Serialized Form

Package pl.poznan.put.circular.exception

Exception pl.poznan.put.circular.exception.InvalidCircularOperationException

class InvalidCircularOperationException extends RuntimeException implements Serializable

Exception pl.poznan.put.circular.exception.InvalidCircularValueException

class InvalidCircularValueException extends RuntimeException implements Serializable

Exception pl.poznan.put.circular.exception.InvalidVectorFormatException

class InvalidVectorFormatException extends RuntimeException implements Serializable

Package pl.poznan.put.pdb

Exception pl.poznan.put.pdb.CifPdbIncompatibilityException

class CifPdbIncompatibilityException extends RuntimeException implements Serializable

Class pl.poznan.put.pdb.ImmutablePdbAtomLine

class 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

class ImmutablePdbExpdtaLine extends PdbExpdtaLine implements Serializable

Serialized Fields

experimentalTechniques

List<ExperimentalTechnique> experimentalTechniques

Class pl.poznan.put.pdb.ImmutablePdbHeaderLine

class ImmutablePdbHeaderLine extends PdbHeaderLine implements Serializable

Serialized Fields

classification

String classification

depositionDate

Date depositionDate

idCode

String idCode

Class pl.poznan.put.pdb.ImmutablePdbModresLine

class 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

class 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

class ImmutablePdbRemark2Line extends PdbRemark2Line implements Serializable

Serialized Fields

resolution

double resolution

Class pl.poznan.put.pdb.ImmutablePdbRemark465Line

class 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

class ImmutablePdbResidueIdentifier extends PdbResidueIdentifier implements Serializable

Serialized Fields

chainIdentifier

String chainIdentifier

insertionCode

String insertionCode

residueNumber

int residueNumber

Class pl.poznan.put.pdb.ImmutablePdbTitleLine

class ImmutablePdbTitleLine extends PdbTitleLine implements Serializable

Serialized Fields

continuation

String continuation

title

String title

Class pl.poznan.put.pdb.PdbAtomLine

class PdbAtomLine extends Object implements Serializable

Class pl.poznan.put.pdb.PdbExpdtaLine

class PdbExpdtaLine extends Object implements Serializable

Class pl.poznan.put.pdb.PdbHeaderLine

class PdbHeaderLine extends Object implements Serializable

Class pl.poznan.put.pdb.PdbModresLine

class PdbModresLine extends Object implements Serializable

Class pl.poznan.put.pdb.PdbNamedResidueIdentifier

class PdbNamedResidueIdentifier extends Object implements Serializable

Exception pl.poznan.put.pdb.PdbParsingException

class PdbParsingException extends RuntimeException implements Serializable

Class pl.poznan.put.pdb.PdbRemark2Line

class PdbRemark2Line extends Object implements Serializable

Class pl.poznan.put.pdb.PdbRemark465Line

class PdbRemark465Line extends Object implements Serializable

Class pl.poznan.put.pdb.PdbResidueIdentifier

class PdbResidueIdentifier extends Object implements Serializable

Class pl.poznan.put.pdb.PdbTitleLine

class PdbTitleLine extends Object implements Serializable

Package pl.poznan.put.pdb.analysis

Class pl.poznan.put.pdb.analysis.AbstractPdbModel

class AbstractPdbModel extends Object implements Serializable

Class pl.poznan.put.pdb.analysis.DefaultCifModel

class DefaultCifModel extends AbstractPdbModel implements Serializable

Class pl.poznan.put.pdb.analysis.DefaultPdbModel

class DefaultPdbModel extends AbstractPdbModel implements Serializable

Class pl.poznan.put.pdb.analysis.DefaultPdbResidue

class DefaultPdbResidue extends Object implements Serializable

Class pl.poznan.put.pdb.analysis.DefaultResidueCollection

class DefaultResidueCollection extends Object implements Serializable

Class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel

class ImmutableDefaultCifModel extends DefaultCifModel implements Serializable

Serialization Methods

readResolve

private Object readResolve()
                    throws ObjectStreamException

Throws:

ObjectStreamException

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

class 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

class 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

class ImmutableDefaultResidueCollection extends DefaultResidueCollection implements Serializable

Serialized Fields

residues

List<PdbResidue> residues

Class pl.poznan.put.pdb.analysis.ImmutablePdbChain

class ImmutablePdbChain extends PdbChain implements Serializable

Serialized Fields

identifier

String identifier

residues

List<PdbResidue> residues

Class pl.poznan.put.pdb.analysis.ImmutablePdbCompactFragment

class ImmutablePdbCompactFragment extends PdbCompactFragment implements Serializable

Serialized Fields

name

String name

residues

List<PdbResidue> residues

Class pl.poznan.put.pdb.analysis.PdbChain

class PdbChain extends Object implements Serializable

Class pl.poznan.put.pdb.analysis.PdbCompactFragment

class PdbCompactFragment extends Object implements Serializable

Package pl.poznan.put.rna

Class pl.poznan.put.rna.ImmutableInteractionType

class 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

class InteractionType extends Object implements Serializable

Package pl.poznan.put.structure

Class pl.poznan.put.structure.AnalyzedBasePair

class AnalyzedBasePair extends Object implements Serializable

Class pl.poznan.put.structure.BasePair

class BasePair extends Object implements Serializable

Class pl.poznan.put.structure.DotBracketSymbol

class DotBracketSymbol extends Object implements Serializable

Class pl.poznan.put.structure.ImmutableAnalyzedBasePair

class 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

stackingTopology

StackingTopology stackingTopology

Class pl.poznan.put.structure.ImmutableBasePair

class ImmutableBasePair extends BasePair implements Serializable

Serialized Fields

left

PdbNamedResidueIdentifier left

right

PdbNamedResidueIdentifier right

Class pl.poznan.put.structure.ImmutableDotBracketSymbol

class ImmutableDotBracketSymbol extends DotBracketSymbol implements Serializable

Serialized Fields

index

int index

sequence

char sequence

structure

char structure

Class pl.poznan.put.structure.ImmutableQuantifiedBasePair

class 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

stackingTopology

StackingTopology stackingTopology

stagger

double stagger

stretch

double stretch

Class pl.poznan.put.structure.QuantifiedBasePair

class QuantifiedBasePair extends Object implements Serializable

Package pl.poznan.put.structure.formats

Class pl.poznan.put.structure.formats.BpSeq

class BpSeq extends Object implements Serializable

Class pl.poznan.put.structure.formats.BpSeq.Entry

class Entry extends Object implements Serializable

Class pl.poznan.put.structure.formats.Ct

class Ct extends Object implements Serializable

Class pl.poznan.put.structure.formats.DefaultDotBracket

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

Class pl.poznan.put.structure.formats.ImmutableBpSeq

class 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

class 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

class 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

class ImmutableEntry extends BpSeq.Entry implements Serializable

Serialized Fields

comment

String comment

index

int index

pair

int pair

seq

char seq