class CalculationsMMFF extends Calculations
Modifier and Type | Class and Description |
---|---|
(package private) class |
CalculationsMMFF.AngleCalc |
(package private) class |
CalculationsMMFF.DistanceCalc |
(package private) class |
CalculationsMMFF.ESCalc |
(package private) class |
CalculationsMMFF.OOPCalc |
(package private) class |
CalculationsMMFF.SBCalc |
(package private) class |
CalculationsMMFF.TorsionCalc |
(package private) class |
CalculationsMMFF.VDWCalc |
Calculations.PairCalc
Modifier and Type | Field and Description |
---|---|
(package private) CalculationsMMFF.AngleCalc |
angleCalc |
(package private) CalculationsMMFF.DistanceCalc |
bondCalc |
static int |
DA_D |
static int |
DA_DA |
(package private) CalculationsMMFF.ESCalc |
esCalc |
private Map<Integer,Object> |
ffParams |
(package private) static double |
FPAR |
(package private) ForceFieldMMFF |
mmff |
(package private) CalculationsMMFF.OOPCalc |
oopCalc |
(package private) CalculationsMMFF.SBCalc |
sbCalc |
(package private) CalculationsMMFF.TorsionCalc |
torsionCalc |
(package private) CalculationsMMFF.VDWCalc |
vdwCalc |
angleCount, atomCount, bondCount, CALC_ANGLE, CALC_DISTANCE, CALC_ES, CALC_MAX, CALC_OOP, CALC_STRETCH_BEND, CALC_TORSION, CALC_VDW, calculations, constraints, da, db, dc, dd, DEG_TO_RAD, ff, gradients, ia, ib, ic, id, isPreliminary, KCAL_TO_KJ, logData, logging, loggingEnabled, minAngles, minAtoms, minBonds, minPositions, minTorsions, RAD_TO_DEG, silent, torsionCount, v1, v2, v3
Constructor and Description |
---|
CalculationsMMFF(ForceField ff,
Map<Integer,Object> ffParams,
MinAtom[] minAtoms,
MinBond[] minBonds,
MinAngle[] minAngles,
MinTorsion[] minTorsions,
MinPosition[] minPositions,
javajs.util.List<Object[]> constraints) |
Modifier and Type | Method and Description |
---|---|
(package private) double |
compute(int iType,
Object[] dataIn) |
(package private) String |
getDebugHeader(int iType) |
(package private) String |
getDebugLine(int iType,
Calculation c) |
(package private) Object |
getParameter(Integer key) |
(package private) Object |
getParameterObj(MinObject a) |
(package private) String |
getUnits() |
private static boolean |
isInvertible(MinAtom a) |
protected boolean |
isLinear(int i) |
(package private) boolean |
setupCalculations() |
addForce, addForces, appendLogData, energyAngle, energyBond, energyES, energyOOP, energyStrBnd, energyStretchBend, energyTorsion, energyVDW, getAtomList, getConstraintList, getDebugFooter, getDebugHeader2, getDebugLineC, getLogData, pairSearch, setAngleVariables, setConstraints, setCoords, setLoggingEnabled, setOopVariables, setPairVariables, setPreliminary, setSilent, setTorsionVariables
static final double FPAR
public static final int DA_D
public static final int DA_DA
CalculationsMMFF.DistanceCalc bondCalc
CalculationsMMFF.AngleCalc angleCalc
CalculationsMMFF.TorsionCalc torsionCalc
CalculationsMMFF.OOPCalc oopCalc
CalculationsMMFF.VDWCalc vdwCalc
CalculationsMMFF.ESCalc esCalc
CalculationsMMFF.SBCalc sbCalc
ForceFieldMMFF mmff
CalculationsMMFF(ForceField ff, Map<Integer,Object> ffParams, MinAtom[] minAtoms, MinBond[] minBonds, MinAngle[] minAngles, MinTorsion[] minTorsions, MinPosition[] minPositions, javajs.util.List<Object[]> constraints)
String getUnits()
getUnits
in class Calculations
boolean setupCalculations()
setupCalculations
in class Calculations
protected boolean isLinear(int i)
private static boolean isInvertible(MinAtom a)
double compute(int iType, Object[] dataIn)
compute
in class Calculations
String getDebugHeader(int iType)
getDebugHeader
in class Calculations
String getDebugLine(int iType, Calculation c)
getDebugLine
in class Calculations