Package org.jmol.minimize.forcefield
Class ForceFieldUFF
- java.lang.Object
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- org.jmol.minimize.forcefield.ForceField
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- org.jmol.minimize.forcefield.ForceFieldUFF
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public class ForceFieldUFF extends ForceField
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Field Summary
Fields Modifier and Type Field Description private static javajs.util.Lst<java.lang.String[]>
atomTypes
private javajs.util.BS
bsAromatic
private java.util.Map<java.lang.Object,java.lang.Object>
ffParams
private boolean
is2D
private static int
PT_CHARGE
private static int
PT_CONNECT
private static int
PT_ELEMENT
private static int
TOKEN_AROMATIC
private static int
TOKEN_ELEMENT_ALLYLIC
private static int
TOKEN_ELEMENT_CHARGED
private static int
TOKEN_ELEMENT_CONNECTED
private static int
TOKEN_ELEMENT_ONLY
private static int
TOKEN_ELEMENT_SP
private static T[][]
tokenTypes
private static java.util.Map<java.lang.Object,java.lang.Object>
uff2DParams
private static java.util.Map<java.lang.Object,java.lang.Object>
uffParams
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Fields inherited from class org.jmol.minimize.forcefield.ForceField
ABI_IJ, ABI_JK, bsFixed, calc, currentStep, EANGLE, EBOND, EELECTROSTATIC, ENERGY, EOOP, ESTRBND, ETORSION, EVDW, minAngles, minAtomCount, minAtoms, minBondCount, minBonds, minimizer, minPositions, minTorsions, name, R3, R4, R5, Raromatic, TBI_AB, TBI_BC, TBI_CD
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Constructor Summary
Constructors Constructor Description ForceFieldUFF(Minimizer minimizer, boolean isQuick)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
clear()
private javajs.util.Lst<java.lang.String[]>
getAtomTypes()
private java.util.Map<java.lang.Object,java.lang.Object>
getParameters()
private javajs.util.BS
getSearch(java.lang.String smarts, int elemnoMax, javajs.util.BS bsElements)
private void
setAtomTypes(javajs.util.BS bsElements, int elemnoMax)
boolean
setModel(javajs.util.BS bsElements, int elemnoMax)
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Methods inherited from class org.jmol.minimize.forcefield.ForceField
detectExplosion, energyAngle, energyBond, energyES, energyFull, energyOOP, energyStretchBend, energyTorsion, energyVDW, getAtomList, getBufferedReader, getCurrentStep, getEnergy, getEnergyDiff, getLogData, getNormalizedDE, log, setConstraints, setModelFields, steepestDescentInitialize, steepestDescentTakeNSteps, toUserUnits
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Field Detail
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atomTypes
private static javajs.util.Lst<java.lang.String[]> atomTypes
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ffParams
private java.util.Map<java.lang.Object,java.lang.Object> ffParams
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uff2DParams
private static java.util.Map<java.lang.Object,java.lang.Object> uff2DParams
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uffParams
private static java.util.Map<java.lang.Object,java.lang.Object> uffParams
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bsAromatic
private javajs.util.BS bsAromatic
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is2D
private boolean is2D
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TOKEN_ELEMENT_ONLY
private static final int TOKEN_ELEMENT_ONLY
- See Also:
- Constant Field Values
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TOKEN_ELEMENT_CHARGED
private static final int TOKEN_ELEMENT_CHARGED
- See Also:
- Constant Field Values
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TOKEN_ELEMENT_CONNECTED
private static final int TOKEN_ELEMENT_CONNECTED
- See Also:
- Constant Field Values
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TOKEN_AROMATIC
private static final int TOKEN_AROMATIC
- See Also:
- Constant Field Values
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TOKEN_ELEMENT_SP
private static final int TOKEN_ELEMENT_SP
- See Also:
- Constant Field Values
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TOKEN_ELEMENT_ALLYLIC
private static final int TOKEN_ELEMENT_ALLYLIC
- See Also:
- Constant Field Values
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PT_ELEMENT
private static final int PT_ELEMENT
- See Also:
- Constant Field Values
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PT_CHARGE
private static final int PT_CHARGE
- See Also:
- Constant Field Values
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PT_CONNECT
private static final int PT_CONNECT
- See Also:
- Constant Field Values
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tokenTypes
private static final T[][] tokenTypes
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Constructor Detail
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ForceFieldUFF
public ForceFieldUFF(Minimizer minimizer, boolean isQuick)
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Method Detail
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clear
public void clear()
- Specified by:
clear
in classForceField
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setModel
public boolean setModel(javajs.util.BS bsElements, int elemnoMax) throws JmolAsyncException
- Specified by:
setModel
in classForceField
- Throws:
JmolAsyncException
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setAtomTypes
private void setAtomTypes(javajs.util.BS bsElements, int elemnoMax)
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getSearch
private javajs.util.BS getSearch(java.lang.String smarts, int elemnoMax, javajs.util.BS bsElements)
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getParameters
private java.util.Map<java.lang.Object,java.lang.Object> getParameters()
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getAtomTypes
private javajs.util.Lst<java.lang.String[]> getAtomTypes() throws JmolAsyncException
- Throws:
JmolAsyncException
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