Package org.jmol.minimize.forcefield
Class Calculations
java.lang.Object
org.jmol.minimize.forcefield.Calculations
- Direct Known Subclasses:
CalculationsMMFF
,CalculationsUFF
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Field Summary
FieldsModifier and TypeFieldDescription(package private) int
(package private) int
(package private) int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) static final int
(package private) javajs.util.Lst<Object[]>[]
private MMConstraint[][]
(package private) final javajs.util.V3d
(package private) final javajs.util.V3d
(package private) final javajs.util.V3d
(package private) final javajs.util.V3d
static final double
(package private) ForceField
(package private) boolean
private boolean
(package private) int
(package private) int
(package private) int
(package private) int
(package private) boolean
(package private) static final double
(package private) javajs.util.SB
(package private) boolean
(package private) boolean
(package private) MinAngle[]
(package private) MinAtom[]
(package private) MinBond[]
private MinPosition[]
(package private) MinTorsion[]
(package private) FFParam
(package private) FFParam
(package private) FFParam
private static final double
static final double
(package private) boolean
(package private) int
private static final double
(package private) final javajs.util.V3d
(package private) final javajs.util.V3d
(package private) final javajs.util.V3d
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Constructor Summary
ConstructorsConstructorDescriptionCalculations
(ForceField ff, MinAtom[] minAtoms, MinBond[] minBonds, MinAngle[] minAngles, MinTorsion[] minTorsions, MinPosition[] minPositions, javajs.util.Lst<MMConstraint> constraints) -
Method Summary
Modifier and TypeMethodDescription(package private) void
addForce
(javajs.util.V3d v, int i, double dE) (package private) void
addForces
(Calculation c, int n) (package private) void
private double
calc
(int iType, boolean gradients, boolean canConstrain) (package private) abstract double
private double
constrainQuadratic
(double value, double targetValue, double k, int iType) private double
constraintEnergy
(int iType) (package private) double
energyAngle
(boolean gradients) (package private) double
energyBond
(boolean gradients) (package private) double
energyES
(boolean gradients) (package private) double
energyOOP
(boolean gradients) (package private) double
energyStrBnd
(boolean gradients) (package private) double
energyStretchBend
(boolean gradients) (package private) double
energyTorsion
(boolean gradients) (package private) double
energyVDW
(boolean gradients) (package private) String
getAtomList
(String title) (package private) void
(package private) String
getDebugFooter
(int iType, double energy) (package private) abstract String
getDebugHeader
(int iType) protected String
getDebugHeader2
(int iType) (package private) String
getDebugLine
(int iType, Calculation c) protected String
getDebugLineC
(int iType, Calculation c) (package private) Object
(package private) abstract Object
(package private) abstract String
getUnits()
(package private) boolean
isLinear
(int i) protected void
pairSearch
(javajs.util.Lst<Object[]> calc1, Calculation pc1, javajs.util.Lst<Object[]> calc2, Calculation pc2) (package private) void
void
setConstraints
(javajs.util.Lst<MMConstraint> constraints) (package private) void
setCoords
(Calculation c, int n) (package private) void
setLoggingEnabled
(boolean TF) (package private) void
setOopVariables
(Calculation c, boolean fixTheta) (package private) void
(package private) void
setPreliminary
(boolean TF) void
setSilent
(boolean TF) (package private) void
(package private) abstract boolean
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Field Details
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RAD_TO_DEG
public static final double RAD_TO_DEG- See Also:
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DEG_TO_RAD
public static final double DEG_TO_RAD- See Also:
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KCAL_TO_KJ
static final double KCAL_TO_KJ- See Also:
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CALC_DISTANCE
static final int CALC_DISTANCE- See Also:
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CALC_ANGLE
static final int CALC_ANGLE- See Also:
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CALC_TORSION
static final int CALC_TORSION- See Also:
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CALC_STRETCH_BEND
static final int CALC_STRETCH_BEND- See Also:
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CALC_OOP
static final int CALC_OOP- See Also:
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CALC_VDW
static final int CALC_VDW- See Also:
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CALC_ES
static final int CALC_ES- See Also:
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CALC_MAX
static final int CALC_MAX- See Also:
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parA
FFParam parA -
parB
FFParam parB -
parC
FFParam parC -
ff
ForceField ff -
calculations
javajs.util.Lst<Object[]>[] calculations -
ffParams
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ac
int ac -
bondCount
int bondCount -
angleCount
int angleCount -
torsionCount
int torsionCount -
minAtoms
MinAtom[] minAtoms -
minBonds
MinBond[] minBonds -
minAngles
MinAngle[] minAngles -
minTorsions
MinTorsion[] minTorsions -
minPositions
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constraintsByType
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haveConstraints
private boolean haveConstraints -
isPreliminary
boolean isPreliminary -
gradients
boolean gradients -
silent
boolean silent -
logData
javajs.util.SB logData -
logging
boolean logging -
loggingEnabled
boolean loggingEnabled -
da
final javajs.util.V3d da -
db
final javajs.util.V3d db -
dc
final javajs.util.V3d dc -
dd
final javajs.util.V3d dd -
ia
int ia -
ib
int ib -
ic
int ic -
id
int id -
v1
final javajs.util.V3d v1 -
v2
final javajs.util.V3d v2 -
v3
final javajs.util.V3d v3 -
PI_OVER_2
private static final double PI_OVER_2- See Also:
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TWO_PI
private static final double TWO_PI- See Also:
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Constructor Details
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Calculations
Calculations(ForceField ff, MinAtom[] minAtoms, MinBond[] minBonds, MinAngle[] minAngles, MinTorsion[] minTorsions, MinPosition[] minPositions, javajs.util.Lst<MMConstraint> constraints)
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Method Details
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getParameterObj
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getParameter
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setupCalculations
abstract boolean setupCalculations() -
getUnits
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compute
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setConstraints
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addForce
void addForce(javajs.util.V3d v, int i, double dE) -
setSilent
public void setSilent(boolean TF) -
getLogData
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appendLogData
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setLoggingEnabled
void setLoggingEnabled(boolean TF) -
setPreliminary
void setPreliminary(boolean TF) -
pairSearch
protected void pairSearch(javajs.util.Lst<Object[]> calc1, Calculation pc1, javajs.util.Lst<Object[]> calc2, Calculation pc2) -
calc
private double calc(int iType, boolean gradients, boolean canConstrain) -
energyStrBnd
double energyStrBnd(boolean gradients) -
energyBond
double energyBond(boolean gradients) -
energyAngle
double energyAngle(boolean gradients) -
energyTorsion
double energyTorsion(boolean gradients) -
energyStretchBend
double energyStretchBend(boolean gradients) -
energyOOP
double energyOOP(boolean gradients) -
energyVDW
double energyVDW(boolean gradients) -
energyES
double energyES(boolean gradients) -
constraintEnergy
private double constraintEnergy(int iType) -
constrainQuadratic
private double constrainQuadratic(double value, double targetValue, double k, int iType) -
getConstraintList
void getConstraintList() -
getAtomList
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getDebugHeader
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getDebugHeader2
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getDebugLine
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getDebugLineC
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setPairVariables
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setAngleVariables
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setOopVariables
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setTorsionVariables
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setCoords
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addForces
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isLinear
boolean isLinear(int i) - Parameters:
i
-- Returns:
- T/F
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