meshi.geometry
Class MatrixRow

java.lang.Object
  meshi.geometry.DistanceList
      meshi.geometry.MatrixRow

All Implemented Interfaces:

java.lang.Iterable<Distance>

Direct Known Subclasses:

MatrixRowCaOnly, MatrixRowNoImageAtoms

public class MatrixRow
extends DistanceList

Field Summary

AtomCore	atom
protected static AtomCore	atom2
protected static int	atom2number
static int	CAPACITY
private static double	d2
protected static Distance	distance
protected static int	lastEmpty
(package private) MatrixRow[]	matrix
private static DistanceMode	mode
int	number
protected double	rMax2
(package private) double	rMaxPlusBuffer2
(package private) int	searchStart
private static boolean[]	toNonBonded
private static double	x1
private static double	y1
private static double	z1

Fields inherited from class meshi.geometry.DistanceList

capacity, filter, internalArray, size

Constructor Summary

MatrixRow(AtomCore atom, MatrixRow[] matrix)

Method Summary

void	addCell(GridCell cell, DistanceList nonBondedList, java.util.ArrayList<DistanceList> energyTermsDistanceLists)
private void	insert(int number, AtomCore atom, AtomCore cellAtom, int cellAtomNumber, double d2, double dx, double dy, double dz, DistanceList nonBondedList, java.util.ArrayList<DistanceList> energyTermsDistanceLists)
Distance	search(int atom2number)
java.lang.String	toString()
void	update(DistanceList nonBondedList, java.util.ArrayList<DistanceList> energyTermsDistanceLists)

Methods inherited from class meshi.geometry.DistanceList

add, clear, get, isEmpty, iterator, size, sort, toArray

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

atom

public final AtomCore atom

number

public final int number

searchStart

int searchStart

matrix

MatrixRow[] matrix

rMax2

protected double rMax2

rMaxPlusBuffer2

double rMaxPlusBuffer2

CAPACITY

public static final int CAPACITY

See Also:

Constant Field Values

atom2number

protected static int atom2number

lastEmpty

protected static int lastEmpty

distance

protected static Distance distance

atom2

protected static AtomCore atom2

x1

private static double x1

y1

private static double y1

z1

private static double z1

d2

private static double d2

mode

private static DistanceMode mode

toNonBonded

private static boolean[] toNonBonded

Constructor Detail

MatrixRow

public MatrixRow(AtomCore atom,
                 MatrixRow[] matrix)

Method Detail

update

public void update(DistanceList nonBondedList,
                   java.util.ArrayList<DistanceList> energyTermsDistanceLists)

search

public Distance search(int atom2number)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

addCell

public void addCell(GridCell cell,
                    DistanceList nonBondedList,
                    java.util.ArrayList<DistanceList> energyTermsDistanceLists)

insert

private void insert(int number,
                    AtomCore atom,
                    AtomCore cellAtom,
                    int cellAtomNumber,
                    double d2,
                    double dx,
                    double dy,
                    double dz,
                    DistanceList nonBondedList,
                    java.util.ArrayList<DistanceList> energyTermsDistanceLists)