org.biojava.bio.structure.align
Class StrucAligParameters

java.lang.Object
  extended by org.biojava.bio.structure.align.StrucAligParameters

public class StrucAligParameters
extends Object

A class that contains all the parameters of the structure alignment algorithm.

Since:
1.5
Version:
%I% %G%
Author:
Andreas Prlic

Constructor Summary
StrucAligParameters()
           
 
Method Summary
 int getAngleDiff()
           
 float getCreate_co()
           
static StrucAligParameters getDBSearchParameters()
           
static StrucAligParameters getDefaultParameters()
           
 float getDensityCutoff()
           
 int getDiagonalDistance()
           
 int getDiagonalDistance2()
           
 float getEvalCutoff()
           
 float getFragCompat()
           
 int getFragmentLength()
           
 float getFragmentMiniDistance()
           
 float getGapExtension()
           
 float getGapOpen()
           
 int getInitialK()
           
 double getJoinRMSCutoff()
           
 int getMaxIter()
           
 int getMaxrefine()
           
 int getPermutationSize()
           
 int getSeedFragmentLength()
           
 float getSeedRmsdCutoff()
           
 String[] getUsedAtomNames()
           
 boolean isDoAngleCheck()
           
 boolean isDoDensityCheck()
           
 boolean isDoDistanceCheck()
           
 boolean isDoRMSCheck()
           
 boolean isJoinFast()
           
 boolean isJoinPlo()
           
 boolean reduceInitialFragments()
          if this is set to false, the time spent to joint the initial fragments (step 2) is increased.
 void setAngleDiff(int angleDiff)
           
 void setCreate_co(float create_co)
           
 void setDensityCutoff(float densityCutoff)
           
 void setDiagonalDistance(int diagonalDistance)
           
 void setDiagonalDistance2(int diagonalDistance2)
           
 void setDoAngleCheck(boolean doAngleCheck)
           
 void setDoDensityCheck(boolean doDensityCheck)
           
 void setDoDistanceCheck(boolean doDistanceCheck)
           
 void setDoRMSCheck(boolean doRMSCheck)
           
 void setEvalCutoff(float evalCutoff)
           
 void setFragCompat(float fragCompat)
           
 void setFragmentLength(int fragmentLength)
           
 void setFragmentMiniDistance(float fragmentMiniDistance)
           
 void setGapExtension(float gapExtension)
           
 void setGapOpen(float gapOpen)
           
 void setInitialK(int initialK)
           
 void setJoinFast(boolean fastJoin)
           
 void setJoinPlo(boolean joinPlo)
           
 void setJoinRMSCutoff(double joinRMSCutoff)
           
 void setMaxIter(int maxIter)
           
 void setMaxrefine(int maxrefine)
           
 void setPermutationSize(int permutationSize)
           
 void setReduceInitialFragments(boolean reduceInitialFragments)
           
 void setSeedFragmentLength(int seedFragmentLength)
           
 void setSeedRmsdCutoff(float seedRmsdCutoff)
           
 void setUsedAtomNames(String[] usedAtomNames)
           
 String toString()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

StrucAligParameters

public StrucAligParameters()
Method Detail

getDefaultParameters

public static StrucAligParameters getDefaultParameters()

toString

public String toString()
Overrides:
toString in class Object

getDBSearchParameters

public static StrucAligParameters getDBSearchParameters()

getDensityCutoff

public float getDensityCutoff()

setDensityCutoff

public void setDensityCutoff(float densityCutoff)

getInitialK

public int getInitialK()

setInitialK

public void setInitialK(int initialK)

getSeedFragmentLength

public int getSeedFragmentLength()

isJoinFast

public boolean isJoinFast()

setJoinFast

public void setJoinFast(boolean fastJoin)

isJoinPlo

public boolean isJoinPlo()

setJoinPlo

public void setJoinPlo(boolean joinPlo)

setSeedFragmentLength

public void setSeedFragmentLength(int seedFragmentLength)

getSeedRmsdCutoff

public float getSeedRmsdCutoff()

setSeedRmsdCutoff

public void setSeedRmsdCutoff(float seedRmsdCutoff)

isDoAngleCheck

public boolean isDoAngleCheck()

setDoAngleCheck

public void setDoAngleCheck(boolean doAngleCheck)

isDoDensityCheck

public boolean isDoDensityCheck()

setDoDensityCheck

public void setDoDensityCheck(boolean doDensityCheck)

isDoDistanceCheck

public boolean isDoDistanceCheck()

setDoDistanceCheck

public void setDoDistanceCheck(boolean doDistanceCheck)

isDoRMSCheck

public boolean isDoRMSCheck()

setDoRMSCheck

public void setDoRMSCheck(boolean doRMSCheck)

getJoinRMSCutoff

public double getJoinRMSCutoff()

setJoinRMSCutoff

public void setJoinRMSCutoff(double joinRMSCutoff)

getEvalCutoff

public float getEvalCutoff()

setEvalCutoff

public void setEvalCutoff(float evalCutoff)

getPermutationSize

public int getPermutationSize()

setPermutationSize

public void setPermutationSize(int permutationSize)

getGapExtension

public float getGapExtension()

setGapExtension

public void setGapExtension(float gapExtension)

getGapOpen

public float getGapOpen()

setGapOpen

public void setGapOpen(float gapOpen)

getMaxIter

public int getMaxIter()

setMaxIter

public void setMaxIter(int maxIter)

getCreate_co

public float getCreate_co()

setCreate_co

public void setCreate_co(float create_co)

reduceInitialFragments

public boolean reduceInitialFragments()
if this is set to false, the time spent to joint the initial fragments (step 2) is increased. - particular for large structures this increases calc. time a lot. advantage: more combinations of fragments are used.

Returns:
a flag if the inital fragments should be reduced

setReduceInitialFragments

public void setReduceInitialFragments(boolean reduceInitialFragments)

getAngleDiff

public int getAngleDiff()

setAngleDiff

public void setAngleDiff(int angleDiff)

getFragCompat

public float getFragCompat()

setFragCompat

public void setFragCompat(float fragCompat)

getMaxrefine

public int getMaxrefine()

setMaxrefine

public void setMaxrefine(int maxrefine)

getUsedAtomNames

public String[] getUsedAtomNames()

setUsedAtomNames

public void setUsedAtomNames(String[] usedAtomNames)

getFragmentLength

public int getFragmentLength()

setFragmentLength

public void setFragmentLength(int fragmentLength)

getDiagonalDistance

public int getDiagonalDistance()

setDiagonalDistance

public void setDiagonalDistance(int diagonalDistance)

getDiagonalDistance2

public int getDiagonalDistance2()

setDiagonalDistance2

public void setDiagonalDistance2(int diagonalDistance2)

getFragmentMiniDistance

public float getFragmentMiniDistance()

setFragmentMiniDistance

public void setFragmentMiniDistance(float fragmentMiniDistance)