Class StrucAligParameters

Method Details

• 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)