public class Minimizer extends java.lang.Object implements MinimizerInterface
Modifier and Type | Class and Description |
---|---|
(package private) class |
Minimizer.MinimizationThread |
Modifier and Type | Field and Description |
---|---|
private int |
atomCount |
private int[] |
atomMap |
Atom[] |
atoms |
private int |
bondCount |
Bond[] |
bonds |
java.util.BitSet |
bsAtoms |
private java.util.BitSet |
bsFixed |
private java.util.BitSet |
bsFixedDefault |
java.util.BitSet |
bsMinFixed |
private java.util.BitSet |
bsSelected |
private java.util.BitSet |
bsTaint |
private java.util.Map<java.lang.String,java.lang.Object[]> |
constraintMap |
java.util.List<java.lang.Object[]> |
constraints |
(package private) double[][] |
coordSaved |
private double |
crit |
private int |
elemnoMax |
private java.lang.String |
ff |
private boolean |
isSilent |
MinAngle[] |
minAngles |
MinAtom[] |
minAtoms |
MinBond[] |
minBonds |
(package private) boolean |
minimizationOn |
private Minimizer.MinimizationThread |
minimizationThread |
MinTorsion[] |
minTorsions |
double[] |
partialCharges |
private ForceField |
pFF |
int |
rawBondCount |
private int |
steps |
java.lang.String |
units |
Viewer |
viewer |
Constructor and Description |
---|
Minimizer() |
Modifier and Type | Method and Description |
---|---|
private void |
addConstraint(java.lang.Object[] c) |
void |
calculatePartialCharges(Bond[] bonds,
int bondCount,
Atom[] atoms,
java.util.BitSet bsAtoms) |
private void |
clear() |
(package private) void |
endMinimization() |
void |
getAngles() |
private void |
getBonds() |
private void |
getEnergyOnly() |
ForceField |
getForceField(java.lang.String ff) |
java.lang.Object |
getProperty(java.lang.String propertyName,
int param) |
void |
getTorsions() |
boolean |
minimize(int steps,
double crit,
java.util.BitSet bsSelected,
java.util.BitSet bsFixed,
boolean haveFixed,
boolean forceSilent,
java.lang.String ff) |
private void |
minimizeWithoutThread() |
void |
report(java.lang.String msg,
boolean isEcho) |
private void |
reportEnergy() |
private void |
restoreCoordinates() |
private void |
saveCoordinates() |
private void |
setAtomPositions() |
private void |
setEnergyUnits() |
private void |
setMinimizationOn(boolean minimizationOn) |
private boolean |
setModel(java.util.BitSet bsElements) |
void |
setProperty(java.lang.String propertyName,
java.lang.Object value) |
private boolean |
setupMinimization() |
boolean |
startMinimization() |
(package private) boolean |
stepMinimization() |
private void |
stopMinimization(boolean coordAreOK) |
(package private) void |
updateAtomXYZ() |
public Viewer viewer
public Atom[] atoms
public Bond[] bonds
public int rawBondCount
public MinAtom[] minAtoms
public MinBond[] minBonds
public MinAngle[] minAngles
public MinTorsion[] minTorsions
public java.util.BitSet bsMinFixed
private int atomCount
private int bondCount
private int[] atomMap
public double[] partialCharges
private int steps
private double crit
public java.lang.String units
private ForceField pFF
private java.lang.String ff
private java.util.BitSet bsTaint
private java.util.BitSet bsSelected
public java.util.BitSet bsAtoms
private java.util.BitSet bsFixedDefault
private java.util.BitSet bsFixed
public java.util.List<java.lang.Object[]> constraints
private boolean isSilent
private java.util.Map<java.lang.String,java.lang.Object[]> constraintMap
private int elemnoMax
boolean minimizationOn
private Minimizer.MinimizationThread minimizationThread
double[][] coordSaved
public void setProperty(java.lang.String propertyName, java.lang.Object value)
setProperty
in interface MinimizerInterface
public java.lang.Object getProperty(java.lang.String propertyName, int param)
getProperty
in interface MinimizerInterface
private void addConstraint(java.lang.Object[] c)
private void clear()
public boolean minimize(int steps, double crit, java.util.BitSet bsSelected, java.util.BitSet bsFixed, boolean haveFixed, boolean forceSilent, java.lang.String ff)
minimize
in interface MinimizerInterface
private void setEnergyUnits()
private boolean setupMinimization()
private boolean setModel(java.util.BitSet bsElements)
private void setAtomPositions()
private void getBonds()
public void getAngles()
public void getTorsions()
public ForceField getForceField(java.lang.String ff)
private void setMinimizationOn(boolean minimizationOn)
private void getEnergyOnly()
private void reportEnergy()
public boolean startMinimization()
boolean stepMinimization()
void endMinimization()
private void saveCoordinates()
private void restoreCoordinates()
private void stopMinimization(boolean coordAreOK)
void updateAtomXYZ()
private void minimizeWithoutThread()
public void report(java.lang.String msg, boolean isEcho)
public void calculatePartialCharges(Bond[] bonds, int bondCount, Atom[] atoms, java.util.BitSet bsAtoms)
calculatePartialCharges
in interface MinimizerInterface