Inheritance diagram for denoptim.integration.tinker.TinkerMolecule:

Collaboration diagram for denoptim.integration.tinker.TinkerMolecule:

Public Member Functions
	TinkerMolecule ()

	TinkerMolecule (String molName, ArrayList< int[]> zadd, ArrayList< int[]> zdel, ArrayList< TinkerAtom > lstAtoms)

ArrayList< Integer >	getConnectedAtoms (int pos)
	Identify the list of connected atoms (only first neighbours are considered) to the atom at the specified position. More...

void	set3DCoordinates (ArrayList< double[]> coords)
	store 3d coordinates of the fragments More...

void	setName (String molName)

void	setAtoms (ArrayList< TinkerAtom > lstAtoms)

void	setBondPairs (ArrayList< int[]> zdel, ArrayList< int[]> zadd)

ArrayList< TinkerAtom >	getAtoms ()

int	getLastAtomNumber ()

String	getName ()

ArrayList< int[]>	getBondAdd ()

ArrayList< int[]>	getBondDel ()

TinkerAtom	getAtom (int pos)
	Returns the atom which has the XYZ index set to pos. More...

Object	clone () throws CloneNotSupportedException
	This method produces a shallow copy of the object. More...

TinkerMolecule	deepCopy ()
	This method produces a deep copy of the object. More...

boolean	isConnected (int atm1, int atm2)

void	addMolecule (TinkerMolecule tmol2)

void	addAtom (TinkerAtom ta)
	Add one atom to this molecule. More...

void	addBond (int a1, int a2)
	Add one bond by appending a pair of indeces into the z-add section. More...

boolean	isTorsionUsed (int t1, int t2)
	Check if the pair of atoms has been used to define a proper torsion. More...

void	printIC ()

Package Attributes
ArrayList< int[]>	zdel

ArrayList< int[]>	zadd

String	molName

Private Attributes
ArrayList< TinkerAtom >	lstAtoms

boolean	debug = false

Detailed Description

Author: Vishwesh Venkatraman; Marco Foscato

Definition at line 30 of file TinkerMolecule.java.

Constructor & Destructor Documentation

◆ TinkerMolecule() [1/2]

denoptim.integration.tinker.TinkerMolecule.TinkerMolecule ( )

Definition at line 41 of file TinkerMolecule.java.

References denoptim.integration.tinker.TinkerMolecule.lstAtoms, denoptim.integration.tinker.TinkerMolecule.molName, denoptim.integration.tinker.TinkerMolecule.zadd, and denoptim.integration.tinker.TinkerMolecule.zdel.

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

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◆ TinkerMolecule() [2/2]

denoptim.integration.tinker.TinkerMolecule.TinkerMolecule	(	String	molName,
		ArrayList< int[]>	zadd,
		ArrayList< int[]>	zdel,
		ArrayList< TinkerAtom >	lstAtoms
	)

Definition at line 51 of file TinkerMolecule.java.

References denoptim.integration.tinker.TinkerMolecule.lstAtoms, denoptim.integration.tinker.TinkerMolecule.molName, denoptim.integration.tinker.TinkerMolecule.zadd, and denoptim.integration.tinker.TinkerMolecule.zdel.

Member Function Documentation

◆ addAtom()

void denoptim.integration.tinker.TinkerMolecule.addAtom ( TinkerAtom ta )

Add one atom to this molecule.

Definition at line 287 of file TinkerMolecule.java.

References denoptim.integration.tinker.TinkerMolecule.lstAtoms.

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

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◆ addBond()

void denoptim.integration.tinker.TinkerMolecule.addBond	(	int	a1,
		int	a2
	)

Add one bond by appending a pair of indeces into the z-add section.

Parameters

a1	first atom index
a2	second atom index

Definition at line 299 of file TinkerMolecule.java.

References denoptim.integration.tinker.TinkerMolecule.zadd.

Referenced by denoptim.molecularmodeling.ChemicalObjectModel.addBond(), and denoptim.integration.tinker.TinkerUtils.getICFromIAC().

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◆ addMolecule()

void denoptim.integration.tinker.TinkerMolecule.addMolecule ( TinkerMolecule tmol2 )

Definition at line 272 of file TinkerMolecule.java.

References denoptim.integration.tinker.TinkerMolecule.getAtoms(), denoptim.integration.tinker.TinkerMolecule.getBondAdd(), denoptim.integration.tinker.TinkerMolecule.getBondDel(), denoptim.integration.tinker.TinkerMolecule.lstAtoms, denoptim.integration.tinker.TinkerMolecule.zadd, and denoptim.integration.tinker.TinkerMolecule.zdel.

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◆ clone()

Object denoptim.integration.tinker.TinkerMolecule.clone ( ) throws CloneNotSupportedException

This method produces a shallow copy of the object.

Definition at line 200 of file TinkerMolecule.java.

Referenced by denoptim.molecularmodeling.ChemicalObjectModel.deepcopy().

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◆ deepCopy()

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

This method produces a deep copy of the object.

Definition at line 210 of file TinkerMolecule.java.

Referenced by denoptim.molecularmodeling.ChemicalObjectModel.deepcopy().

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◆ getAtom()

TinkerAtom denoptim.integration.tinker.TinkerMolecule.getAtom ( int pos )

Returns the atom which has the XYZ index set to pos.

Parameters

pos

Returns: the TinkerAtom at the specified position

Definition at line 181 of file TinkerMolecule.java.

References denoptim.integration.tinker.TinkerAtom.getXYZIndex(), and denoptim.integration.tinker.TinkerMolecule.lstAtoms.

Referenced by denoptim.integration.tinker.TinkerMolecule.getConnectedAtoms(), denoptim.integration.tinker.TinkerMolecule.isConnected(), denoptim.integration.tinker.ConformationalSearchPSSROT.performPSSROT(), denoptim.molecularmodeling.RingClosureTool.saturateRingClosingAttractor(), and denoptim.molecularmodeling.ChemicalObjectModel.updateXYZFromINT().

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◆ getAtoms()

ArrayList< TinkerAtom > denoptim.integration.tinker.TinkerMolecule.getAtoms ( )

Definition at line 140 of file TinkerMolecule.java.

References denoptim.integration.tinker.TinkerMolecule.lstAtoms.

Referenced by denoptim.integration.tinker.TinkerMolecule.addMolecule(), and denoptim.integration.tinker.ConformationalSearchPSSROT.performPSSROT().

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◆ getBondAdd()

ArrayList< int[]> denoptim.integration.tinker.TinkerMolecule.getBondAdd ( )

Definition at line 161 of file TinkerMolecule.java.

References denoptim.integration.tinker.TinkerMolecule.zadd.

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

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◆ getBondDel()

ArrayList< int[]> denoptim.integration.tinker.TinkerMolecule.getBondDel ( )

Definition at line 168 of file TinkerMolecule.java.

References denoptim.integration.tinker.TinkerMolecule.zdel.

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

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◆ getConnectedAtoms()

ArrayList< Integer > denoptim.integration.tinker.TinkerMolecule.getConnectedAtoms ( int pos )

Identify the list of connected atoms (only first neighbours are considered) to the atom at the specified position.

Parameters

pos

Returns: list of connected atoms

Definition at line 70 of file TinkerMolecule.java.

References denoptim.integration.tinker.TinkerMolecule.getAtom(), denoptim.integration.tinker.TinkerAtom.getAtomNeighbours(), denoptim.integration.tinker.TinkerAtom.getXYZIndex(), and denoptim.integration.tinker.TinkerMolecule.lstAtoms.

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◆ getLastAtomNumber()

int denoptim.integration.tinker.TinkerMolecule.getLastAtomNumber ( )

Definition at line 147 of file TinkerMolecule.java.

References denoptim.integration.tinker.TinkerMolecule.lstAtoms.

◆ getName()

String denoptim.integration.tinker.TinkerMolecule.getName ( )

Definition at line 154 of file TinkerMolecule.java.

References denoptim.integration.tinker.TinkerMolecule.molName.

Referenced by denoptim.integration.tinker.ConformationalSearchPSSROT.performPSSROT().

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◆ isConnected()

boolean denoptim.integration.tinker.TinkerMolecule.isConnected	(	int	atm1,
		int	atm2
	)

Definition at line 254 of file TinkerMolecule.java.

References denoptim.integration.tinker.TinkerMolecule.getAtom(), and denoptim.integration.tinker.TinkerAtom.getAtomNeighbours().

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◆ isTorsionUsed()

boolean denoptim.integration.tinker.TinkerMolecule.isTorsionUsed	(	int	t1,
		int	t2
	)

Check if the pair of atoms has been used to define a proper torsion.

Parameters

t1
t2

Returns: true if the atoms have been used already

Definition at line 316 of file TinkerMolecule.java.

References denoptim.integration.tinker.TinkerMolecule.debug, and denoptim.integration.tinker.TinkerMolecule.lstAtoms.

◆ printIC()

void denoptim.integration.tinker.TinkerMolecule.printIC ( )

Definition at line 341 of file TinkerMolecule.java.

References denoptim.integration.tinker.TinkerAtom.getAtomNeighbours(), denoptim.integration.tinker.TinkerAtom.getAtomString(), denoptim.integration.tinker.TinkerAtom.getAtomType(), denoptim.integration.tinker.TinkerAtom.getDistAngle(), denoptim.integration.tinker.TinkerAtom.getXYZIndex(), denoptim.integration.tinker.TinkerMolecule.lstAtoms, and denoptim.integration.tinker.TinkerMolecule.molName.

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

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◆ set3DCoordinates()

void denoptim.integration.tinker.TinkerMolecule.set3DCoordinates ( ArrayList< double[]> coords )

store 3d coordinates of the fragments

Parameters

coords

Definition at line 105 of file TinkerMolecule.java.

References denoptim.integration.tinker.TinkerMolecule.lstAtoms, and denoptim.integration.tinker.TinkerAtom.moveTo().

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◆ setAtoms()

void denoptim.integration.tinker.TinkerMolecule.setAtoms ( ArrayList< TinkerAtom > lstAtoms )

Definition at line 125 of file TinkerMolecule.java.

References denoptim.integration.tinker.TinkerMolecule.lstAtoms.

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

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◆ setBondPairs()

void denoptim.integration.tinker.TinkerMolecule.setBondPairs	(	ArrayList< int[]>	zdel,
		ArrayList< int[]>	zadd
	)

Definition at line 132 of file TinkerMolecule.java.

References denoptim.integration.tinker.TinkerMolecule.zadd, and denoptim.integration.tinker.TinkerMolecule.zdel.

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

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◆ setName()

void denoptim.integration.tinker.TinkerMolecule.setName ( String molName )

Definition at line 118 of file TinkerMolecule.java.

References denoptim.integration.tinker.TinkerMolecule.molName.

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

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Member Data Documentation

◆ debug

boolean denoptim.integration.tinker.TinkerMolecule.debug = false

private

Definition at line 37 of file TinkerMolecule.java.

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

◆ lstAtoms

ArrayList<TinkerAtom> denoptim.integration.tinker.TinkerMolecule.lstAtoms

private

Definition at line 32 of file TinkerMolecule.java.

◆ molName

String denoptim.integration.tinker.TinkerMolecule.molName

package

Definition at line 35 of file TinkerMolecule.java.

Referenced by denoptim.integration.tinker.TinkerMolecule.deepCopy(), denoptim.integration.tinker.TinkerMolecule.getName(), denoptim.integration.tinker.TinkerMolecule.printIC(), denoptim.integration.tinker.TinkerMolecule.setName(), and denoptim.integration.tinker.TinkerMolecule.TinkerMolecule().

◆ zadd

ArrayList<int[]> denoptim.integration.tinker.TinkerMolecule.zadd

package

Definition at line 34 of file TinkerMolecule.java.

Referenced by denoptim.integration.tinker.TinkerMolecule.addBond(), denoptim.integration.tinker.TinkerMolecule.addMolecule(), denoptim.integration.tinker.TinkerMolecule.deepCopy(), denoptim.integration.tinker.TinkerMolecule.getBondAdd(), denoptim.integration.tinker.TinkerMolecule.setBondPairs(), and denoptim.integration.tinker.TinkerMolecule.TinkerMolecule().

◆ zdel

ArrayList<int[]> denoptim.integration.tinker.TinkerMolecule.zdel

package

Definition at line 33 of file TinkerMolecule.java.

Referenced by denoptim.integration.tinker.TinkerMolecule.addMolecule(), denoptim.integration.tinker.TinkerMolecule.deepCopy(), denoptim.integration.tinker.TinkerMolecule.getBondDel(), denoptim.integration.tinker.TinkerMolecule.setBondPairs(), and denoptim.integration.tinker.TinkerMolecule.TinkerMolecule().

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

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

Public Member Functions

Package Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ TinkerMolecule() [1/2]

◆ TinkerMolecule() [2/2]

Member Function Documentation

◆ addAtom()

◆ addBond()

◆ addMolecule()

◆ clone()

◆ deepCopy()

◆ getAtom()

◆ getAtoms()

◆ getBondAdd()

◆ getBondDel()

◆ getConnectedAtoms()

◆ getLastAtomNumber()

◆ getName()

◆ isConnected()

◆ isTorsionUsed()

◆ printIC()

◆ set3DCoordinates()

◆ setAtoms()

◆ setBondPairs()

◆ setName()

Member Data Documentation

◆ debug

◆ lstAtoms

◆ molName

◆ zadd

◆ zdel