META-INF/MANIFEST.MF
META-INF/SELFSIGN.SF
META-INF/SELFSIGN.RSA
META-INF/
org/
org/jmol/
org/jmol/minimize/
org/jmol/minimize/forcefield/
org/jmol/minimize/MinAtom.class
<Unknown>
package org.jmol.minimize
public org.jmol.minimize.MinAtom extends java.lang.Object {
	int index
	public org.jmol.modelset.Atom atom
	public double[] coord
	public double[] force
	public java.util.Vector bonds
	public int nBonds
	public String type
	int[] bondedAtoms
	void <init> (int, org.jmol.modelset.Atom, double[], java.lang.String) 
	void set () 
	public org.jmol.minimize.MinBond getBondTo (int) 
	public int[] getBondedAtomIndexes () 
	public java.lang.String getIdentity () 
}

org/jmol/minimize/MinBond.class
<Unknown>
package org.jmol.minimize
public org.jmol.minimize.MinBond extends java.lang.Object {
	public int[] atomIndexes
	public boolean isAromatic
	public boolean isAmide
	void <init> (int[], boolean, boolean) 
	public int getOtherAtom (int) 
}

org/jmol/minimize/Minimizer$MinimizationThread.class
<Unknown>
package org.jmol.minimize
 org.jmol.minimize.Minimizer$MinimizationThread extends java.lang.Thread implements java.lang.Runnable  {
	private final org.jmol.minimize.Minimizer this$0
	void <init> (org.jmol.minimize.Minimizer) 
	public void run () 
}

org/jmol/minimize/Minimizer.class
<Unknown>
package org.jmol.minimize
public org.jmol.minimize.Minimizer extends java.lang.Object implements org.jmol.api.MinimizerInterface  {
	public org.jmol.viewer.Viewer viewer
	public org.jmol.modelset.Atom[] atoms
	public org.jmol.minimize.MinAtom[] minAtoms
	public org.jmol.minimize.MinBond[] minBonds
	public java.util.BitSet bsMinFixed
	private int atomCount
	private int bondCount
	private int atomCountFull
	private int[] atomMap
	public int[][] angles
	public int[][] torsions
	public double[] partialCharges
	private int steps
	private double crit
	private static java.util.Vector atomTypes
	private org.jmol.minimize.forcefield.ForceField pFF
	private String ff
	private java.util.BitSet bsTaint
	private java.util.BitSet bsSelected
	private java.util.BitSet bsAtoms
	private java.util.BitSet bsFixed
	public java.util.Vector constraints
	java.util.Hashtable constraintMap
	static final int TOKEN_ELEMENT_ONLY
	static final int TOKEN_ELEMENT_CHARGED
	static final int TOKEN_ELEMENT_CONNECTED
	static final int TOKEN_ELEMENT_AROMATIC
	static final int TOKEN_ELEMENT_SP
	static final int TOKEN_ELEMENT_SP2
	static final int PT_ELEMENT
	static final int PT_CHARGE
	static final int PT_CONNECT
	static final org.jmol.viewer.Token[][] tokenTypes
	boolean minimizationOn
	private org.jmol.minimize.Minimizer$MinimizationThread minimizationThread
	double[][] coordSaved
	public void <init> () 
	public void setProperty (java.lang.String, java.lang.Object) 
	public java.lang.Object getProperty (java.lang.String, int) 
	private void addConstraint (java.lang.Object[]) 
	private void clear () 
	public boolean minimize (int, double, java.util.BitSet) 
	private boolean setupMinimization () 
	private void setAtomPositions () 
	private java.util.BitSet getSearch (java.lang.String, int, java.util.BitSet) 
	public void getAngles () 
	public void getTorsions () 
	public org.jmol.minimize.forcefield.ForceField getForceField () 
	public java.util.Vector getAtomTypes () 
	private void setMinimizationOn (boolean) 
	private void getEnergyOnly () 
	public boolean startMinimization () 
	boolean stepMinimization () 
	void endMinimization () 
	private void saveCoordinates () 
	private void restoreCoordinates () 
	private void stopMinimization (boolean) 
	void updateAtomXYZ () 
	private void minimizeWithoutThread () 
	static void <clinit> () 
}

org/jmol/minimize/Util.class
<Unknown>
package org.jmol.minimize
public org.jmol.minimize.Util extends java.lang.Object {
	public static final double RAD_TO_DEG
	public static final double DEG_TO_RAD
	static final double max_squarable_double
	static final double min_squarable_double
	public void <init> () 
	public static void sub (double[], double[], javax.vecmath.Vector3d) 
	public static void putCoord (javax.vecmath.Vector3d, double[]) 
	public static double distance2 (double[], double[]) 
	public static double distance2 (javax.vecmath.Vector3d, javax.vecmath.Vector3d) 
	public static double getAngleRadiansABC (double[], double[], double[]) 
	public static boolean isApprox (javax.vecmath.Vector3d, javax.vecmath.Vector3d, double) 
	public static boolean canBeSquared (double) 
	public static boolean isNegligible (double, double) 
	public static boolean isFinite (double) 
	public static boolean isNegligible (double, double, double) 
	public static boolean isNear (double, double) 
	public static boolean isNear (double, double, double) 
	public static boolean isNearZero (double) 
	public static boolean isNearZero (double, double) 
	public static boolean canBeNormalized (javax.vecmath.Vector3d) 
	public static double pointPlaneAngleRadians (javax.vecmath.Vector3d, javax.vecmath.Vector3d, javax.vecmath.Vector3d, javax.vecmath.Vector3d, javax.vecmath.Vector3d, javax.vecmath.Vector3d, javax.vecmath.Vector3d) 
	private static double vectorAngleRadians (javax.vecmath.Vector3d, javax.vecmath.Vector3d) 
	public static double getTorsionAngleRadians (double[], double[], double[], double[], javax.vecmath.Vector3d, javax.vecmath.Vector3d, javax.vecmath.Vector3d) 
	public static double restorativeForceAndDistance (javax.vecmath.Vector3d, javax.vecmath.Vector3d, javax.vecmath.Vector3d) 
	private static void randomizeUnitVector (javax.vecmath.Vector3d) 
	public static double restorativeForceAndAngleRadians (javax.vecmath.Vector3d, javax.vecmath.Vector3d, javax.vecmath.Vector3d) 
	public static double restorativeForceAndOutOfPlaneAngleRadians (javax.vecmath.Vector3d, javax.vecmath.Vector3d, javax.vecmath.Vector3d, javax.vecmath.Vector3d, javax.vecmath.Vector3d, javax.vecmath.Vector3d, javax.vecmath.Vector3d) 
	public static double restorativeForceAndTorsionAngleRadians (javax.vecmath.Vector3d, javax.vecmath.Vector3d, javax.vecmath.Vector3d, javax.vecmath.Vector3d) 
}

org/jmol/minimize/forcefield/Calculation.class
<Unknown>
package org.jmol.minimize.forcefield
abstract org.jmol.minimize.forcefield.Calculation extends java.lang.Object {
	double dE
	org.jmol.minimize.forcefield.FFParam parA
	org.jmol.minimize.forcefield.FFParam parB
	org.jmol.minimize.forcefield.FFParam parC
	org.jmol.minimize.MinAtom a
	org.jmol.minimize.MinAtom b
	org.jmol.minimize.MinAtom c
	org.jmol.minimize.MinAtom d
	int ia
	int ib
	int ic
	int id
	int[] iData
	double[] dData
	double delta
	double rab
	double theta
	double energy
	void <init> () 
	abstract double compute (java.lang.Object[]) 
	double getEnergy () 
	void getPointers (java.lang.Object[]) 
}

org/jmol/minimize/forcefield/Calculations.class
<Unknown>
package org.jmol.minimize.forcefield
abstract org.jmol.minimize.forcefield.Calculations extends java.lang.Object {
	public static final double RAD_TO_DEG
	public static final double DEG_TO_RAD
	static final double KCAL_TO_KJ
	static final int CALC_DISTANCE
	static final int CALC_ANGLE
	static final int CALC_TORSION
	static final int CALC_OOP
	static final int CALC_VDW
	static final int CALC_ES
	static final int CALC_MAX
	org.jmol.minimize.forcefield.ForceField ff
	java.util.Vector[] calculations
	public java.util.Hashtable ffParams
	int atomCount
	int bondCount
	org.jmol.minimize.MinAtom[] atoms
	org.jmol.minimize.MinBond[] bonds
	int[][] angles
	int[][] torsions
	double[] partialCharges
	boolean havePartialCharges
	java.util.Vector constraints
	boolean isPreliminary
	boolean gradients
	boolean silent
	StringBuffer logData
	boolean logging
	boolean loggingEnabled
	final javax.vecmath.Vector3d da
	final javax.vecmath.Vector3d db
	final javax.vecmath.Vector3d dc
	final javax.vecmath.Vector3d dd
	int ia
	int ib
	int ic
	int id
	final javax.vecmath.Vector3d v1
	final javax.vecmath.Vector3d v2
	final javax.vecmath.Vector3d v3
	private static final double PI_OVER_2
	private static final double TWO_PI
	public void setConstraints (java.util.Vector) 
	void <init> (org.jmol.minimize.forcefield.ForceField, org.jmol.minimize.MinAtom[], org.jmol.minimize.MinBond[], int[][], int[][], double[], java.util.Vector) 
	boolean haveParams () 
	void setParams (java.util.Hashtable) 
	static org.jmol.minimize.forcefield.FFParam getParameter (java.lang.String, java.util.Hashtable) 
	abstract boolean setupCalculations () 
	abstract java.lang.String getAtomList (java.lang.String) 
	abstract boolean setupElectrostatics () 
	abstract java.lang.String getDebugHeader (int) 
	abstract java.lang.String getDebugFooter (int, double) 
	abstract java.lang.String getUnit () 
	abstract double compute (int, java.lang.Object[]) 
	void addForce (javax.vecmath.Vector3d, int, double) 
	public void setSilent (boolean) 
	public java.lang.String getLogData () 
	void appendLogData (java.lang.String) 
	void setLoggingEnabled (boolean) 
	void setPreliminary (boolean) 
	private double calc (int, boolean) 
	double energyStrBnd (boolean) 
	double energyBond (boolean) 
	double energyAngle (boolean) 
	double energyTorsion (boolean) 
	double energyOOP (boolean) 
	double energyVDW (boolean) 
	double energyES (boolean) 
	private double constraintEnergy (int) 
	private double constrainQuadratic (double, double, double, int) 
}

org/jmol/minimize/forcefield/CalculationsUFF$AngleCalc.class
<Unknown>
package org.jmol.minimize.forcefield
 org.jmol.minimize.forcefield.CalculationsUFF$AngleCalc extends org.jmol.minimize.forcefield.Calculation {
	private final org.jmol.minimize.forcefield.CalculationsUFF this$0
	void <init> (org.jmol.minimize.forcefield.CalculationsUFF) 
	void setData (java.util.Vector, int) 
	double compute (java.lang.Object[]) 
}

org/jmol/minimize/forcefield/CalculationsUFF$DistanceCalc.class
<Unknown>
package org.jmol.minimize.forcefield
 org.jmol.minimize.forcefield.CalculationsUFF$DistanceCalc extends org.jmol.minimize.forcefield.Calculation {
	double r0
	double kb
	private final org.jmol.minimize.forcefield.CalculationsUFF this$0
	void <init> (org.jmol.minimize.forcefield.CalculationsUFF) 
	void setData (java.util.Vector, int, int, double) 
	double compute (java.lang.Object[]) 
}

org/jmol/minimize/forcefield/CalculationsUFF$ESCalc.class
<Unknown>
package org.jmol.minimize.forcefield
 org.jmol.minimize.forcefield.CalculationsUFF$ESCalc extends org.jmol.minimize.forcefield.CalculationsUFF$PairCalc {
	private final org.jmol.minimize.forcefield.CalculationsUFF this$0
	void <init> (org.jmol.minimize.forcefield.CalculationsUFF) 
	void setData (java.util.Vector, int, int) 
	double compute (java.lang.Object[]) 
}

org/jmol/minimize/forcefield/CalculationsUFF$OOPCalc.class
<Unknown>
package org.jmol.minimize.forcefield
 org.jmol.minimize.forcefield.CalculationsUFF$OOPCalc extends org.jmol.minimize.forcefield.Calculation {
	private final org.jmol.minimize.forcefield.CalculationsUFF this$0
	void <init> (org.jmol.minimize.forcefield.CalculationsUFF) 
	void setData (java.util.Vector, int, int) 
	double compute (java.lang.Object[]) 
}

org/jmol/minimize/forcefield/CalculationsUFF$PairCalc.class
<Unknown>
package org.jmol.minimize.forcefield
abstract org.jmol.minimize.forcefield.CalculationsUFF$PairCalc extends org.jmol.minimize.forcefield.Calculation {
	private final org.jmol.minimize.forcefield.CalculationsUFF this$0
	void <init> (org.jmol.minimize.forcefield.CalculationsUFF) 
	abstract void setData (java.util.Vector, int, int) 
}

org/jmol/minimize/forcefield/CalculationsUFF$TorsionCalc.class
<Unknown>
package org.jmol.minimize.forcefield
 org.jmol.minimize.forcefield.CalculationsUFF$TorsionCalc extends org.jmol.minimize.forcefield.Calculation {
	private final org.jmol.minimize.forcefield.CalculationsUFF this$0
	void <init> (org.jmol.minimize.forcefield.CalculationsUFF) 
	void setData (java.util.Vector, int) 
	double compute (java.lang.Object[]) 
}

org/jmol/minimize/forcefield/CalculationsUFF$VDWCalc.class
<Unknown>
package org.jmol.minimize.forcefield
 org.jmol.minimize.forcefield.CalculationsUFF$VDWCalc extends org.jmol.minimize.forcefield.CalculationsUFF$PairCalc {
	private final org.jmol.minimize.forcefield.CalculationsUFF this$0
	void <init> (org.jmol.minimize.forcefield.CalculationsUFF) 
	void setData (java.util.Vector, int, int) 
	double compute (java.lang.Object[]) 
}

org/jmol/minimize/forcefield/CalculationsUFF.class
<Unknown>
package org.jmol.minimize.forcefield
 org.jmol.minimize.forcefield.CalculationsUFF extends org.jmol.minimize.forcefield.Calculations {
	public static final int PAR_R
	public static final int PAR_THETA
	public static final int PAR_X
	public static final int PAR_D
	public static final int PAR_ZETA
	public static final int PAR_Z
	public static final int PAR_V
	public static final int PAR_U
	public static final int PAR_XI
	public static final int PAR_HARD
	public static final int PAR_RADIUS
	org.jmol.minimize.forcefield.CalculationsUFF$DistanceCalc bondCalc
	org.jmol.minimize.forcefield.CalculationsUFF$AngleCalc angleCalc
	org.jmol.minimize.forcefield.CalculationsUFF$TorsionCalc torsionCalc
	org.jmol.minimize.forcefield.CalculationsUFF$OOPCalc oopCalc
	org.jmol.minimize.forcefield.CalculationsUFF$VDWCalc vdwCalc
	org.jmol.minimize.forcefield.CalculationsUFF$ESCalc esCalc
	static final double KCAL644
	static final double KCAL6
	static final double KCAL22
	static final double KCAL44
	static final double KCAL332
	void <init> (org.jmol.minimize.forcefield.ForceField, org.jmol.minimize.MinAtom[], org.jmol.minimize.MinBond[], int[][], int[][], double[], java.util.Vector) 
	java.lang.String getUnit () 
	boolean setupCalculations () 
	private boolean isInvertible (int) 
	private void pairSearch (java.util.Vector, org.jmol.minimize.forcefield.CalculationsUFF$PairCalc) 
	boolean setupElectrostatics () 
	static double calculateR0 (double, double, double, double, double) 
	double compute (int, java.lang.Object[]) 
	java.lang.String getAtomList (java.lang.String) 
	java.lang.String getDebugHeader (int) 
	java.lang.String getDebugLine (int, org.jmol.minimize.forcefield.Calculation) 
	java.lang.String getDebugFooter (int, double) 
}

org/jmol/minimize/forcefield/FFParam.class
<Unknown>
package org.jmol.minimize.forcefield
public org.jmol.minimize.forcefield.FFParam extends java.lang.Object {
	int[] iVal
	double[] dVal
	String[] sVal
	public void <init> () 
}

org/jmol/minimize/forcefield/ForceField.class
<Unknown>
package org.jmol.minimize.forcefield
public abstract org.jmol.minimize.forcefield.ForceField extends java.lang.Object {
	static final int ENERGY
	static final int EBOND
	static final int EANGLE
	static final int ESTRBND
	static final int ETORSION
	static final int EOOP
	static final int EVDW
	static final int EELECTROSTATIC
	org.jmol.minimize.forcefield.Calculations calc
	private double criterion
	private double e0
	private double dE
	private int currentStep
	private int stepMax
	private double[][] coordSaved
	int atomCount
	int bondCount
	org.jmol.viewer.Viewer viewer
	org.jmol.minimize.MinAtom[] atoms
	org.jmol.minimize.MinBond[] bonds
	java.util.BitSet bsFixed
	private java.lang.String getUnits () 
	public abstract java.util.Vector getAtomTypes () 
	protected abstract java.util.Hashtable getFFParameters () 
	public void <init> () 
	public void setModel (org.jmol.minimize.Minimizer) 
	public void setConstraints (org.jmol.minimize.Minimizer) 
	public boolean setup () 
	public void steepestDescentInitialize (int, double) 
	private void clearForces () 
	public boolean steepestDescentTakeNSteps (int) 
	private double getEnergy (int, boolean) 
	private void setForcesUsingNumericalDerivative (org.jmol.minimize.MinAtom, int) 
	private double getDE (org.jmol.minimize.MinAtom, int, int, double) 
	public double energyFull (boolean, boolean) 
	double energyStrBnd (boolean) 
	double energyBond (boolean) 
	double energyAngle (boolean) 
	double energyTorsion (boolean) 
	double energyOOP (boolean) 
	double energyVDW (boolean) 
	double energyES (boolean) 
	private void linearSearch () 
	private void saveCoordinates () 
	private void restoreCoordinates () 
	public boolean detectExplosion () 
	public int getCurrentStep () 
	public double getEnergy () 
	public java.lang.String getAtomList (java.lang.String) 
	public double getEnergyDiff () 
	public java.lang.String getLogData () 
	double getNormalizedDE () 
}

org/jmol/minimize/forcefield/ForceFieldUFF.class
<Unknown>
package org.jmol.minimize.forcefield
public org.jmol.minimize.forcefield.ForceFieldUFF extends org.jmol.minimize.forcefield.ForceField {
	public void <init> () 
	public void setModel (org.jmol.minimize.Minimizer) 
	protected java.util.Hashtable getFFParameters () 
	public java.util.Vector getAtomTypes () 
}

org/jmol/minimize/forcefield/UFF.txt