new ChemStructureConnector()
Implements the concept of a connections between two or more structure nodes.
Properties:
Name | Type | Description |
---|---|---|
connectedChemNodes |
Array | Nodes connected with this connector. |
parity |
Int | Stereo parity of connector. |
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Extends
Methods
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appendConnectedObj(obj)
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Add a object to connectedObjs array. If obj already in connectedObjs, nothing will be done.
Parameters:
Name Type Description obj
Kekule.ChemStructureObject - Inherited From:
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appendLinkedConnector(connector)
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Link a connector to this node.
Parameters:
Name Type Description connector
Kekule.ChemStructureConnector - Inherited From:
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assertConnectedObjLegal(obj) → {Bool}
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Check if an obj can be added to connectedObjs array. Generally, an object with same owner of current connector can be added. If not so, a exception will be raised.
Parameters:
Name Type Description obj
Kekule.ChemStructureObject - Inherited From:
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Returns:
- Type
- Bool
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clearConnectedObjs()
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Clear all connected objects.
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compareStructure(targetObj, options) → {Int}
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Explicit set compare method to chem structure and compare to targetObj.
Parameters:
Name Type Description targetObj
Kekule.ChemObject options
Hash - Inherited From:
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Returns:
- Type
- Int
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equalStructure(targetObj, options) → {Bool}
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Check if this object and targetObj has equivalent chem structure.
Parameters:
Name Type Description targetObj
Kekule.ChemObject options
Hash - Inherited From:
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Returns:
- Type
- Bool
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getAbsBaseCoord(coordMode) → {Hash}
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Get center absolute coord of object.
Parameters:
Name Type Description coordMode
Int Bool - Inherited From:
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Returns:
- Type
- Hash
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getAllAutoScaleRefLengths(coordMode, allowCoordBorrow) → {Array}
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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 Returns:
- Type
- Array
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getBaseCoord(coordMode, allowCoordBorrow) → {Hash}
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Get center coord of object. Param coordMode determinate which coord (2D or 3D) will be returned.
Parameters:
Name Type Description coordMode
Int allowCoordBorrow
Bool - Inherited From:
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Returns:
- Type
- Hash
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getBelongedRingMinSize() → {Int}
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Returns the min size of all belonged rings.
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Returns:
Min ring node count. If the object is not belonged to any ring, null will be returned.- Type
- Int
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getBelongedSssrRings() → {Array}
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Returns SSSR ring that this object belonged.
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Returns:
- Type
- Array
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getConnectedChemNodeCount() → {Int}
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Get count of connected chem nodes.
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Returns:
- Type
- Int
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getConnectedExposedObjs() → {Array}
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Returns only connected objects exposed to renderer.
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Returns:
- Type
- Array
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getConnectedNonHydrogenObjs() → {Array}
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Returns connected objects except hydrogen atoms.
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Returns:
- Type
- Array
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getConnectedObjAt(index) → {Kekule.ChemStructureObject}
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Get connectedObj at index.
Parameters:
Name Type Description index
Int - Inherited From:
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Returns:
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getConnectedObjCount() → {Int}
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Get count of connected objects.
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Returns:
- Type
- Int
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getConnectedSiblings() → {Array}
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Returns connected objects with the same parent of this connector. For example, connector connected to a child node in subgroup, then the subgroup rather than the child node will be returned.
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Returns:
- Type
- Array
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getConnectorTo(obj) → {Kekule.ChemStructureConnector}
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Get connector between this object and another object.
Parameters:
Name Type Description obj
Kekule.ChemStructureObject - Inherited From:
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Returns:
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getCoordDependentObjects() → {Array}
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If coord is calculated from other objects, this function will return them.
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Returns:
- Type
- Array
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getCoordDeterminateObjects() → {Array}
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If this object determinate other object's coord, this method should returns them.
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Returns:
- Type
- Array
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getCurrConnectableObj() → {Kekule.ChemStructureObject}
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Returns self or child object that can directly linked to a connector. For atom or other simple chem objetc, this function should just returns self, for structure fragment, this function need to returns an anchor node.
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Returns:
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getLength(coordMode, allowCoordBorrow) → {Float}
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Return distance between two connected object. If more than two objects are connected, this function will return null.
Parameters:
Name Type Description coordMode
Int allowCoordBorrow
Bool - Inherited From:
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Returns:
- Type
- Float
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getLength2D(allowCoordBorrow) → {Float}
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Return 2D distance between two connected object. If more than two objects are connected, this function will return null.
Parameters:
Name Type Description allowCoordBorrow
Bool - Inherited From:
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Returns:
- Type
- Float
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getLength3D(allowCoordBorrow) → {Float}
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Return 3D distance between two connected object. If more than two objects are connected, this function will return null.
Parameters:
Name Type Description allowCoordBorrow
Bool - Inherited From:
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Returns:
- Type
- Float
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getLinkedConnectorAt(index) → {Kekule.ChemStructureConnector}
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Get linked connector object at index.
Parameters:
Name Type Description index
Int - Inherited From:
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Returns:
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getLinkedConnectorCount() → {Int}
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Return count of linkedConnectors.
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Returns:
- Type
- Int
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getLinkedHydrogenAtoms() → {Array}
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Returns linked hydrogen atoms.
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Returns:
- Type
- Array
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getLinkedNonHydrogenConnectors() → {Array}
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Returns connectors that connected to a non hydrogen node.
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Returns:
- Type
- Array
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getLinkedNonHydrogenObjs() → {Array}
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Returns linked objects except hydrogen atoms.
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Returns:
- Type
- Array
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getLinkedObjsOnConnector() → {Array}
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Returns other objects connected to this one through connector.
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Returns:
- Type
- Array
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getParentFragment() → {Kekule.StructureFragment}
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If Kekule.ChemStructureObject#parent is a Kekule.StructureFragment, returns this fragment.
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Returns:
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getRootFragment() → {Kekule.StructureFragment}
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Returns the root parent of Kekule.StructureFragment, rather than subgroups.
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Returns:
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hasConnectedObj(obj)
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Check if a object is connected with this connector.
Parameters:
Name Type Description obj
Kekule.ChemStructureObject - Inherited From:
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indexOfConnectedObj(obj) → {Int}
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Get index of obj in connectedObjs array.
Parameters:
Name Type Description obj
Kekule.ChemStructureObject - Inherited From:
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Returns:
- Type
- Int
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indexOfLinkedConnector(connector) → {Int}
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Returns index of connector connected to node.
Parameters:
Name Type Description connector
Kekule.ChemStructureConnector - Inherited From:
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Returns:
- Type
- Int
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insertConnectedObjAt(obj, index)
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Insert obj at index of connectedObjs array. If index is not set, obj will be put as the first obj.
Parameters:
Name Type Description obj
Kekule.ChemStructureObject index
Int - Inherited From:
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isConnectingConnector()
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Check if this connector connected to another connector (e.g, bond ends with another bond).
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isConnectingWithObj(obj)
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Check if a object is connected with this connector. Same as Kekule.ChemStructureConnector#hasConnectedObj
Parameters:
Name Type Description obj
Kekule.ChemStructureObject - Inherited From:
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isCoordDependent() → {Bool}
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Whether the coord of chem object is not calculated from other object (like connector).
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Returns:
- Type
- Bool
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isNormalConnectorToHydrogen() → {Bool}
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Whether this connector connect hydrogen atom to another node.
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Returns:
- Type
- Bool
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move(delta, coordMode)
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Move connector by delta. Actually this action will move all nodes connected with this connector.
Parameters:
Name Type Description delta
Hash coordMode
Int - Inherited From:
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move2D(delta) → {Hash}
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Move connector 2D coord by delta.
Parameters:
Name Type Description delta
Hash - Inherited From:
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Returns:
New coord after moving.- Type
- Hash
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move3D(delta) → {Hash}
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Move connector 3D coord by delta.
Parameters:
Name Type Description delta
Hash - Inherited From:
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Returns:
New coord after moving.- Type
- Hash
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removeConnectedObj(obj)
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Remove a object in connectedObjs property.
Parameters:
Name Type Description obj
Kekule.ChemStructureObject - Inherited From:
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removeConnectedObjAt(index)
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Remove object at index in connectedObjs property.
Parameters:
Name Type Description index
Int - Inherited From:
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removeLinkedConnector(connector)
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Remove a connector in linkedContainer.
Parameters:
Name Type Description connector
Kekule.ChemStructureConnector - Inherited From:
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removeLinkedConnectorAt(index)
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Remove connector at index of linkedConnectors.
Parameters:
Name Type Description index
Int - Inherited From:
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removeThisFromConnectedObjs()
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Remove this connector from all linked objects. Ths method should be called before a connector is removed from a structure.
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removeThisFromLinkedConnector()
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Remove this node from all linked connectors. Ths method should be called before a object is removed from a structure.
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replaceConnectedObj(oldObj, newObj)
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Replace old connected object with new one and remove connection to old object.
Parameters:
Name Type Description oldObj
Kekule.ChemStructureObject newObj
Kekule.ChemStructureObject - Inherited From:
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reverseConnectedObjOrder()
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Reverse the order of connected object.
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setAbsBaseCoord(value, coordMode)
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Set absolute center coord of connector. Actually mode all conntected nodes.
Parameters:
Name Type Description value
Hash coordMode
Int - Inherited From:
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setConnectedObjAt(index, value)
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Set connectedObj at index.
Parameters:
Name Type Description index
Int value
Kekule.ChemStructureObject - Inherited From:
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sortConnectedObjs(compareFunc)
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Sort the array of connected objs.
Parameters:
Name Type Description compareFunc
function - Inherited From:
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Events
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structureChange
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Invoked when object is changed and the change is related with structure (e.g. modify a bond, change a atomic number...). Event has field: {origin: the change source object (may be a child of event.target}.
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