BasePairParameters (biojava-structure 5.4.0 API)

java.lang.Object
- org.biojava.nbio.structure.basepairs.BasePairParameters

All Implemented Interfaces:

java.io.Serializable

Direct Known Subclasses:

MismatchedBasePairParameters, TertiaryBasePairParameters
```
public class BasePairParameters
extends java.lang.Object
implements java.io.Serializable
```
This module calculates the el Hassan-Calladine Base Pairing and Base-pair Step Parameters for any nucleic acid containing structure that has the information about the core base-pair rings. Citation: https://www.ncbi.nlm.nih.gov/pubmed/11601858 The method that is usually overridden is findPairs(), this base implementation is used for a large-scale analysis of the most proper helical regions in almost 4000 protein-DNA structures, almost 2000 structures containing only DNA, or almost 1300 structures containing only RNA. (as of 7/2017). Those who study tertiary structures for RNA folding should use the TertiaryBasePairParameters, because this base class is only looking for base pairs between separate strands that exactly line up. To relax the lining up policy and allow for non-canonical base pairs, use the MismatchedBasePairParameters class, which will not consider intra-strand base pairing.

Since:

5.0.0

Author:

Luke Czapla

See Also:

Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`protected static java.lang.String[]`	`BASE_LIST_DNA`
`protected static java.lang.String[]`	`BASE_LIST_RNA`
`protected static java.util.Map<java.lang.String,java.lang.Integer>`	`BASE_MAP`
`protected boolean`	`canonical`
`protected boolean`	`nonredundant`
`protected java.util.List<java.lang.String>`	`pairingNames`
`protected double[][]`	`pairingParameters`
`protected double[]`	`pairParameters`
`protected java.lang.String`	`pairSequence`
`protected java.util.List<javax.vecmath.Matrix4d>`	`referenceFrames`
`protected static java.util.Map<java.lang.Integer,java.util.List<java.lang.String>>`	`RING_MAP`
`static java.lang.String[]`	`STANDARD_BASES`
`protected double[][]`	`stepParameters`
`protected Structure`	`structure`
`protected boolean`	`useRNA`

Constructor Summary

Constructors
Constructor and Description
`BasePairParameters(Structure structure)` This constructor takes a Structure object, finds base pair and base-pair step parameters for double-helical regions within the structure for only canonical DNA pairs.
`BasePairParameters(Structure structure, boolean useRNA)` This constructor takes a Structure object, and whether to use the RNA standard bases.
`BasePairParameters(Structure structure, boolean useRNA, boolean removeDups)` This constructor takes a Structure object, whether to use RNA, and whether to remove duplicate sequences.
`BasePairParameters(Structure structure, boolean useRNA, boolean removeDups, boolean canonical)` This constructor takes a Structure object, finds base pair and base-pair step parameters for double-helical regions within the structure.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`BasePairParameters`	`analyze()` This method is the main function call to extract all step parameters, pairing parameters, and sequence information from the Structure object provided to the constructor.
`javax.vecmath.Matrix4d`	`basePairReferenceFrame(Pair<Group> pair)` This method calculates the central frame (4x4 transformation matrix) of a single base pair.
`static double[]`	`calculateTp(javax.vecmath.Matrix4d input)` This method calculates pairing and step parameters from 4x4 transformation matrices (used internally) that comes out as a Matrix4d.
`protected static char`	`complementBase(char base, boolean RNA)` This method returns the complement of a base.
`java.util.List<Pair<Group>>`	`findPairs(java.util.List<Chain> chains)` This method performs a search for base pairs in the structure.
`java.lang.Double`	`getBuckle(int bp)` This method returns the buckle in degrees for the given base pair
`int`	`getLength()` This method returns the total number of base pairs that were found, used after the call to analyze().
`java.util.List<Chain>`	`getNucleicChains(boolean removeDups)` This method reports all the nucleic acid chains and has an option to remove duplicates if you are considering an analysis of only unique DNA or RNA helices in the Structure.
`java.lang.Double`	`getOpening(int bp)` This method returns the opening in degrees for the given base pair
`java.util.List<java.lang.String>`	`getPairingNames()` This method returns the names of the pairs in terms of A, G, T/U, and C for each base pair group in the list.
`double[][]`	`getPairingParameters()` This method reports all the pair parameters, in the order of: buckle, propeller, opening (in degrees), shear, stagger, stretch (in Å).
`java.lang.String`	`getPairSequence()` This method returns the primary strand's sequence where parameters were found.
`java.lang.Double`	`getPropeller(int bp)` This method returns the propeller ("propeller-twist") in degrees for the given base pair
`java.util.List<javax.vecmath.Matrix4d>`	`getReferenceFrames()`
`java.lang.Double`	`getRise(int bp)` This method returns the rise for the given base pair, relative to the one before it.
`java.lang.Double`	`getRoll(int bp)` This method returns the roll for the given base pair, relative to the one before it.
`java.lang.Double`	`getShear(int bp)` This method returns the shear in Å for the given base pair
`java.lang.Double`	`getShift(int bp)` Return the shift for the given base pair, relative to the one before it.
`java.lang.Double`	`getSlide(int bp)` This method returns the slide for the given base pair, relative to the one before it.
`java.lang.Double`	`getStagger(int bp)` This method returns the stagger in Å for the given base pair
`double[][]`	`getStepParameters()` This method reports all the base-pair step parameters, in the order of: tilt, roll, twist (in degrees), shift, slide, rise (in Å).
`java.lang.Double`	`getStretch(int bp)` This method returns the stretch in Å for the given base pair
`java.lang.Double`	`getTilt(int bp)` This method returns the tilt for the given base pair, relative to the one before it.
`java.lang.Double`	`getTwist(int bp)` This method returns the twist for the given base pair, relative to the one before it.
`protected static boolean`	`match(char a, char b, boolean RNA)` This returns true if a is the complement of b, false otherwise.
`java.lang.String`	`toString()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - STANDARD_BASES
```
public static final java.lang.String[] STANDARD_BASES
```
  - BASE_LIST_DNA
```
protected static final java.lang.String[] BASE_LIST_DNA
```
  - BASE_LIST_RNA
```
protected static final java.lang.String[] BASE_LIST_RNA
```
  - BASE_MAP
```
protected static final java.util.Map<java.lang.String,java.lang.Integer> BASE_MAP
```
  - RING_MAP
```
protected static final java.util.Map<java.lang.Integer,java.util.List<java.lang.String>> RING_MAP
```
  - structure
```
protected Structure structure
```
  - canonical
```
protected boolean canonical
```
  - useRNA
```
protected boolean useRNA
```
  - nonredundant
```
protected boolean nonredundant
```
  - pairParameters
```
protected double[] pairParameters
```
  - pairSequence
```
protected java.lang.String pairSequence
```
  - pairingParameters
```
protected double[][] pairingParameters
```
  - stepParameters
```
protected double[][] stepParameters
```
  - pairingNames
```
protected java.util.List<java.lang.String> pairingNames
```
  - referenceFrames
```
protected java.util.List<javax.vecmath.Matrix4d> referenceFrames
```
- Constructor Detail
  - BasePairParameters
```
public BasePairParameters(Structure structure,
                          boolean useRNA,
                          boolean removeDups,
                          boolean canonical)
```
    This constructor takes a Structure object, finds base pair and base-pair step parameters for double-helical regions within the structure.
    
    Parameters:
    
    structure - The already-loaded structure to analyze.
    
    useRNA - whether to look for canonical RNA pairs. By default (false) it analyzes DNA.
    
    removeDups - whether to only look for base-pair parameters for each unique sequence in the structure (if set to true)
    
    canonical - Whether to consider only Watson-Crick base pairs
  - BasePairParameters
```
public BasePairParameters(Structure structure,
                          boolean useRNA,
                          boolean removeDups)
```
    This constructor takes a Structure object, whether to use RNA, and whether to remove duplicate sequences.
    
    Parameters:
    
    structure - The already-loaded structure to analyze.
    
    useRNA - if true, the RNA standard bases will be used. Otherwise, if false, it will work on standard DNA bases.
    
    removeDups - if true, duplicate sequences will not be considered. This is for the analysis of X-ray structures from RCSB, where there may be identical or similar units.
  - BasePairParameters
```
public BasePairParameters(Structure structure,
                          boolean useRNA)
```
    This constructor takes a Structure object, and whether to use the RNA standard bases.
    
    Parameters:
    
    structure - The already-loaded structure to analyze.
    
    useRNA - if true, the RNA standard bases will be used. Otherwise, if false, it will work on standard DNA bases.
  - BasePairParameters
```
public BasePairParameters(Structure structure)
```
    This constructor takes a Structure object, finds base pair and base-pair step parameters for double-helical regions within the structure for only canonical DNA pairs.
    
    Parameters:
    
    structure - The already-loaded structure to analyze.
- Method Detail
  - analyze
```
public BasePairParameters analyze()
```
    This method is the main function call to extract all step parameters, pairing parameters, and sequence information from the Structure object provided to the constructor.
    
    Returns:
    
    This same object with the populated data, convenient for output (e.g. log.info(new BasePairParameters(structure).analyze());)
  - getLength
```
public int getLength()
```
    This method returns the total number of base pairs that were found, used after the call to analyze().
    
    Returns:
    
    An integer value, number of base pairs
  - getPairingParameters
```
public double[][] getPairingParameters()
```
    This method reports all the pair parameters, in the order of: buckle, propeller, opening (in degrees), shear, stagger, stretch (in Å).
    
    Returns:
    
    A double[][] with length equal to number of base pairs for rows, and 6 columns
  - getStepParameters
```
public double[][] getStepParameters()
```
    This method reports all the base-pair step parameters, in the order of: tilt, roll, twist (in degrees), shift, slide, rise (in Å).
    
    Returns:
    
    A double[][] with length equal to number of base pairs (the first row 0 has no step and therefore is six zeroes), and 6 columns.
  - getPairSequence
```
public java.lang.String getPairSequence()
```
    This method returns the primary strand's sequence where parameters were found. There are spaces in the string anywhere there was a break in the helix or when it goes from one helix to another helix in the structure. (the "step" is still returned)
    
    Returns:
    
    String of primary sequence with spaces between gaps and new helices.
  - getPairingNames
```
public java.util.List<java.lang.String> getPairingNames()
```
    This method returns the names of the pairs in terms of A, G, T/U, and C for each base pair group in the list. The first character is the leading strand base and the second character is the complementary base
    
    Returns:
  - getReferenceFrames
```
public java.util.List<javax.vecmath.Matrix4d> getReferenceFrames()
```
  - getBuckle
```
public java.lang.Double getBuckle(int bp)
```
    This method returns the buckle in degrees for the given base pair
    
    Parameters:
    
    bp - the number of the base pair (starting with 0)
    
    Returns:
    
    the value as a double (in degrees)
  - getPropeller
```
public java.lang.Double getPropeller(int bp)
```
    This method returns the propeller ("propeller-twist") in degrees for the given base pair
    
    Parameters:
    
    bp - the number of the base pair (starting with 0)
    
    Returns:
    
    the value as a double (in degrees)
  - getOpening
```
public java.lang.Double getOpening(int bp)
```
    This method returns the opening in degrees for the given base pair
    
    Parameters:
    
    bp - the number of the base pair (starting with 0)
    
    Returns:
    
    the value as a double (in degrees)
  - getShear
```
public java.lang.Double getShear(int bp)
```
    This method returns the shear in Å for the given base pair
    
    Parameters:
    
    bp - the number of the base pair (starting with 0)
    
    Returns:
    
    the value as a double (in Å)
  - getStretch
```
public java.lang.Double getStretch(int bp)
```
    This method returns the stretch in Å for the given base pair
    
    Parameters:
    
    bp - the number of the base pair (starting with 0)
    
    Returns:
    
    the value as a double (in Å)
  - getStagger
```
public java.lang.Double getStagger(int bp)
```
    This method returns the stagger in Å for the given base pair
    
    Parameters:
    
    bp - the number of the base pair (starting with 0)
    
    Returns:
    
    the value as a double (in Å)
  - getTilt
```
public java.lang.Double getTilt(int bp)
```
    This method returns the tilt for the given base pair, relative to the one before it.
    
    Parameters:
    
    bp - the number of the base pair (starting with 0)
    
    Returns:
    
    the value as a double (in degrees)
  - getRoll
```
public java.lang.Double getRoll(int bp)
```
    This method returns the roll for the given base pair, relative to the one before it.
    
    Parameters:
    
    bp - the number of the base pair (starting with 0)
    
    Returns:
    
    the value as a double (in degrees)
  - getTwist
```
public java.lang.Double getTwist(int bp)
```
    This method returns the twist for the given base pair, relative to the one before it.
    
    Parameters:
    
    bp - the number of the base pair (starting with 0)
    
    Returns:
    
    the value as a double (in degrees)
  - getShift
```
public java.lang.Double getShift(int bp)
```
    Return the shift for the given base pair, relative to the one before it.
    
    Parameters:
    
    bp - the number of the base pair (starting with 0)
    
    Returns:
    
    the value as a double (in Å)
  - getSlide
```
public java.lang.Double getSlide(int bp)
```
    This method returns the slide for the given base pair, relative to the one before it.
    
    Parameters:
    
    bp - the number of the base pair (starting with 0)
    
    Returns:
    
    the value as a double (in Å)
  - getRise
```
public java.lang.Double getRise(int bp)
```
    This method returns the rise for the given base pair, relative to the one before it.
    
    Parameters:
    
    bp - the number of the base pair (starting with 0)
    
    Returns:
    
    the value as a double (in Å)
  - getNucleicChains
```
public java.util.List<Chain> getNucleicChains(boolean removeDups)
```
    This method reports all the nucleic acid chains and has an option to remove duplicates if you are considering an analysis of only unique DNA or RNA helices in the Structure.
    
    Parameters:
    
    removeDups - If true, it will ignore duplicate chains
    
    Returns:
    
    A list of all the nucleic acid chains in order of the Structure
  - findPairs
```
public java.util.List<Pair<Group>> findPairs(java.util.List<Chain> chains)
```
    This method performs a search for base pairs in the structure. The criteria is alignment of sequences and the canonical base pairs of DNA or RNA. Use MismatchedBasePairParameters or TertiaryBasePairParameters for finding higher-order associations.
    
    Parameters:
    
    chains - The list of chains already found to be nucleic acids
    
    Returns:
    
    The list of corresponding Watson-Crick groups as pairs, as a Pair of nucleic acid Groups
  - basePairReferenceFrame
```
public javax.vecmath.Matrix4d basePairReferenceFrame(Pair<Group> pair)
```
    This method calculates the central frame (4x4 transformation matrix) of a single base pair.
    
    Parameters:
    
    pair - An array of the two groups that make a hypothetical pair
    
    Returns:
    
    The middle frame of the center of the base-pair formed
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class java.lang.Object
  - calculateTp
```
public static double[] calculateTp(javax.vecmath.Matrix4d input)
```
    This method calculates pairing and step parameters from 4x4 transformation matrices (used internally) that comes out as a Matrix4d.
    
    Parameters:
    
    input - the 4x4 matrix representing the transformation from strand II -> strand I or pair i to pair i+1
    
    Returns:
    
    Six parameters as double[6]
  - complementBase
```
protected static char complementBase(char base,
                                     boolean RNA)
```
    This method returns the complement of a base. (used internally)
    
    Parameters:
    
    base - The letter of the base
    
    RNA - Whether it is RNA (if false, it is DNA)
    
    Returns:
    
    The character representing the complement of the base
  - match
```
protected static boolean match(char a,
                               char b,
                               boolean RNA)
```
    This returns true if a is the complement of b, false otherwise. (used internally)
    
    Parameters:
    
    a - First letter
    
    b - Potential matching letter
    
    RNA - Whether it is RNA (if false, DNA rules are used)
    
    Returns:
    
    True if the bases are complementary.

Class BasePairParameters

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

STANDARD_BASES

BASE_LIST_DNA

BASE_LIST_RNA

BASE_MAP

RING_MAP

structure

canonical

useRNA

nonredundant

pairParameters

pairSequence

pairingParameters

stepParameters

pairingNames

referenceFrames

Constructor Detail

BasePairParameters

BasePairParameters

BasePairParameters

BasePairParameters

Method Detail

analyze

getLength

getPairingParameters

getStepParameters

getPairSequence

getPairingNames

getReferenceFrames

getBuckle

getPropeller

getOpening

getShear

getStretch

getStagger

getTilt

getRoll

getTwist

getShift

getSlide

getRise

getNucleicChains

findPairs

basePairReferenceFrame

toString

calculateTp

complementBase

match