org.biojava.bio.structure.align
Class StrucAligParameters
java.lang.Object
org.biojava.bio.structure.align.StrucAligParameters
public class StrucAligParameters
- extends Object
StrucAligParameters
public StrucAligParameters()
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()
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)