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