Class: Pseudoatom

Kekule. Pseudoatom

new Pseudoatom(id, atomType, coord2D, coord3D)

Represent an unreal atom, such as dummy atom (A point or object with no chemical semantics), a "any atom" and so on. Examples can be centroids, bond-midpoints, orienting "atoms" in small z-matrices.
Parameters:
Name Type Description
id String Id of this node.
atomType String Unreal atom type, value from Kekule.PseudoatomType.
coord2D Object The 2D coordinates of node, {x, y}, can be null.
coord3D Object The 3D coordinates of node, {x, y, z}, can be null.
Properties:
Name Type Description
atomType String Unreal atom type, value from Kekule.PseudoatomType.
symbol String User custom symbol. Meanless if atomType != Kekule.PseudoatomType.CUSTOM.
Source:

Extends

Methods

appendLinkedConnector(connector)

Link a connector to this node.
Parameters:
Name Type Description
connector Kekule.ChemStructureConnector
Inherited From:
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compareStructure(targetObj, options) → {Int}

Explicit set compare method to chem structure and compare to targetObj.
Parameters:
Name Type Description
targetObj Kekule.ChemObject
options Hash
Inherited From:
Source:
Returns:
Type
Int

equalStructure(targetObj, options) → {Bool}

Check if this object and targetObj has equivalent chem structure.
Parameters:
Name Type Description
targetObj Kekule.ChemObject
options Hash
Inherited From:
Source:
Returns:
Type
Bool

fetchChargeMarker() → {Kekule.ChemMarker.ChemPropertyMarker}

Get charge marker of node. If no such a marker currently and canCreate is true, a new marker will be created.
Inherited From:
Source:
Returns:
Type
Kekule.ChemMarker.ChemPropertyMarker

fetchRadicalMarker() → {Kekule.ChemMarker.ChemPropertyMarker}

Get radical marker of node. If no such a marker currently and canCreate is true, a new marker will be created.
Inherited From:
Source:
Returns:
Type
Kekule.ChemMarker.ChemPropertyMarker

getAbsBaseCoord(coordMode, allowCoordBorrow) → {Hash}

Get absolute center coord of object.
Parameters:
Name Type Description
coordMode Int
allowCoordBorrow Bool
Inherited From:
Source:
Returns:
Type
Hash

getBaseCoord(coordMode, allowCoordBorrow) → {Hash}

Get center coord of object.
Parameters:
Name Type Description
coordMode Int
allowCoordBorrow Bool
Inherited From:
Source:
Returns:
Type
Hash

getBelongedRingMinSize() → {Int}

Returns the min size of all belonged rings.
Inherited From:
Source:
Returns:
Min ring node count. If the object is not belonged to any ring, null will be returned.
Type
Int

getBelongedSssrRings() → {Array}

Returns SSSR ring that this object belonged.
Inherited From:
Source:
Returns:
Type
Array

getConnectorTo(obj) → {Kekule.ChemStructureConnector}

Get connector between this object and another object.
Parameters:
Name Type Description
obj Kekule.ChemStructureObject
Inherited From:
Source:
Returns:
Type
Kekule.ChemStructureConnector

getContainerBox(coordMode, allowCoordBorrow) → {Hash}

Calculate the box to contain the object. Descendants may override this method.
Parameters:
Name Type Description
coordMode Int Determine to calculate 2D or 3D box. Value from Kekule.CoordMode.
allowCoordBorrow Bool
Inherited From:
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 contain the object.
Parameters:
Name Type Description
allowCoordBorrow Bool
Inherited From:
Source:
Returns:
Box information. {x1, y1, z1, x2, y2, z2} (in 2D mode z1 and z2 will not be set).
Type
Hash

getContainerBox3D(allowCoordBorrow) → {Hash}

Calculate the 3D box to contain the object.
Parameters:
Name Type Description
allowCoordBorrow Bool
Inherited From:
Source:
Returns:
Box information. {x1, y1, z1, x2, y2, z2} (in 2D mode z1 and z2 will not be set).
Type
Hash

getCoordDeterminateObjects() → {Array}

If this object determinate other object's coord, this method should returns them.
Inherited From:
Source:
Returns:
Type
Array

getCurrConnectableObj() → {Kekule.ChemStructureObject}

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.
Inherited From:
Source:
Returns:
Type
Kekule.ChemStructureObject

getDisplayRichText(hydrogenDisplayLevel, showCharge)

Get label to display the atom.
Parameters:
Name Type Description
hydrogenDisplayLevel Int Value from Kekule.Render.HydrogenDisplayLevel.
showCharge Bool Whether display charge of node.
Inherited From:
Source:

getHydrogenCount(includingBondedHydrogen)

Returns hydrogen count linked to this atom. Same as getExplicitHydrogenCount if includingBondedHydrogen is false.
Parameters:
Name Type Description
includingBondedHydrogen Bool If true, hydrogen siblings will also be take into consideration.
Inherited From:
Source:

getLinkedBonds(bondType) → {Array}

Returns linked instances of Kekule.Bond to this node.
Parameters:
Name Type Description
bondType Int
Inherited From:
Source:
Returns:
Type
Array

getLinkedChemNodes(ignoreHydrogenAtoms) → {Array}

Returns neighbor nodes linked to this node through proper connectors.
Parameters:
Name Type Description
ignoreHydrogenAtoms Bool Whether explicit hydrogen atoms are returned. Default is false.
Inherited From:
Source:
Returns:
Type
Array

getLinkedConnectorAt(index) → {Kekule.ChemStructureConnector}

Get linked connector object at index.
Parameters:
Name Type Description
index Int
Inherited From:
Source:
Returns:
Type
Kekule.ChemStructureConnector

getLinkedConnectorCount() → {Int}

Return count of linkedConnectors.
Inherited From:
Source:
Returns:
Type
Int

getLinkedDoubleBonds() → {Array}

Returns linked double covalent bond to this node.
Inherited From:
Source:
Returns:
Type
Array

getLinkedHydrogenAtoms() → {Array}

Returns linked hydrogen atoms.
Inherited From:
Source:
Returns:
Type
Array

getLinkedMultipleBonds() → {Array}

Returns linked multiple covalent bond to this node.
Inherited From:
Source:
Returns:
Type
Array

getLinkedNonHydrogenConnectors() → {Array}

Returns connectors that connected to a non hydrogen node.
Inherited From:
Source:
Returns:
Type
Array

getLinkedNonHydrogenObjs() → {Array}

Returns linked objects except hydrogen atoms.
Inherited From:
Source:
Returns:
Type
Array

getLinkedObjsOnConnector() → {Array}

Returns other objects connected to this one through connector.
Inherited From:
Source:
Returns:
Type
Array

getParentFragment() → {Kekule.StructureFragment}

If Kekule.ChemStructureObject#parent is a Kekule.StructureFragment, returns this fragment.
Inherited From:
Source:
Returns:
Type
Kekule.StructureFragment

getRootFragment() → {Kekule.StructureFragment}

Returns the root parent of Kekule.StructureFragment, rather than subgroups.
Inherited From:
Source:
Returns:
Type
Kekule.StructureFragment

indexOfLinkedConnector(connector) → {Int}

Returns index of connector connected to node.
Parameters:
Name Type Description
connector Kekule.ChemStructureConnector
Inherited From:
Source:
Returns:
Type
Int

isCoordDependent() → {Bool}

Whether the coord of chem object is calculated from other object (like connector).
Inherited From:
Source:
Returns:
Type
Bool

isHydrogenAtom() → {Bool}

Returns whether this node is a H atom (but not D or T).
Inherited From:
Source:
Returns:
Type
Bool

isSaturated() → {Bool}

Returns whether this atom is a saturated one.
Inherited From:
Source:
Returns:
Type
Bool

mayContainElement(atomicNumberOrSymbol) → {Bool}

Returns when this node is an atom of certain element or maybe or may include element (peusdo atom or atom list).
Parameters:
Name Type Description
atomicNumberOrSymbol Variant
Inherited From:
Source:
Returns:
Type
Bool

move(delta, coordMode) → {Hash}

Move node by delta.
Parameters:
Name Type Description
delta Hash
coordMode Int
Inherited From:
Source:
Returns:
New coord after moving.
Type
Hash

move2D(delta) → {Hash}

Move node 2D coord by delta.
Parameters:
Name Type Description
delta Hash
Inherited From:
Source:
Returns:
New coord after moving.
Type
Hash

move3D(delta) → {Hash}

Move node 3D coord by delta.
Parameters:
Name Type Description
delta Hash
Inherited From:
Source:
Returns:
New coord after moving.
Type
Hash

removeLinkedConnector(connector)

Remove a connector in linkedContainer.
Parameters:
Name Type Description
connector Kekule.ChemStructureConnector
Inherited From:
Source:

removeLinkedConnectorAt(index)

Remove connector at index of linkedConnectors.
Parameters:
Name Type Description
index Int
Inherited From:
Source:

removeThisFromLinkedConnector()

Remove this node from all linked connectors. Ths method should be called before a object is removed from a structure.
Inherited From:
Source:

setHydrogenCount(value)

Same as setExplicitHydrogenCount.
Parameters:
Name Type Description
value Int
Inherited From:
Source:

Events

structureChange

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}.
Inherited From:
Source:

Kekule. Pseudoatom

new Pseudoatom()

Source:

Methods

appendLinkedConnector(connector)

Link a connector to this node.
Parameters:
Name Type Description
connector Kekule.ChemStructureConnector
Inherited From:
Source:

compareStructure(targetObj, options) → {Int}

Explicit set compare method to chem structure and compare to targetObj.
Parameters:
Name Type Description
targetObj Kekule.ChemObject
options Hash
Inherited From:
Source:
Returns:
Type
Int

equalStructure(targetObj, options) → {Bool}

Check if this object and targetObj has equivalent chem structure.
Parameters:
Name Type Description
targetObj Kekule.ChemObject
options Hash
Inherited From:
Source:
Returns:
Type
Bool

fetchChargeMarker() → {Kekule.ChemMarker.ChemPropertyMarker}

Get charge marker of node. If no such a marker currently and canCreate is true, a new marker will be created.
Inherited From:
Source:
Returns:
Type
Kekule.ChemMarker.ChemPropertyMarker

fetchRadicalMarker() → {Kekule.ChemMarker.ChemPropertyMarker}

Get radical marker of node. If no such a marker currently and canCreate is true, a new marker will be created.
Inherited From:
Source:
Returns:
Type
Kekule.ChemMarker.ChemPropertyMarker

getAbsBaseCoord(coordMode, allowCoordBorrow) → {Hash}

Get absolute center coord of object.
Parameters:
Name Type Description
coordMode Int
allowCoordBorrow Bool
Inherited From:
Source:
Returns:
Type
Hash

getBaseCoord(coordMode, allowCoordBorrow) → {Hash}

Get center coord of object.
Parameters:
Name Type Description
coordMode Int
allowCoordBorrow Bool
Inherited From:
Source:
Returns:
Type
Hash

getBelongedRingMinSize() → {Int}

Returns the min size of all belonged rings.
Inherited From:
Source:
Returns:
Min ring node count. If the object is not belonged to any ring, null will be returned.
Type
Int

getBelongedSssrRings() → {Array}

Returns SSSR ring that this object belonged.
Inherited From:
Source:
Returns:
Type
Array

getConnectorTo(obj) → {Kekule.ChemStructureConnector}

Get connector between this object and another object.
Parameters:
Name Type Description
obj Kekule.ChemStructureObject
Inherited From:
Source:
Returns:
Type
Kekule.ChemStructureConnector

getContainerBox(coordMode, allowCoordBorrow) → {Hash}

Calculate the box to contain the object. Descendants may override this method.
Parameters:
Name Type Description
coordMode Int Determine to calculate 2D or 3D box. Value from Kekule.CoordMode.
allowCoordBorrow Bool
Inherited From:
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 contain the object.
Parameters:
Name Type Description
allowCoordBorrow Bool
Inherited From:
Source:
Returns:
Box information. {x1, y1, z1, x2, y2, z2} (in 2D mode z1 and z2 will not be set).
Type
Hash

getContainerBox3D(allowCoordBorrow) → {Hash}

Calculate the 3D box to contain the object.
Parameters:
Name Type Description
allowCoordBorrow Bool
Inherited From:
Source:
Returns:
Box information. {x1, y1, z1, x2, y2, z2} (in 2D mode z1 and z2 will not be set).
Type
Hash

getCoordDeterminateObjects() → {Array}

If this object determinate other object's coord, this method should returns them.
Inherited From:
Source:
Returns:
Type
Array

getCurrConnectableObj() → {Kekule.ChemStructureObject}

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.
Inherited From:
Source:
Returns:
Type
Kekule.ChemStructureObject

getDisplayRichText(hydrogenDisplayLevel, showCharge)

Get label to display the atom.
Parameters:
Name Type Description
hydrogenDisplayLevel Int Value from Kekule.Render.HydrogenDisplayLevel.
showCharge Bool Whether display charge of node.
Inherited From:
Source:

getHydrogenCount(includingBondedHydrogen)

Returns hydrogen count linked to this atom. Same as getExplicitHydrogenCount if includingBondedHydrogen is false.
Parameters:
Name Type Description
includingBondedHydrogen Bool If true, hydrogen siblings will also be take into consideration.
Inherited From:
Source:

getLinkedBonds(bondType) → {Array}

Returns linked instances of Kekule.Bond to this node.
Parameters:
Name Type Description
bondType Int
Inherited From:
Source:
Returns:
Type
Array

getLinkedChemNodes(ignoreHydrogenAtoms) → {Array}

Returns neighbor nodes linked to this node through proper connectors.
Parameters:
Name Type Description
ignoreHydrogenAtoms Bool Whether explicit hydrogen atoms are returned. Default is false.
Inherited From:
Source:
Returns:
Type
Array

getLinkedConnectorAt(index) → {Kekule.ChemStructureConnector}

Get linked connector object at index.
Parameters:
Name Type Description
index Int
Inherited From:
Source:
Returns:
Type
Kekule.ChemStructureConnector

getLinkedConnectorCount() → {Int}

Return count of linkedConnectors.
Inherited From:
Source:
Returns:
Type
Int

getLinkedDoubleBonds() → {Array}

Returns linked double covalent bond to this node.
Inherited From:
Source:
Returns:
Type
Array

getLinkedHydrogenAtoms() → {Array}

Returns linked hydrogen atoms.
Inherited From:
Source:
Returns:
Type
Array

getLinkedMultipleBonds() → {Array}

Returns linked multiple covalent bond to this node.
Inherited From:
Source:
Returns:
Type
Array

getLinkedNonHydrogenConnectors() → {Array}

Returns connectors that connected to a non hydrogen node.
Inherited From:
Source:
Returns:
Type
Array

getLinkedNonHydrogenObjs() → {Array}

Returns linked objects except hydrogen atoms.
Inherited From:
Source:
Returns:
Type
Array

getLinkedObjsOnConnector() → {Array}

Returns other objects connected to this one through connector.
Inherited From:
Source:
Returns:
Type
Array

getParentFragment() → {Kekule.StructureFragment}

If Kekule.ChemStructureObject#parent is a Kekule.StructureFragment, returns this fragment.
Inherited From:
Source:
Returns:
Type
Kekule.StructureFragment

getRootFragment() → {Kekule.StructureFragment}

Returns the root parent of Kekule.StructureFragment, rather than subgroups.
Inherited From:
Source:
Returns:
Type
Kekule.StructureFragment

indexOfLinkedConnector(connector) → {Int}

Returns index of connector connected to node.
Parameters:
Name Type Description
connector Kekule.ChemStructureConnector
Inherited From:
Source:
Returns:
Type
Int

isCoordDependent() → {Bool}

Whether the coord of chem object is calculated from other object (like connector).
Inherited From:
Source:
Returns:
Type
Bool

isHydrogenAtom() → {Bool}

Returns whether this node is a H atom (but not D or T).
Inherited From:
Source:
Returns:
Type
Bool

isSaturated() → {Bool}

Returns whether this atom is a saturated one.
Inherited From:
Source:
Returns:
Type
Bool

mayContainElement(atomicNumberOrSymbol) → {Bool}

Returns when this node is an atom of certain element or maybe or may include element (peusdo atom or atom list).
Parameters:
Name Type Description
atomicNumberOrSymbol Variant
Inherited From:
Source:
Returns:
Type
Bool

move(delta, coordMode) → {Hash}

Move node by delta.
Parameters:
Name Type Description
delta Hash
coordMode Int
Inherited From:
Source:
Returns:
New coord after moving.
Type
Hash

move2D(delta) → {Hash}

Move node 2D coord by delta.
Parameters:
Name Type Description
delta Hash
Inherited From:
Source:
Returns:
New coord after moving.
Type
Hash

move3D(delta) → {Hash}

Move node 3D coord by delta.
Parameters:
Name Type Description
delta Hash
Inherited From:
Source:
Returns:
New coord after moving.
Type
Hash

removeLinkedConnector(connector)

Remove a connector in linkedContainer.
Parameters:
Name Type Description
connector Kekule.ChemStructureConnector
Inherited From:
Source:

removeLinkedConnectorAt(index)

Remove connector at index of linkedConnectors.
Parameters:
Name Type Description
index Int
Inherited From:
Source:

removeThisFromLinkedConnector()

Remove this node from all linked connectors. Ths method should be called before a object is removed from a structure.
Inherited From:
Source:

setHydrogenCount(value)

Same as setExplicitHydrogenCount.
Parameters:
Name Type Description
value Int
Inherited From:
Source:

Events

structureChange

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}.
Inherited From:
Source: