Package com.actelion.research.chem.coords

Class InventorFragment

java.lang.Object

com.actelion.research.chem.coords.InventorFragment

public class InventorFragment
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field	Description
protected double[]	mAtomX
protected double[]	mAtomY
protected int[]	mGlobalAtom
protected int[]	mGlobalBond
protected int[]	mGlobalToLocalAtom
protected boolean	mKeepMarkedAtoms
protected int[]	mPriority

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	InventorFragment(InventorFragment f)
protected	InventorFragment(StereoMolecule mol, int atoms, boolean keepMarkedAtoms)

Method Summary

Modifier and Type	Method	Description
protected void	arrangeWith(InventorFragment f)
protected double	calculatePreferredAttachmentAngle(double x, double y, int neighbourAtomCount, double padding)
protected boolean	equals(InventorFragment f)
protected void	flip(double x, double y, double mirrorAngle)
protected void	flipOneSide(int bond)
protected double	getAtomX(int index)
protected double	getAtomY(int index)
protected java.util.ArrayList<int[]>	getCollisionList()
protected double	getCollisionPanalty()
protected int	getGlobalAtom(int localAtom)
protected double	getHeight()
protected int	getLocalAtom(int globalAtom)
protected double	getWidth()
protected boolean	isMember(int globalAtom)
protected void	locateBonds()
protected void	optimizeAtomCoordinates(int atom)
protected void	rotate(double x, double y, double angleDif)
protected int	size()
protected void	translate(double dx, double dy)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

mGlobalAtom

protected int[] mGlobalAtom

mGlobalBond

protected int[] mGlobalBond

mGlobalToLocalAtom

protected int[] mGlobalToLocalAtom

mPriority

protected int[] mPriority

mAtomX

protected double[] mAtomX

mAtomY

protected double[] mAtomY

mKeepMarkedAtoms

protected boolean mKeepMarkedAtoms

Constructor Detail

InventorFragment

protected InventorFragment(StereoMolecule mol,
                           int atoms,
                           boolean keepMarkedAtoms)

InventorFragment

protected InventorFragment(InventorFragment f)

Method Detail

size

protected int size()

equals

protected boolean equals(InventorFragment f)

getAtomX

protected double getAtomX(int index)

getAtomY

protected double getAtomY(int index)

getWidth

protected double getWidth()

getHeight

protected double getHeight()

isMember

protected boolean isMember(int globalAtom)

getGlobalAtom

protected int getGlobalAtom(int localAtom)

getLocalAtom

protected int getLocalAtom(int globalAtom)

translate

protected void translate(double dx,
                         double dy)

rotate

protected void rotate(double x,
                      double y,
                      double angleDif)

flip

protected void flip(double x,
                    double y,
                    double mirrorAngle)

flipOneSide

protected void flipOneSide(int bond)

arrangeWith

protected void arrangeWith(InventorFragment f)

getCollisionList

protected java.util.ArrayList<int[]> getCollisionList()

getCollisionPanalty

protected double getCollisionPanalty()

locateBonds

protected void locateBonds()

optimizeAtomCoordinates

protected void optimizeAtomCoordinates(int atom)

calculatePreferredAttachmentAngle

protected double calculatePreferredAttachmentAngle(double x,
                                                   double y,
                                                   int neighbourAtomCount,
                                                   double padding)

Parameters:

x -

y -

Returns:

angle