meshi.energy.sideChainModelingSolvate
Class SideChainSolvateParametersList

java.lang.Object
  java.util.AbstractCollection<E>
      java.util.AbstractList<E>
          java.util.ArrayList
              meshi.energy.sideChainModelingSolvate.SideChainSolvateParametersList

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Iterable, java.util.Collection, java.util.List, java.util.RandomAccess, Parameters

public class SideChainSolvateParametersList
extends java.util.ArrayList
implements Parameters

This class is a truncated form of the corresponding class in the "meshi.energy.solvate" package. It was designed solely for accelerating the application SCMOD (concurrent sidechain modeling), and should not be used for other purposes. Please do not use it!

See Also:

Serialized Form

Field Summary

int[]	atomicTypeConverter
Spline1D[]	atomTypeSplines
double[][]	Cend
double[][]	Cp1
double[][]	Cp2
double[][]	CvalAtp1
double[][]	CvalAtp2
double[][]	HBend
double[][]	HBp1
double[][]	HBp2
double[][]	HBvalAtp1
double[][]	HBvalAtp2
double	maxEnd
int	NTsai

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

SideChainSolvateParametersList(java.lang.String[] parameterFiles)
The parameter to the constructor is an array of 12 Strings, giving the 12 files required as parameters.

Method Summary

Parameters	createParameters(java.lang.String s)
Parameters	parameters(java.lang.Object obj)
private void	readSigmoidValueFile(double[][] ar, java.lang.String filename)

Methods inherited from class java.util.ArrayList

add, add, addAll, addAll, clear, clone, contains, ensureCapacity, get, indexOf, isEmpty, lastIndexOf, remove, remove, removeRange, set, size, toArray, toArray, trimToSize

Methods inherited from class java.util.AbstractList

equals, hashCode, iterator, listIterator, listIterator, subList

Methods inherited from class java.util.AbstractCollection

containsAll, removeAll, retainAll, toString

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.List

containsAll, equals, hashCode, iterator, listIterator, listIterator, removeAll, retainAll, subList

Field Detail

NTsai

public final int NTsai

See Also:

Constant Field Values

atomicTypeConverter

public final int[] atomicTypeConverter

maxEnd

public final double maxEnd

atomTypeSplines

public final Spline1D[] atomTypeSplines

Cend

public final double[][] Cend

Cp1

public final double[][] Cp1

Cp2

public final double[][] Cp2

CvalAtp1

public final double[][] CvalAtp1

CvalAtp2

public final double[][] CvalAtp2

HBend

public final double[][] HBend

HBp1

public final double[][] HBp1

HBp2

public final double[][] HBp2

HBvalAtp1

public final double[][] HBvalAtp1

HBvalAtp2

public final double[][] HBvalAtp2

Constructor Detail

SideChainSolvateParametersList

public SideChainSolvateParametersList(java.lang.String[] parameterFiles)

The parameter to the constructor is an array of 12 Strings, giving the 12 files required as parameters. See the MeshiPotential class for a detailed list.

Method Detail

createParameters

public Parameters createParameters(java.lang.String s)

parameters

public Parameters parameters(java.lang.Object obj)

readSigmoidValueFile

private void readSigmoidValueFile(double[][] ar,
                                  java.lang.String filename)