Logo Search packages:      
Sourcecode: jmol version File versions  Download package

Public Member Functions | Public Attributes | Static Public Attributes | Package Functions | Static Package Functions | Package Attributes | Static Package Attributes | Private Member Functions | Static Private Attributes

org::jmol::minimize::forcefield::Calculations Class Reference

Inheritance diagram for org::jmol::minimize::forcefield::Calculations:
Inheritance graph
Collaboration diagram for org::jmol::minimize::forcefield::Calculations:
Collaboration graph

List of all members.

Public Member Functions

String getLogData ()
void setConstraints (List constraints)
void setSilent (boolean TF)

Public Attributes

Hashtable ffParams

Static Public Attributes

final static double DEG_TO_RAD = (Math.PI / 180.0)
final static double RAD_TO_DEG = (180.0 / Math.PI)

Package Functions

void addForce (Vector3d v, int i, double dE)
void appendLogData (String s)
 Calculations (ForceField ff, MinAtom[] minAtoms, MinBond[] minBonds, int[][] angles, int[][] torsions, double[] partialCharges, List constraints)
abstract double compute (int iType, Object[] dataIn)
double energyAngle (boolean gradients)
double energyBond (boolean gradients)
double energyES (boolean gradients)
double energyOOP (boolean gradients)
double energyStrBnd (boolean gradients)
double energyTorsion (boolean gradients)
double energyVDW (boolean gradients)
abstract String getAtomList (String title)
abstract String getDebugFooter (int iType, double energy)
abstract String getDebugHeader (int iType)
abstract String getUnit ()
boolean haveParams ()
void setLoggingEnabled (boolean TF)
void setParams (Hashtable temp)
void setPreliminary (boolean TF)
abstract boolean setupCalculations ()
abstract boolean setupElectrostatics ()

Static Package Functions

static FFParam getParameter (String a, Hashtable ffParams)

Package Attributes

int[][] angles
int atomCount
MinAtom[] atoms
int bondCount
MinBond[] bonds
List[] calculations = new ArrayList[CALC_MAX]
List constraints
final Vector3d da = new Vector3d()
final Vector3d db = new Vector3d()
final Vector3d dc = new Vector3d()
final Vector3d dd = new Vector3d()
ForceField ff
boolean gradients
boolean havePartialCharges
int ia
int ib
int ic
int id
boolean isPreliminary
StringBuffer logData = new StringBuffer()
boolean logging
boolean loggingEnabled
double[] partialCharges
boolean silent
int[][] torsions
final Vector3d v1 = new Vector3d()
final Vector3d v2 = new Vector3d()
final Vector3d v3 = new Vector3d()

Static Package Attributes

static final int CALC_ANGLE = 1
static final int CALC_DISTANCE = 0
static final int CALC_ES = 5
static final int CALC_MAX = 6
static final int CALC_OOP = 3
static final int CALC_TORSION = 2
static final int CALC_VDW = 4
static final double KCAL_TO_KJ = 4.1868

Private Member Functions

double calc (int iType, boolean gradients)
double constrainQuadratic (double value, double targetValue, double k, int iType)
double constraintEnergy (int iType)

Static Private Attributes

static final double PI_OVER_2 = Math.PI / 2
static final double TWO_PI = Math.PI * 2

Detailed Description

Definition at line 37 of file Calculations.java.

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

Generated by  Doxygen 1.6.0   Back to index