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