public class Minimizer extends java.lang.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 java.util.List<java.lang.String[]> |
atomTypes |
private int |
bondCount |
private java.util.BitSet |
bsAromatic |
private java.util.BitSet |
bsAtoms |
private java.util.BitSet |
bsFixed |
private java.util.BitSet |
bsFixedDefault |
java.util.BitSet |
bsMinFixed |
private java.util.BitSet |
bsSelected |
private java.util.BitSet |
bsTaint |
private java.util.Map<java.lang.String,java.lang.Object[]> |
constraintMap |
java.util.List<java.lang.Object[]> |
constraints |
(package private) double[][] |
coordSaved |
private double |
crit |
private java.lang.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(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() |
public Viewer viewer
public Atom[] atoms
public MinAtom[] minAtoms
public MinBond[] minBonds
public java.util.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 static java.util.List<java.lang.String[]> atomTypes
private ForceField pFF
private java.lang.String ff
private java.util.BitSet bsTaint
private java.util.BitSet bsSelected
private java.util.BitSet bsAtoms
private java.util.BitSet bsFixedDefault
private java.util.BitSet bsFixed
private java.util.BitSet bsAromatic
public java.util.List<java.lang.Object[]> constraints
private boolean isSilent
private java.util.Map<java.lang.String,java.lang.Object[]> constraintMap
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(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, java.util.BitSet bsSelected, java.util.BitSet bsFixed, boolean haveFixed, boolean forceSilent)
minimize
in interface MinimizerInterface
private boolean setupMinimization()
private void setAtomPositions()
private java.util.BitSet getSearch(java.lang.String smarts, int elemnoMax, java.util.BitSet bsElements)
public void getAngles()
public void getTorsions()
public ForceField getForceField()
public java.util.List<java.lang.String[]> getAtomTypes()
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(java.lang.String msg, boolean isEcho)