Package pl.poznan.put.structure.formats

Class DefaultDotBracketFromPdb

java.lang.Object

pl.poznan.put.structure.formats.DefaultDotBracketFromPdb

All Implemented Interfaces:

DotBracket, DotBracketFromPdb

Direct Known Subclasses:

ImmutableDefaultDotBracketFromPdb

@Immutable
public abstract class DefaultDotBracketFromPdb
extends Object
implements DotBracketFromPdb

A default implementation of a dot-bracket structure which is mapped to data from 3D coordinates.

Constructor Summary

Constructors

Constructor	Description
DefaultDotBracketFromPdb()

Method Summary

Modifier and Type	Method	Description
protected List<List<Strand>>	candidatesToCombine()
List<DotBracket>	combineStrands()	Combines strands which share a base pair into a new dot-bracket instance and returns a list of those.
List<DotBracketFromPdb>	combineStrands(List<ClassifiedBasePair> nonCanonical)	Combines strands which are connected via canonical or non-canonical base pairs.
boolean	contains(PdbResidueIdentifier residueIdentifier)	Checks if this structure contains a mapping for the given residue identifier.
PdbResidueIdentifier	identifier(DotBracketSymbol symbol)	Maps the given dot-bracket symbol to its corresponding residue identifier.
abstract PdbModel	model()
int	originalIndex(DotBracketSymbol symbol)	Returns the index of a dot-bracket symbol according to some external source like PDB numbering.
Map<DotBracketSymbol,DotBracketSymbol>	pairs()
protected Map<PdbResidueIdentifier,DotBracketSymbol>	residueToSymbol()
abstract String	sequence()
List<Strand>	strands()
abstract String	structure()
DotBracketSymbol	symbol(PdbResidueIdentifier residueIdentifier)	Maps the given residue identifier to its corresponding dot-bracket symbol.
List<DotBracketSymbol>	symbols()
protected Map<DotBracketSymbol,PdbResidueIdentifier>	symbolToResidue()
protected DefaultDotBracketFromPdb	validate()

Methods inherited from class java.lang.Object

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

Methods inherited from interface pl.poznan.put.structure.formats.DotBracket

containsMissing, findStrand, length, missingInternal, missingTerminal, pseudoknotOrder, sequence, structure, symbols, toStringWithStrands

Methods inherited from interface pl.poznan.put.structure.formats.DotBracketFromPdb

identifierSet

Constructor Detail

DefaultDotBracketFromPdb

public DefaultDotBracketFromPdb()

Method Detail

model

@Parameter(order=3)
public abstract PdbModel model()

combineStrands

public final List<DotBracket> combineStrands()

Description copied from interface: DotBracket

Combines strands which share a base pair into a new dot-bracket instance and returns a list of those.

Specified by:

combineStrands in interface DotBracket

Returns:

The list of dot-bracket instances, each containing strands which only pair with each other.

originalIndex

public final int originalIndex(DotBracketSymbol symbol)

Description copied from interface: DotBracket

Returns the index of a dot-bracket symbol according to some external source like PDB numbering.

Specified by:

originalIndex in interface DotBracket

Parameters:

symbol - Dot-bracket symbol for which the original index is sought.

Returns:

An index which reflects the numbering in real structure (e.g. PDB).

strands

@Default
@Auxiliary
public List<Strand> strands()

Specified by:

strands in interface DotBracket

Returns:

The list of strands.

sequence

@Parameter(order=1)
public abstract String sequence()

Specified by:

sequence in interface DotBracket

Returns:

The sequence of nucleotides.

structure

@Parameter(order=2)
public abstract String structure()

Specified by:

structure in interface DotBracket

Returns:

The sequence of dots and brackets representing paired and unpaired residues.

pairs

@Lazy
@Auxiliary
public Map<DotBracketSymbol,DotBracketSymbol> pairs()

Specified by:

pairs in interface DotBracket

identifier

public final PdbResidueIdentifier identifier(DotBracketSymbol symbol)

Description copied from interface: DotBracketFromPdb

Maps the given dot-bracket symbol to its corresponding residue identifier.

Specified by:

identifier in interface DotBracketFromPdb

Parameters:

symbol - The symbol to look for.

Returns:

The PDB residue identifier.

symbol

public final DotBracketSymbol symbol(PdbResidueIdentifier residueIdentifier)

Description copied from interface: DotBracketFromPdb

Maps the given residue identifier to its corresponding dot-bracket symbol.

Specified by:

symbol in interface DotBracketFromPdb

Parameters:

residueIdentifier - The residue identifier to look for.

Returns:

The dot-bracket symbol.

contains

public final boolean contains(PdbResidueIdentifier residueIdentifier)

Description copied from interface: DotBracketFromPdb

Checks if this structure contains a mapping for the given residue identifier.

Specified by:

contains in interface DotBracketFromPdb

Parameters:

residueIdentifier - The residue identifier to check.

Returns:

True, if there is a mapping for the given residue identifier.

combineStrands

public final List<DotBracketFromPdb> combineStrands(List<ClassifiedBasePair> nonCanonical)

Description copied from interface: DotBracketFromPdb

Combines strands which are connected via canonical or non-canonical base pairs.

Specified by:

combineStrands in interface DotBracketFromPdb

Parameters:

nonCanonical - The list of non-canonical base pairs to take into account.

Returns:

The list of dot-bracket structures from the combined strands.

residueToSymbol

@Lazy
protected Map<PdbResidueIdentifier,DotBracketSymbol> residueToSymbol()

symbolToResidue

@Lazy
protected Map<DotBracketSymbol,PdbResidueIdentifier> symbolToResidue()

validate

@Check
protected DefaultDotBracketFromPdb validate()

symbols

public List<DotBracketSymbol> symbols()

Specified by:

symbols in interface DotBracket

Returns:

The list of dot-bracket symbols.

candidatesToCombine

protected final List<List<Strand>> candidatesToCombine()