Package org.biojava.nbio.structure.basepairs

Class MismatchedBasePairParameters

java.lang.Object

org.biojava.nbio.structure.basepairs.BasePairParameters

org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters

All Implemented Interfaces:

Serializable

public class MismatchedBasePairParameters
extends BasePairParameters

This class allows for finding inter-strand base pairs that are not necessarily canonical Watson-Crick pairs. The implementation of findPair is different than that of the base class. This class does not consider intra-strand base pairing and for that, the TertiaryBasePairParameters class should be used.

Since:

5.0.0

Author:

Luke Czapla

See Also:

• Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
static final double	DEFAULT_MAX_PROPELLER
static final double	DEFAULT_MAX_SHEAR
static final double	DEFAULT_MAX_STAGGER
static final double	DEFAULT_MAX_STRETCH

Fields inherited from class org.biojava.nbio.structure.basepairs.BasePairParameters

BASE_LIST_DNA, BASE_LIST_RNA, BASE_MAP, canonical, nonredundant, pairingNames, pairingParameters, pairParameters, pairSequence, referenceFrames, RING_MAP, STANDARD_BASES, stepParameters, structure, useRNA

Constructor Summary

Constructors

Constructor	Description
MismatchedBasePairParameters(Structure structure, boolean RNA, boolean removeDups, boolean canonical)	This constructor is used to create the TertiaryBasePairParameters object.

Method Summary

Modifier and Type	Method	Description
List<Pair<Group>>	findPairs(List<Chain> chains)	This is an implementation for finding non-canonical base pairs when there may be missing or overhanging bases.
double	getMaxPropeller()	This method returns the maximum propeller twist between bases used as criteria for the characterization of two bases as being paired.
double	getMaxShear()	This method returns the maximum shear between bases used as criteria for the characterization of two bases as being paired.
double	getMaxStagger()	This method returns the maximum stagger between bases used as criteria for the characterization of two bases as being paired.
double	getMaxStretch()	This method returns the maximum stretch between bases used as criteria for the characterization of two bases as being paired.
void	setMaxPropeller(double maxPropeller)	This method sets the maximum propeller allowed for a base pair, prior to analyze() call
void	setMaxShear(double maxShear)	This method sets the maximum shear allowed for a base pair, prior to analyze() call
void	setMaxStagger(double maxStagger)	This method sets the maximum stagger allowed for a base pair, prior to analyze() call
void	setMaxStretch(double maxStretch)	This method sets the maximum stretch allowed for a base pair, prior to analyze() call.

Methods inherited from class org.biojava.nbio.structure.basepairs.BasePairParameters

analyze, basePairReferenceFrame, calculateTp, complementBase, getBuckle, getLength, getNucleicChains, getOpening, getPairingNames, getPairingParameters, getPairSequence, getPropeller, getReferenceFrames, getRise, getRoll, getShear, getShift, getSlide, getStagger, getStepParameters, getStretch, getTilt, getTwist, match, toString

Methods inherited from class java.lang.Object

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

Field Details

DEFAULT_MAX_STAGGER

public static final double DEFAULT_MAX_STAGGER

See Also:

• Constant Field Values

DEFAULT_MAX_PROPELLER

public static final double DEFAULT_MAX_PROPELLER

See Also:

• Constant Field Values

DEFAULT_MAX_SHEAR

public static final double DEFAULT_MAX_SHEAR

See Also:

• Constant Field Values

DEFAULT_MAX_STRETCH

public static final double DEFAULT_MAX_STRETCH

See Also:

• Constant Field Values

Constructor Details

MismatchedBasePairParameters

public MismatchedBasePairParameters(Structure structure,
 boolean RNA,
 boolean removeDups,
 boolean canonical)

This constructor is used to create the TertiaryBasePairParameters object. The parent constructors are valid as well, but for this class, it makes the most sense to specify the exact parameters for the analysis.

Parameters:

structure - The Structure to analyze

RNA - Whether to analyze RNA (if false, it will analyze DNA)

removeDups - Whether to remove duplicate sequences (useful for RCSB data with redundant units).

canonical - Whether to only consider canonical Watson-Crick base pairs. If false, any pairing will be identified as long it falls below the maximum values of stagger, shear, and stretch.

Method Details

findPairs

public List<Pair<Group>> findPairs(List<Chain> chains)

This is an implementation for finding non-canonical base pairs when there may be missing or overhanging bases.

Overrides:

findPairs in class BasePairParameters

Parameters:

chains - The list of chains already found to be nucleic acids.

Returns:

The list of the atom groups (residues) that are pairs, as a Pair of nucleic acid Groups.

getMaxStagger

public double getMaxStagger()

This method returns the maximum stagger between bases used as criteria for the characterization of two bases as being paired.

Returns:

the maximum propeller ("propeller-twist", in degrees) allowed.

setMaxStagger

public void setMaxStagger(double maxStagger)

This method sets the maximum stagger allowed for a base pair, prior to analyze() call

Parameters:

maxStagger - The maximum propeller (in Å) allowed to consider two bases paired

getMaxShear

public double getMaxShear()

This method returns the maximum shear between bases used as criteria for the characterization of two bases as being paired.

Returns:

the maximum shear (in Å) allowed.

setMaxShear

public void setMaxShear(double maxShear)

This method sets the maximum shear allowed for a base pair, prior to analyze() call

Parameters:

maxShear - The maximum shear (in Å) allowed to consider two bases paired

getMaxStretch

public double getMaxStretch()

This method returns the maximum stretch between bases used as criteria for the characterization of two bases as being paired.

Returns:

the maximum stretch (in Å) allowed.

setMaxStretch

public void setMaxStretch(double maxStretch)

This method sets the maximum stretch allowed for a base pair, prior to analyze() call.

Parameters:

maxStretch - The maximum stretch (in Å) allowed to consider two bases paired

getMaxPropeller

public double getMaxPropeller()

This method returns the maximum propeller twist between bases used as criteria for the characterization of two bases as being paired.

Returns:

the maximum propeller ("propeller-twist", in degrees) allowed.

setMaxPropeller

public void setMaxPropeller(double maxPropeller)

This method sets the maximum propeller allowed for a base pair, prior to analyze() call

Parameters:

maxPropeller - The maximum propeller ("propeller-twist", in degrees) allowed to consider two bases paired