Package org.biojava.nbio.structure.basepairs

Class TertiaryBasePairParameters

java.lang.Object

org.biojava.nbio.structure.basepairs.BasePairParameters

org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters

All Implemented Interfaces:

Serializable

public class TertiaryBasePairParameters
extends BasePairParameters

This class also finds the base pairing and base-pair step parameters but has a broader definition of a base pair so that non-canonical-WC base pairs will be detected and reported. This is useful for RNA that has folded into different regions, and for higher-order DNA structures. Intra-strand pairings are considered in this class (but in not the base class or MismatchedBasePairParameters class)

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_STAGGER

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
TertiaryBasePairParameters(Structure structure, boolean RNA, boolean removeDups)

Method Summary

Modifier and Type	Method	Description
List<Pair<Group>>	findPairs(List<Chain> chains)	This is an alternative implementation of findPair() that looks for anything that would fit the criteria for a base-pair, useful for the context of tertiary structure of RNA.
double	getMaxPropeller()	This method returns the maximum propeller twist 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.
void	setMaxPropeller(double maxPropeller)	This method sets the maximum propeller 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

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

Constructor Details

TertiaryBasePairParameters

public TertiaryBasePairParameters(Structure structure,
 boolean RNA,
 boolean removeDups)

Method Details

findPairs

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

This is an alternative implementation of findPair() that looks for anything that would fit the criteria for a base-pair, useful for the context of tertiary structure of RNA. Intra-strand base pairs are found with this algorithm.

Overrides:

findPairs in class BasePairParameters

Parameters:

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

Returns:

A list of the Pair of groups that match the base pair criteria, including intra-strand 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 stagger (in Å) 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 stagger (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