org.jmol.minimize
Class Minimizer
java.lang.Object
org.jmol.minimize.Minimizer
- All Implemented Interfaces:
- MinimizerInterface
public class Minimizer
- extends java.lang.Object
- implements MinimizerInterface
Method Summary |
private void |
addConstraint(java.lang.Object[] c)
|
private void |
clear()
|
(package private) void |
endMinimization()
|
void |
getAngles()
|
java.util.List<java.lang.String[]> |
getAtomTypes()
|
private void |
getEnergyOnly()
|
ForceField |
getForceField()
|
java.lang.Object |
getProperty(java.lang.String propertyName,
int param)
|
private java.util.BitSet |
getSearch(java.lang.String smarts,
int elemnoMax,
java.util.BitSet bsElements)
|
void |
getTorsions()
|
boolean |
minimize(int steps,
double crit,
java.util.BitSet bsSelected,
java.util.BitSet bsFixed,
boolean haveFixed,
boolean forceSilent)
|
private void |
minimizeWithoutThread()
|
void |
report(java.lang.String msg,
boolean isEcho)
|
private void |
restoreCoordinates()
|
private void |
saveCoordinates()
|
private void |
setAtomPositions()
|
private void |
setMinimizationOn(boolean minimizationOn)
|
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()
|
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
viewer
public Viewer viewer
atoms
public Atom[] atoms
minAtoms
public MinAtom[] minAtoms
minBonds
public MinBond[] minBonds
bsMinFixed
public java.util.BitSet bsMinFixed
atomCount
private int atomCount
bondCount
private int bondCount
atomMap
private int[] atomMap
angles
public int[][] angles
torsions
public int[][] torsions
partialCharges
public double[] partialCharges
steps
private int steps
crit
private double crit
atomTypes
private static java.util.List<java.lang.String[]> atomTypes
pFF
private ForceField pFF
ff
private java.lang.String ff
bsTaint
private java.util.BitSet bsTaint
bsSelected
private java.util.BitSet bsSelected
bsAtoms
private java.util.BitSet bsAtoms
bsFixedDefault
private java.util.BitSet bsFixedDefault
bsFixed
private java.util.BitSet bsFixed
bsAromatic
private java.util.BitSet bsAromatic
constraints
public java.util.List<java.lang.Object[]> constraints
isSilent
private boolean isSilent
constraintMap
private java.util.Map<java.lang.String,java.lang.Object[]> constraintMap
TOKEN_ELEMENT_ONLY
private static final int TOKEN_ELEMENT_ONLY
- See Also:
- Constant Field Values
TOKEN_ELEMENT_CHARGED
private static final int TOKEN_ELEMENT_CHARGED
- See Also:
- Constant Field Values
TOKEN_ELEMENT_CONNECTED
private static final int TOKEN_ELEMENT_CONNECTED
- See Also:
- Constant Field Values
TOKEN_AROMATIC
private static final int TOKEN_AROMATIC
- See Also:
- Constant Field Values
TOKEN_ELEMENT_SP
private static final int TOKEN_ELEMENT_SP
- See Also:
- Constant Field Values
TOKEN_ELEMENT_ALLYLIC
private static final int TOKEN_ELEMENT_ALLYLIC
- See Also:
- Constant Field Values
PT_ELEMENT
private static final int PT_ELEMENT
- See Also:
- Constant Field Values
PT_CHARGE
private static final int PT_CHARGE
- See Also:
- Constant Field Values
PT_CONNECT
private static final int PT_CONNECT
- See Also:
- Constant Field Values
tokenTypes
private static final Token[][] tokenTypes
minimizationOn
boolean minimizationOn
minimizationThread
private Minimizer.MinimizationThread minimizationThread
coordSaved
double[][] coordSaved
Minimizer
public Minimizer()
setProperty
public void setProperty(java.lang.String propertyName,
java.lang.Object value)
- Specified by:
setProperty
in interface MinimizerInterface
getProperty
public java.lang.Object getProperty(java.lang.String propertyName,
int param)
- Specified by:
getProperty
in interface MinimizerInterface
addConstraint
private void addConstraint(java.lang.Object[] c)
clear
private void clear()
minimize
public boolean minimize(int steps,
double crit,
java.util.BitSet bsSelected,
java.util.BitSet bsFixed,
boolean haveFixed,
boolean forceSilent)
- Specified by:
minimize
in interface MinimizerInterface
setupMinimization
private boolean setupMinimization()
setAtomPositions
private void setAtomPositions()
getSearch
private java.util.BitSet getSearch(java.lang.String smarts,
int elemnoMax,
java.util.BitSet bsElements)
getAngles
public void getAngles()
getTorsions
public void getTorsions()
getForceField
public ForceField getForceField()
getAtomTypes
public java.util.List<java.lang.String[]> getAtomTypes()
setMinimizationOn
private void setMinimizationOn(boolean minimizationOn)
getEnergyOnly
private void getEnergyOnly()
startMinimization
public boolean startMinimization()
stepMinimization
boolean stepMinimization()
endMinimization
void endMinimization()
saveCoordinates
private void saveCoordinates()
restoreCoordinates
private void restoreCoordinates()
stopMinimization
private void stopMinimization(boolean coordAreOK)
updateAtomXYZ
void updateAtomXYZ()
minimizeWithoutThread
private void minimizeWithoutThread()
report
public void report(java.lang.String msg,
boolean isEcho)