Package org.jmol.minimize
Class Minimizer
java.lang.Object
org.jmol.minimize.Minimizer
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Field Summary
FieldsModifier and TypeFieldDescriptionprivate int
private int[]
Atom[]
private int
Bond[]
javajs.util.BS
javajs.util.BS
private javajs.util.BS
private javajs.util.BS
javajs.util.BS
private javajs.util.BS
private javajs.util.BS
private Map
<String, MMConstraint> javajs.util.Lst
<MMConstraint> (package private) double[][]
private double
private int
private String
private boolean
private boolean
MinAngle[]
MinAtom[]
MinBond[]
private boolean
private MinimizationThread
private javajs.util.P3
double[]
private ForceField
int
private int
private double
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprivate void
addConstraint
(Object[] o) void
calculatePartialCharges
(ModelSet ms, javajs.util.BS bsAtoms, javajs.util.BS bsReport) private void
clear()
void
void
private void
getBonds()
private void
getForceField
(String ff) getProperty
(String propertyName, int param) void
boolean
boolean
minimize
(int steps, double crit, javajs.util.BS bsSelected, javajs.util.BS bsFixed, javajs.util.BS bsBasis, int flags, String ff) private void
void
private void
private void
private void
private void
private void
private void
setMinimizationOn
(boolean minimizationOn) private boolean
setModel
(javajs.util.BS bsElements) setProperty
(String propertyName, Object value) private boolean
boolean
boolean
void
stopMinimization
(boolean coordAreOK) (package private) void
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Field Details
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vwr
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atoms
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bonds
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rawBondCount
public int rawBondCount -
minAtoms
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minBonds
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minAngles
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minTorsions
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minPositions
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bsMinFixed
public javajs.util.BS bsMinFixed -
ac
private int ac -
bondCount
private int bondCount -
atomMap
private int[] atomMap -
partialCharges
public double[] partialCharges -
steps
private int steps -
crit
private double crit -
units
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pFF
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ff
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bsTaint
private javajs.util.BS bsTaint -
bsSelected
private javajs.util.BS bsSelected -
bsAtoms
public javajs.util.BS bsAtoms -
bsFixedDefault
private javajs.util.BS bsFixedDefault -
bsFixed
private javajs.util.BS bsFixed -
constraints
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bsBasis
public javajs.util.BS bsBasis -
isSilent
private boolean isSilent -
constraintMap
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elemnoMax
private int elemnoMax -
isQuick
private boolean isQuick -
minimizationOn
private boolean minimizationOn -
minimizationThread
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trustRadius
private double trustRadius -
coordSaved
double[][] coordSaved -
p
private javajs.util.P3 p
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Constructor Details
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Minimizer
public Minimizer()
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Method Details
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setProperty
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minimize
public boolean minimize(int steps, double crit, javajs.util.BS bsSelected, javajs.util.BS bsFixed, javajs.util.BS bsBasis, int flags, String ff) throws JmolAsyncException - Throws:
JmolAsyncException
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getProperty
- Parameters:
propertyName
-param
-- Returns:
- Object
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addConstraint
- Parameters:
o
- [ [natoms a1 a2 a3...] value ]
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clear
private void clear() -
setEnergyUnits
private void setEnergyUnits() -
setupMinimization
- Throws:
JmolAsyncException
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setModel
- Throws:
JmolAsyncException
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setAtomPositions
private void setAtomPositions() -
getBonds
private void getBonds() -
getAngles
public void getAngles() -
getTorsions
public void getTorsions() -
getForceField
- Throws:
JmolAsyncException
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minimizationOn
public boolean minimizationOn() -
getThread
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setMinimizationOn
private void setMinimizationOn(boolean minimizationOn) -
getEnergyOnly
private void getEnergyOnly() -
reportEnergy
private void reportEnergy() -
startMinimization
public boolean startMinimization() -
stepMinimization
public boolean stepMinimization() -
endMinimization
public void endMinimization() -
saveCoordinates
private void saveCoordinates() -
restoreCoordinates
private void restoreCoordinates() -
stopMinimization
public void stopMinimization(boolean coordAreOK) -
updateAtomXYZ
void updateAtomXYZ() -
minimizeWithoutThread
private void minimizeWithoutThread() -
report
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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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