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org::jmol::minimize::Minimizer Class Reference

Inheritance diagram for org::jmol::minimize::Minimizer:
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List of all members.


class  MinimizationThread

Public Member Functions

void getAngles ()
List getAtomTypes ()
ForceField getForceField ()
Object getProperty (String propertyName, int param)
void getTorsions ()
boolean minimize (int steps, double crit, BitSet bsSelected, BitSet bsFixed, boolean haveFixed, boolean forceSilent)
void report (String msg, boolean isEcho)
void setProperty (String propertyName, Object value)
boolean startMinimization ()

Public Attributes

int[][] angles
Atom[] atoms
BitSet bsMinFixed
List constraints
MinAtom[] minAtoms
MinBond[] minBonds
double[] partialCharges
int[][] torsions
Viewer viewer

Package Functions

void endMinimization ()
boolean stepMinimization ()
void updateAtomXYZ ()

Package Attributes

BitSet bsAtoms
BitSet bsSelected
double[][] coordSaved
boolean minimizationOn

Private Member Functions

void addConstraint (Object[] c)
void clear ()
void getEnergyOnly ()
BitSet getSearch (String smarts, int elemnoMax, BitSet bsElements)
void minimizeWithoutThread ()
void restoreCoordinates ()
void saveCoordinates ()
void setAtomPositions ()
void setMinimizationOn (boolean minimizationOn)
boolean setupMinimization ()
void stopMinimization (boolean coordAreOK)

Private Attributes

int atomCount
int[] atomMap
int bondCount
BitSet bsAromatic
BitSet bsFixed
BitSet bsFixedDefault
BitSet bsTaint
Hashtable constraintMap
double crit = 1e-3
String ff = "UFF"
boolean isSilent
MinimizationThread minimizationThread
ForceField pFF
int steps = 50

Static Private Attributes

static List atomTypes
static final int PT_CHARGE = 5
static final int PT_CONNECT = 6
static final int PT_ELEMENT = 2
static final int TOKEN_AROMATIC = 3
static final int TOKEN_ELEMENT_ALLYLIC = 6
static final int TOKEN_ELEMENT_CHARGED = 1
static final int TOKEN_ELEMENT_CONNECTED = 2
static final int TOKEN_ELEMENT_ONLY = 0
static final int TOKEN_ELEMENT_SP = 4
static final Token[][] tokenTypes

Detailed Description

Definition at line 49 of file Minimizer.java.

The documentation for this class was generated from the following file:

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