Package org.openmolecules.chem.conf.so

Class ConformationRule

java.lang.Object

org.openmolecules.chem.conf.so.ConformationRule

Direct Known Subclasses:

AxialStereoRule, DistanceRule, PlaneRule, StraightLineRule, TetrahedralStereoRule, TorsionRule

public abstract class ConformationRule
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field	Description
protected int[]	mAtom
protected boolean	mIsEnabled
static java.lang.String[]	RULE_NAME
static int	RULE_TYPE_BINAP
static int	RULE_TYPE_DISTANCE
static int	RULE_TYPE_LINE
static int	RULE_TYPE_PLANE
static int	RULE_TYPE_STEREO
static int	RULE_TYPE_TORSION

Constructor Summary

Constructors

Constructor	Description
ConformationRule(int[] atom)

Method Summary

Modifier and Type	Method	Description
protected void	addAtomList(java.lang.StringBuilder sb)
abstract double	addStrain(Conformer conformer, double[] atomStrain)
abstract boolean	apply(Conformer conformer, double cycleFactor)
protected int[]	getAtomList()
abstract int	getRuleType()
boolean	isEnabled()
protected void	moveAtomWithUnboundedNeighbors(Conformer conformer, int atom, double dx, double dy, double dz)
protected void	moveGroup(Conformer conformer, int atom, int[] notList, double dx, double dy, double dz)	Move one atom and all non-ring-bond substituents, provided attachment atom is not part of the notList.
protected void	moveSubstituent(Conformer conformer, int rootAtom, int firstAtom, double dx, double dy, double dz)	Moves all atoms of the substituent connected to rootAtom starting with firstAtom.
protected void	rotateAtom(Conformer conformer, int atom, int refAtom, Coordinates unit, double theta)
void	setEnabled(boolean b)
abstract java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

RULE_TYPE_DISTANCE

public static final int RULE_TYPE_DISTANCE

See Also:

Constant Field Values

RULE_TYPE_PLANE

public static final int RULE_TYPE_PLANE

See Also:

Constant Field Values

RULE_TYPE_LINE

public static final int RULE_TYPE_LINE

See Also:

Constant Field Values

RULE_TYPE_TORSION

public static final int RULE_TYPE_TORSION

See Also:

Constant Field Values

RULE_TYPE_STEREO

public static final int RULE_TYPE_STEREO

See Also:

Constant Field Values

RULE_TYPE_BINAP

public static final int RULE_TYPE_BINAP

See Also:

Constant Field Values

RULE_NAME

public static final java.lang.String[] RULE_NAME

mAtom

protected int[] mAtom

mIsEnabled

protected boolean mIsEnabled

Constructor Detail

ConformationRule

public ConformationRule(int[] atom)

Method Detail

isEnabled

public boolean isEnabled()

setEnabled

public void setEnabled(boolean b)

apply

public abstract boolean apply(Conformer conformer,
                              double cycleFactor)

addStrain

public abstract double addStrain(Conformer conformer,
                                 double[] atomStrain)

getRuleType

public abstract int getRuleType()

toString

public abstract java.lang.String toString()

Overrides:

toString in class java.lang.Object

getAtomList

protected int[] getAtomList()

addAtomList

protected void addAtomList(java.lang.StringBuilder sb)

moveGroup

protected void moveGroup(Conformer conformer,
                         int atom,
                         int[] notList,
                         double dx,
                         double dy,
                         double dz)

Move one atom and all non-ring-bond substituents, provided attachment atom is not part of the notList.

Parameters:

conformer -

atom -

notList - atom list that are not moved

dx -

dy -

dz -

moveSubstituent

protected void moveSubstituent(Conformer conformer,
                               int rootAtom,
                               int firstAtom,
                               double dx,
                               double dy,
                               double dz)

Moves all atoms of the substituent connected to rootAtom starting with firstAtom.

Parameters:

conformer -

rootAtom -

firstAtom -

dx -

dy -

dz -

moveAtomWithUnboundedNeighbors

protected void moveAtomWithUnboundedNeighbors(Conformer conformer,
                                              int atom,
                                              double dx,
                                              double dy,
                                              double dz)

rotateAtom

protected void rotateAtom(Conformer conformer,
                          int atom,
                          int refAtom,
                          Coordinates unit,
                          double theta)