Package org.biojava.nbio.structure.align.ce

Class CeParameters

java.lang.Object

org.biojava.nbio.structure.align.ce.CeParameters

All Implemented Interfaces:

ConfigStrucAligParams

Direct Known Subclasses:

CECPParameters, CESymmParameters, OptimalCECPParameters

public class CeParameters
extends Object
implements ConfigStrucAligParams

Contains the parameters that can be sent to CE

Author:

Andreas Prlic

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	CeParameters.ScoringStrategy

Field Summary

Fields

Modifier and Type	Field	Description
protected static double	DEFAULT_GAP_EXTENSION
protected static double	DEFAULT_GAP_OPEN
protected static double	DEFAULT_oRmsdThr
protected static String	DEFAULT_SUBSTITUTION_MATRIX
protected static double	DISTANCE_INCREMENT
protected double	distanceIncrement
protected double	gapExtension
protected double	gapOpen
protected int	maxGapSize
protected int	maxNrIterationsForOptimization
protected double	maxOptRMSD
protected double	oRmsdThr
protected double	rmsdThr
protected double	rmsdThrJoin
protected CeParameters.ScoringStrategy	scoringStrategy
protected double	seqWeight
protected boolean	showAFPRanges
protected int	sideChainScoringType
protected SubstitutionMatrix<AminoAcidCompound>	substitutionMatrix
protected int	winSize

Constructor Summary

Constructors

Constructor	Description
CeParameters()

Method Summary

Modifier and Type	Method	Description
Double	getDistanceIncrement()
Double	getGapExtension()
Double	getGapOpen()
Integer	getMaxGapSize()	the Max gap size parameter G . default is 30, which was described to obtained empirically in the CE paper.
int	getMaxNrIterationsForOptimization()	Get the maximum nr of times the (slow) optimiziation of alignment should iterate.
Double	getMaxOptRMSD()	Returns the maximum RMSD cutoff to be applied during alignment optimization (default: 99 = unlimited)
Double	getORmsdThr()	Get the Original RMSD threshold from which the alignment optimization is started
Double	getRmsdThr()	RMSD Threshold
Double	getRmsdThrJoin()	RMSD threshold for joining of AFPs
CeParameters.ScoringStrategy	getScoringStrategy()
double	getSeqWeight()	Should sequence conservation be considered as part of the alignment?
SubstitutionMatrix<AminoAcidCompound>	getSubstitutionMatrix()	Sets the substitution matrix to be used for influencing the alignment with sequence conservation information.
List<String>	getUserConfigHelp()	The help text for each of these parameters.
List<String>	getUserConfigParameterNames()	The labels to be displayed to the user for each parameter
List<String>	getUserConfigParameters()	get the list of parameters that the user can change through the user interface.
List<Class>	getUserConfigTypes()	Get the data types of the parameters
Integer	getWinSize()	The window size to look at
boolean	isOptimizeAlignment()	Whether the CE algorithm should extend the best found trace with dynamic programming, while keeping RMSD at about the same level.
boolean	isShowAFPRanges()
void	reset()	Set the parameters to the default.
void	setDistanceIncrement(Double distanceIncrement)
void	setGapExtension(Double gapExtension)
void	setGapOpen(Double gapOpen)
void	setMaxGapSize(Integer maxGapSize)	Set the Max gap size parameter.
void	setMaxNrIterationsForOptimization(int maxNrIterationsForOptimization)	Set the maximum nr of times the (slow) optimiziation of alignment should iterate.
void	setMaxOptRMSD(Double param)	set the maximum RMSD cutoff to be applied during alignment optimization.
void	setOptimizeAlignment(boolean optimizeAlignment)	Whether the CE algorithm should extend the best found trace with dynamic programming, while keeping RMSD at about the same level.
void	setORmsdThr(Double oRmsdThr)	Set the Original RMSD threshold from which the alignment optimization is started
void	setRmsdThr(Double rmsdThr)
void	setRmsdThrJoin(Double rmsdThrJoin)
void	setScoringStrategy(CeParameters.ScoringStrategy scoringStrategy)	Set the scoring strategy to use. 0 is default CE scoring scheme. 1 uses Side chain orientation.
void	setSeqWeight(double seqWeight)	Should sequence conservation be considered as part of the alignment?
void	setShowAFPRanges(boolean showAFPRanges)
void	setSubstitutionMatrix(SubstitutionMatrix<AminoAcidCompound> substitutionMatrix)	Sets the substitution matrix to be used for influencing the alignment with sequence conservation information.
void	setWinSize(Integer winSize)
String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

winSize

protected int winSize

rmsdThr

protected double rmsdThr

rmsdThrJoin

protected double rmsdThrJoin

maxOptRMSD

protected double maxOptRMSD

scoringStrategy

protected CeParameters.ScoringStrategy scoringStrategy

maxGapSize

protected int maxGapSize

showAFPRanges

protected boolean showAFPRanges

sideChainScoringType

protected int sideChainScoringType

DEFAULT_GAP_OPEN

protected static final double DEFAULT_GAP_OPEN

See Also:

Constant Field Values

DEFAULT_GAP_EXTENSION

protected static final double DEFAULT_GAP_EXTENSION

See Also:

Constant Field Values

DISTANCE_INCREMENT

protected static final double DISTANCE_INCREMENT

See Also:

Constant Field Values

DEFAULT_oRmsdThr

protected static final double DEFAULT_oRmsdThr

See Also:

Constant Field Values

DEFAULT_SUBSTITUTION_MATRIX

protected static final String DEFAULT_SUBSTITUTION_MATRIX

See Also:

Constant Field Values

gapOpen

protected double gapOpen

gapExtension

protected double gapExtension

distanceIncrement

protected double distanceIncrement

oRmsdThr

protected double oRmsdThr

maxNrIterationsForOptimization

protected int maxNrIterationsForOptimization

substitutionMatrix

protected SubstitutionMatrix<AminoAcidCompound> substitutionMatrix

seqWeight

protected double seqWeight

Constructor Detail

CeParameters

public CeParameters()

Method Detail

toString

public String toString()

Overrides:

toString in class Object

reset

public void reset()

Description copied from interface: ConfigStrucAligParams

Set the parameters to the default.

Specified by:

reset in interface ConfigStrucAligParams

getWinSize

public Integer getWinSize()

The window size to look at

Returns:

window size

setWinSize

public void setWinSize(Integer winSize)

getRmsdThr

public Double getRmsdThr()

RMSD Threshold

Returns:

RMSD threshold

setRmsdThr

public void setRmsdThr(Double rmsdThr)

getRmsdThrJoin

public Double getRmsdThrJoin()

RMSD threshold for joining of AFPs

Returns:

rmsd threshold

setRmsdThrJoin

public void setRmsdThrJoin(Double rmsdThrJoin)

getScoringStrategy

public CeParameters.ScoringStrategy getScoringStrategy()

setScoringStrategy

public void setScoringStrategy(CeParameters.ScoringStrategy scoringStrategy)

Set the scoring strategy to use. 0 is default CE scoring scheme. 1 uses Side chain orientation.

Parameters:

scoringStrategy -

setMaxGapSize

public void setMaxGapSize(Integer maxGapSize)

Set the Max gap size parameter. Default 30. For unlimited gaps set to -1

Parameters:

maxGapSize -

getMaxGapSize

public Integer getMaxGapSize()

the Max gap size parameter G . default is 30, which was described to obtained empirically in the CE paper. the larger the max gap size, the longer the compute time, but in same cases drastically improved results. Set to -1 for unlimited gap size.

Returns:

max gap size parameter

getUserConfigHelp

public List<String> getUserConfigHelp()

Description copied from interface: ConfigStrucAligParams

The help text for each of these parameters.

Specified by:

getUserConfigHelp in interface ConfigStrucAligParams

Returns:

help strings

getUserConfigParameters

public List<String> getUserConfigParameters()

Description copied from interface: ConfigStrucAligParams

get the list of parameters that the user can change through the user interface. Parameter names are the same names as the corresponding Get/Set methods.

Specified by:

getUserConfigParameters in interface ConfigStrucAligParams

Returns:

list of parameters

getUserConfigParameterNames

public List<String> getUserConfigParameterNames()

Description copied from interface: ConfigStrucAligParams

The labels to be displayed to the user for each parameter

Specified by:

getUserConfigParameterNames in interface ConfigStrucAligParams

Returns:

list of parameter names

getUserConfigTypes

public List<Class> getUserConfigTypes()

Description copied from interface: ConfigStrucAligParams

Get the data types of the parameters

Specified by:

getUserConfigTypes in interface ConfigStrucAligParams

Returns:

list of parameter classes

isShowAFPRanges

public boolean isShowAFPRanges()

Returns:

whether information about AFPs should be printed

setShowAFPRanges

public void setShowAFPRanges(boolean showAFPRanges)

setMaxOptRMSD

public void setMaxOptRMSD(Double param)

set the maximum RMSD cutoff to be applied during alignment optimization. (default: 99 = unlimited)

Parameters:

param - maxOptRMSD

getMaxOptRMSD

public Double getMaxOptRMSD()

Returns the maximum RMSD cutoff to be applied during alignment optimization (default: 99 = unlimited)

Returns:

maxOptRMSD

getGapOpen

public Double getGapOpen()

setGapOpen

public void setGapOpen(Double gapOpen)

getGapExtension

public Double getGapExtension()

setGapExtension

public void setGapExtension(Double gapExtension)

getDistanceIncrement

public Double getDistanceIncrement()

setDistanceIncrement

public void setDistanceIncrement(Double distanceIncrement)

getORmsdThr

public Double getORmsdThr()

Get the Original RMSD threshold from which the alignment optimization is started

Returns:

oRMSDThreshold

setORmsdThr

public void setORmsdThr(Double oRmsdThr)

Set the Original RMSD threshold from which the alignment optimization is started

Parameters:

oRmsdThr - the threshold

getMaxNrIterationsForOptimization

public int getMaxNrIterationsForOptimization()

Get the maximum nr of times the (slow) optimiziation of alignment should iterate. Default: unlimited

Parameters:

maxNrIterationsForOptimization -

setMaxNrIterationsForOptimization

public void setMaxNrIterationsForOptimization(int maxNrIterationsForOptimization)

Set the maximum nr of times the (slow) optimiziation of alignment should iterate. Default: unlimited

Parameters:

maxNrIterationsForOptimization -

getSeqWeight

public double getSeqWeight()

Should sequence conservation be considered as part of the alignment? If yes, this weight factor allows to determine how much. By default this is set to 0, meaning no contribution of the sequence alignment score.

Returns:

seqWeight the weight factor (default 0)

setSeqWeight

public void setSeqWeight(double seqWeight)

Should sequence conservation be considered as part of the alignment? If yes, this weight factor allows to determine how much. By default this is set to 0, meaning no contribution of the sequence alignment score.

Parameters:

seqWeight - the weight factor (default 0)

getSubstitutionMatrix

public SubstitutionMatrix<AminoAcidCompound> getSubstitutionMatrix()

Sets the substitution matrix to be used for influencing the alignment with sequence conservation information. Default: SDM matrix (Prlic et al 2000)

Returns:

substitutionMatrix

setSubstitutionMatrix

public void setSubstitutionMatrix(SubstitutionMatrix<AminoAcidCompound> substitutionMatrix)

Sets the substitution matrix to be used for influencing the alignment with sequence conservation information. Default: SDM matrix (Prlic et al 2000)

Parameters:

substitutionMatrix -

isOptimizeAlignment

public boolean isOptimizeAlignment()

Whether the CE algorithm should extend the best found trace with dynamic programming, while keeping RMSD at about the same level. This is useful for edge cases with remote homology, but can be slow for large structures.

Returns:

optimizeAlignment

setOptimizeAlignment

public void setOptimizeAlignment(boolean optimizeAlignment)

Whether the CE algorithm should extend the best found trace with dynamic programming, while keeping RMSD at about the same level. This is useful for edge cases with remote homology, but can be slow for large structures.

Parameters:

optimizeAlignment -