORWARD
reactants	Molecule[]	The list of the reactants of the reaction.
agents	Molecule[]	The list of the agents of the reaction.
products	Molecule[]	The list of the products of the reaction.

MarkushStructure

A Markush structure object. A Markush structure is defined by a scaffold, a list of Definitions and an optional Logic to describe extra rules for Definition substitutions.

Fields

field	type	description
id	string	Reference id of this object. Should be unique for the entire document.
scaffold	{ [k: string]: any; }	The scaffold (root structure) of this Markush.
definitions	Definitions[]?	The list of the variable Definitions for this Markush.
logic	Logic[]?	The extra rules for the Definiton substitutions

Definitions

Markush Definitons is a list of alternatives the R-atoms can be substituted with.

Fields

field	type	description
name	string?	The name of the definition. Usually the label of the corresponding R-atom. Functions as an id as well, so it has to be unique within this Markush structure.
alternatives	Molecule[]?	The applicable alternatives for this definition. This definition can be substituted with any of these alternatives.

Logic

The extra rules for the Definiton substitutions

Fields

field	type	description
targetDefinition	string?	The name of the Definition this logic defined for.
occurenceCount	string?	The desired substitution count of the target Definition as a string. The value represents either an exact count or an open or closed range.
restH	boolean?	This Logic triggers if and only if all substitutions of the R-atoms of the scaffold are either an alternative from the target or a Hydrogen atom.
thenDefinition	string?	Makes this Logic an if-then type conditional Logic and specifies the then-definition name.

Atom

An atom object. Basic building block of molecule objects. Either can be a natural chemical element, or a logical placeholder for custom entities, such as groups attachment points, query entities or Markush atoms.

Fields

field	type	description
id	string	Reference id of this object. Should be unique for the entire document
label	string	The label of this Atom, which is the symbol from the periodic table for natural elements, or a custom label for logical Atoms.
nature	AtomNature	Logical property of the Atom, marking its type from cheminformatical point of view. SUPERATOM is for legacy purposes only, do not use.
alias	string?	A custom label to override the label of this Atom in some cases.
charge	number?	The electrical charge (formal charge) of this Atom as a signed integer. Should be omitted for uncharged Atoms.
isotope	number?	The isotopical mass (sum of the count of protons and count of neutrons in the nucleus) of this Atom as a positive integer.
location	Location?	The coordinate of this Atom. If omitted, it should be considered as (0;0;0).
mapping	number?	Atom-to-Atom mapping index: correspondence of Atoms in different structures. Do not confuse with numbering, which is a dynamic, calculated value, stored as the name of the numbering algorithm for the entire document.
radical	AtomRadical?	Free radical value of the Atom.
stereo	Stereo?	The stereochemistry-properties attached to this atom
implicitHydrogenCount	number?	Indicates the suggested number of implicit hydrogens bound to this Atom. Correct values can vary in different systems. When the value is considered incorrect it can be ignored. This is not a query property.
properties	{ [k: string]: any; }?	Key-value pairs of additional custom properties.

Location

Three dimensional coordinate to mark a Location. In CXON it is a molecular Cartesian coordinate in Angstroms.

Fields

field	type	description
x	number	X-coordinate.
y	number	Y-coordinate.
z	number	Z-coordinate.

Bond

A Bond object, which is a basic building block of Molecule objects. Can be a chemical bond or a query bond.

Fields

field	type	description
id	string	Reference id of this object. Should be unique for the entire document.
type	BondType	Type of this Bond. Can be a chemical covalent bond (SINGLE, DOUBLE, TRIPLE, AROMATIC, COORDINATE) or stereochemically enhanced covalent bond (UP, DOWN, UP_OR_DOWN), or a query bond (ANY, CIS_OR_TRANS, SINGLE_OR_AROMATIC, SINGLE_OR_DOUBLE, DOUBLE_OR_AROMATIC, UP_OR_DOWN).
startAtom	string	The reference id of the Atom this bond starts at. The direction is not important in most cases, but relevant for stereochemical and dative bonds.
endAtom	string	The reference id of the Atom this bond ends at. The direction is not important in most cases, but relevant for stereochemical and dative bonds.
query	BondQuery?	The query features attached to this bond

Group

Work in progress

Fields

field	type	description
id	string	Reference id of this object. Should be unique for the entire document
type	GroupType	Type of this Group
name	string?	The name of this Group. In case of abbreviation this is the default label.
location	Location?	The coordinate of this Group. This location should be used if the group is contracted. If omitted, it should be considered as (0;0;0).
atoms	string[]	The reference ids of the Atoms in this Group.
bonds	string[]?	The reference ids of the Bonds in this Group.
attachmentPoints	AttachmentPoint[]?	The AttachmentPoints of this group.

AttachmentPoint

AttachmentPoint descriptor object. Describes a site in this Group on which it can bond with other substances. It has an order which can have conventional meaning, such as in case of amino acids the amid bonds are formed from one amino acid's 2nd AttachmentPoint to another's 1st AttachmentPoint.

Fields

field	type	description
atom	string?	The reference id of the Atom that serves as the site of chemical bonding with other substances.
order	number?	The unique order of the AttachmentPoint. The AttachmentPoint orders in a Group should be a sequential set of positive integers starting from 1.

Paragraph

Paragraphs are newline separated portions of a text. Paragraph consists of an array of sections, which are independently formattable portions of text.

Fields

field	type	description
sections	Section[]	The content of the Paragraph. An array of formatted Sections, which are continuous portions of text separated only for formatting, the content should be joined without any additional delimiter.

Section

Sections of a Paragraph separated only for formatting purposes. Each Section has one formatting setup, there are no embedded sections, hence no style inheritance. Any formatting option not specified in the section falls back to the default value of the Textbox

Fields

field	type	description
text	string	Plain textual content of the Section without formatting.
font	Font?	The font properties of the Section. If not specified, then the visualizer/renderer chooses the font.
formula	boolean?	Indicates if this Section contains a chemical formula or not. Purely for marker purposes, to mark the intentions of the editor.
color	string?	The color of the Section's text, specified as a HTML color code.
backgroundColor	string?	The background-color of the Section's text, specified as a HTML color code.

Font

Font descriptor object.

Fields

field	type	description
family	string?	The actual font family, such as 'Arial' or 'Times New Roman', or a logical family such as 'Serif'.
size	number?	The size of the Font in points.
style	FontStyle[]?	The Font's style.

Stroke

An object to specify properties for lines, borders, etc.

Fields

field	type	description
style	StrokeStyle?	The style of this Stroke, modifies the line style of this Stroke.
color	string?	The color of this Stroke, specified as a HTML color code.
thickness	number?	The thickness of this Stroke in points. For best results, use positive integer values.

Arrow

A graphical Arrow, which is a directed line from one Location to another.

Fields

field	type	description
id	string	Reference id of this object. Should be unique for the entire document.
shape	string	Has to be ARROW
arrowType	ArrowType?	Type of this Arrow: SINGLE(----->), DOUBLE(=====>), BLOCK(====	>), CROSSED(–x–>), CURVED(a curved SINGLE arrow), DASHED(- - ->), EQUILIBRIUM(´=====,), HASHED(--//–>) or RESONANCE(<----->)
head	{ [k: string]: any; }	Properties of the Head of this Arrow. The Head is at the Location this Arrow is directed to.
tail	{ [k: string]: any; }	Properties of the Tail of this Arrow. The Tail is at the Location this Arrow is directed from.
line	Stroke?	The line of this Arrow. In most cases it is the arrow itself, but for example in case of BLOCK arrow, it is the outline.
arc	{ [k: string]: any; }?	The arc of this arrow. Should be specified only for CURVED arrows. This property describes an SVG arc. The SVG path's d attribute that describes this arc is: M headLocationX headLocationY A rx ry xAxisRotation largeArcFlag sweepFlag tailLocationX tailLocationY where tail and head location values are the corresponding properties of the arrow. For further details please visit https://www.w3.org/TR/SVG/paths.html#PathDataEllipticalArcCommands
properties	{ [k: string]: any; }?	Key-value pairs of additional custom properties.

Bracket

A graphical Bracket, which is a pair of brackets enclosing an area.

Fields

field	type	description
id	string	Reference id of this object. Should be unique for the entire document.
shape	string	Has to be BRACKET
points	Location[]	The corner points of the bracketed area in the order top-left, top-right, bottom-right and bottom-left.
line	Stroke?	The line of this Bracket
type	BracketType?	The type of this Bracket. If not specified, it is considered SQUARE([]). Also can be ROUND(()), BRACES({}), or CHEVRONS(<>)
properties	{ [k: string]: any; }?	Key-value pairs of additional custom properties.

Ellipse

A graphical Ellipse.

Fields

field	type	description
id	string	Reference id of this object. Should be unique for the entire document.
shape	string	Has to be ELLIPSE
points	Location[]	The corners of the bounding rectangle in the order top-left, top-right, bottom-right and bottom-left. The corners has to be defined in the atomic space to keep the relative position to the chemical content. The defined rectangle scaled up into the graphical space gives the area the shape should be rendered into.
background	string?	The background color of this Ellipse, specified as a HTML color code. Not specified means transparent.
border	Stroke?	The border of this Ellipse. An object of border properties. Right now only the color and thickness can be specified.
properties	{ [k: string]: any; }?	Key-value pairs of additional custom properties.

Image

An Image that can be remote or embedded into this document as a base64 encoded image.

Fields

field	type	description
id	string	Reference id of this object. Should be unique for the entire document.
shape	string	Has to be IMAGE
points	Location[]	The corners of the bounding rectangle in the order top-left, top-right, bottom-right and bottom-left. The corners has to be defined in the atomic space to keep the relative position to the chemical content. The defined rectangle scaled up into the graphical space gives the area the image should be rendered into.
url	string?	The URL of this Image
placeholder	string?	Base64 encoded image to render if the remote image is not available, or while it is loading
image	string?	Base64 encoded image
properties	{ [k: string]: any; }?	Key-value pairs of additional custom properties.

Line

A graphical undirected, straight Line.

Fields

field	type	description
id	string	Reference id of this object. Should be unique for the entire document.
shape	string	Has to be LINE
points	Location[]	The endpoints of this Line
line	Stroke?	The graphical properties of this Line.
properties	{ [k: string]: any; }?	Key-value pairs of additional custom properties.

Path

Work in progress

Fields

field	type	description
id	string	Reference id of this object. Should be unique for the entire document.
shape	string	Has to be PATH
points	Location[]	The corners of the bounding rectangle in the order top-left, top-right, bottom-right and bottom-left. The corners has to be defined in the atomic space to keep the relative position to the chemical content. The defined rectangle scaled up into the graphical space gives the area the shape should be rendered into.
svgPath	string	This Path described as an SVG path. See the 'd' property of SVG path at https://www.w3.org/TR/SVG/paths.html
background	string?	The background color of this Path, specified as a HTML color code. Not specified means transparent. Only applicable for closed paths.
line	Stroke?	Work in progress
properties	{ [k: string]: any; }?	Key-value pairs of additional custom properties.

Rectangle

A graphical Rectangle.

Fields

field	type	description
id	string	Reference id of this object. Should be unique for the entire document.
shape	string	Has to be RECTANGLE
points	Location[]	The corners of the bounding rectangle in the order top-left, top-right, bottom-right and bottom-left. The corners has to be defined in the atomic space to keep the relative position to the chemical content. The defined rectangle scaled up into the graphical space gives the area the shape should be rendered into.
background	string?	The background color of this Rectangle, specified as a HTML color code. Not specified means transparent.
border	Stroke?	The border of this Rectangle. An object of border properties. Right now only the color can be specified.
properties	{ [k: string]: any; }?	Key-value pairs of additional custom properties.

TextBox

A Textbox, which is a formatted textual content that should be rendered into a rectangular area.

Fields

field	type	description
id	string	Reference id of this object. Should be unique for the entire document.
shape	string	Has to be TEXTBOX
points	Location[]	The corners of the bounding rectangle in the order top-left, top-right, bottom-right and bottom-left. The corners has to be defined in the atomic space to keep the relative position to the chemical content. The defined rectangle scaled up into the graphical space gives the area the textbox should be rendered into.
font	Font?	The default font for the Textbox. If a section of the Textbox does not specify some, or any of the font properties, this should be used for missing values. If this value is not set either, it is up to the renderer what font is used.
color	string?	The default color for the Textbox, specified as a HTML color code. If a section of the Textbox does not specify a color, this should be used.
paragraphs	Paragraph[]	The content of the Textbox. An array of Paragraphs, which are newline separated portions of the whole textual content.
autoResize	boolean?	Marks whether this Textbox should change its size on change of the content. If not set, it is considered false.
background	string?	The background color of the Textbox, specified as a HTML color code. Not specified means transparent.
align	TextBoxAlign?	The horizontal alignment of the content. If not specified, it is considered LEFT
verticalAlign	TextBoxVerticalAlign?	The vertical alignment of the content. If not specified, it is considered TOP.
border	Stroke?	The border of this Textbox. An object of border properties. Right now only the color can be specified.
properties	{ [k: string]: any; }?	Key-value pairs of additional custom properties.

PlusSign

A graphical PlusSign

Fields

field	type	description
id	string	Reference id of this object. Should be unique for the entire document.
shape	string	Has to be PLUSSIGN
points	Location[]	The corners of the bounding rectangle in the order top-left, top-right, bottom-right and bottom-left.
line	Stroke?	The line of the a PlusSign
properties	{ [k: string]: any; }?	Key-value pairs of additional custom properties.

DisplayProperties

Describes the rendering hints for the content of this document.

Fields

field	type	description
saveProperties	boolean?	Marks whether these properties should be saved or not after editing the document.
scale	number?	The scale for rendering the elements in this document. The coordinates in this format are in Angstroms, so this property is basically a multiplier that transforms coordinates from Angstroms to pixels.
background	string?	The color of the background in HTML color code.
atomDisplayProperties	AtomDisplayProperties?	Rendering hints for Atoms.
bondDisplayProperties	BondDisplayProperties?	Rendering hints for Bonds.
moleculeDisplayProperties	MoleculeDisplayProperties?	Rendering hints for Molecules.
reactionDisplayProperties	ReactionDisplayProperties?	Rendering hints for Reactions.
groupDisplayProperties	GroupDisplayProperties?	Rendering hints for Groups.
z-index	string[]?	Stores ordering of objects on the z-axis.

AtomDisplayProperties

Describes the rendering hints for Atoms. If an Atom has rendering hints in the customized section, then it should be used, otherwise the rendering hints in this section, and if there are no rendering hints in this section, it is the renderer's choice how to render the Atom.

Fields

field	type	description
labelFont	Font?	The default font for atom labels.
color	string?	The default color for atom labels in HTML color code.
mapColor	string?	The default color for atom map labels in HTML color code.
chargeColor	string?	The default color for charge labels in HTML color code.
stereoColor	string?	The default color for stereo labels in HTML color code.
atomNumberingType	AtomDisplayPropertiesAtomNumberingType?	The numbering algorithm for atoms.
atomPropertiesVisible	boolean?	Sets whether atom properties (extra properties added in a key-value pair) are visible or not.
atomMappingVisible	boolean?	Sets whether atom mapping is visible or not.
lonePairsVisible	boolean?	Sets whether the lone pairs should be rendered or not.
lonePairsAsLine	boolean?	Sets whether the lone pairs should be rendered as lines (true) or as dots (false). If this property is not specified, the default is the latter.
calculateLonePairs	boolean?	Sets whether the lone pairs should be calculated for each atom (true) or use the precalculated values only (false).
carbonVisibility	AtomDisplayPropertiesCarbonVisibility?	sets the visibility property for carbon atoms.
charge	AtomDisplayPropertiesCharge?	sets the display property for charges on atoms.
peptide	AtomDisplayPropertiesPeptide?	sets the display property for peptides.
customized	AtomDisplayProperty[]?	List of specific display properties for atoms that have unique rendering specifications, like font or color, etc.

AtomDisplayProperty

Descriptor of display properties for customized atoms

Fields

field	type	description
id	string	The internal reference id of the customized atom. The same id as in the atoms array of a molecule.
labelFont	Font?	The font for the atom label.
color	string?	The color for the atom label of a given atom in HTML color code.
mapColor	string?	The color for atom map label of a given atom in HTML color code.
chargeColor	string?	The color for charge label of a given atom in HTML color code.
stereoColor	string?	The color for stereo label of a given atom in HTML color code.
formattedLabel	Section[]?	The atom label with formatting. An array of formatted sections, which are continuous portions of text separated only for formatting, the content should be joined without any delimiter.
atomMappingLocation	Location?	Display location information for atom mapping label, relative to atom.
stereoLabelLocation	Location?	Display location information for stereo label, relative to atom.
chargeLocation	Location?	Display location information for charge label, relative to atom.

BondDisplayProperties

Describes the rendering hints for Bonds. If a Bond has rendering hints in the customized section, then it should be used, otherwise the rendering hints in this section, and if there are no rendering hints in this section, it is the renderer's choice how to render the Bond.

Fields

field	type	description
bondLength	number?	The default rendered bond length in points.
aminoAcidBondColoringEnabled	boolean?	If true, then the amino acid bridge (usually S-S bridges) bonds are colored.
bondLengthVisible	boolean?	If true, then the bond length values (in Angstrom) are displayed next to the bonds.
coordinateBondStyle	string?	Sets the style of coordinate bonds.
coordinateBondStyleAtMulticenter	string?	Sets the style of coordinate bonds if the bond points from or to a multicenter (also known as position variation bond).
boldBondWidth	number?	Sets the width of bold bonds in points.
bondSpacing	number?	Sets the gap between double (aromatic and some query bonds as well) and triple bonds in points.
bondHashSpacing	number?	Sets the spacing between the hashed lines for single down wedged bonds and hashed bonds in points.
wireThickness	number?	Bond thickness in wireframe mode in points.
stickThickness	number?	The stick diameter for ball and stick mode in points.
downWedge	BondDisplayPropertiesDownWedge?	Wedge bond display convention. Down wedge points downward in MDL's convention, upward (at the chiral center) in Daylight's.
anyBond	string?	The bond-style to draw any-bonds with.
customized	BondDisplayProperty[]?	List of bond specific display properties for bonds that have unique rendering specifications, such as color.

BondDisplayProperty

Descriptor of display properties for customized bonds

Fields

field	type	description
id	string	The internal reference id of the customized bond. The same id as in the bonds array of a molecule.
bondStyle	string?	The style for the bond.
color	string?	The color for the bond in HTML color code.
doubleBondAlignment	BondDisplayPropertyDoubleBondAlignment?	Double bond alignment between two atoms, defined from the viewpoint of the start atom towards the end atom.
stereoLabelLocation	Location?	Display location information for stereo label, relative to the midpoint of bond.

MoleculeDisplayProperties

Describes the rendering hints for Molecules.

Fields

field	type	description
ezVisible	boolean?	Whether to show E/Z labels.
mpVisible	boolean?	Whether to show M/P labels.
valenceErrorVisible	boolean?	Whether to show valence errors.
absoluteLabelVisible	boolean?	Whether to show absolute stereo configuration labels.
colorScheme	MoleculeDisplayPropertiesColorScheme?	Color scheme. (MONO=monochrome, CPK=Corey-Pauling-Kultun, SHAPELY=shapely (residue types), GROUP=residue sequence numbers).

ReactionDisplayProperties

Describes the rendering hints for Reactions.

Fields

field	type	description
automaticReactionDetection	boolean?	Marks whether the content of this document should be automatically converted to a reaction. This conversion will only take place if the content was not a reaction and there is exactly one graphical arrow in the document.
sketchArrowHeadLength	number?	Length of the head of the (graphical) reaction arrow in points.
sketchArrowHeadWidth	number?	Width of the head of the (graphical) reaction arrow in points.
sketchArrowTailLength	number?	Length of the tail of the (graphical) reaction arrow in points.
sketchArrowTailWidth	number?	Width of the tail of the (graphical) reaction arrow in points.
customized	ReactionDisplayProperty[]?	List of reaction specific display properties for reactions that have unique rendering specifications, such as a custom arrow.

ReactionDisplayProperty

Descriptor of display properties for customized reactions

Fields

field	type	description
id	string	The internal reference id of the customized reaction. The same id as in the reactions array of the document.
arrow	Arrow?	The custom arrow for the reaction. If not present, the reaction arrow should be generated by the renderer based on the reaction's direction property.

GroupDisplayProperties

Describes the rendering hints for Groups.

Fields

field	type	description
customized	GroupDisplayProperty[]?	List of group specific display properties for groups that have custom rendering specifications.

GroupDisplayProperty

Descriptor of display properties for customized groups

Fields

field	type	description
id	string	The internal reference id of the customized group.
contracted	boolean?	Marks whether the group is represented in a contracted form or not.
formattedLabel	Section[]?	Group label as formatted text. An array of formatted sections, which are continuous portions of text separated only for formatting, the content should be joined without any delimiter.

Stereo

The stereochemistry-properties attached to this atom

Fields

field	type	description
enhanced	EnhancedStereo?	The stereo representation matching MDL's Enhanced Stereo Representation

EnhancedStereo

The stereo representation matching MDL's Enhanced Stereo Representation

Fields

field	type	description
type	EnhancedStereoType	The way to connect groups according to this representation. Note, that "AND" and "OR" does not make sense without a group, while "ABSOLUTE" does not make sense with a group.
group	number?	Serves as the basis to connect type "AND" or "OR" enhanced stereo-atoms. (A complete enhanced stereochemical representation is made of all the atoms having the same type and group enhanced stereo descriptors)

BondQuery

The query features attached to this bond

Fields

field	type	description
topology	string?	Queries will match only if this bond is part of a chain or ring (as per the value of this property)

BondStyle

The style for the bond

Values

Hashed = "HASHED", Dashed = "DASHED", Bold = "BOLD", Wavy = "WAVY", Down = "DOWN", Up = "UP", Up_Or_Down = "UP_OR_DOWN", Default = "DEFAULT", Arrow = "ARROW", Auto = "AUTO", Solid = "SOLID"

BondTopology

Queries will match only if this bond is part of a chain or ring (as per the value of this property)

Values

In_Ring = "IN_RING", In_Chain = "IN_CHAIN"

MoleculeNature

Logical property of the molecule, marking its type from cheminformatical point of view. PLAIN is for regular molecules, NO_STRUCTURE for placeholder molecule for search purposes.

Values

Plain = "PLAIN", No_Structure = "NO_STRUCTURE"

ReactionDirection

The direction of the reaction. If omitted, the reaction direction is FORWARD

Values

Forward = "FORWARD", Backward = "BACKWARD", Equilibrium = "EQUILIBRIUM"

AtomNature

Logical property of the Atom, marking its type from cheminformatical point of view. SUPERATOM is for legacy purposes only, do not use.

Values

Natural = "NATURAL", Attachment_Point = "ATTACHMENT_POINT", Conventional = "CONVENTIONAL", Pseudo = "PSEUDO", Query = "QUERY", R_Atom = "R_ATOM", Superatom = "SUPERATOM"

AtomRadical

Free radical value of the Atom.

Values

None = "NONE", Monovalent = "MONOVALENT", Divalent = "DIVALENT", Divalent_Singlet = "DIVALENT_SINGLET", Divalent_Triplet = "DIVALENT_TRIPLET", Trivalent = "TRIVALENT", Trivalent_Doublet = "TRIVALENT_DOUBLET", Trivalent_Quartet = "TRIVALENT_QUARTET"

BondType

Type of this Bond. Can be a chemical covalent bond (SINGLE, DOUBLE, TRIPLE, AROMATIC, COORDINATE) or stereochemically enhanced covalent bond (UP, DOWN, UP_OR_DOWN), or a query bond (ANY, CIS_OR_TRANS, SINGLE_OR_AROMATIC, SINGLE_OR_DOUBLE, DOUBLE_OR_AROMATIC, UP_OR_DOWN).

Values

Any = "ANY", Aromatic = "AROMATIC", Cis_Or_Trans = "CIS_OR_TRANS", Coordinate = "COORDINATE", Double = "DOUBLE", Double_Or_Aromatic = "DOUBLE_OR_AROMATIC", Down = "DOWN", Single = "SINGLE", Single_Or_Aromatic = "SINGLE_OR_AROMATIC", Single_Or_Double = "SINGLE_OR_DOUBLE", Triple = "TRIPLE", Up = "UP", Up_Or_Down = "UP_OR_DOWN"

GroupType

Type of this Group

Values

Abbreviation = "ABBREVIATION", Amino_Acid = "AMINO_ACID"

FontStyle

Values

Plain = "PLAIN", Bold = "BOLD", Italic = "ITALIC", Underline = "UNDERLINE", Subscript = "SUBSCRIPT", Superscript = "SUPERSCRIPT"

StrokeStyle

The style of this Stroke, modifies the line style of this Stroke.

Values

Solid = "SOLID", Dashed = "DASHED"

ArrowType

Type of this Arrow: SINGLE(----->), DOUBLE(=====>), BLOCK(====|>), CROSSED(–x–>), CURVED(a curved SINGLE arrow), DASHED(- - ->), EQUILIBRIUM(´=====,), HASHED(--//–>) or RESONANCE(<----->)

Values

Single = "SINGLE", Double = "DOUBLE", Block = "BLOCK", Crossed = "CROSSED", Curved = "CURVED", Dashed = "DASHED", Equilibrium = "EQUILIBRIUM", Hashed = "HASHED", Resonance = "RESONANCE"

BracketType

The type of this Bracket. If not specified, it is considered SQUARE([]). Also can be ROUND(()), BRACES({}), or CHEVRONS(<>)

Values

Square = "SQUARE", Round = "ROUND", Braces = "BRACES", Chevrons = "CHEVRONS"

TextBoxAlign

The horizontal alignment of the content. If not specified, it is considered LEFT

Values

Center = "CENTER", Left = "LEFT", Right = "RIGHT"

TextBoxVerticalAlign

The vertical alignment of the content. If not specified, it is considered TOP.

Values

Middle = "MIDDLE", Top = "TOP", Bottom = "BOTTOM"

AtomDisplayPropertiesAtomNumberingType

The numbering algorithm for atoms.

Values

None = "NONE", Default = "DEFAULT", Iupac = "IUPAC"

AtomDisplayPropertiesCarbonVisibility

sets the visibility property for carbon atoms.

Values

Always = "ALWAYS", Never = "NEVER", On_Demand = "ON_DEMAND"

AtomDisplayPropertiesCharge

sets the display property for charges on atoms.

Values

Plain = "PLAIN", Circled = "CIRCLED"

AtomDisplayPropertiesPeptide

sets the display property for peptides.

Values

One_Letter = "ONE_LETTER", Three_Letter = "THREE_LETTER"

BondDisplayPropertiesDownWedge

Wedge bond display convention. Down wedge points downward in MDL's convention, upward (at the chiral center) in Daylight's.

Values

Mdl = "MDL", Daylight = "DAYLIGHT"

BondDisplayPropertyDoubleBondAlignment

Double bond alignment between two atoms, defined from the viewpoint of the start atom towards the end atom.

Values

Left = "LEFT", Right = "RIGHT", Center = "CENTER"

MoleculeDisplayPropertiesColorScheme

Color scheme. (MONO=monochrome, CPK=Corey-Pauling-Kultun, SHAPELY=shapely (residue types), GROUP=residue sequence numbers).

Values

Mono = "MONO", Cpk = "CPK", Shapely = "SHAPELY", Group = "GROUP"

EnhancedStereoType

The way to connect groups according to this representation. Note, that "AND" and "OR" does not make sense without a group, while "ABSOLUTE" does not make sense with a group.

Values

And = "AND", Or = "OR", Absolute = "ABSOLUTE"