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

All Methods Static Methods Instance Methods Concrete Methods
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 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)

Class StrucAligParameters

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

StrucAligParameters

Method Detail

getDefaultParameters

toString

getDBSearchParameters

getDensityCutoff

setDensityCutoff

getInitialK

setInitialK

getSeedFragmentLength

isJoinFast

setJoinFast

isJoinPlo

setJoinPlo

setSeedFragmentLength

getSeedRmsdCutoff

setSeedRmsdCutoff

isDoAngleCheck

setDoAngleCheck

isDoDensityCheck

setDoDensityCheck

isDoDistanceCheck

setDoDistanceCheck

isDoRMSCheck

setDoRMSCheck

getJoinRMSCutoff

setJoinRMSCutoff

getEvalCutoff

setEvalCutoff

getPermutationSize

setPermutationSize

getGapExtension

setGapExtension

getGapOpen

setGapOpen

getMaxIter

setMaxIter

getCreate_co

setCreate_co

reduceInitialFragments

setReduceInitialFragments

getAngleDiff

setAngleDiff

getFragCompat

setFragCompat

getMaxrefine

setMaxrefine

getUsedAtomNames

setUsedAtomNames

getFragmentLength

setFragmentLength

getDiagonalDistance

setDiagonalDistance

getDiagonalDistance2

setDiagonalDistance2

getFragmentMiniDistance

setFragmentMiniDistance