Class Optimize.OptimizeLogger

java.lang.Object
  java.util.AbstractCollection<E>
      java.util.AbstractList<E>
          java.util.ArrayList<java.lang.String>
              meshi.util.string.StringList
                  Optimize.OptimizeLogger

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Iterable<java.lang.String>, java.util.Collection<java.lang.String>, java.util.List<java.lang.String>, java.util.RandomAccess, Logger

Enclosing class:

Optimize

private static class Optimize.OptimizeLogger
extends StringList
implements Logger

Field Summary

private CommandList	commands
private Protein	model
private java.lang.String	outFileName
private MeshiWriter	output
private Protein	reference
private boolean	referenceExists

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

Optimize.OptimizeLogger(Protein model, CommandList commands, java.lang.String nativeFileName, java.lang.String outFileName)

Method Summary

void	afterRelax(Protein target, TotalEnergy energy, java.lang.String label)
void	mcm(TotalEnergy energy, int i)
void	mcm(TotalEnergy energy, int i, java.lang.String label)

Methods inherited from class meshi.util.string.StringList

filter, filterEndsWith, filterEndsWith, filterGrep, filterGrep, filterStartsWith, filterStartsWith, lastString, print, setComment, standardSeparators, startsWith, stringParseAt, stringParseAt, stringParseAt

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

referenceExists

private boolean referenceExists

model

private Protein model

reference

private Protein reference

outFileName

private java.lang.String outFileName

commands

private CommandList commands

output

private MeshiWriter output

Constructor Detail

Optimize.OptimizeLogger

public Optimize.OptimizeLogger(Protein model,
                               CommandList commands,
                               java.lang.String nativeFileName,
                               java.lang.String outFileName)

Method Detail

afterRelax

public void afterRelax(Protein target,
                       TotalEnergy energy,
                       java.lang.String label)

mcm

public void mcm(TotalEnergy energy,
                int i,
                java.lang.String label)

mcm

public void mcm(TotalEnergy energy,
                int i)

Specified by:

mcm in interface Logger