public class Minimizer extends java.lang.Object implements MinimizerInterface
Modifier and Type | Field and Description |
---|---|
private int |
ac |
private int[] |
atomMap |
Atom[] |
atoms |
private int |
bondCount |
Bond[] |
bonds |
BS |
bsAtoms |
private BS |
bsFixed |
private BS |
bsFixedDefault |
BS |
bsMinFixed |
private BS |
bsSelected |
private BS |
bsTaint |
private java.util.Map<java.lang.String,java.lang.Object[]> |
constraintMap |
javajs.util.Lst<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 |
private boolean |
minimizationOn |
private MinimizationThread |
minimizationThread |
MinPosition[] |
minPositions |
MinTorsion[] |
minTorsions |
double[] |
partialCharges |
private ForceField |
pFF |
int |
rawBondCount |
private int |
steps |
java.lang.String |
units |
Viewer |
vwr |
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,
BS bsAtoms) |
private void |
clear() |
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) |
JmolThread |
getThread() |
void |
getTorsions() |
boolean |
minimizationOn() |
boolean |
minimize(int steps,
double crit,
BS bsSelected,
BS 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(BS bsElements) |
MinimizerInterface |
setProperty(java.lang.String propertyName,
java.lang.Object value) |
private boolean |
setupMinimization() |
boolean |
startMinimization() |
boolean |
stepMinimization() |
void |
stopMinimization(boolean coordAreOK) |
(package private) void |
updateAtomXYZ() |
public Viewer vwr
public Atom[] atoms
public Bond[] bonds
public int rawBondCount
public MinAtom[] minAtoms
public MinBond[] minBonds
public MinAngle[] minAngles
public MinTorsion[] minTorsions
public MinPosition[] minPositions
public BS bsMinFixed
private int ac
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 BS bsTaint
private BS bsSelected
public BS bsAtoms
private BS bsFixedDefault
private BS bsFixed
public javajs.util.Lst<java.lang.Object[]> constraints
private boolean isSilent
private java.util.Map<java.lang.String,java.lang.Object[]> constraintMap
private int elemnoMax
private boolean minimizationOn
private MinimizationThread minimizationThread
double[][] coordSaved
public MinimizerInterface 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, BS bsSelected, BS bsFixed, boolean haveFixed, boolean forceSilent, java.lang.String ff) throws JmolAsyncException
minimize
in interface MinimizerInterface
JmolAsyncException
private void setEnergyUnits()
private boolean setupMinimization() throws JmolAsyncException
JmolAsyncException
private boolean setModel(BS bsElements) throws JmolAsyncException
JmolAsyncException
private void setAtomPositions()
private void getBonds()
public void getAngles()
public void getTorsions()
public ForceField getForceField(java.lang.String ff) throws JmolAsyncException
JmolAsyncException
public boolean minimizationOn()
minimizationOn
in interface MinimizerInterface
public JmolThread getThread()
getThread
in interface MinimizerInterface
private void setMinimizationOn(boolean minimizationOn)
private void getEnergyOnly()
private void reportEnergy()
public boolean startMinimization()
startMinimization
in interface MinimizerInterface
public boolean stepMinimization()
stepMinimization
in interface MinimizerInterface
public void endMinimization()
endMinimization
in interface MinimizerInterface
private void saveCoordinates()
private void restoreCoordinates()
public 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, BS bsAtoms) throws JmolAsyncException
calculatePartialCharges
in interface MinimizerInterface
JmolAsyncException