Package pl.poznan.put.structure.formats
Class CombinedStrandFromPdb
- java.lang.Object
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- pl.poznan.put.structure.formats.AbstractCombinedStrand
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- pl.poznan.put.structure.formats.CombinedStrandFromPdb
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- 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.
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Constructor Summary
Constructors Constructor Description CombinedStrandFromPdb()
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Method Summary
All Methods Instance Methods Abstract Methods Concrete Methods Modifier and Type Method Description List<DotBracketFromPdb>combineStrands(List<ClassifiedBasePair> unused)Combines strands which are connected via canonical or non-canonical base pairs.booleancontains(PdbResidueIdentifier residueIdentifier)Checks if this structure contains a mapping for the given residue identifier.PdbResidueIdentifieridentifier(DotBracketSymbol symbol)Maps the given dot-bracket symbol to its corresponding residue identifier.Set<PdbResidueIdentifier>identifierSet()protected abstract List<Strand>inputStrands()protected abstract Map<DotBracketSymbol,PdbResidueIdentifier>inputSymbolToResidue()protected org.apache.commons.collections4.BidiMap<DotBracketSymbol,PdbResidueIdentifier>mapping()intoriginalIndex(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()DotBracketSymbolsymbol(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 java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface pl.poznan.put.structure.formats.DotBracket
combineStrands, containsMissing, findStrand, length, missingInternal, missingTerminal, pseudoknotOrder, sequence, sequence, structure, structure, toStringWithStrands
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Method Detail
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inputStrands
@Parameter(order=1) protected abstract List<Strand> inputStrands()
- Specified by:
inputStrandsin classAbstractCombinedStrand- Returns:
- The list of input strands.
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symbols
@Lazy public List<DotBracketSymbol> symbols()
- Specified by:
symbolsin interfaceDotBracket- Overrides:
symbolsin classAbstractCombinedStrand- Returns:
- The list of dot-bracket symbols.
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strands
@Lazy public List<Strand> strands()
- Specified by:
strandsin interfaceDotBracket- Overrides:
strandsin classAbstractCombinedStrand- Returns:
- The list of strands.
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inputSymbolToResidue
@Parameter(order=2) protected abstract Map<DotBracketSymbol,PdbResidueIdentifier> inputSymbolToResidue()
- Returns:
- The mapping of dot-bracket symbols with corresponding PDB identifiers.
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originalIndex
public final int originalIndex(DotBracketSymbol symbol)
Description copied from interface:DotBracketReturns the index of a dot-bracket symbol according to some external source like PDB numbering.- Specified by:
originalIndexin interfaceDotBracket- 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).
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pairs
@Lazy @Auxiliary public Map<DotBracketSymbol,DotBracketSymbol> pairs()
- Specified by:
pairsin interfaceDotBracket
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identifier
public final PdbResidueIdentifier identifier(DotBracketSymbol symbol)
Description copied from interface:DotBracketFromPdbMaps the given dot-bracket symbol to its corresponding residue identifier.- Specified by:
identifierin interfaceDotBracketFromPdb- Parameters:
symbol- The symbol to look for.- Returns:
- The PDB residue identifier.
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symbol
public final DotBracketSymbol symbol(PdbResidueIdentifier residueIdentifier)
Description copied from interface:DotBracketFromPdbMaps the given residue identifier to its corresponding dot-bracket symbol.- Specified by:
symbolin interfaceDotBracketFromPdb- Parameters:
residueIdentifier- The residue identifier to look for.- Returns:
- The dot-bracket symbol.
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contains
public final boolean contains(PdbResidueIdentifier residueIdentifier)
Description copied from interface:DotBracketFromPdbChecks if this structure contains a mapping for the given residue identifier.- Specified by:
containsin interfaceDotBracketFromPdb- Parameters:
residueIdentifier- The residue identifier to check.- Returns:
- True, if there is a mapping for the given residue identifier.
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combineStrands
public final List<DotBracketFromPdb> combineStrands(List<ClassifiedBasePair> unused)
Description copied from interface:DotBracketFromPdbCombines strands which are connected via canonical or non-canonical base pairs.- Specified by:
combineStrandsin interfaceDotBracketFromPdb- Parameters:
unused- The list of non-canonical base pairs to take into account.- Returns:
- The list of dot-bracket structures from the combined strands.
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identifierSet
public final Set<PdbResidueIdentifier> identifierSet()
- Specified by:
identifierSetin interfaceDotBracketFromPdb- Returns:
- The set of residue identifiers used in this structure.
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symbolToResidue
@Lazy @Auxiliary protected Map<DotBracketSymbol,PdbResidueIdentifier> symbolToResidue()
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mapping
@Lazy @Auxiliary protected org.apache.commons.collections4.BidiMap<DotBracketSymbol,PdbResidueIdentifier> mapping()
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