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org::jmol::minimize::forcefield::CalculationsUFF Class Reference

Inheritance diagram for org::jmol::minimize::forcefield::CalculationsUFF:
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Collaboration diagram for org::jmol::minimize::forcefield::CalculationsUFF:
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List of all members.


class  AngleCalc
class  DistanceCalc
class  ESCalc
class  OOPCalc
class  PairCalc
class  TorsionCalc
class  VDWCalc

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)
static final int PAR_D = 3
static final int PAR_HARD = 9
static final int PAR_R = 0
static final int PAR_RADIUS = 10
static final int PAR_THETA = 1
static final int PAR_U = 7
static final int PAR_V = 6
static final int PAR_X = 2
static final int PAR_XI = 8
static final int PAR_Z = 5
static final int PAR_ZETA = 4
final static double RAD_TO_DEG = (180.0 / Math.PI)

Package Functions

void addForce (Vector3d v, int i, double dE)
void appendLogData (String s)
 CalculationsUFF (ForceField ff, MinAtom[] minAtoms, MinBond[] minBonds, int[][] angles, int[][] torsions, double[] partialCharges, List constraints)
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)
String getAtomList (String title)
String getDebugFooter (int iType, double energy)
String getDebugHeader (int iType)
String getDebugLine (int iType, Calculation c)
String getUnit ()
boolean haveParams ()
void setLoggingEnabled (boolean TF)
void setParams (Hashtable temp)
void setPreliminary (boolean TF)
boolean setupCalculations ()
boolean setupElectrostatics ()

Static Package Functions

static double calculateR0 (double ri, double rj, double chiI, double chiJ, double bondorder)
static FFParam getParameter (String a, Hashtable ffParams)

Package Attributes

AngleCalc angleCalc
int[][] angles
int atomCount
MinAtom[] atoms
DistanceCalc bondCalc
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()
ESCalc esCalc
ForceField ff
boolean gradients
boolean havePartialCharges
int ia
int ib
int ic
int id
boolean isPreliminary
StringBuffer logData = new StringBuffer()
boolean logging
boolean loggingEnabled
OOPCalc oopCalc
double[] partialCharges
boolean silent
TorsionCalc torsionCalc
int[][] torsions
final Vector3d v1 = new Vector3d()
final Vector3d v2 = new Vector3d()
final Vector3d v3 = new Vector3d()
VDWCalc vdwCalc

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 KCAL22 = 22.0 * KCAL_TO_KJ
static final double KCAL332 = KCAL_TO_KJ * 332.0637
static final double KCAL44 = 44.0 * KCAL_TO_KJ
static final double KCAL6 = 6.0 * KCAL_TO_KJ
static final double KCAL644 = 644.12 * KCAL_TO_KJ
static final double KCAL_TO_KJ = 4.1868

Private Member Functions

boolean isInvertible (int n)
void pairSearch (List calc, PairCalc type)

Detailed Description

Definition at line 50 of file CalculationsUFF.java.

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

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