Based on the code from ffx.kenai.com Michael J. More...

Inheritance diagram for denoptim.integration.tinker.TinkerAtom:

Collaboration diagram for denoptim.integration.tinker.TinkerAtom:

Public Member Functions
	TinkerAtom ()

	TinkerAtom (int xyzIndex, String atomStr, int ffAtomType, double[] xyz, int[] atmNb, double[] distAngles)

void	setAtomNeighbours (int[] atmNb)

int[]	getAtomNeighbours ()

void	setDistAngle (double[] distAngles)

double[]	getDistAngle ()

void	moveTo (double[] d)
	Add a vector to the Atom's current position vector. More...

void	moveTo (double a, double b, double c)

void	setXYZ (double[] xyz)

double[]	getXYZ ()

void	getXYZ (double[] x)

int	getXYZIndex ()
	Gets the XYZ Index. More...

void	setXYZIndex (int xyzIndex)

String	getAtomString ()

void	setAtomString (String atomStr)

int	getAtomType ()

void	setAtomType (int ffAtomType)

void	setVertexId (long vidx)

long	getVertexId ()

boolean	usesProperTorsion ()
	Evaluates whether this TinkerAtom's line refers to a torsion (chiral flag is 0) or to an inproper torsion (chiral flag is +/-1). More...

String	toString ()

Private Attributes
int	ffAtomType

String	atomStr

double[]	xyz

int	xyzIndex

double[]	distAngles

int[]	atmNb

long	vtxId

Detailed Description

Based on the code from ffx.kenai.com Michael J.

Schnieders

Author: Vishwesh Venkatraman

Definition at line 25 of file TinkerAtom.java.

Constructor & Destructor Documentation

◆ TinkerAtom() [1/2]

denoptim.integration.tinker.TinkerAtom.TinkerAtom ( )

Definition at line 66 of file TinkerAtom.java.

◆ TinkerAtom() [2/2]

denoptim.integration.tinker.TinkerAtom.TinkerAtom	(	int	xyzIndex,
		String	atomStr,
		int	ffAtomType,
		double[]	xyz,
		int[]	atmNb,
		double[]	distAngles
	)

Definition at line 72 of file TinkerAtom.java.

References denoptim.integration.tinker.TinkerAtom.atmNb, denoptim.integration.tinker.TinkerAtom.atomStr, denoptim.integration.tinker.TinkerAtom.distAngles, denoptim.integration.tinker.TinkerAtom.ffAtomType, denoptim.integration.tinker.TinkerAtom.xyz, and denoptim.integration.tinker.TinkerAtom.xyzIndex.

Member Function Documentation

◆ getAtomNeighbours()

int[] denoptim.integration.tinker.TinkerAtom.getAtomNeighbours ( )

Definition at line 100 of file TinkerAtom.java.

References denoptim.integration.tinker.TinkerAtom.atmNb.

Referenced by denoptim.integration.tinker.TinkerMolecule.deepCopy(), denoptim.integration.tinker.TinkerMolecule.getConnectedAtoms(), denoptim.integration.tinker.TinkerMolecule.isConnected(), denoptim.integration.tinker.TinkerMolecule.printIC(), denoptim.molecularmodeling.ChemicalObjectModel.updateXYZFromINT(), and denoptim.integration.tinker.TinkerUtils.writeIC().

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◆ getAtomString()

String denoptim.integration.tinker.TinkerAtom.getAtomString ( )

Definition at line 210 of file TinkerAtom.java.

References denoptim.integration.tinker.TinkerAtom.atomStr.

Referenced by denoptim.integration.tinker.TinkerMolecule.deepCopy(), denoptim.integration.tinker.TinkerMolecule.printIC(), denoptim.molecularmodeling.RingClosureTool.setTinkerTypes(), denoptim.integration.tinker.TinkerUtils.setTinkerTypes(), and denoptim.integration.tinker.TinkerUtils.writeIC().

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◆ getAtomType()

int denoptim.integration.tinker.TinkerAtom.getAtomType ( )

Definition at line 224 of file TinkerAtom.java.

References denoptim.integration.tinker.TinkerAtom.ffAtomType.

Referenced by denoptim.integration.tinker.TinkerMolecule.deepCopy(), denoptim.integration.tinker.TinkerMolecule.printIC(), and denoptim.integration.tinker.TinkerUtils.writeIC().

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◆ getDistAngle()

double[] denoptim.integration.tinker.TinkerAtom.getDistAngle ( )

Definition at line 114 of file TinkerAtom.java.

References denoptim.integration.tinker.TinkerAtom.distAngles.

Referenced by denoptim.integration.tinker.TinkerMolecule.deepCopy(), denoptim.integration.tinker.ConformationalSearchPSSROT.performPSSROT(), denoptim.integration.tinker.TinkerMolecule.printIC(), denoptim.molecularmodeling.RingClosureTool.saturateRingClosingAttractor(), denoptim.molecularmodeling.ChemicalObjectModel.updateXYZFromINT(), and denoptim.integration.tinker.TinkerUtils.writeIC().

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◆ getVertexId()

long denoptim.integration.tinker.TinkerAtom.getVertexId ( )

Definition at line 245 of file TinkerAtom.java.

References denoptim.integration.tinker.TinkerAtom.vtxId.

Referenced by denoptim.integration.tinker.TinkerMolecule.deepCopy().

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◆ getXYZ() [1/2]

double[] denoptim.integration.tinker.TinkerAtom.getXYZ ( )

getXYZ

Returns: an array of double.

Definition at line 169 of file TinkerAtom.java.

References denoptim.integration.tinker.TinkerAtom.xyz.

Referenced by denoptim.integration.tinker.TinkerMolecule.deepCopy().

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◆ getXYZ() [2/2]

void denoptim.integration.tinker.TinkerAtom.getXYZ ( double[] x )

getXYZ

Parameters

x	an array of double.

Definition at line 181 of file TinkerAtom.java.

References denoptim.integration.tinker.TinkerAtom.xyz.

◆ getXYZIndex()

int denoptim.integration.tinker.TinkerAtom.getXYZIndex ( )

Gets the XYZ Index.

Returns: XYZ Index

Definition at line 195 of file TinkerAtom.java.

References denoptim.integration.tinker.TinkerAtom.xyzIndex.

Referenced by denoptim.integration.tinker.TinkerMolecule.getAtom(), denoptim.integration.tinker.TinkerMolecule.getConnectedAtoms(), denoptim.integration.tinker.TinkerMolecule.printIC(), denoptim.integration.tinker.TinkerBond.TinkerBond(), and denoptim.integration.tinker.TinkerUtils.writeIC().

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◆ moveTo() [1/2]

void denoptim.integration.tinker.TinkerAtom.moveTo	(	double	a,
		double	b,
		double	c
	)

moveTo

Parameters

a	a double.
b	a double.
c	a double.

Definition at line 142 of file TinkerAtom.java.

References denoptim.integration.tinker.TinkerAtom.xyz.

◆ moveTo() [2/2]

void denoptim.integration.tinker.TinkerAtom.moveTo ( double[] d )

Add a vector to the Atom's current position vector.

Parameters

d	Vector to add to the current position

Definition at line 126 of file TinkerAtom.java.

References denoptim.integration.tinker.TinkerAtom.xyz.

Referenced by denoptim.integration.tinker.TinkerMolecule.set3DCoordinates(), and denoptim.molecularmodeling.ChemicalObjectModel.updateXYZFromINT().

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◆ setAtomNeighbours()

void denoptim.integration.tinker.TinkerAtom.setAtomNeighbours ( int[] atmNb )

Definition at line 93 of file TinkerAtom.java.

References denoptim.integration.tinker.TinkerAtom.atmNb.

◆ setAtomString()

void denoptim.integration.tinker.TinkerAtom.setAtomString ( String atomStr )

Definition at line 217 of file TinkerAtom.java.

References denoptim.integration.tinker.TinkerAtom.atomStr.

Referenced by denoptim.molecularmodeling.RingClosureTool.saturateRingClosingAttractor().

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◆ setAtomType()

void denoptim.integration.tinker.TinkerAtom.setAtomType ( int ffAtomType )

Definition at line 231 of file TinkerAtom.java.

References denoptim.integration.tinker.TinkerAtom.ffAtomType.

Referenced by denoptim.molecularmodeling.RingClosureTool.setTinkerTypes(), and denoptim.integration.tinker.TinkerUtils.setTinkerTypes().

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◆ setDistAngle()

void denoptim.integration.tinker.TinkerAtom.setDistAngle ( double[] distAngles )

Definition at line 107 of file TinkerAtom.java.

References denoptim.integration.tinker.TinkerAtom.distAngles.

Referenced by denoptim.integration.tinker.ConformationalSearchPSSROT.performPSSROT(), and denoptim.molecularmodeling.RingClosureTool.saturateRingClosingAttractor().

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◆ setVertexId()

void denoptim.integration.tinker.TinkerAtom.setVertexId ( long vidx )

Definition at line 238 of file TinkerAtom.java.

Referenced by denoptim.integration.tinker.TinkerMolecule.deepCopy(), and denoptim.integration.tinker.TinkerUtils.getICFromIAC().

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◆ setXYZ()

void denoptim.integration.tinker.TinkerAtom.setXYZ ( double[] xyz )

setXYZ

Parameters

xyz	an array of double.

Definition at line 157 of file TinkerAtom.java.

References denoptim.integration.tinker.TinkerAtom.xyz.

◆ setXYZIndex()

void denoptim.integration.tinker.TinkerAtom.setXYZIndex ( int xyzIndex )

Definition at line 202 of file TinkerAtom.java.

References denoptim.integration.tinker.TinkerAtom.xyzIndex.

◆ toString()

String denoptim.integration.tinker.TinkerAtom.toString ( )

Definition at line 275 of file TinkerAtom.java.

References denoptim.integration.tinker.TinkerAtom.atmNb, denoptim.integration.tinker.TinkerAtom.atomStr, denoptim.integration.tinker.TinkerAtom.distAngles, denoptim.integration.tinker.TinkerAtom.ffAtomType, denoptim.integration.tinker.TinkerAtom.vtxId, denoptim.integration.tinker.TinkerAtom.xyz, and denoptim.integration.tinker.TinkerAtom.xyzIndex.

Referenced by denoptim.integration.tinker.TinkerUtils.getICFromIAC().

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◆ usesProperTorsion()

boolean denoptim.integration.tinker.TinkerAtom.usesProperTorsion ( )

Evaluates whether this TinkerAtom's line refers to a torsion (chiral flag is 0) or to an inproper torsion (chiral flag is +/-1).

For the position to be defined by a proper torsion, all 3 neighbouring atoms has to be defined (!= 0).

Returns: true if this TinkerAtom makes use of a proper torsion

Definition at line 261 of file TinkerAtom.java.

Member Data Documentation

◆ atmNb

int [] denoptim.integration.tinker.TinkerAtom.atmNb

private

Definition at line 57 of file TinkerAtom.java.

Referenced by denoptim.integration.tinker.TinkerAtom.getAtomNeighbours(), denoptim.integration.tinker.TinkerAtom.setAtomNeighbours(), denoptim.integration.tinker.TinkerAtom.TinkerAtom(), and denoptim.integration.tinker.TinkerAtom.toString().

◆ atomStr

String denoptim.integration.tinker.TinkerAtom.atomStr

private

Definition at line 35 of file TinkerAtom.java.

Referenced by denoptim.integration.tinker.TinkerAtom.getAtomString(), denoptim.integration.tinker.TinkerAtom.setAtomString(), denoptim.integration.tinker.TinkerAtom.TinkerAtom(), and denoptim.integration.tinker.TinkerAtom.toString().

◆ distAngles

double [] denoptim.integration.tinker.TinkerAtom.distAngles

private

Definition at line 50 of file TinkerAtom.java.

Referenced by denoptim.integration.tinker.TinkerAtom.getDistAngle(), denoptim.integration.tinker.TinkerAtom.setDistAngle(), denoptim.integration.tinker.TinkerAtom.TinkerAtom(), and denoptim.integration.tinker.TinkerAtom.toString().

◆ ffAtomType

int denoptim.integration.tinker.TinkerAtom.ffAtomType

private

Definition at line 30 of file TinkerAtom.java.

Referenced by denoptim.integration.tinker.TinkerAtom.getAtomType(), denoptim.integration.tinker.TinkerAtom.setAtomType(), denoptim.integration.tinker.TinkerAtom.TinkerAtom(), and denoptim.integration.tinker.TinkerAtom.toString().

◆ vtxId

long denoptim.integration.tinker.TinkerAtom.vtxId

private

Definition at line 62 of file TinkerAtom.java.

Referenced by denoptim.integration.tinker.TinkerAtom.getVertexId(), and denoptim.integration.tinker.TinkerAtom.toString().

◆ xyz

double [] denoptim.integration.tinker.TinkerAtom.xyz

private

Definition at line 40 of file TinkerAtom.java.

Referenced by denoptim.integration.tinker.TinkerAtom.getXYZ(), denoptim.integration.tinker.TinkerAtom.moveTo(), denoptim.integration.tinker.TinkerAtom.setXYZ(), denoptim.integration.tinker.TinkerAtom.TinkerAtom(), and denoptim.integration.tinker.TinkerAtom.toString().

◆ xyzIndex

int denoptim.integration.tinker.TinkerAtom.xyzIndex

private

Definition at line 45 of file TinkerAtom.java.

Referenced by denoptim.integration.tinker.TinkerAtom.getXYZIndex(), denoptim.integration.tinker.TinkerAtom.setXYZIndex(), denoptim.integration.tinker.TinkerAtom.TinkerAtom(), and denoptim.integration.tinker.TinkerAtom.toString().

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

/github/workspace/src/main/java/denoptim/integration/tinker/TinkerAtom.java

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ TinkerAtom() [1/2]

◆ TinkerAtom() [2/2]

Member Function Documentation

◆ getAtomNeighbours()

◆ getAtomString()

◆ getAtomType()

◆ getDistAngle()

◆ getVertexId()

◆ getXYZ() [1/2]

◆ getXYZ() [2/2]

◆ getXYZIndex()

◆ moveTo() [1/2]

◆ moveTo() [2/2]

◆ setAtomNeighbours()

◆ setAtomString()

◆ setAtomType()

◆ setDistAngle()

◆ setVertexId()

◆ setXYZ()

◆ setXYZIndex()

◆ toString()

◆ usesProperTorsion()

Member Data Documentation

◆ atmNb

◆ atomStr

◆ distAngles

◆ ffAtomType

◆ vtxId

◆ xyz

◆ xyzIndex