Class: StructureConnectionTable

Kekule. StructureConnectionTable

new StructureConnectionTable(owner, parent)

A connection table for representing a complex (especially organic) molecule or group.
Parameters:
Name Type Description
owner Kekule.ChemSpace Owner for each objects in connection table.
parent Kekule.StructureFragment Parent to hold this Ctab.
Properties:
Name Type Description
owner Kekule.ChemSpace Owner for each objects in connection table.
parent Kekule.StructureFragment Parent to hold this Ctab. Read only.
nodes Array All structure nodes in this connection table.
anchorNodes Array Nodes that can have bond connected to other structure fragments.
connectors Array Connectors (usually bonds) in this connection table.
nonHydrogenNodes Array All structure nodes except hydrogen atoms in this connection table.
nonHydrogenConnectors Array Connectors except ones connected to hydrogen atoms in this connection table.
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Extends

Methods

addEventListener(eventName, listener, thisArg) → {Object}

Add an event handler.
Parameters:
Name Type Description
eventName String Name of event.
listener function Handler function.
thisArg Object The scope object applied when the handler is called.
Inherited From:
Source:
Returns:
Handler info object on success, null on fail.
Type
Object

addOnceEventListener(eventName, listener, thisArg) → {Object}

Add an event handler that will only be evoked once.
Parameters:
Name Type Description
eventName String Name of event.
listener function Handler function.
thisArg Object The scope object applied when the handler is called.
Inherited From:
Source:
Returns:
Handler info object on success, null on fail.
Type
Object

afterInitialization()

Do jobs after initialization, desendants can override this method
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analysisRings(options) → {Hash}

Returns ring system details of ctab.
Parameters:
Name Type Description
options Hash Options to find rings. Can include the following fields: { bondTypes: [] } If this param is not set, Kekule.globalOptions.algorithm.ringSearch will be used.
Source:
Returns:
Ring info of ctab, now has one field {ringBlocks: []} in which ringBlocks is An array, each items in it is a cycle block detail. Item containing a series of hash with fields: { connectors: Array of all vertexes in cycle block. nodes: Array of all edges in cycle block. allRings: Array of all rings in cycle block, each item list connectors and nodes of one ring. sssrRings: Array, each item containing connectors and nodes in a SSSR member ring. }
Type
Hash

appendAnchorNode(node)

Add anchor node of connection table. If node not in nodes, nothing will be done.
Parameters:
Name Type Description
node Kekule.ChemStructureNode
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appendBond(nodesOrIndexes, bondOrder, bondType) → {Kekule.Bond}

A util method to create a new bond object connected with nodes and append to current connection table.
Parameters:
Name Type Description
nodesOrIndexes Array Array of connected nodes or indexes of those nodes
bondOrder Int Order of bond.
bondType Int Type of bond.
Source:
Returns:
Type
Kekule.Bond

appendConnector(connector)

Add connector to connection table.
Parameters:
Name Type Description
connector Kekule.ChemStructureConnector
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appendNode(node)

Add node to connection table. If node already inside, nothing will be done.
Parameters:
Name Type Description
node Kekule.ChemStructureNode
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assign(srcObj)

Assign data in srcObj to this object.
Parameters:
Name Type Description
srcObj ObjectEx
Inherited From:
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assignTo(targetObj)

Assign data in this object to targetObj.
Parameters:
Name Type Description
targetObj ObjectEx
Inherited From:
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beginUpdate()

Begin to update multiple properties of object. In update state, all changed properties will not invoke propertySet event until method endUpdate is called.
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calcFormula() → {Kekule.MolecularFormula}

Calculate molecular formula from this connection table.
Source:
Returns:
Type
Kekule.MolecularFormula

canonicalize(canonicalizerId)

Canonicalize a structure fragment by canonicalizer. If canonicalizerId is not set, the default one will be used.
Parameters:
Name Type Description
canonicalizerId String
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clear()

Clear all nodes, anchor nodes and connectors in connection table.
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clearAnchorNodes()

Remove all anchor nodes from connection table.
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clearConnectors()

Remove all connectors from connection table.
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clearNodes()

Remove all nodes from connection table.
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clone() → {ObjectEx}

Returns a cloned object.
Inherited From:
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Returns:
Type
ObjectEx

copyPropsTo(dest)

Copy property values to dest object. Dest must be a desendant of ObjectEx.
Parameters:
Name Type Description
dest ObjectEx
Inherited From:
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defineEvent(eventName) → {Object}

Define an event in class. Event is actually a special property with type Class.EventHandlerList
Parameters:
Name Type Description
eventName String Name of event.
Inherited From:
Deprecated:
  • Yes
Source:
Returns:
Property info object created.
Type
Object

defineProp(propName, options) → {Object}

Define a property in class.
Parameters:
Name Type Description
propName String Name of property, case sensitive.
options Object A hash object, may contains the following fields: { dataType: type of property data, a string constant in DataType or a class name. //storeField: field in object to store property value, // not allowed for running speed getter: getter function, setter: setter function, if set to null, the property will be read-only, serializable: boolean, whether the property should be save or restore in serialization. Default is true. defaultValue: default value of property, can only be simple type (number, string, bool...) }
Inherited From:
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Returns:
Property info object added to property list.
Type
Object

deleteChildObj(childObj, cascadeDelete)

Remove and free childObj from connection table.
Parameters:
Name Type Description
childObj Variant A child node or connector.
cascadeDelete Bool Whether delete related objects (e.g., bond connected to an atom).
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doEndUpdate()

Actual work of endUpdate, just invoke all property change events.
Inherited From:
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doPropChanged(propName, newValue)

Do some job when a property value is changed. Descendants can override this.
Parameters:
Name Type Description
propName String Name of property.
newValue Variant New value of the property.
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endUpdate()

Update end and notify all properties changed after calling of beginUpdate.
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finalize()

Free resources used. Like finalize method in Java.
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findAllRings() → {Array}

Returns all rings in a ctab.
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Returns:
An array containing a series of hash with fields: { connectors: Array of all found connectors. nodes: Array of all found nodes. } Each array item marks a ring.
Type
Array

findAromaticRings(allowUncertainRings, candidateRings) → {Array}

Perceive and all aromatic rings in ctab, same as method perceiveAromaticRings.
Parameters:
Name Type Description
allowUncertainRings Bool Whether uncertain rings (e.g., with variable atom) be included in result.
candidateRings Array Rings in ctab that the detection will be performed. If this param is not set, all memebers of SSSR of ctab will be checked.
Source:
Returns:
Found aromatic rings.
Type
Array

findCycleBlocks() → {Array}

Returns all nodes and connectors in cylce block.
Source:
Returns:
An array containing a series of hash with fields: { connectors: Array of all found connectors. nodes: Array of all found nodes. } Each array item marks a cycle block.
Type
Array

findDirectChildOfObj(originObj) → {Kekule.ChemStructureNode}

Returns the direct node/substructure that contains originObj. originObj may be a child node or connector of substructure in this ctab. If originObj is actually not in this ctab, null will be returned.
Parameters:
Name Type Description
originObj Kekule.ChemStructureObject
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Returns:
Type
Kekule.ChemStructureNode

findSSSR() → {Array}

Returns Smallest set of smallest rings of ctab.
Source:
Returns:
An array containing a series of hash with fields: { nodes: Array of all found nodes. connectors: Array of all found connectors. } Each array item marks a SSSR ring.
Type
Array

getAllAutoScaleRefLengths(coordMode, allowCoordBorrow) → {Array}

Returns all length factors in object to help the scale ratio in autoscale mode. To molecule, typically this is the all of bond lengths. If no length can be found in this object, [] will be returned.
Parameters:
Name Type Description
coordMode Int
allowCoordBorrow Bool
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Returns:
Type
Array

getAllChildConnectors() → {Array}

Return all bonds in structure as well as in sub structure.
Source:
Returns:
Array of {Kekule.ChemStructureConnector}.
Type
Array

getAllContainingConnectors() → {Array}

Return all bonds in structure as well as in sub structure.
Source:
Returns:
Array of {Kekule.ChemStructureConnector}.
Type
Array

getAllPropList() → {Class.PropList}

Get list of all properties in this class, including ones inherited from parent class.
Inherited From:
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Returns:
Type
Class.PropList

getAnchorNodeAt(index) → {Kekule.ChemStructureNode}

Get anchor node at index.
Parameters:
Name Type Description
index Int
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Returns:
Type
Kekule.ChemStructureNode

getAnchorNodeCount() → {Int}

Return count of anchorNodes.
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Returns:
Type
Int

getChildAt(index) → {Variant}

Get child object (including both nodes and connectors) at index.
Parameters:
Name Type Description
index Int
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Returns:
Type
Variant

getChildAtIndexStack(indexStack) → {Kekule.ChemStructureObject}

Get child object at indexStack. For example, indexStack is [2, 3, 1], then this.getChildAt(2).getChildAt(3).getChildAt(1) will be returned.
Parameters:
Name Type Description
indexStack Array Array of integers.
Source:
Returns:
Type
Kekule.ChemStructureObject

getChildCount() → {Int}

Get count of child objects (including both nodes and connectors).
Source:
Returns:
Type
Int

getClass() → {Object}

Get class of this object.
Inherited From:
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Returns:
Class object.
Type
Object

getClassLocalName() → {String}

Get last part of class name of this object. For example, 'Atom' will be returned by instance of class 'Kekule.Atom'.
Inherited From:
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Returns:
Last part of class name of object.
Type
String

getClassName() → {String}

Get class name of this object, usually returns CLASS_NAME field.
Inherited From:
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Returns:
Class name of object.
Type
String

getConnectorAt(index) → {Kekule.ChemStructureConnector}

Get connector at index.
Parameters:
Name Type Description
index Int
Source:
Returns:
Type
Kekule.ChemStructureConnector

getConnectorAtIndexStack(indexStack) → {Kekule.ChemStructureNode}

Get connector at indexStack. For example, indexStack is [2, 3, 1], then this.getNodeAt(2).getNodeAt(3).getConnectorAt(1) will be returned.
Parameters:
Name Type Description
indexStack Array Array of integers.
Source:
Returns:
Type
Kekule.ChemStructureNode

getConnectorById(id) → {Kekule.ChemStructureConnector}

Get a structure connector object with a specified id.
Parameters:
Name Type Description
id String
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Returns:
Type
Kekule.ChemStructureConnector

getConnectorCount() → {Int}

Return count of connectors.
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Returns:
Type
Int

getConnectorLengthMedian(coordMode, allowCoordBorrow) → {Float}

Returns median of all connector lengths.
Parameters:
Name Type Description
coordMode Int
allowCoordBorrow Bool
Source:
Returns:
Type
Float

getContainerBox(coordMode, allowCoordBorrow) → {Hash}

Calculate the box to fit all nodes in CTable of molecule.
Parameters:
Name Type Description
coordMode Int Determine to calculate 2D or 3D box. Value from Kekule.CoordMode.
allowCoordBorrow Bool
Source:
Returns:
Box information. {x1, y1, z1, x2, y2, z2} (in 2D mode z1 and z2 will not be set).
Type
Hash

getContainerBox2D(allowCoordBorrow) → {Hash}

Calculate the 2D box to fit all nodes in CTable.
Parameters:
Name Type Description
allowCoordBorrow Bool
Source:
Returns:
2D box information. {x1, y1, x2, y2, width, height}.
Type
Hash

getContainerBox3D(allowCoordBorrow) → {Hash}

Calculate the 3D box to fit all nodes in CTable.
Parameters:
Name Type Description
allowCoordBorrow Bool
Source:
Returns:
3D box information. {x1, y1, z1, x2, y2, z2, deltaX, deltaY, deltaZ}.
Type
Hash

getEventHandlerList(eventName) → {Class.EventHandlerList}

Get the handler list of a event.
Parameters:
Name Type Description
eventName String Name of event.
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Returns:
Handler list of event. If this event does not exist, null is returned.
Type
Class.EventHandlerList

getLeafNodes() → {Array}

Get all leaf nodes (node that do not have children, usually atom). Note if a sub group has no children, it will be regarded as leaf node too.
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Returns:
Array of Kekule.ChemStructureNode.
Type
Array

getNextSiblingOfChild(childObj) → {Variant}

Returns next sibling node or connector to childObj.
Parameters:
Name Type Description
childObj Variant Node or connector.
Source:
Returns:
Type
Variant

getNodeAt(index) → {Kekule.ChemStructureNode}

Get node at index.
Parameters:
Name Type Description
index Int
Source:
Returns:
Type
Kekule.ChemStructureNode

getNodeAtIndexStack(indexStack) → {Kekule.ChemStructureNode}

Get node at indexStack. For example, indexStack is [2, 3, 1], then this.getNodeAt(2).getNodeAt(3).getNodeAt(1) will be returned.
Parameters:
Name Type Description
indexStack Array Array of integers.
Source:
Returns:
Type
Kekule.ChemStructureNode

getNodeById(id) → {Kekule.ChemStructureNode}

Get a structure node object with a specified id.
Parameters:
Name Type Description
id String
Source:
Returns:
Type
Kekule.ChemStructureNode

getNodeCount() → {Int}

Return count of nodes.
Source:
Returns:
Type
Int

getNodesContainBox(nodes, coordMode, allowCoordBorrow) → {Hash}

Calculate the absolute box to fit all nodes.
Parameters:
Name Type Description
nodes Array
coordMode Int Determine to calculate 2D or 3D box. Value from Kekule.CoordMode.
allowCoordBorrow Bool
Source:
Returns:
Box information. {x1, y1, z1, x2, y2, z2} (in 2D mode z1 and z2 will not be set).
Type
Hash

getObjectById(id) → {Kekule.ChemStructureObject}

Get a structure node or connector object with a specified id.
Parameters:
Name Type Description
id String
Source:
Returns:
Type
Kekule.ChemStructureObject

getOwnPropList() → {Class.PropList}

Get property list of this class. The properties inherited from parent class will not be returned.
Inherited From:
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Returns:
Type
Class.PropList

getPropertyDataType(propName) → {String}

Returns type constants of property.
Parameters:
Name Type Description
propName String
Inherited From:
Source:
Returns:
Values from DataType.
Type
String

getPropInfo(propName, ownPropertyOnly) → {Object}

Get property info object from the property list of current class.
Parameters:
Name Type Description
propName String Name of property.
ownPropertyOnly Bool If true, only property defined in this class will be checked.
Inherited From:
Source:
Returns:
Property info object found. If there is no such a property, null is returned.
Type
Object

getPropListOfScopes(scopes) → {Class.PropList}

Get list of all properties of certain scopes in this class, including ones inherited from parent class.
Parameters:
Name Type Description
scopes Array Array item from Class.PropertyScope.
Inherited From:
Source:
Returns:
Type
Class.PropList

getPropStoreFieldValue(propName) → {Variant}

Get value of a property's store field. Use this method to get property value and avoid the call of property getter. Note: if the property has no store field, this method may returns null or undefined.
Parameters:
Name Type Description
propName String Name of property.
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Returns:
Value of property. If property does not exists, null is returned.
Type
Variant

getPropValue(propName) → {Variant}

Get value of a property.
Parameters:
Name Type Description
propName String Name of property.
Inherited From:
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Returns:
Value of property. If property does not exists, null is returned.
Type
Variant

getPropValues(propNames) → {Hash}

Returns values of a series of properties.
Parameters:
Name Type Description
propNames Variant Can be an array of property names, also can be an object while the direct field names of object will be regarded as property names.
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Returns:
Stores all property name-value pair.
Type
Hash

getPrototype() → {Object}

Get prototype of this object.
Inherited From:
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Returns:
Type
Object

getRingAromaticType(ring, refRings)

Returns aromatic type of a ring.
Parameters:
Name Type Description
ring Object
refRings Array Should list all related rings to ring, help to determine the p electron number. If this value is not set, SSSR of ctab will be used instead.
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getSerializationName() → {String}

Returns a name to be used in serialization. Descendants can override this.
Inherited From:
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Returns:
Type
String

getSubFragments() → {Array}

Get all sub fragments (node that have children, usually SubGroup). Note if a sub group has no children, it will not be regarded as sub fragment.
Source:
Returns:
Array of Kekule.StructureFragment.
Type
Array

getSuperClass() → {Object}

Get super class of this object.
Inherited From:
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Returns:
Class object.
Type
Object

getSuperClassPrototype() → {Object}

Get prototype of super class.
Inherited From:
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Returns:
If there is no super class, null is returned.
Type
Object

hasChildObj(childObj) → {Bool}

Check if childObj is a child node or connector of this ctab.
Parameters:
Name Type Description
childObj Kekule.ChemObject
Source:
Returns:
Type
Bool

hasConnector(connector, checkNestedStructure) → {Bool}

Check if a connector exists in structure.
Parameters:
Name Type Description
connector Kekule.ChemStructureConnector Connector to seek.
checkNestedStructure Bool If true the nested sub groups will also be checked.
Source:
Returns:
Type
Bool

hasDirectProperty(propName) → {Boolean}

Check if property is defined in current class (not inherited from super class).
Parameters:
Name Type Description
propName String Name of property.
Inherited From:
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Returns:
Type
Boolean

hasNode(node, checkNestedStructure) → {Bool}

Check if a node exists in structure.
Parameters:
Name Type Description
node Kekule.ChemStructureNode Node to seek.
checkNestedStructure Bool If true the nested sub groups will also be checked.
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Returns:
Type
Bool

hasProperty(propName) → {Boolean}

Check if property exists in current class.
Parameters:
Name Type Description
propName String Name of property.
Inherited From:
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Returns:
Type
Boolean

hasSubFragments() → {Bool}

Returns whether there are sub fragment(s) (node that have children, usually SubGroup) in this ctab. Note if a sub group has no children, it will not be regarded as sub fragment.
Source:
Returns:
Type
Bool

indexOfAnchorNode(node) → {Int}

Get index of node in anchorNodes list.
Parameters:
Name Type Description
node Kekule.ChemStructureNode
Source:
Returns:
Type
Int

indexOfChild(obj) → {Int}

Get the index of obj in children list.
Parameters:
Name Type Description
obj Variant
Source:
Returns:
Index of obj or -1 when not found.
Type
Int

indexOfConnector(connector) → {Int}

Get index of connector in connectors list.
Parameters:
Name Type Description
connector Kekule.ChemStructureConnector
Source:
Returns:
Type
Int

indexOfNode(node) → {Int}

Get index of node in nodes list.
Parameters:
Name Type Description
node Kekule.ChemStructureNode
Source:
Returns:
Type
Int

indexStackOfChild(indexStack) → {Kekule.ChemStructureObject}

Get child object at indexStack. For example, indexStack is [2, 3, 1], then this.getNodeAt(2).getNodeAt(3).getChildAt(1) will be returned.
Parameters:
Name Type Description
indexStack Array Array of integers.
Source:
Returns:
Type
Kekule.ChemStructureObject

indexStackOfConnector(connector) → {Variant}

Returns index of connector. If connector exists in nested sub group, index in sub group will be pushed to stack as well.
Parameters:
Name Type Description
connector Kekule.ChemStructureConnector
Source:
Returns:
If connector is the direct child of this structure, returns {Int}, otherwise stack {Array} will be returned.
Type
Variant

indexStackOfNode(node) → {Variant}

Returns index of node. If node exists in nested sub group, index in sub group will be pushed to stack as well.
Parameters:
Name Type Description
node Kekule.ChemStructureNode
Source:
Returns:
If node is the direct child of this structure, returns {Int}, otherwise stack {Array} will be returned.
Type
Variant

insertBefore(obj, refChild) → {Int}

Insert obj before refChild in node or connector list. If refChild is null or does not exists, obj will be append to tail of list.
Parameters:
Name Type Description
obj Variant A node or connector.
refChild Variant Ref node or connector
Source:
Returns:
Index of obj after inserting.
Type
Int

insertConnectorAt(connector, index)

Insert connector to index. If index is not set, node will be inserted as the first connector of ctab.
Parameters:
Name Type Description
connector Kekule.ChemStructureConnector
index Int
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insertNodeAt(node, index)

Insert node to index. If index is not set, node will be inserted to the tail of node list of ctab.
Parameters:
Name Type Description
node Kekule.ChemStructureNode
index Int
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invokeEvent(eventName, event)

Invoke an event and call all corresponding handlers (listeners).
Parameters:
Name Type Description
eventName String Event to be invoked.
event Object A hash object with information about event. At least should include the following fields: { name: name of event, target: which object invoke this event, generally this object } If this parameter is not set, the default value {eventName, this} will be used.
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isEmpty() → {Bool}

Returns if this fragment has no formula or ctab, or ctab has no nodes or connectors.
Source:
Returns:
Type
Bool

isEventHandlerList(value) → {bool}

Check if a object is Class.EventHandlerList.
Parameters:
Name Type Description
value Object
Inherited From:
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Returns:
True or false.
Type
bool

isPropertySerializable(propName) → {Bool}

Returns if property is serializable.
Parameters:
Name Type Description
propName String
Inherited From:
Source:
Returns:
Type
Bool

isPropUpdated(propName)

Check whether property is changed in begin/endUpdate procedure.
Parameters:
Name Type Description
propName Object
Inherited From:
Source:

isSubFragment(node) → {Bool}

Check if a node has a sub structure (has child nodes). Note if a sub group has no children, it will not be regarded as sub fragment.
Parameters:
Name Type Description
node Kekule.ChemStructureNode
Source:
Returns:
Type
Bool

isUpdating()

Check if object is in updating state.
Inherited From:
Source:

loadObj(srcNode, serializerOrName)

load current object from srcNode.
Parameters:
Name Type Description
srcNode Object Storage node to load object. Different serializer requires different node.
serializerOrName Variant A ObjSerializer instance or name registered in ObjSerializerFactory. Can be null to use the default serializer.
Inherited From:
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nodesHasCoord2D(allowCoordBorrow) → {Bool}

Check if child nodes has 2D coord.
Parameters:
Name Type Description
allowCoordBorrow Bool
Source:
Returns:
Type
Bool

nodesHasCoord3D(allowCoordBorrow) → {Bool}

Check if child nodes has 3D coord.
Parameters:
Name Type Description
allowCoordBorrow Bool
Source:
Returns:
Type
Bool

notifyPropSet(propName, newValue)

Notify that a property value is set
Parameters:
Name Type Description
propName String Name of property.
newValue Variant New value of the property.
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objectChange()

Called when object is changed.
Inherited From:
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off(eventName, listener, thisArg)

Remove an event handler, shortcut for (@link ObjectEx.removeEventListener}.
Parameters:
Name Type Description
eventName String Name of event.
listener function Handler function.
thisArg Object The scope object applied when the handler is called. If not set, all listenr function in list will be removed.
Inherited From:
Source:

on(eventName, listener, thisArg) → {Object}

Add an event handler, shortcut for ObjectEx.addEventListener.
Parameters:
Name Type Description
eventName String Name of event.
listener function Handler function.
thisArg Object The scope object applied when the handler is called.
Inherited From:
Source:
Returns:
Handler info object on success, null on fail.
Type
Object

once(eventName, listener, thisArg) → {Object}

Add an event handler that will only be evoked once, shortcut for ObjectEx.addOnceEventListener.
Parameters:
Name Type Description
eventName String Name of event.
listener function Handler function.
thisArg Object The scope object applied when the handler is called.
Inherited From:
Source:
Returns:
Handler info object on success, null on fail.
Type
Object

overwriteMethod(methodName, newMethod) → {ObjectEx}

Overwrite method of object instance (rather than prototype) with a new one.
Parameters:
Name Type Description
methodName String
newMethod Func New function. The arguments of function should be same as overwritten one plus a extra leading param stores the old method. e.g. Overwrite getPropValue method:
var obj = new ObjectEx();
obj.overwriteMethod('getPropValue', function($old, propName)
{
console.log('new method'); return $old(propName); });
Inherited From:
Source:
Returns:
Type
ObjectEx

perceiveAromaticRings(allowUncertainRings, candidateRings) → {Array}

Perceive and all aromatic rings in ctab.
Parameters:
Name Type Description
allowUncertainRings Bool Whether uncertain rings (e.g., with variable atom) be included in result.
candidateRings Array Rings in ctab that the detection will be performed. If this param is not set, all memebers of SSSR of ctab will be checked.
Source:
Returns:
Found aromatic rings.
Type
Array

relayEvent(eventName, event)

Relay event from child of this object.
Parameters:
Name Type Description
eventName String Event to be invoked.
event Object A hash object with information about event.
Inherited From:
Source:

removeAnchorNode(node)

Remove a node in anchorNodes.
Parameters:
Name Type Description
node Kekule.ChemStructureNode
Source:

removeAnchorNodeAt(index)

Remove node at index of anchorNodes.
Parameters:
Name Type Description
index Int
Source:

removeChild(childObj)

Remove child obj directly from connection table.
Parameters:
Name Type Description
childObj Variant A child node or connector.
Source:

removeChildObj(childObj, cascadeRemove, freeRemoved)

Remove childObj from connection table.
Parameters:
Name Type Description
childObj Variant A child node or connector.
cascadeRemove Bool Whether remove related objects (e.g., bond connected to an atom).
freeRemoved Bool Whether free all removed objects.
Source:

removeConnector(connector, preserveConnectedObjs)

Remove a connector in connection table.
Parameters:
Name Type Description
connector Kekule.ChemStructureConnector
preserveConnectedObjs Bool Whether delte relations between this connector and related nodes.
Source:

removeConnectorAt(index, preserveConnectedObjs)

Remove connector at index of connectors.
Parameters:
Name Type Description
index Int
preserveConnectedObjs Bool Whether delte relations between this connector and related nodes.
Source:

removeEventListener(eventName, listener, thisArg)

Remove an event handler.
Parameters:
Name Type Description
eventName String Name of event.
listener function Handler function.
thisArg Object The scope object applied when the handler is called. If not set, all listenr function in list will be removed.
Inherited From:
Source:

removeNode(node, preserveLinkedConnectors)

Remove a node in connection table.
Parameters:
Name Type Description
node Kekule.ChemStructureNode
preserveLinkedConnectors Bool Whether remove relations between this node and linked connectors.
Source:

removeNodeAt(index, preserveLinkedConnectors)

Remove node at index in connection table.
Parameters:
Name Type Description
index Int
preserveLinkedConnectors Bool Whether remove relations between this node and linked connectors.
Source:

replaceNode(oldNode, newNode)

Replace oldNode with new one, preserve coords and all linked connectors.
Parameters:
Name Type Description
oldNode Kekule.ChemStructureNode Must be direct child of current ctab (node in nested structure fragment will be ignored).
newNode Kekule.ChemStructureNode
Source:

saved()

Called after this object is saved through a serialization system. Descendants may override this.
Inherited From:
Source:

saveObj(destNode, serializerOrName, options)

Save current object to destNode.
Parameters:
Name Type Description
destNode Object Storage node to save object. Different serializer requires different node.
serializerOrName Variant A ObjSerializer instance or name registered in ObjSerializerFactory. Can be null to use the default serializer.
options Hash
Inherited From:
Source:

setConnectorIndex(connector, index)

Change index of connector.
Parameters:
Name Type Description
connector Kekule.ChemStructureConnector
index Int
Source:

setNodeIndex(node, index)

Change index of node.
Parameters:
Name Type Description
node Kekule.ChemStructureNode
index Int
Source:

setPropStoreFieldValue(propName) → {Variant}

Set value of a property's store field. Use this method to set property value and avoid the call of property setter. Readonly property can also be changed in this method. Note: if the property has no store field, this method will has no effect on property.
Parameters:
Name Type Description
propName String Name of property.
Inherited From:
Source:
Returns:
Value of property. If property does not exists, null is returned.
Type
Variant

setPropValue(propName, value, ignoreReadOnly)

Set value of a property.
Parameters:
Name Type Description
propName String Name of property.
value Variant Value of the property.
ignoreReadOnly bool Try set the value directly through store field even if the property is a readonly one (without a setter).
Inherited From:
Source:

setPropValues(hash, ignoreReadOnly)

Set a series of property.
Parameters:
Name Type Description
hash Hash A hash object, its key and values will be used to set property value.
ignoreReadOnly bool Try set the value directly through store field even if the property is a readonly one (without a setter).
Inherited From:
Source:

setPropValueX()

Set value of a property. Similar to ObjectEx.setPropValue but can pass in multiple params. The first param is always the property name while the rest will be put into setter method (setXXX).
Inherited From:
Source:

sortConnectors(sortFunc)

Sort direct child connectors in ctab.
Parameters:
Name Type Description
sortFunc function Function to determine the priority of connectors.
Source:

sortNodes(sortFunc)

Sort direct child nodes in ctab.
Parameters:
Name Type Description
sortFunc function Function to determine the priority of nodes.
Source:

stopEventPropagation(event)

Stop propagation of event, disallow it to bubble to higher level.
Parameters:
Name Type Description
event Object
Inherited From:
Source:

traverse(callback, startingNode, breadthFirst, partialNodes) → {Hash}

Traverse the nodes in connection tab through a depth or breadth first spanning tree algorithm.
Parameters:
Name Type Description
callback Func Function called when meet a new node or connector, has two params: callback(currNodeOrConnector, isConnector)
startingNode Kekule.StructureNode Starting position of travers.
breadthFirst Bool Set to true to use breadth first algorithm or false to use depth first algorithm.
partialNodes Array If this param is set, only part of the structure will be traversed.
Source:
Returns:
A hash object containing all the nodes and connectors sequence traversed. {nodes, connectors}. Note that all nodes but not all connectors (e.g., the one in ring) may be traversed.
Type
Hash

Events

change

Invoked when the object has been modified. event param of it has one fields: {changedPropNames: Array}
Inherited From:
Source:

finalize

Invoked when ObjectEx#finalize is called and the object is released. event param of it has one fields: {obj}
Inherited From:
Source:

propValueSet

Invoked when a property value is set by its setter event param of it has two fields: {propName, propValue} If property enablePropValueSetEvent is false, this event will never be fired.
Inherited From:
Source:

Kekule. StructureConnectionTable

new StructureConnectionTable()

Source:

Methods

addEventListener(eventName, listener, thisArg) → {Object}

Add an event handler.
Parameters:
Name Type Description
eventName String Name of event.
listener function Handler function.
thisArg Object The scope object applied when the handler is called.
Inherited From:
Source:
Returns:
Handler info object on success, null on fail.
Type
Object

addOnceEventListener(eventName, listener, thisArg) → {Object}

Add an event handler that will only be evoked once.
Parameters:
Name Type Description
eventName String Name of event.
listener function Handler function.
thisArg Object The scope object applied when the handler is called.
Inherited From:
Source:
Returns:
Handler info object on success, null on fail.
Type
Object

afterInitialization()

Do jobs after initialization, desendants can override this method
Inherited From:
Source:

analysisRings(options) → {Hash}

Returns ring system details of ctab.
Parameters:
Name Type Description
options Hash Options to find rings. Can include the following fields: { bondTypes: [] } If this param is not set, Kekule.globalOptions.algorithm.ringSearch will be used.
Source:
Returns:
Ring info of ctab, now has one field {ringBlocks: []} in which ringBlocks is An array, each items in it is a cycle block detail. Item containing a series of hash with fields: { connectors: Array of all vertexes in cycle block. nodes: Array of all edges in cycle block. allRings: Array of all rings in cycle block, each item list connectors and nodes of one ring. sssrRings: Array, each item containing connectors and nodes in a SSSR member ring. }
Type
Hash

appendAnchorNode(node)

Add anchor node of connection table. If node not in nodes, nothing will be done.
Parameters:
Name Type Description
node Kekule.ChemStructureNode
Source:

appendBond(nodesOrIndexes, bondOrder, bondType) → {Kekule.Bond}

A util method to create a new bond object connected with nodes and append to current connection table.
Parameters:
Name Type Description
nodesOrIndexes Array Array of connected nodes or indexes of those nodes
bondOrder Int Order of bond.
bondType Int Type of bond.
Source:
Returns:
Type
Kekule.Bond

appendConnector(connector)

Add connector to connection table.
Parameters:
Name Type Description
connector Kekule.ChemStructureConnector
Source:

appendNode(node)

Add node to connection table. If node already inside, nothing will be done.
Parameters:
Name Type Description
node Kekule.ChemStructureNode
Source:

assign(srcObj)

Assign data in srcObj to this object.
Parameters:
Name Type Description
srcObj ObjectEx
Inherited From:
Source:

assignTo(targetObj)

Assign data in this object to targetObj.
Parameters:
Name Type Description
targetObj ObjectEx
Inherited From:
Source:

beginUpdate()

Begin to update multiple properties of object. In update state, all changed properties will not invoke propertySet event until method endUpdate is called.
Inherited From:
Source:

calcFormula() → {Kekule.MolecularFormula}

Calculate molecular formula from this connection table.
Source:
Returns:
Type
Kekule.MolecularFormula

canonicalize(canonicalizerId)

Canonicalize a structure fragment by canonicalizer. If canonicalizerId is not set, the default one will be used.
Parameters:
Name Type Description
canonicalizerId String
Source:

clear()

Clear all nodes, anchor nodes and connectors in connection table.
Source:

clearAnchorNodes()

Remove all anchor nodes from connection table.
Source:

clearConnectors()

Remove all connectors from connection table.
Source:

clearNodes()

Remove all nodes from connection table.
Source:

clone() → {ObjectEx}

Returns a cloned object.
Inherited From:
Source:
Returns:
Type
ObjectEx

copyPropsTo(dest)

Copy property values to dest object. Dest must be a desendant of ObjectEx.
Parameters:
Name Type Description
dest ObjectEx
Inherited From:
Source:

defineEvent(eventName) → {Object}

Define an event in class. Event is actually a special property with type Class.EventHandlerList
Parameters:
Name Type Description
eventName String Name of event.
Inherited From:
Deprecated:
  • Yes
Source:
Returns:
Property info object created.
Type
Object

defineProp(propName, options) → {Object}

Define a property in class.
Parameters:
Name Type Description
propName String Name of property, case sensitive.
options Object A hash object, may contains the following fields: { dataType: type of property data, a string constant in DataType or a class name. //storeField: field in object to store property value, // not allowed for running speed getter: getter function, setter: setter function, if set to null, the property will be read-only, serializable: boolean, whether the property should be save or restore in serialization. Default is true. defaultValue: default value of property, can only be simple type (number, string, bool...) }
Inherited From:
Source:
Returns:
Property info object added to property list.
Type
Object

deleteChildObj(childObj, cascadeDelete)

Remove and free childObj from connection table.
Parameters:
Name Type Description
childObj Variant A child node or connector.
cascadeDelete Bool Whether delete related objects (e.g., bond connected to an atom).
Source:

doEndUpdate()

Actual work of endUpdate, just invoke all property change events.
Inherited From:
Source:

doPropChanged(propName, newValue)

Do some job when a property value is changed. Descendants can override this.
Parameters:
Name Type Description
propName String Name of property.
newValue Variant New value of the property.
Inherited From:
Source:

endUpdate()

Update end and notify all properties changed after calling of beginUpdate.
Inherited From:
Source:

finalize()

Free resources used. Like finalize method in Java.
Inherited From:
Source:

findAllRings() → {Array}

Returns all rings in a ctab.
Source:
Returns:
An array containing a series of hash with fields: { connectors: Array of all found connectors. nodes: Array of all found nodes. } Each array item marks a ring.
Type
Array

findAromaticRings(allowUncertainRings, candidateRings) → {Array}

Perceive and all aromatic rings in ctab, same as method perceiveAromaticRings.
Parameters:
Name Type Description
allowUncertainRings Bool Whether uncertain rings (e.g., with variable atom) be included in result.
candidateRings Array Rings in ctab that the detection will be performed. If this param is not set, all memebers of SSSR of ctab will be checked.
Source:
Returns:
Found aromatic rings.
Type
Array

findCycleBlocks() → {Array}

Returns all nodes and connectors in cylce block.
Source:
Returns:
An array containing a series of hash with fields: { connectors: Array of all found connectors. nodes: Array of all found nodes. } Each array item marks a cycle block.
Type
Array

findDirectChildOfObj(originObj) → {Kekule.ChemStructureNode}

Returns the direct node/substructure that contains originObj. originObj may be a child node or connector of substructure in this ctab. If originObj is actually not in this ctab, null will be returned.
Parameters:
Name Type Description
originObj Kekule.ChemStructureObject
Source:
Returns:
Type
Kekule.ChemStructureNode

findSSSR() → {Array}

Returns Smallest set of smallest rings of ctab.
Source:
Returns:
An array containing a series of hash with fields: { nodes: Array of all found nodes. connectors: Array of all found connectors. } Each array item marks a SSSR ring.
Type
Array

getAllAutoScaleRefLengths(coordMode, allowCoordBorrow) → {Array}

Returns all length factors in object to help the scale ratio in autoscale mode. To molecule, typically this is the all of bond lengths. If no length can be found in this object, [] will be returned.
Parameters:
Name Type Description
coordMode Int
allowCoordBorrow Bool
Source:
Returns:
Type
Array

getAllChildConnectors() → {Array}

Return all bonds in structure as well as in sub structure.
Source:
Returns:
Array of {Kekule.ChemStructureConnector}.
Type
Array

getAllContainingConnectors() → {Array}

Return all bonds in structure as well as in sub structure.
Source:
Returns:
Array of {Kekule.ChemStructureConnector}.
Type
Array

getAllPropList() → {Class.PropList}

Get list of all properties in this class, including ones inherited from parent class.
Inherited From:
Source:
Returns:
Type
Class.PropList

getAnchorNodeAt(index) → {Kekule.ChemStructureNode}

Get anchor node at index.
Parameters:
Name Type Description
index Int
Source:
Returns:
Type
Kekule.ChemStructureNode

getAnchorNodeCount() → {Int}

Return count of anchorNodes.
Source:
Returns:
Type
Int

getChildAt(index) → {Variant}

Get child object (including both nodes and connectors) at index.
Parameters:
Name Type Description
index Int
Source:
Returns:
Type
Variant

getChildAtIndexStack(indexStack) → {Kekule.ChemStructureObject}

Get child object at indexStack. For example, indexStack is [2, 3, 1], then this.getChildAt(2).getChildAt(3).getChildAt(1) will be returned.
Parameters:
Name Type Description
indexStack Array Array of integers.
Source:
Returns:
Type
Kekule.ChemStructureObject

getChildCount() → {Int}

Get count of child objects (including both nodes and connectors).
Source:
Returns:
Type
Int

getClass() → {Object}

Get class of this object.
Inherited From:
Source:
Returns:
Class object.
Type
Object

getClassLocalName() → {String}

Get last part of class name of this object. For example, 'Atom' will be returned by instance of class 'Kekule.Atom'.
Inherited From:
Source:
Returns:
Last part of class name of object.
Type
String

getClassName() → {String}

Get class name of this object, usually returns CLASS_NAME field.
Inherited From:
Source:
Returns:
Class name of object.
Type
String

getConnectorAt(index) → {Kekule.ChemStructureConnector}

Get connector at index.
Parameters:
Name Type Description
index Int
Source:
Returns:
Type
Kekule.ChemStructureConnector

getConnectorAtIndexStack(indexStack) → {Kekule.ChemStructureNode}

Get connector at indexStack. For example, indexStack is [2, 3, 1], then this.getNodeAt(2).getNodeAt(3).getConnectorAt(1) will be returned.
Parameters:
Name Type Description
indexStack Array Array of integers.
Source:
Returns:
Type
Kekule.ChemStructureNode

getConnectorById(id) → {Kekule.ChemStructureConnector}

Get a structure connector object with a specified id.
Parameters:
Name Type Description
id String
Source:
Returns:
Type
Kekule.ChemStructureConnector

getConnectorCount() → {Int}

Return count of connectors.
Source:
Returns:
Type
Int

getConnectorLengthMedian(coordMode, allowCoordBorrow) → {Float}

Returns median of all connector lengths.
Parameters:
Name Type Description
coordMode Int
allowCoordBorrow Bool
Source:
Returns:
Type
Float

getContainerBox(coordMode, allowCoordBorrow) → {Hash}

Calculate the box to fit all nodes in CTable of molecule.
Parameters:
Name Type Description
coordMode Int Determine to calculate 2D or 3D box. Value from Kekule.CoordMode.
allowCoordBorrow Bool
Source:
Returns:
Box information. {x1, y1, z1, x2, y2, z2} (in 2D mode z1 and z2 will not be set).
Type
Hash

getContainerBox2D(allowCoordBorrow) → {Hash}

Calculate the 2D box to fit all nodes in CTable.
Parameters:
Name Type Description
allowCoordBorrow Bool
Source:
Returns:
2D box information. {x1, y1, x2, y2, width, height}.
Type
Hash

getContainerBox3D(allowCoordBorrow) → {Hash}

Calculate the 3D box to fit all nodes in CTable.
Parameters:
Name Type Description
allowCoordBorrow Bool
Source:
Returns:
3D box information. {x1, y1, z1, x2, y2, z2, deltaX, deltaY, deltaZ}.
Type
Hash

getEventHandlerList(eventName) → {Class.EventHandlerList}

Get the handler list of a event.
Parameters:
Name Type Description
eventName String Name of event.
Inherited From:
Source:
Returns:
Handler list of event. If this event does not exist, null is returned.
Type
Class.EventHandlerList

getLeafNodes() → {Array}

Get all leaf nodes (node that do not have children, usually atom). Note if a sub group has no children, it will be regarded as leaf node too.
Source:
Returns:
Array of Kekule.ChemStructureNode.
Type
Array

getNextSiblingOfChild(childObj) → {Variant}

Returns next sibling node or connector to childObj.
Parameters:
Name Type Description
childObj Variant Node or connector.
Source:
Returns:
Type
Variant

getNodeAt(index) → {Kekule.ChemStructureNode}

Get node at index.
Parameters:
Name Type Description
index Int
Source:
Returns:
Type
Kekule.ChemStructureNode

getNodeAtIndexStack(indexStack) → {Kekule.ChemStructureNode}

Get node at indexStack. For example, indexStack is [2, 3, 1], then this.getNodeAt(2).getNodeAt(3).getNodeAt(1) will be returned.
Parameters:
Name Type Description
indexStack Array Array of integers.
Source:
Returns:
Type
Kekule.ChemStructureNode

getNodeById(id) → {Kekule.ChemStructureNode}

Get a structure node object with a specified id.
Parameters:
Name Type Description
id String
Source:
Returns:
Type
Kekule.ChemStructureNode

getNodeCount() → {Int}

Return count of nodes.
Source:
Returns:
Type
Int

getNodesContainBox(nodes, coordMode, allowCoordBorrow) → {Hash}

Calculate the absolute box to fit all nodes.
Parameters:
Name Type Description
nodes Array
coordMode Int Determine to calculate 2D or 3D box. Value from Kekule.CoordMode.
allowCoordBorrow Bool
Source:
Returns:
Box information. {x1, y1, z1, x2, y2, z2} (in 2D mode z1 and z2 will not be set).
Type
Hash

getObjectById(id) → {Kekule.ChemStructureObject}

Get a structure node or connector object with a specified id.
Parameters:
Name Type Description
id String
Source:
Returns:
Type
Kekule.ChemStructureObject

getOwnPropList() → {Class.PropList}

Get property list of this class. The properties inherited from parent class will not be returned.
Inherited From:
Source:
Returns:
Type
Class.PropList

getPropertyDataType(propName) → {String}

Returns type constants of property.
Parameters:
Name Type Description
propName String
Inherited From:
Source:
Returns:
Values from DataType.
Type
String

getPropInfo(propName, ownPropertyOnly) → {Object}

Get property info object from the property list of current class.
Parameters:
Name Type Description
propName String Name of property.
ownPropertyOnly Bool If true, only property defined in this class will be checked.
Inherited From:
Source:
Returns:
Property info object found. If there is no such a property, null is returned.
Type
Object

getPropListOfScopes(scopes) → {Class.PropList}

Get list of all properties of certain scopes in this class, including ones inherited from parent class.
Parameters:
Name Type Description
scopes Array Array item from Class.PropertyScope.
Inherited From:
Source:
Returns:
Type
Class.PropList

getPropStoreFieldValue(propName) → {Variant}

Get value of a property's store field. Use this method to get property value and avoid the call of property getter. Note: if the property has no store field, this method may returns null or undefined.
Parameters:
Name Type Description
propName String Name of property.
Inherited From:
Source:
Returns:
Value of property. If property does not exists, null is returned.
Type
Variant

getPropValue(propName) → {Variant}

Get value of a property.
Parameters:
Name Type Description
propName String Name of property.
Inherited From:
Source:
Returns:
Value of property. If property does not exists, null is returned.
Type
Variant

getPropValues(propNames) → {Hash}

Returns values of a series of properties.
Parameters:
Name Type Description
propNames Variant Can be an array of property names, also can be an object while the direct field names of object will be regarded as property names.
Inherited From:
Source:
Returns:
Stores all property name-value pair.
Type
Hash

getPrototype() → {Object}

Get prototype of this object.
Inherited From:
Source:
Returns:
Type
Object

getRingAromaticType(ring, refRings)

Returns aromatic type of a ring.
Parameters:
Name Type Description
ring Object
refRings Array Should list all related rings to ring, help to determine the p electron number. If this value is not set, SSSR of ctab will be used instead.
Source:

getSerializationName() → {String}

Returns a name to be used in serialization. Descendants can override this.
Inherited From:
Source:
Returns:
Type
String

getSubFragments() → {Array}

Get all sub fragments (node that have children, usually SubGroup). Note if a sub group has no children, it will not be regarded as sub fragment.
Source:
Returns:
Array of Kekule.StructureFragment.
Type
Array

getSuperClass() → {Object}

Get super class of this object.
Inherited From:
Source:
Returns:
Class object.
Type
Object

getSuperClassPrototype() → {Object}

Get prototype of super class.
Inherited From:
Source:
Returns:
If there is no super class, null is returned.
Type
Object

hasChildObj(childObj) → {Bool}

Check if childObj is a child node or connector of this ctab.
Parameters:
Name Type Description
childObj Kekule.ChemObject
Source:
Returns:
Type
Bool

hasConnector(connector, checkNestedStructure) → {Bool}

Check if a connector exists in structure.
Parameters:
Name Type Description
connector Kekule.ChemStructureConnector Connector to seek.
checkNestedStructure Bool If true the nested sub groups will also be checked.
Source:
Returns:
Type
Bool

hasDirectProperty(propName) → {Boolean}

Check if property is defined in current class (not inherited from super class).
Parameters:
Name Type Description
propName String Name of property.
Inherited From:
Source:
Returns:
Type
Boolean

hasNode(node, checkNestedStructure) → {Bool}

Check if a node exists in structure.
Parameters:
Name Type Description
node Kekule.ChemStructureNode Node to seek.
checkNestedStructure Bool If true the nested sub groups will also be checked.
Source:
Returns:
Type
Bool

hasProperty(propName) → {Boolean}

Check if property exists in current class.
Parameters:
Name Type Description
propName String Name of property.
Inherited From:
Source:
Returns:
Type
Boolean

hasSubFragments() → {Bool}

Returns whether there are sub fragment(s) (node that have children, usually SubGroup) in this ctab. Note if a sub group has no children, it will not be regarded as sub fragment.
Source:
Returns:
Type
Bool

indexOfAnchorNode(node) → {Int}

Get index of node in anchorNodes list.
Parameters:
Name Type Description
node Kekule.ChemStructureNode
Source:
Returns:
Type
Int

indexOfChild(obj) → {Int}

Get the index of obj in children list.
Parameters:
Name Type Description
obj Variant
Source:
Returns:
Index of obj or -1 when not found.
Type
Int

indexOfConnector(connector) → {Int}

Get index of connector in connectors list.
Parameters:
Name Type Description
connector Kekule.ChemStructureConnector
Source:
Returns:
Type
Int

indexOfNode(node) → {Int}

Get index of node in nodes list.
Parameters:
Name Type Description
node Kekule.ChemStructureNode
Source:
Returns:
Type
Int

indexStackOfChild(indexStack) → {Kekule.ChemStructureObject}

Get child object at indexStack. For example, indexStack is [2, 3, 1], then this.getNodeAt(2).getNodeAt(3).getChildAt(1) will be returned.
Parameters:
Name Type Description
indexStack Array Array of integers.
Source:
Returns:
Type
Kekule.ChemStructureObject

indexStackOfConnector(connector) → {Variant}

Returns index of connector. If connector exists in nested sub group, index in sub group will be pushed to stack as well.
Parameters:
Name Type Description
connector Kekule.ChemStructureConnector
Source:
Returns:
If connector is the direct child of this structure, returns {Int}, otherwise stack {Array} will be returned.
Type
Variant

indexStackOfNode(node) → {Variant}

Returns index of node. If node exists in nested sub group, index in sub group will be pushed to stack as well.
Parameters:
Name Type Description
node Kekule.ChemStructureNode
Source:
Returns:
If node is the direct child of this structure, returns {Int}, otherwise stack {Array} will be returned.
Type
Variant

insertBefore(obj, refChild) → {Int}

Insert obj before refChild in node or connector list. If refChild is null or does not exists, obj will be append to tail of list.
Parameters:
Name Type Description
obj Variant A node or connector.
refChild Variant Ref node or connector
Source:
Returns:
Index of obj after inserting.
Type
Int

insertConnectorAt(connector, index)

Insert connector to index. If index is not set, node will be inserted as the first connector of ctab.
Parameters:
Name Type Description
connector Kekule.ChemStructureConnector
index Int
Source:

insertNodeAt(node, index)

Insert node to index. If index is not set, node will be inserted to the tail of node list of ctab.
Parameters:
Name Type Description
node Kekule.ChemStructureNode
index Int
Source:

invokeEvent(eventName, event)

Invoke an event and call all corresponding handlers (listeners).
Parameters:
Name Type Description
eventName String Event to be invoked.
event Object A hash object with information about event. At least should include the following fields: { name: name of event, target: which object invoke this event, generally this object } If this parameter is not set, the default value {eventName, this} will be used.
Inherited From:
Source:

isEmpty() → {Bool}

Returns if this fragment has no formula or ctab, or ctab has no nodes or connectors.
Source:
Returns:
Type
Bool

isEventHandlerList(value) → {bool}

Check if a object is Class.EventHandlerList.
Parameters:
Name Type Description
value Object
Inherited From:
Source:
Returns:
True or false.
Type
bool

isPropertySerializable(propName) → {Bool}

Returns if property is serializable.
Parameters:
Name Type Description
propName String
Inherited From:
Source:
Returns:
Type
Bool

isPropUpdated(propName)

Check whether property is changed in begin/endUpdate procedure.
Parameters:
Name Type Description
propName Object
Inherited From:
Source:

isSubFragment(node) → {Bool}

Check if a node has a sub structure (has child nodes). Note if a sub group has no children, it will not be regarded as sub fragment.
Parameters:
Name Type Description
node Kekule.ChemStructureNode
Source:
Returns:
Type
Bool

isUpdating()

Check if object is in updating state.
Inherited From:
Source:

loadObj(srcNode, serializerOrName)

load current object from srcNode.
Parameters:
Name Type Description
srcNode Object Storage node to load object. Different serializer requires different node.
serializerOrName Variant A ObjSerializer instance or name registered in ObjSerializerFactory. Can be null to use the default serializer.
Inherited From:
Source:

nodesHasCoord2D(allowCoordBorrow) → {Bool}

Check if child nodes has 2D coord.
Parameters:
Name Type Description
allowCoordBorrow Bool
Source:
Returns:
Type
Bool

nodesHasCoord3D(allowCoordBorrow) → {Bool}

Check if child nodes has 3D coord.
Parameters:
Name Type Description
allowCoordBorrow Bool
Source:
Returns:
Type
Bool

notifyPropSet(propName, newValue)

Notify that a property value is set
Parameters:
Name Type Description
propName String Name of property.
newValue Variant New value of the property.
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objectChange()

Called when object is changed.
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off(eventName, listener, thisArg)

Remove an event handler, shortcut for (@link ObjectEx.removeEventListener}.
Parameters:
Name Type Description
eventName String Name of event.
listener function Handler function.
thisArg Object The scope object applied when the handler is called. If not set, all listenr function in list will be removed.
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on(eventName, listener, thisArg) → {Object}

Add an event handler, shortcut for ObjectEx.addEventListener.
Parameters:
Name Type Description
eventName String Name of event.
listener function Handler function.
thisArg Object The scope object applied when the handler is called.
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Returns:
Handler info object on success, null on fail.
Type
Object

once(eventName, listener, thisArg) → {Object}

Add an event handler that will only be evoked once, shortcut for ObjectEx.addOnceEventListener.
Parameters:
Name Type Description
eventName String Name of event.
listener function Handler function.
thisArg Object The scope object applied when the handler is called.
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Returns:
Handler info object on success, null on fail.
Type
Object

overwriteMethod(methodName, newMethod) → {ObjectEx}

Overwrite method of object instance (rather than prototype) with a new one.
Parameters:
Name Type Description
methodName String
newMethod Func New function. The arguments of function should be same as overwritten one plus a extra leading param stores the old method. e.g. Overwrite getPropValue method:
var obj = new ObjectEx();
obj.overwriteMethod('getPropValue', function($old, propName)
{
console.log('new method'); return $old(propName); });
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Returns:
Type
ObjectEx

perceiveAromaticRings(allowUncertainRings, candidateRings) → {Array}

Perceive and all aromatic rings in ctab.
Parameters:
Name Type Description
allowUncertainRings Bool Whether uncertain rings (e.g., with variable atom) be included in result.
candidateRings Array Rings in ctab that the detection will be performed. If this param is not set, all memebers of SSSR of ctab will be checked.
Source:
Returns:
Found aromatic rings.
Type
Array

relayEvent(eventName, event)

Relay event from child of this object.
Parameters:
Name Type Description
eventName String Event to be invoked.
event Object A hash object with information about event.
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removeAnchorNode(node)

Remove a node in anchorNodes.
Parameters:
Name Type Description
node Kekule.ChemStructureNode
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removeAnchorNodeAt(index)

Remove node at index of anchorNodes.
Parameters:
Name Type Description
index Int
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removeChild(childObj)

Remove child obj directly from connection table.
Parameters:
Name Type Description
childObj Variant A child node or connector.
Source:

removeChildObj(childObj, cascadeRemove, freeRemoved)

Remove childObj from connection table.
Parameters:
Name Type Description
childObj Variant A child node or connector.
cascadeRemove Bool Whether remove related objects (e.g., bond connected to an atom).
freeRemoved Bool Whether free all removed objects.
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removeConnector(connector, preserveConnectedObjs)

Remove a connector in connection table.
Parameters:
Name Type Description
connector Kekule.ChemStructureConnector
preserveConnectedObjs Bool Whether delte relations between this connector and related nodes.
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removeConnectorAt(index, preserveConnectedObjs)

Remove connector at index of connectors.
Parameters:
Name Type Description
index Int
preserveConnectedObjs Bool Whether delte relations between this connector and related nodes.
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removeEventListener(eventName, listener, thisArg)

Remove an event handler.
Parameters:
Name Type Description
eventName String Name of event.
listener function Handler function.
thisArg Object The scope object applied when the handler is called. If not set, all listenr function in list will be removed.
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removeNode(node, preserveLinkedConnectors)

Remove a node in connection table.
Parameters:
Name Type Description
node Kekule.ChemStructureNode
preserveLinkedConnectors Bool Whether remove relations between this node and linked connectors.
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removeNodeAt(index, preserveLinkedConnectors)

Remove node at index in connection table.
Parameters:
Name Type Description
index Int
preserveLinkedConnectors Bool Whether remove relations between this node and linked connectors.
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replaceNode(oldNode, newNode)

Replace oldNode with new one, preserve coords and all linked connectors.
Parameters:
Name Type Description
oldNode Kekule.ChemStructureNode Must be direct child of current ctab (node in nested structure fragment will be ignored).
newNode Kekule.ChemStructureNode
Source:

saved()

Called after this object is saved through a serialization system. Descendants may override this.
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saveObj(destNode, serializerOrName, options)

Save current object to destNode.
Parameters:
Name Type Description
destNode Object Storage node to save object. Different serializer requires different node.
serializerOrName Variant A ObjSerializer instance or name registered in ObjSerializerFactory. Can be null to use the default serializer.
options Hash
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setConnectorIndex(connector, index)

Change index of connector.
Parameters:
Name Type Description
connector Kekule.ChemStructureConnector
index Int
Source:

setNodeIndex(node, index)

Change index of node.
Parameters:
Name Type Description
node Kekule.ChemStructureNode
index Int
Source:

setPropStoreFieldValue(propName) → {Variant}

Set value of a property's store field. Use this method to set property value and avoid the call of property setter. Readonly property can also be changed in this method. Note: if the property has no store field, this method will has no effect on property.
Parameters:
Name Type Description
propName String Name of property.
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Returns:
Value of property. If property does not exists, null is returned.
Type
Variant

setPropValue(propName, value, ignoreReadOnly)

Set value of a property.
Parameters:
Name Type Description
propName String Name of property.
value Variant Value of the property.
ignoreReadOnly bool Try set the value directly through store field even if the property is a readonly one (without a setter).
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setPropValues(hash, ignoreReadOnly)

Set a series of property.
Parameters:
Name Type Description
hash Hash A hash object, its key and values will be used to set property value.
ignoreReadOnly bool Try set the value directly through store field even if the property is a readonly one (without a setter).
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setPropValueX()

Set value of a property. Similar to ObjectEx.setPropValue but can pass in multiple params. The first param is always the property name while the rest will be put into setter method (setXXX).
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sortConnectors(sortFunc)

Sort direct child connectors in ctab.
Parameters:
Name Type Description
sortFunc function Function to determine the priority of connectors.
Source:

sortNodes(sortFunc)

Sort direct child nodes in ctab.
Parameters:
Name Type Description
sortFunc function Function to determine the priority of nodes.
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stopEventPropagation(event)

Stop propagation of event, disallow it to bubble to higher level.
Parameters:
Name Type Description
event Object
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traverse(callback, startingNode, breadthFirst, partialNodes) → {Hash}

Traverse the nodes in connection tab through a depth or breadth first spanning tree algorithm.
Parameters:
Name Type Description
callback Func Function called when meet a new node or connector, has two params: callback(currNodeOrConnector, isConnector)
startingNode Kekule.StructureNode Starting position of travers.
breadthFirst Bool Set to true to use breadth first algorithm or false to use depth first algorithm.
partialNodes Array If this param is set, only part of the structure will be traversed.
Source:
Returns:
A hash object containing all the nodes and connectors sequence traversed. {nodes, connectors}. Note that all nodes but not all connectors (e.g., the one in ring) may be traversed.
Type
Hash

Events

change

Invoked when the object has been modified. event param of it has one fields: {changedPropNames: Array}
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finalize

Invoked when ObjectEx#finalize is called and the object is released. event param of it has one fields: {obj}
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propValueSet

Invoked when a property value is set by its setter event param of it has two fields: {propName, propValue} If property enablePropValueSetEvent is false, this event will never be fired.
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