org.jmol.minimize
public class Minimizer extends Object implements MinimizerInterface
Modifier and Type | Class and Description |
---|---|
(package private) class |
Minimizer.MinimizationThread |
Modifier and Type | Field and Description |
---|---|
int[][] |
angles |
private int |
atomCount |
private int[] |
atomMap |
Atom[] |
atoms |
private static List<String[]> |
atomTypes |
private int |
bondCount |
private BitSet |
bsAromatic |
private BitSet |
bsAtoms |
private BitSet |
bsFixed |
private BitSet |
bsFixedDefault |
BitSet |
bsMinFixed |
private BitSet |
bsSelected |
private BitSet |
bsTaint |
private Map<String,Object[]> |
constraintMap |
List<Object[]> |
constraints |
(package private) double[][] |
coordSaved |
private double |
crit |
private String |
ff |
private boolean |
isSilent |
MinAtom[] |
minAtoms |
MinBond[] |
minBonds |
(package private) boolean |
minimizationOn |
private Minimizer.MinimizationThread |
minimizationThread |
double[] |
partialCharges |
private ForceField |
pFF |
private static int |
PT_CHARGE |
private static int |
PT_CONNECT |
private static int |
PT_ELEMENT |
private int |
steps |
private static int |
TOKEN_AROMATIC |
private static int |
TOKEN_ELEMENT_ALLYLIC |
private static int |
TOKEN_ELEMENT_CHARGED |
private static int |
TOKEN_ELEMENT_CONNECTED |
private static int |
TOKEN_ELEMENT_ONLY |
private static int |
TOKEN_ELEMENT_SP |
private static Token[][] |
tokenTypes |
int[][] |
torsions |
Viewer |
viewer |
Constructor and Description |
---|
Minimizer() |
Modifier and Type | Method and Description |
---|---|
private void |
addConstraint(Object[] c) |
private void |
clear() |
(package private) void |
endMinimization() |
void |
getAngles() |
List<String[]> |
getAtomTypes() |
private void |
getEnergyOnly() |
ForceField |
getForceField() |
Object |
getProperty(String propertyName,
int param) |
private BitSet |
getSearch(String smarts,
int elemnoMax,
BitSet bsElements) |
void |
getTorsions() |
boolean |
minimize(int steps,
double crit,
BitSet bsSelected,
BitSet bsFixed,
boolean haveFixed,
boolean forceSilent) |
private void |
minimizeWithoutThread() |
void |
report(String msg,
boolean isEcho) |
private void |
restoreCoordinates() |
private void |
saveCoordinates() |
private void |
setAtomPositions() |
private void |
setMinimizationOn(boolean minimizationOn) |
void |
setProperty(String propertyName,
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 MinAtom[] minAtoms
public MinBond[] minBonds
public BitSet bsMinFixed
private int atomCount
private int bondCount
private int[] atomMap
public int[][] angles
public int[][] torsions
public double[] partialCharges
private int steps
private double crit
private ForceField pFF
private String ff
private BitSet bsTaint
private BitSet bsSelected
private BitSet bsAtoms
private BitSet bsFixedDefault
private BitSet bsFixed
private BitSet bsAromatic
private boolean isSilent
private static final int TOKEN_ELEMENT_ONLY
private static final int TOKEN_ELEMENT_CHARGED
private static final int TOKEN_ELEMENT_CONNECTED
private static final int TOKEN_AROMATIC
private static final int TOKEN_ELEMENT_SP
private static final int TOKEN_ELEMENT_ALLYLIC
private static final int PT_ELEMENT
private static final int PT_CHARGE
private static final int PT_CONNECT
private static final Token[][] tokenTypes
boolean minimizationOn
private Minimizer.MinimizationThread minimizationThread
double[][] coordSaved
public void setProperty(String propertyName, Object value)
setProperty
in interface MinimizerInterface
public Object getProperty(String propertyName, int param)
getProperty
in interface MinimizerInterface
private void addConstraint(Object[] c)
private void clear()
public boolean minimize(int steps, double crit, BitSet bsSelected, BitSet bsFixed, boolean haveFixed, boolean forceSilent)
minimize
in interface MinimizerInterface
private boolean setupMinimization()
private void setAtomPositions()
public void getAngles()
public void getTorsions()
public ForceField getForceField()
private void setMinimizationOn(boolean minimizationOn)
private void getEnergyOnly()
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(String msg, boolean isEcho)