Package org.jmol.minimize
Class Minimizer
- java.lang.Object
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- org.jmol.minimize.Minimizer
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public class Minimizer extends Object
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Field Summary
Fields Modifier and Type Field Description private int
ac
private int[]
atomMap
Atom[]
atoms
private int
bondCount
Bond[]
bonds
javajs.util.BS
bsAtoms
private javajs.util.BS
bsFixed
private javajs.util.BS
bsFixedDefault
javajs.util.BS
bsMinFixed
private javajs.util.BS
bsSelected
private javajs.util.BS
bsTaint
private Map<String,MMConstraint>
constraintMap
javajs.util.Lst<MMConstraint>
constraints
(package private) double[][]
coordSaved
private double
crit
private int
elemnoMax
private 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
String
units
Viewer
vwr
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Constructor Summary
Constructors Constructor Description Minimizer()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description private void
addConstraint(Object[] o)
void
calculatePartialCharges(ModelSet ms, javajs.util.BS bsAtoms, javajs.util.BS bsReport)
private void
clear()
void
endMinimization()
void
getAngles()
private void
getBonds()
private void
getEnergyOnly()
ForceField
getForceField(String ff)
Object
getProperty(String propertyName, int param)
JmolThread
getThread()
void
getTorsions()
boolean
minimizationOn()
boolean
minimize(int steps, double crit, javajs.util.BS bsSelected, javajs.util.BS bsFixed, boolean haveFixed, boolean forceSilent, String ff)
private void
minimizeWithoutThread()
void
report(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(javajs.util.BS bsElements)
Minimizer
setProperty(String propertyName, Object value)
private boolean
setupMinimization()
boolean
startMinimization()
boolean
stepMinimization()
void
stopMinimization(boolean coordAreOK)
(package private) void
updateAtomXYZ()
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Field Detail
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vwr
public Viewer vwr
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atoms
public Atom[] atoms
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bonds
public Bond[] bonds
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rawBondCount
public int rawBondCount
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minAtoms
public MinAtom[] minAtoms
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minBonds
public MinBond[] minBonds
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minAngles
public MinAngle[] minAngles
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minTorsions
public MinTorsion[] minTorsions
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minPositions
public MinPosition[] minPositions
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bsMinFixed
public javajs.util.BS bsMinFixed
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ac
private int ac
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bondCount
private int bondCount
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atomMap
private int[] atomMap
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partialCharges
public double[] partialCharges
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steps
private int steps
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crit
private double crit
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units
public String units
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pFF
private ForceField pFF
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ff
private String ff
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bsTaint
private javajs.util.BS bsTaint
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bsSelected
private javajs.util.BS bsSelected
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bsAtoms
public javajs.util.BS bsAtoms
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bsFixedDefault
private javajs.util.BS bsFixedDefault
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bsFixed
private javajs.util.BS bsFixed
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constraints
public javajs.util.Lst<MMConstraint> constraints
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isSilent
private boolean isSilent
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constraintMap
private Map<String,MMConstraint> constraintMap
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elemnoMax
private int elemnoMax
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minimizationOn
private boolean minimizationOn
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minimizationThread
private MinimizationThread minimizationThread
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coordSaved
double[][] coordSaved
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Method Detail
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getProperty
public Object getProperty(String propertyName, int param)
- Parameters:
propertyName
-param
-- Returns:
- Object
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addConstraint
private void addConstraint(Object[] o)
- Parameters:
o
- [ [natoms a1 a2 a3...] value ]
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clear
private void clear()
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minimize
public boolean minimize(int steps, double crit, javajs.util.BS bsSelected, javajs.util.BS bsFixed, boolean haveFixed, boolean forceSilent, String ff) throws JmolAsyncException
- Throws:
JmolAsyncException
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setEnergyUnits
private void setEnergyUnits()
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setupMinimization
private boolean setupMinimization() throws JmolAsyncException
- Throws:
JmolAsyncException
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setModel
private boolean setModel(javajs.util.BS bsElements) throws JmolAsyncException
- Throws:
JmolAsyncException
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setAtomPositions
private void setAtomPositions()
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getBonds
private void getBonds()
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getAngles
public void getAngles()
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getTorsions
public void getTorsions()
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getForceField
public ForceField getForceField(String ff) throws JmolAsyncException
- Throws:
JmolAsyncException
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minimizationOn
public boolean minimizationOn()
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getThread
public JmolThread getThread()
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setMinimizationOn
private void setMinimizationOn(boolean minimizationOn)
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getEnergyOnly
private void getEnergyOnly()
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reportEnergy
private void reportEnergy()
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startMinimization
public boolean startMinimization()
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stepMinimization
public boolean stepMinimization()
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endMinimization
public void endMinimization()
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saveCoordinates
private void saveCoordinates()
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restoreCoordinates
private void restoreCoordinates()
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stopMinimization
public void stopMinimization(boolean coordAreOK)
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updateAtomXYZ
void updateAtomXYZ()
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minimizeWithoutThread
private void minimizeWithoutThread()
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report
public void report(String msg, boolean isEcho)
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calculatePartialCharges
public void calculatePartialCharges(ModelSet ms, javajs.util.BS bsAtoms, javajs.util.BS bsReport) throws JmolAsyncException
- Throws:
JmolAsyncException
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