Representation of an atom in the ZMatrix. More...

Collaboration diagram for denoptim.molecularmodeling.zmatrix.ZMatrixAtom:

Public Member Functions
	ZMatrixAtom (int id, String symbol, String type, ZMatrixAtom bondRefAtom, ZMatrixAtom angleRefAtom, ZMatrixAtom angle2RefAtom, Double bondLength, Double angleValue, Double angle2Value, Integer chiralFlag)
	Constructor for ZMatrixAtom. More...

int	getId ()
	Get the id of the atom. More...

void	setId (int id)
	Set the id of the atom. More...

String	getSymbol ()
	Get the symbol of the atom. More...

void	setSymbol (String symbol)
	Set the symbol of the atom. More...

String	getType ()
	Get the type of the atom. More...

void	setType (String type)
	Set the type of the atom. More...

ZMatrixAtom	getBondRefAtom ()
	Get the bond reference atom. More...

ZMatrixAtom	getAngleRefAtom ()
	Get the angle reference atom. More...

ZMatrixAtom	getAngle2RefAtom ()
	Get the angle2 reference atom. More...

Double	getBondLength ()
	Get the bond length. More...

Double	getAngleValue ()
	Get the angle value. More...

Double	getAngle2Value ()
	Get the angle2 value. More...

void	setBondLength (Double bondLength)
	Set the bond length. More...

void	setAngleValue (Double angleValue)
	Set the angle value. More...

void	setAngle2Value (Double angle2Value)
	Set the angle2 value. More...

void	setChiralFlag (Integer chiralFlag)
	Set the chiral flag. More...

Integer	getChiralFlag ()
	Get the chiral flag. More...

boolean	usesProperTorsion ()
	Check if the atom uses proper torsion. More...

boolean	equals (Object o)
	Get the string representation of the atom. More...

int	hashCode ()

String	toString ()

Package Functions
void	setBondRefAtom (ZMatrixAtom bondRefAtom)
	Package-private setter for bond reference atom (used for cloning). More...

void	setAngleRefAtom (ZMatrixAtom angleRefAtom)
	Package-private setter for angle reference atom (used for cloning). More...

void	setAngle2RefAtom (ZMatrixAtom angle2RefAtom)
	Package-private setter for angle2 reference atom (used for cloning). More...

Private Attributes
int	id

String	symbol

String	type

ZMatrixAtom	bondRefAtom

ZMatrixAtom	angleRefAtom

ZMatrixAtom	angle2RefAtom

Double	bondLength

Double	angleValue

Double	angle2Value

Integer	chiralFlag

Detailed Description

Representation of an atom in the ZMatrix.

Definition at line 8 of file ZMatrixAtom.java.

Constructor & Destructor Documentation

◆ ZMatrixAtom()

denoptim.molecularmodeling.zmatrix.ZMatrixAtom.ZMatrixAtom	(	int	id,
		String	symbol,
		String	type,
		ZMatrixAtom	bondRefAtom,
		ZMatrixAtom	angleRefAtom,
		ZMatrixAtom	angle2RefAtom,
		Double	bondLength,
		Double	angleValue,
		Double	angle2Value,
		Integer	chiralFlag
	)

Constructor for ZMatrixAtom.

Parameters

id	The id of the atom
symbol	The symbol of the atom
type	The type of the atom
bondRefAtom	The bond reference atom
angleRefAtom	The angle reference atom
angle2RefAtom	The angle2 reference atom
bondLength	The bond length
angleValue	The angle value
angle2Value	The angle2 value
chiralFlag	The chiral flag

Definition at line 36 of file ZMatrixAtom.java.

Referenced by denoptim.molecularmodeling.zmatrix.ZMatrixAtom.equals().

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Member Function Documentation

◆ equals()

boolean denoptim.molecularmodeling.zmatrix.ZMatrixAtom.equals ( Object o )

Get the string representation of the atom.

Returns: The string representation of the atom

Definition at line 290 of file ZMatrixAtom.java.

Referenced by denoptim.molecularmodeling.zmatrix.ZMatrixBond.equals().

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◆ getAngle2RefAtom()

ZMatrixAtom denoptim.molecularmodeling.zmatrix.ZMatrixAtom.getAngle2RefAtom ( )

Get the angle2 reference atom.

Returns: The angle2 reference atom or null if not set

Definition at line 147 of file ZMatrixAtom.java.

References denoptim.molecularmodeling.zmatrix.ZMatrixAtom.angle2RefAtom.

Referenced by denoptim.molecularmodeling.zmatrix.ZMatrix.clone(), and denoptim.molecularmodeling.zmatrix.ZMatrix.getAngle2RefAtom().

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◆ getAngle2Value()

Double denoptim.molecularmodeling.zmatrix.ZMatrixAtom.getAngle2Value ( )

Get the angle2 value.

Returns: The angle2 value or null if not set

Definition at line 180 of file ZMatrixAtom.java.

References denoptim.molecularmodeling.zmatrix.ZMatrixAtom.angle2Value.

Referenced by denoptim.molecularmodeling.zmatrix.ZMatrix.getAngle2Value(), and denoptim.integration.tinker.ConformationalSearchPSSROT.performPSSROT().

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◆ getAngleRefAtom()

ZMatrixAtom denoptim.molecularmodeling.zmatrix.ZMatrixAtom.getAngleRefAtom ( )

Get the angle reference atom.

Returns: The angle reference atom or null if not set

Definition at line 136 of file ZMatrixAtom.java.

References denoptim.molecularmodeling.zmatrix.ZMatrixAtom.angleRefAtom.

Referenced by denoptim.molecularmodeling.zmatrix.ZMatrix.clone(), and denoptim.molecularmodeling.zmatrix.ZMatrix.getAngleRefAtom().

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◆ getAngleValue()

Double denoptim.molecularmodeling.zmatrix.ZMatrixAtom.getAngleValue ( )

Get the angle value.

Returns: The angle value or null if not set

Definition at line 169 of file ZMatrixAtom.java.

References denoptim.molecularmodeling.zmatrix.ZMatrixAtom.angleValue.

Referenced by denoptim.molecularmodeling.zmatrix.ZMatrix.getAngleValue(), and denoptim.integration.tinker.ConformationalSearchPSSROT.performPSSROT().

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◆ getBondLength()

Double denoptim.molecularmodeling.zmatrix.ZMatrixAtom.getBondLength ( )

Get the bond length.

Returns: The bond length or null if not set

Definition at line 158 of file ZMatrixAtom.java.

References denoptim.molecularmodeling.zmatrix.ZMatrixAtom.bondLength.

Referenced by denoptim.molecularmodeling.zmatrix.ZMatrix.getBondLength(), and denoptim.integration.tinker.ConformationalSearchPSSROT.performPSSROT().

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◆ getBondRefAtom()

ZMatrixAtom denoptim.molecularmodeling.zmatrix.ZMatrixAtom.getBondRefAtom ( )

Get the bond reference atom.

Returns: The bond reference atom or null if not set

Definition at line 125 of file ZMatrixAtom.java.

References denoptim.molecularmodeling.zmatrix.ZMatrixAtom.bondRefAtom.

Referenced by denoptim.molecularmodeling.zmatrix.ZMatrix.clone(), denoptim.molecularmodeling.zmatrix.ZMatrix.getBondRefAtom(), and denoptim.molecularmodeling.zmatrix.ZMatrix.getBondsToDel().

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◆ getChiralFlag()

Integer denoptim.molecularmodeling.zmatrix.ZMatrixAtom.getChiralFlag ( )

Get the chiral flag.

Returns: The chiral flag or null if not set

Definition at line 235 of file ZMatrixAtom.java.

References denoptim.molecularmodeling.zmatrix.ZMatrixAtom.chiralFlag.

Referenced by denoptim.molecularmodeling.zmatrix.ZMatrix.getChiralFlag(), and denoptim.integration.tinker.ConformationalSearchPSSROT.performPSSROT().

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◆ getId()

int denoptim.molecularmodeling.zmatrix.ZMatrixAtom.getId ( )

Get the id of the atom.

Returns: The id of the atom

Definition at line 59 of file ZMatrixAtom.java.

References denoptim.molecularmodeling.zmatrix.ZMatrixAtom.id.

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◆ getSymbol()

String denoptim.molecularmodeling.zmatrix.ZMatrixAtom.getSymbol ( )

Get the symbol of the atom.

Returns: The symbol of the atom

Definition at line 81 of file ZMatrixAtom.java.

References denoptim.molecularmodeling.zmatrix.ZMatrixAtom.symbol.

Referenced by denoptim.integration.rcoserver.RCOSocketServerClient.getZMatrixAsJsonArray(), denoptim.integration.tinker.ConformationalSearchPSSROT.setTinkerTypes(), denoptim.molecularmodeling.zmatrix.ZMatrixTest.testClone(), and denoptim.integration.tinker.TinkerUtils.writeTinkerINT().

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◆ getType()

String denoptim.molecularmodeling.zmatrix.ZMatrixAtom.getType ( )

Get the type of the atom.

Returns: The type of the atom

Definition at line 103 of file ZMatrixAtom.java.

References denoptim.molecularmodeling.zmatrix.ZMatrixAtom.type.

Referenced by denoptim.molecularmodeling.zmatrix.ZMatrixTest.testClone(), and denoptim.integration.tinker.TinkerUtils.writeTinkerINT().

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◆ hashCode()

int denoptim.molecularmodeling.zmatrix.ZMatrixAtom.hashCode ( )

Definition at line 393 of file ZMatrixAtom.java.

Referenced by denoptim.molecularmodeling.zmatrix.ZMatrixAtomTest.testZMatrixAtomHashCode().

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◆ setAngle2RefAtom()

void denoptim.molecularmodeling.zmatrix.ZMatrixAtom.setAngle2RefAtom ( ZMatrixAtom angle2RefAtom )

package

Package-private setter for angle2 reference atom (used for cloning).

Definition at line 276 of file ZMatrixAtom.java.

References denoptim.molecularmodeling.zmatrix.ZMatrixAtom.angle2RefAtom.

Referenced by denoptim.molecularmodeling.zmatrix.ZMatrix.clone(), and denoptim.molecularmodeling.zmatrix.ZMatrixAtomTest.testEquals().

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◆ setAngle2Value()

void denoptim.molecularmodeling.zmatrix.ZMatrixAtom.setAngle2Value ( Double angle2Value )

Set the angle2 value.

Parameters

angle2Value The angle2 value to set

Definition at line 213 of file ZMatrixAtom.java.

References denoptim.molecularmodeling.zmatrix.ZMatrixAtom.angle2Value.

Referenced by denoptim.integration.tinker.ConformationalSearchPSSROT.performPSSROT(), denoptim.integration.rcoserver.RCOSocketServerClient.runConformationalOptimization(), and denoptim.molecularmodeling.zmatrix.ZMatrixAtomTest.testEquals().

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◆ setAngleRefAtom()

void denoptim.molecularmodeling.zmatrix.ZMatrixAtom.setAngleRefAtom ( ZMatrixAtom angleRefAtom )

package

Package-private setter for angle reference atom (used for cloning).

Definition at line 266 of file ZMatrixAtom.java.

References denoptim.molecularmodeling.zmatrix.ZMatrixAtom.angleRefAtom.

Referenced by denoptim.molecularmodeling.zmatrix.ZMatrix.clone(), and denoptim.molecularmodeling.zmatrix.ZMatrixAtomTest.testEquals().

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◆ setAngleValue()

void denoptim.molecularmodeling.zmatrix.ZMatrixAtom.setAngleValue ( Double angleValue )

Set the angle value.

Parameters

angleValue The angle value to set

Definition at line 202 of file ZMatrixAtom.java.

References denoptim.molecularmodeling.zmatrix.ZMatrixAtom.angleValue.

Referenced by denoptim.integration.tinker.ConformationalSearchPSSROT.performPSSROT(), denoptim.integration.rcoserver.RCOSocketServerClient.runConformationalOptimization(), and denoptim.molecularmodeling.zmatrix.ZMatrixAtomTest.testEquals().

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◆ setBondLength()

void denoptim.molecularmodeling.zmatrix.ZMatrixAtom.setBondLength ( Double bondLength )

Set the bond length.

Parameters

bondLength The bond length to set

Definition at line 191 of file ZMatrixAtom.java.

References denoptim.molecularmodeling.zmatrix.ZMatrixAtom.bondLength.

Referenced by denoptim.integration.tinker.ConformationalSearchPSSROT.performPSSROT(), denoptim.integration.rcoserver.RCOSocketServerClient.runConformationalOptimization(), denoptim.molecularmodeling.RingClosureTool.saturateRingClosingAttractor(), and denoptim.molecularmodeling.zmatrix.ZMatrixAtomTest.testEquals().

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◆ setBondRefAtom()

void denoptim.molecularmodeling.zmatrix.ZMatrixAtom.setBondRefAtom ( ZMatrixAtom bondRefAtom )

package

Package-private setter for bond reference atom (used for cloning).

Definition at line 256 of file ZMatrixAtom.java.

References denoptim.molecularmodeling.zmatrix.ZMatrixAtom.bondRefAtom.

Referenced by denoptim.molecularmodeling.zmatrix.ZMatrix.clone(), and denoptim.molecularmodeling.zmatrix.ZMatrixAtomTest.testEquals().

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◆ setChiralFlag()

void denoptim.molecularmodeling.zmatrix.ZMatrixAtom.setChiralFlag ( Integer chiralFlag )

Set the chiral flag.

Parameters

chiralFlag The chiral flag to set

Definition at line 224 of file ZMatrixAtom.java.

References denoptim.molecularmodeling.zmatrix.ZMatrixAtom.chiralFlag.

Referenced by denoptim.integration.tinker.ConformationalSearchPSSROT.performPSSROT(), denoptim.integration.rcoserver.RCOSocketServerClient.runConformationalOptimization(), and denoptim.molecularmodeling.zmatrix.ZMatrixAtomTest.testEquals().

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◆ setId()

void denoptim.molecularmodeling.zmatrix.ZMatrixAtom.setId ( int id )

Set the id of the atom.

Parameters

id	The id of the atom to set

Definition at line 70 of file ZMatrixAtom.java.

References denoptim.molecularmodeling.zmatrix.ZMatrixAtom.id.

Referenced by denoptim.molecularmodeling.zmatrix.ZMatrixAtomTest.testEquals(), and denoptim.molecularmodeling.zmatrix.ZMatrixAtomTest.testZMatrixAtomHashCode().

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◆ setSymbol()

void denoptim.molecularmodeling.zmatrix.ZMatrixAtom.setSymbol ( String symbol )

Set the symbol of the atom.

Parameters

symbol The symbol of the atom to set

Definition at line 92 of file ZMatrixAtom.java.

References denoptim.molecularmodeling.zmatrix.ZMatrixAtom.symbol.

Referenced by denoptim.molecularmodeling.RingClosureTool.saturateRingClosingAttractor(), and denoptim.molecularmodeling.zmatrix.ZMatrixAtomTest.testEquals().

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◆ setType()

void denoptim.molecularmodeling.zmatrix.ZMatrixAtom.setType ( String type )

Set the type of the atom.

Parameters

type	The type of the atom to set

Definition at line 114 of file ZMatrixAtom.java.

References denoptim.molecularmodeling.zmatrix.ZMatrixAtom.type.

Referenced by denoptim.integration.tinker.ConformationalSearchPSSROT.setTinkerTypes(), and denoptim.molecularmodeling.zmatrix.ZMatrixAtomTest.testEquals().

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◆ toString()

String denoptim.molecularmodeling.zmatrix.ZMatrixAtom.toString ( )

Definition at line 412 of file ZMatrixAtom.java.

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◆ usesProperTorsion()

boolean denoptim.molecularmodeling.zmatrix.ZMatrixAtom.usesProperTorsion ( )

Check if the atom uses proper torsion.

Returns: True if the atom uses proper torsion, false otherwise

Definition at line 246 of file ZMatrixAtom.java.

References denoptim.molecularmodeling.zmatrix.ZMatrixAtom.chiralFlag.

Member Data Documentation

◆ angle2RefAtom

ZMatrixAtom denoptim.molecularmodeling.zmatrix.ZMatrixAtom.angle2RefAtom

private

Definition at line 15 of file ZMatrixAtom.java.

Referenced by denoptim.molecularmodeling.zmatrix.ZMatrixAtom.equals(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.getAngle2RefAtom(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.hashCode(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.setAngle2RefAtom(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.toString(), and denoptim.molecularmodeling.zmatrix.ZMatrixAtom.ZMatrixAtom().

◆ angle2Value

Double denoptim.molecularmodeling.zmatrix.ZMatrixAtom.angle2Value

private

Definition at line 18 of file ZMatrixAtom.java.

Referenced by denoptim.molecularmodeling.zmatrix.ZMatrixAtom.equals(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.getAngle2Value(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.hashCode(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.setAngle2Value(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.toString(), and denoptim.molecularmodeling.zmatrix.ZMatrixAtom.ZMatrixAtom().

◆ angleRefAtom

ZMatrixAtom denoptim.molecularmodeling.zmatrix.ZMatrixAtom.angleRefAtom

private

Definition at line 14 of file ZMatrixAtom.java.

Referenced by denoptim.molecularmodeling.zmatrix.ZMatrixAtom.equals(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.getAngleRefAtom(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.hashCode(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.setAngleRefAtom(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.toString(), and denoptim.molecularmodeling.zmatrix.ZMatrixAtom.ZMatrixAtom().

◆ angleValue

Double denoptim.molecularmodeling.zmatrix.ZMatrixAtom.angleValue

private

Definition at line 17 of file ZMatrixAtom.java.

Referenced by denoptim.molecularmodeling.zmatrix.ZMatrixAtom.equals(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.getAngleValue(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.hashCode(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.setAngleValue(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.toString(), and denoptim.molecularmodeling.zmatrix.ZMatrixAtom.ZMatrixAtom().

◆ bondLength

Double denoptim.molecularmodeling.zmatrix.ZMatrixAtom.bondLength

private

Definition at line 16 of file ZMatrixAtom.java.

Referenced by denoptim.molecularmodeling.zmatrix.ZMatrixAtom.equals(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.getBondLength(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.hashCode(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.setBondLength(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.toString(), and denoptim.molecularmodeling.zmatrix.ZMatrixAtom.ZMatrixAtom().

◆ bondRefAtom

ZMatrixAtom denoptim.molecularmodeling.zmatrix.ZMatrixAtom.bondRefAtom

private

Definition at line 13 of file ZMatrixAtom.java.

Referenced by denoptim.molecularmodeling.zmatrix.ZMatrixAtom.equals(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.getBondRefAtom(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.hashCode(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.setBondRefAtom(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.toString(), and denoptim.molecularmodeling.zmatrix.ZMatrixAtom.ZMatrixAtom().

◆ chiralFlag

Integer denoptim.molecularmodeling.zmatrix.ZMatrixAtom.chiralFlag

private

Definition at line 19 of file ZMatrixAtom.java.

Referenced by denoptim.molecularmodeling.zmatrix.ZMatrixAtom.equals(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.getChiralFlag(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.hashCode(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.setChiralFlag(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.toString(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.usesProperTorsion(), and denoptim.molecularmodeling.zmatrix.ZMatrixAtom.ZMatrixAtom().

◆ id

int denoptim.molecularmodeling.zmatrix.ZMatrixAtom.id

private

Definition at line 10 of file ZMatrixAtom.java.

Referenced by denoptim.molecularmodeling.zmatrix.ZMatrixAtom.equals(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.getId(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.hashCode(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.setId(), and denoptim.molecularmodeling.zmatrix.ZMatrixAtom.ZMatrixAtom().

◆ symbol

String denoptim.molecularmodeling.zmatrix.ZMatrixAtom.symbol

private

Definition at line 11 of file ZMatrixAtom.java.

Referenced by denoptim.molecularmodeling.zmatrix.ZMatrixAtom.equals(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.getSymbol(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.hashCode(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.setSymbol(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.toString(), and denoptim.molecularmodeling.zmatrix.ZMatrixAtom.ZMatrixAtom().

◆ type

String denoptim.molecularmodeling.zmatrix.ZMatrixAtom.type

private

Definition at line 12 of file ZMatrixAtom.java.

Referenced by denoptim.molecularmodeling.zmatrix.ZMatrixAtom.equals(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.getType(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.hashCode(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.setType(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.toString(), and denoptim.molecularmodeling.zmatrix.ZMatrixAtom.ZMatrixAtom().

The documentation for this class was generated from the following file:

/github/workspace/src/main/java/denoptim/molecularmodeling/zmatrix/ZMatrixAtom.java

Public Member Functions

Package Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ZMatrixAtom()

Member Function Documentation

◆ equals()

◆ getAngle2RefAtom()

◆ getAngle2Value()

◆ getAngleRefAtom()

◆ getAngleValue()

◆ getBondLength()

◆ getBondRefAtom()

◆ getChiralFlag()

◆ getId()

◆ getSymbol()

◆ getType()

◆ hashCode()

◆ setAngle2RefAtom()

◆ setAngle2Value()

◆ setAngleRefAtom()

◆ setAngleValue()

◆ setBondLength()

◆ setBondRefAtom()

◆ setChiralFlag()

◆ setId()

◆ setSymbol()

◆ setType()

◆ toString()

◆ usesProperTorsion()

Member Data Documentation

◆ angle2RefAtom

◆ angle2Value

◆ angleRefAtom

◆ angleValue

◆ bondLength

◆ bondRefAtom

◆ chiralFlag

◆ id

◆ symbol

◆ type