Class StrucAligParameters


  • public class StrucAligParameters
    extends java.lang.Object
    A class that contains all the parameters of the structure alignment algorithm.
    Since:
    1.5
    Version:
    %I% %G%
    Author:
    Andreas Prlic
    • Constructor Detail

      • StrucAligParameters

        public StrucAligParameters()
    • Method Detail

      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object
      • 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 java.lang.String[] getUsedAtomNames()
      • setUsedAtomNames

        public void setUsedAtomNames​(java.lang.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)