Package org.biojava.nbio.structure.align

Class StrucAligParameters

java.lang.Object

org.biojava.nbio.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

Constructors

Constructor	Description
StrucAligParameters()

Method Summary

Modifier and Type	Method	Description
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. - particular for large structures this increases calc. time a lot.
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 Details

StrucAligParameters

public 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)