Package pl.poznan.put.structure.formats

Class CombinedStrandFromPdb

java.lang.Object

pl.poznan.put.structure.formats.AbstractCombinedStrand

pl.poznan.put.structure.formats.CombinedStrandFromPdb

All Implemented Interfaces:

DotBracket, DotBracketFromPdb

Direct Known Subclasses:

ImmutableCombinedStrandFromPdb

@Immutable
public abstract class CombinedStrandFromPdb
extends AbstractCombinedStrand
implements DotBracketFromPdb

A dot-bracket encoded structure made from combining one or more strands. This structure has one-to-one correspondence with a 3D structure.

Constructor Summary

Constructors

Constructor	Description
CombinedStrandFromPdb()

Method Summary

Modifier and Type	Method	Description
final List<DotBracketFromPdb>	combineStrands(List<ClassifiedBasePair> unused)	Combines strands which are connected via canonical or non-canonical base pairs.
final boolean	contains(PdbResidueIdentifier residueIdentifier)	Checks if this structure contains a mapping for the given residue identifier.
final PdbResidueIdentifier	identifier(DotBracketSymbol symbol)	Maps the given dot-bracket symbol to its corresponding residue identifier.
final Set<PdbResidueIdentifier>	identifierSet()
protected abstract List<Strand>	inputStrands()
protected abstract Map<DotBracketSymbol,PdbResidueIdentifier>	inputSymbolToResidue()
protected org.apache.commons.collections4.BidiMap<DotBracketSymbol,PdbResidueIdentifier>	mapping()
final int	originalIndex(DotBracketSymbol symbol)	Returns the index of a dot-bracket symbol according to some external source like PDB numbering.
Map<DotBracketSymbol,DotBracketSymbol>	pairs()
List<Strand>	strands()
final DotBracketSymbol	symbol(PdbResidueIdentifier residueIdentifier)	Maps the given residue identifier to its corresponding dot-bracket symbol.
List<DotBracketSymbol>	symbols()
protected Map<DotBracketSymbol,PdbResidueIdentifier>	symbolToResidue()

Methods inherited from class pl.poznan.put.structure.formats.AbstractCombinedStrand

combineStrands

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

combineStrands, containsMissing, findStrand, isIsolated, isolatedSymbols, length, missingInternal, missingTerminal, pseudoknotOrder, sequence, sequence, structure, structure, toStringWithStrands

Constructor Details

CombinedStrandFromPdb

public CombinedStrandFromPdb()

Method Details

inputStrands

@Parameter(order=1)
protected abstract List<Strand> inputStrands()

Specified by:

inputStrands in class AbstractCombinedStrand

Returns:

The list of input strands.

symbols

@Lazy
public List<DotBracketSymbol> symbols()

Specified by:

symbols in interface DotBracket

Overrides:

symbols in class AbstractCombinedStrand

Returns:

The list of dot-bracket symbols.

strands

@Lazy
public List<Strand> strands()

Specified by:

strands in interface DotBracket

Overrides:

strands in class AbstractCombinedStrand

Returns:

The list of strands.

inputSymbolToResidue

@Parameter(order=2)
protected abstract Map<DotBracketSymbol,PdbResidueIdentifier> inputSymbolToResidue()

Returns:

The mapping of dot-bracket symbols with corresponding PDB identifiers.

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).

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> unused)

Description copied from interface: DotBracketFromPdb

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

Specified by:

combineStrands in interface DotBracketFromPdb

Parameters:

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

Returns:

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

identifierSet

public final Set<PdbResidueIdentifier> identifierSet()

Specified by:

identifierSet in interface DotBracketFromPdb

Returns:

The set of residue identifiers used in this structure.

symbolToResidue

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

mapping

@Lazy
@Auxiliary
protected org.apache.commons.collections4.BidiMap<DotBracketSymbol,PdbResidueIdentifier> mapping()