Serialized Form

Package pl.poznan.put.circular.exception

Class pl.poznan.put.circular.exception.InvalidCircularOperationException extends RuntimeException implements Serializable

Class pl.poznan.put.circular.exception.InvalidCircularValueException extends RuntimeException implements Serializable

Class pl.poznan.put.circular.exception.InvalidVectorFormatException extends RuntimeException implements Serializable

Package pl.poznan.put.pdb

Class pl.poznan.put.pdb.CifPdbIncompatibilityException extends RuntimeException implements Serializable

Class pl.poznan.put.pdb.ImmutablePdbAtomLine extends PdbAtomLine implements Serializable

Serialized Fields

alternateLocation

String alternateLocation

atomName

String atomName

chainIdentifier

String chainIdentifier

charge

String charge

elementSymbol

String elementSymbol

insertionCode

String insertionCode

occupancy

double occupancy

residueName

String residueName

residueNumber

int residueNumber

serialNumber

int serialNumber

temperatureFactor

double temperatureFactor

x

double x

y

double y

z

double z

Class pl.poznan.put.pdb.ImmutablePdbExpdtaLine extends PdbExpdtaLine implements Serializable

Serialized Fields

experimentalTechniques

List<ExperimentalTechnique> experimentalTechniques

Class pl.poznan.put.pdb.ImmutablePdbHeaderLine extends PdbHeaderLine implements Serializable

Serialized Fields

classification

String classification

depositionDate

Date depositionDate

idCode

String idCode

Class pl.poznan.put.pdb.ImmutablePdbModresLine extends PdbModresLine implements Serializable

Serialized Fields

chainIdentifier

String chainIdentifier

comment

String comment

idCode

String idCode

insertionCode

String insertionCode

residueName

String residueName

residueNumber

int residueNumber

standardResidueName

String standardResidueName

Class pl.poznan.put.pdb.ImmutablePdbNamedResidueIdentifier extends PdbNamedResidueIdentifier implements Serializable

Serialized Fields

chainIdentifier

String chainIdentifier

insertionCode

String insertionCode

oneLetterName

char oneLetterName

residueNumber

int residueNumber

Class pl.poznan.put.pdb.ImmutablePdbRemark2Line extends PdbRemark2Line implements Serializable

Serialized Fields

resolution

double resolution

Class pl.poznan.put.pdb.ImmutablePdbRemark465Line extends PdbRemark465Line implements Serializable

Serialized Fields

chainIdentifier

String chainIdentifier

insertionCode

String insertionCode

modelNumber

int modelNumber

residueName

String residueName

residueNumber

int residueNumber

Class pl.poznan.put.pdb.ImmutablePdbResidueIdentifier extends PdbResidueIdentifier implements Serializable

Serialized Fields

chainIdentifier

String chainIdentifier

insertionCode

String insertionCode

residueNumber

int residueNumber

Class pl.poznan.put.pdb.ImmutablePdbTitleLine extends PdbTitleLine implements Serializable

Serialized Fields

continuation

String continuation

title

String title

Class pl.poznan.put.pdb.PdbAtomLine extends Object implements Serializable

Class pl.poznan.put.pdb.PdbExpdtaLine extends Object implements Serializable

Class pl.poznan.put.pdb.PdbHeaderLine extends Object implements Serializable

Class pl.poznan.put.pdb.PdbModresLine extends Object implements Serializable

Class pl.poznan.put.pdb.PdbNamedResidueIdentifier extends Object implements Serializable

Class pl.poznan.put.pdb.PdbParsingException extends RuntimeException implements Serializable

Class pl.poznan.put.pdb.PdbRemark2Line extends Object implements Serializable

Class pl.poznan.put.pdb.PdbRemark465Line extends Object implements Serializable

Class pl.poznan.put.pdb.PdbResidueIdentifier extends Object implements Serializable

Class pl.poznan.put.pdb.PdbTitleLine extends Object implements Serializable

Package pl.poznan.put.pdb.analysis

Class pl.poznan.put.pdb.analysis.AbstractPdbModel extends Object implements Serializable

Class pl.poznan.put.pdb.analysis.DefaultCifModel extends AbstractPdbModel implements Serializable

Class pl.poznan.put.pdb.analysis.DefaultPdbModel extends AbstractPdbModel implements Serializable

Class pl.poznan.put.pdb.analysis.DefaultPdbResidue extends Object implements Serializable

Class pl.poznan.put.pdb.analysis.DefaultResidueCollection extends Object implements Serializable

Class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel extends DefaultCifModel implements Serializable

Serialized Fields

atoms

List<PdbAtomLine> atoms

basePairs

List<QuantifiedBasePair> basePairs

chainTerminatedAfter

Set<PdbResidueIdentifier> chainTerminatedAfter

experimentalData

PdbExpdtaLine experimentalData

header

PdbHeaderLine header

missingResidues

List<PdbRemark465Line> missingResidues

modelNumber

int modelNumber

modifiedResidues

List<PdbModresLine> modifiedResidues

resolution

PdbRemark2Line resolution

title

String title

Class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel extends DefaultPdbModel implements Serializable

Serialization Methods

readResolve

private Object readResolve()
                    throws ObjectStreamException

Throws:

ObjectStreamException

Serialized Fields

atoms

List<PdbAtomLine> atoms

chainTerminatedAfter

Set<PdbResidueIdentifier> chainTerminatedAfter

experimentalData

PdbExpdtaLine experimentalData

header

PdbHeaderLine header

missingResidues

List<PdbRemark465Line> missingResidues

modelNumber

int modelNumber

modifiedResidues

List<PdbModresLine> modifiedResidues

resolution

PdbRemark2Line resolution

title

String title

Class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbResidue extends DefaultPdbResidue implements Serializable

Serialized Fields

atoms

List<PdbAtomLine> atoms

identifier

PdbResidueIdentifier identifier

modifiedResidueName

String modifiedResidueName

standardResidueName

String standardResidueName

Class pl.poznan.put.pdb.analysis.ImmutableDefaultResidueCollection extends DefaultResidueCollection implements Serializable

Serialized Fields

residues

List<PdbResidue> residues

Class pl.poznan.put.pdb.analysis.ImmutablePdbChain extends PdbChain implements Serializable

Serialized Fields

identifier

String identifier

residues

List<PdbResidue> residues

Class pl.poznan.put.pdb.analysis.ImmutablePdbCompactFragment extends PdbCompactFragment implements Serializable

Serialized Fields

name

String name

residues

List<PdbResidue> residues

Class pl.poznan.put.pdb.analysis.PdbChain extends Object implements Serializable

Class pl.poznan.put.pdb.analysis.PdbCompactFragment extends Object implements Serializable

Package pl.poznan.put.rna

Class pl.poznan.put.rna.ImmutableInteractionType extends InteractionType implements Serializable

Serialized Fields

description

String description

isPairing

boolean isPairing

left

NucleotideComponentType left

right

NucleotideComponentType right

Class pl.poznan.put.rna.InteractionType extends Object implements Serializable

Package pl.poznan.put.structure

Class pl.poznan.put.structure.AnalyzedBasePair extends Object implements Serializable

Class pl.poznan.put.structure.BasePair extends Object implements Serializable

Class pl.poznan.put.structure.DotBracketSymbol extends Object implements Serializable

Class pl.poznan.put.structure.ImmutableAnalyzedBasePair extends AnalyzedBasePair implements Serializable

Serialized Fields

basePair

BasePair basePair

bph

BPh bph

br

BR br

interactionType

InteractionType interactionType

isRepresented

boolean isRepresented

leontisWesthof

LeontisWesthof leontisWesthof

saenger

Saenger saenger

Class pl.poznan.put.structure.ImmutableBasePair extends BasePair implements Serializable

Serialized Fields

left

PdbNamedResidueIdentifier left

right

PdbNamedResidueIdentifier right

Class pl.poznan.put.structure.ImmutableDotBracketSymbol extends DotBracketSymbol implements Serializable

Serialized Fields

index

int index

sequence

char sequence

structure

char structure

Class pl.poznan.put.structure.ImmutableQuantifiedBasePair extends QuantifiedBasePair implements Serializable

Serialized Fields

basePair

BasePair basePair

bph

BPh bph

br

BR br

buckle

double buckle

interactionType

InteractionType interactionType

isRepresented

boolean isRepresented

leontisWesthof

LeontisWesthof leontisWesthof

opening

double opening

propeller

double propeller

saenger

Saenger saenger

shear

double shear

stagger

double stagger

stretch

double stretch

Class pl.poznan.put.structure.QuantifiedBasePair extends Object implements Serializable

Package pl.poznan.put.structure.formats

Class pl.poznan.put.structure.formats.BpSeq extends Object implements Serializable

Class pl.poznan.put.structure.formats.BpSeq.Entry extends Object implements Serializable

Class pl.poznan.put.structure.formats.Ct extends Object implements Serializable

Class pl.poznan.put.structure.formats.DefaultDotBracket extends pl.poznan.put.structure.formats.AbstractDotBracket implements Serializable

Class pl.poznan.put.structure.formats.ImmutableBpSeq extends BpSeq implements Serializable

Serialization Methods

readResolve

private Object readResolve()
                    throws ObjectStreamException

Throws:

ObjectStreamException

Serialized Fields

entries

SortedSet<BpSeq.Entry> entries

Class pl.poznan.put.structure.formats.ImmutableCt extends Ct implements Serializable

Serialization Methods

readResolve

private Object readResolve()
                    throws ObjectStreamException

Throws:

ObjectStreamException

Serialized Fields

entries

SortedSet<Ct.ExtendedEntry> entries

Class pl.poznan.put.structure.formats.ImmutableDefaultDotBracket extends DefaultDotBracket implements Serializable

Serialization Methods

readResolve

private Object readResolve()
                    throws ObjectStreamException

Throws:

ObjectStreamException

Serialized Fields

sequence

String sequence

strands

List<Strand> strands

structure

String structure

Class pl.poznan.put.structure.formats.ImmutableEntry extends BpSeq.Entry implements Serializable

Serialized Fields

comment

String comment

index

int index

pair

int pair

seq

char seq