Serialized Form (biojava 4.2.9 API)

Package demo
- Class demo.GetColorGradient extends JPanel implements Serializable
  
  serialVersionUID:
  
  -4954397192682351367L
  - Serialized Fields
    - colors
```
Color[] colors
```
Package org.biojava.nbio.alignment
- Class org.biojava.nbio.alignment.SimpleGapPenalty extends Object implements Serializable
  
  serialVersionUID:
  
  3945671344135815456L
  - Serialized Fields
    - type
```
GapPenalty.Type type
```
    - gop
```
int gop
```
    - gep
```
int gep
```
Package org.biojava.nbio.core.alignment
- Class org.biojava.nbio.core.alignment.SimpleAlignedSequence extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - prev
```
AlignedSequence<S extends Sequence<C>,C extends Compound> prev
```
    - original
```
Sequence<C extends Compound> original
```
    - length
```
int length
```
    - numBefore
```
int numBefore
```
    - numAfter
```
int numAfter
```
    - location
```
Location location
```
    - numGaps
```
int numGaps
```
    - numGapPositions
```
int numGapPositions
```
    - alignmentFromSequence
```
int[] alignmentFromSequence
```
    - sequenceFromAlignment
```
int[] sequenceFromAlignment
```
- Class org.biojava.nbio.core.alignment.SimpleProfile extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - list
```
List<E> list
```
    - originals
```
List<E> originals
```
    - length
```
int length
```
- Class org.biojava.nbio.core.alignment.SimpleProfilePair extends SimpleProfile<S extends Sequence<C>,C extends Compound> implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - query
```
Profile<S extends Sequence<C>,C extends Compound> query
```
    - target
```
Profile<S extends Sequence<C>,C extends Compound> target
```
- Class org.biojava.nbio.core.alignment.SimpleSequencePair extends SimpleProfile<S extends Sequence<C>,C extends Compound> implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - identicals
```
int identicals
```
    - similars
```
int similars
```
Package org.biojava.nbio.core.alignment.matrices
- Class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix extends Object implements Serializable
  
  serialVersionUID:
  
  -2645265638108462479L
  - Serialized Fields
    - compoundSet
```
CompoundSet<C extends Compound> compoundSet
```
    - description
```
String description
```
    - name
```
String name
```
    - matrix
```
short[][] matrix
```
    - max
```
short max
```
    - min
```
short min
```
    - rows
```
List<E> rows
```
    - cols
```
List<E> cols
```
- Class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper extends Object implements Serializable
  
  serialVersionUID:
  
  148491724604653225L
Package org.biojava.nbio.core.exceptions
- Class org.biojava.nbio.core.exceptions.CompoundNotFoundException extends Exception implements Serializable
  
  serialVersionUID:
  
  1L
- Class org.biojava.nbio.core.exceptions.ParserException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  -4101924035353204493L
- Class org.biojava.nbio.core.exceptions.TranslationException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  -3017433758219757440L
Package org.biojava.nbio.core.sequence.compound
- Class org.biojava.nbio.core.sequence.compound.AminoAcidCompound extends AbstractCompound implements Serializable
  
  serialVersionUID:
  
  -1955116496725902319L
  - Serialized Fields
    - compoundSet
```
AminoAcidCompoundSet compoundSet
```
- Class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet extends Object implements Serializable
  
  serialVersionUID:
  
  4000344194364133456L
  - Serialized Fields
    - aminoAcidCompoundCache
```
Map<K,V> aminoAcidCompoundCache
```
    - aminoAcidCompoundCache3Letter
```
Map<K,V> aminoAcidCompoundCache3Letter
```
    - equivalentsCache
```
Map<K,V> equivalentsCache
```
Package org.biojava.nbio.core.sequence.location
- Class org.biojava.nbio.core.sequence.location.FuzzyPoint extends SimplePoint implements Serializable
  - Serialized Fields
    - min
```
int min
```
    - max
```
int max
```
    - resolver
```
Point.Resolver<T extends Point> resolver
```
- Class org.biojava.nbio.core.sequence.location.InsdcLocations.BondLocation extends AbstractLocation implements Serializable
- Class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation extends SimpleLocation implements Serializable
- Class org.biojava.nbio.core.sequence.location.InsdcLocations.OneOfLocation extends AbstractLocation implements Serializable
- Class org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation extends SimpleLocation implements Serializable
- Class org.biojava.nbio.core.sequence.location.SequenceLocation extends SimpleLocation implements Serializable
  - Serialized Fields
    - sequence
```
AbstractSequence<C extends Compound> sequence
```
- Class org.biojava.nbio.core.sequence.location.SimpleLocation extends AbstractLocation implements Serializable
- Class org.biojava.nbio.core.sequence.location.SimplePoint extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - position
```
int position
```
    - unknown
```
boolean unknown
```
    - uncertain
```
boolean uncertain
```
Package org.biojava.nbio.core.sequence.location.template
- Class org.biojava.nbio.core.sequence.location.template.AbstractLocation extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - start
```
Point start
```
    - end
```
Point end
```
    - strand
```
Strand strand
```
    - subLocations
```
List<E> subLocations
```
    - circular
```
boolean circular
```
    - betweenCompounds
```
boolean betweenCompounds
```
    - accession
```
AccessionID accession
```
    - partialOn5prime
```
boolean partialOn5prime
```
    - partialOn3prime
```
boolean partialOn3prime
```
Package org.biojava.nbio.genome.parsers.cytoband
- Class org.biojava.nbio.genome.parsers.cytoband.Cytoband extends Object implements Serializable
  
  serialVersionUID:
  
  2805976387404499650L
  - Serialized Fields
    - chromosome
```
String chromosome
```
    - start
```
Integer start
```
    - end
```
Integer end
```
    - locus
```
String locus
```
    - type
```
StainType type
```
Package org.biojava.nbio.genome.parsers.genename
- Class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition extends Object implements Serializable
  
  serialVersionUID:
  
  -6886306238993367835L
  - Serialized Fields
    - geneName
```
String geneName
```
    - genebankId
```
String genebankId
```
    - chromosome
```
String chromosome
```
    - orientation
```
Character orientation
```
    - transcriptionStart
```
Integer transcriptionStart
```
    - transcriptionEnd
```
Integer transcriptionEnd
```
    - cdsStart
```
Integer cdsStart
```
    - cdsEnd
```
Integer cdsEnd
```
    - exonCount
```
int exonCount
```
    - exonStarts
```
List<E> exonStarts
```
    - exonEnds
```
List<E> exonEnds
```
- Class org.biojava.nbio.genome.parsers.genename.GeneName extends Object implements Serializable
  
  serialVersionUID:
  
  -7163977639324764020L
  - Serialized Fields
    - hgncId
```
String hgncId
```
    - approvedSymbol
```
String approvedSymbol
```
    - approvedName
```
String approvedName
```
    - status
```
String status
```
    - previousSymbols
```
String previousSymbols
```
    - previousNames
```
String previousNames
```
    - synonyms
```
String synonyms
```
    - chromosome
```
String chromosome
```
    - accessionNr
```
String accessionNr
```
    - refseqIds
```
String refseqIds
```
    - uniprot
```
String uniprot
```
    - omimId
```
String omimId
```
    - ensemblGeneId
```
String ensemblGeneId
```
Package org.biojava.nbio.genome.parsers.gff
- Class org.biojava.nbio.genome.parsers.gff.FeatureList extends ArrayList<FeatureI> implements Serializable
  - Serialized Fields
    - featindex
```
Map<K,V> featindex
```
    - mLocation
```
Location mLocation
```
Package org.biojava.nbio.ontology
- Class org.biojava.nbio.ontology.AlreadyExistsException extends OntologyException implements Serializable
  
  serialVersionUID:
  
  1L
- Class org.biojava.nbio.ontology.DefaultOps extends Object implements Serializable
  
  serialVersionUID:
  
  1L
- Class org.biojava.nbio.ontology.InvalidTermException extends OntologyException implements Serializable
  
  serialVersionUID:
  
  1L
- Class org.biojava.nbio.ontology.Ontology.Impl extends Object implements Serializable
  
  serialVersionUID:
  
  -8064461497813727957L
  - Serialized Fields
    - terms
```
Map<K,V> terms
```
    - triples
```
Set<E> triples
```
    - subjectTriples
```
Map<K,V> subjectTriples
```
    - objectTriples
```
Map<K,V> objectTriples
```
    - relationTriples
```
Map<K,V> relationTriples
```
    - remoteTerms
```
Map<K,V> remoteTerms
```
    - localRemoteTerms
```
Set<E> localRemoteTerms
```
    - name
```
String name
```
    - description
```
String description
```
    - ops
```
OntologyOps ops
```
- Class org.biojava.nbio.ontology.OntologyException extends Exception implements Serializable
  
  serialVersionUID:
  
  1L
- Class org.biojava.nbio.ontology.OntologyTerm.Impl extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - ontology
```
Ontology ontology
```
    - target
```
Ontology target
```
    - synonyms
```
Set<E> synonyms
```
- Class org.biojava.nbio.ontology.RemoteTerm.Impl extends AbstractTerm implements Serializable
  
  serialVersionUID:
  
  922700041939183676L
  - Serialized Fields
    - ontology
```
Ontology ontology
```
    - remoteTerm
```
Term remoteTerm
```
    - name
```
String name
```
    - synonyms
```
Set<E> synonyms
```
- Class org.biojava.nbio.ontology.Term.Impl extends AbstractTerm implements Serializable
  
  serialVersionUID:
  
  6561668917514377417L
  - Serialized Fields
    - name
```
String name
```
    - ontology
```
Ontology ontology
```
    - annotation
```
Annotation annotation
```
    - synonyms
```
Set<E> synonyms
```
- Class org.biojava.nbio.ontology.Triple.Impl extends Object implements Serializable
  
  serialVersionUID:
  
  3807331980372839221L
  - Serialized Fields
    - subject
```
Term subject
```
    - object
```
Term object
```
    - predicate
```
Term predicate
```
    - name
```
String name
```
    - description
```
String description
```
    - synonyms
```
Set<E> synonyms
```
- Class org.biojava.nbio.ontology.Variable.Impl extends Term.Impl implements Serializable
  
  serialVersionUID:
  
  1L
Package org.biojava.nbio.ontology.utils
- Class org.biojava.nbio.ontology.utils.AbstractAnnotation extends Object implements Serializable
  
  serialVersionUID:
  
  2753449055959952873L
- Class org.biojava.nbio.ontology.utils.AssertionFailure extends AssertionError implements Serializable
- Class org.biojava.nbio.ontology.utils.SmallAnnotation extends AbstractAnnotation implements Serializable
  - Serialized Fields
    - properties
```
Map<K,V> properties
```
- Class org.biojava.nbio.ontology.utils.SmallMap extends AbstractMap implements Serializable
  - Serialized Fields
    - mappings
```
Object[] mappings
```
    - numMappings
```
int numMappings
```
- Class org.biojava.nbio.ontology.utils.StaticMemberPlaceHolder extends Object implements Serializable
  - Serialization Methods
    - readResolve
```
public Object readResolve()
                   throws ObjectStreamException
```
      Throws:
      
      ObjectStreamException
  - Serialized Fields
    - className
```
String className
```
    - fieldName
```
String fieldName
```
Package org.biojava.nbio.protmod.structure
- Class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl extends Object implements Serializable
  
  serialVersionUID:
  
  1656563037849815427L
  - Serialized Fields
    - originalModification
```
ProteinModification originalModification
```
    - modification
```
ProteinModification modification
```
    - groups
```
Set<E> groups
```
    - atomLinkages
```
Map<K,V> atomLinkages
```
Package org.biojava.nbio.structure
- Class org.biojava.nbio.structure.AminoAcidImpl extends HetatomImpl implements Serializable
  
  serialVersionUID:
  
  -6018854413829044230L
  - Serialized Fields
    - amino_char
```
Character amino_char
```
      IUPAC amino acid residue names
    - recordType
```
String recordType
```
- Class org.biojava.nbio.structure.AtomImpl extends Object implements Serializable
  
  serialVersionUID:
  
  -2258364127420562883L
  - Serialized Fields
    - name
```
String name
```
    - element
```
Element element
```
    - coords
```
double[] coords
```
    - pdbserial
```
int pdbserial
```
    - charge
```
short charge
```
    - occupancy
```
float occupancy
```
    - tempfactor
```
float tempfactor
```
    - altLoc
```
char altLoc
```
    - parent
```
Group parent
```
    - bonds
```
List<E> bonds
```
- Class org.biojava.nbio.structure.Author extends Object implements Serializable
  
  serialVersionUID:
  
  4840370515056666418L
  - Serialized Fields
    - surname
```
String surname
```
    - initials
```
String initials
```
- Class org.biojava.nbio.structure.BondImpl extends Object implements Serializable
  
  serialVersionUID:
  
  8836120946858134380L
  - Serialized Fields
    - atomA
```
Atom atomA
```
    - atomB
```
Atom atomB
```
    - bondOrder
```
int bondOrder
```
- Class org.biojava.nbio.structure.ChainImpl extends Object implements Serializable
  
  serialVersionUID:
  
  1990171805277911840L
  - Serialized Fields
    - swissprot_id
```
String swissprot_id
```
    - chainID
```
String chainID
```
    - groups
```
List<E> groups
```
    - seqResGroups
```
List<E> seqResGroups
```
    - id
```
Long id
```
    - mol
```
Compound mol
```
    - parent
```
Structure parent
```
    - pdbResnumMap
```
Map<K,V> pdbResnumMap
```
    - internalChainID
```
String internalChainID
```
    - seqMisMatches
```
List<E> seqMisMatches
```
- Class org.biojava.nbio.structure.Compound extends Object implements Serializable
  
  serialVersionUID:
  
  2991897825657586356L
  - Serialized Fields
    - chains
```
List<E> chains
```
      The list of chains that are described by this Compound
    - molId
```
int molId
```
      The Molecule identifier, called entity_id in mmCIF dictionary
    - chains2pdbResNums2ResSerials
```
Map<K,V> chains2pdbResNums2ResSerials
```
      A map to cache residue number mapping, between ResidueNumbers and index (1-based) in aligned sequences (SEQRES). Initialised lazily upon call to Compound.getAlignedResIndex(Group, Chain)
    - refChainId
```
String refChainId
```
    - molName
```
String molName
```
    - title
```
String title
```
    - synonyms
```
List<E> synonyms
```
    - ecNums
```
List<E> ecNums
```
    - engineered
```
String engineered
```
    - mutation
```
String mutation
```
    - biologicalUnit
```
String biologicalUnit
```
    - details
```
String details
```
    - numRes
```
String numRes
```
    - resNames
```
String resNames
```
    - headerVars
```
String headerVars
```
    - synthetic
```
String synthetic
```
    - fragment
```
String fragment
```
    - organismScientific
```
String organismScientific
```
    - organismTaxId
```
String organismTaxId
```
    - organismCommon
```
String organismCommon
```
    - strain
```
String strain
```
    - variant
```
String variant
```
    - cellLine
```
String cellLine
```
    - atcc
```
String atcc
```
    - organ
```
String organ
```
    - tissue
```
String tissue
```
    - cell
```
String cell
```
    - organelle
```
String organelle
```
    - secretion
```
String secretion
```
    - gene
```
String gene
```
    - cellularLocation
```
String cellularLocation
```
    - expressionSystem
```
String expressionSystem
```
    - expressionSystemTaxId
```
String expressionSystemTaxId
```
    - expressionSystemStrain
```
String expressionSystemStrain
```
    - expressionSystemVariant
```
String expressionSystemVariant
```
    - expressionSystemCellLine
```
String expressionSystemCellLine
```
    - expressionSystemAtccNumber
```
String expressionSystemAtccNumber
```
    - expressionSystemOrgan
```
String expressionSystemOrgan
```
    - expressionSystemTissue
```
String expressionSystemTissue
```
    - expressionSystemCell
```
String expressionSystemCell
```
    - expressionSystemOrganelle
```
String expressionSystemOrganelle
```
    - expressionSystemCellularLocation
```
String expressionSystemCellularLocation
```
    - expressionSystemVectorType
```
String expressionSystemVectorType
```
    - expressionSystemVector
```
String expressionSystemVector
```
    - expressionSystemPlasmid
```
String expressionSystemPlasmid
```
    - expressionSystemGene
```
String expressionSystemGene
```
    - expressionSystemOtherDetails
```
String expressionSystemOtherDetails
```
    - id
```
Long id
```
- Class org.biojava.nbio.structure.DBRef extends Object implements Serializable
  
  serialVersionUID:
  
  -1050178577542224379L
  - Serialized Fields
    - parent
```
Structure parent
```
    - idCode
```
String idCode
```
    - chainId
```
String chainId
```
    - seqbegin
```
int seqbegin
```
    - insertBegin
```
char insertBegin
```
    - seqEnd
```
int seqEnd
```
    - insertEnd
```
char insertEnd
```
    - database
```
String database
```
    - dbAccession
```
String dbAccession
```
    - dbIdCode
```
String dbIdCode
```
    - dbSeqBegin
```
int dbSeqBegin
```
    - idbnsBegin
```
char idbnsBegin
```
    - dbSeqEnd
```
int dbSeqEnd
```
    - idbnsEnd
```
char idbnsEnd
```
    - id
```
Long id
```
- Class org.biojava.nbio.structure.HetatomImpl extends Object implements Serializable
  
  serialVersionUID:
  
  4491470432023820382L
  - Serialized Fields
    - properties
```
Map<K,V> properties
```
    - id
```
long id
```
    - pdb_flag
```
boolean pdb_flag
```
      stores if 3d coordinates are available.
    - pdb_name
```
String pdb_name
```
      3 letter name of amino acid in pdb file.
    - residueNumber
```
ResidueNumber residueNumber
```
    - atoms
```
List<E> atoms
```
    - parent
```
Chain parent
```
    - atomNameLookup
```
Map<K,V> atomNameLookup
```
    - chemComp
```
ChemComp chemComp
```
    - altLocs
```
List<E> altLocs
```
- Class org.biojava.nbio.structure.JournalArticle extends Object implements Serializable
  
  serialVersionUID:
  
  5062668226159515468L
  - Serialized Fields
    - authorList
```
List<E> authorList
```
    - editorList
```
List<E> editorList
```
    - title
```
String title
```
    - ref
```
String ref
```
    - journalName
```
String journalName
```
    - volume
```
String volume
```
    - startPage
```
String startPage
```
    - publicationDate
```
int publicationDate
```
    - publisher
```
String publisher
```
    - refn
```
String refn
```
    - pmid
```
String pmid
```
    - doi
```
String doi
```
    - published
```
boolean published
```
- Class org.biojava.nbio.structure.NucleotideImpl extends HetatomImpl implements Serializable
  
  serialVersionUID:
  
  -7467726932980288712L
- Class org.biojava.nbio.structure.PDBCrystallographicInfo extends Object implements Serializable
  
  serialVersionUID:
  
  -7949886749566087669L
  - Serialized Fields
    - cell
```
CrystalCell cell
```
    - sg
```
SpaceGroup sg
```
    - ncsOperators
```
javax.vecmath.Matrix4d[] ncsOperators
```
      Some PDB files contain NCS operators necessary to create the full AU. Usually this happens for viral proteins. See http://www.wwpdb.org/documentation/format33/sect8.html#MTRIXn . Note that the "given" operators (iGiven field =1 in PDB format, "given" string in _struct_ncs_oper.code in mmCIF format) are not stored.
    - nonStandardSg
```
boolean nonStandardSg
```
      Whether this structure has a non-standard space group not supported by Biojava. If this is true the sg member will be null.
      
      Since:
      
      4.2.5
    - nonStandardCoordFrameConvention
```
boolean nonStandardCoordFrameConvention
```
      Whether this structure is non-standard coordinate frame convention, for which our scale matrix calculation and thus the crystal reconstruction will be incorrect. There's ~ 200 old structures in the PDB affected by the non-standard frame problem, hopefully they will be remediated in the future. For more info see: https://github.com/eppic-team/owl/issues/4
      
      Since:
      
      4.2.5
- Class org.biojava.nbio.structure.PDBHeader extends Object implements Serializable
  
  serialVersionUID:
  
  -5834326174085429508L
  - Serialized Fields
    - title
```
String title
```
    - description
```
String description
```
    - idCode
```
String idCode
```
    - classification
```
String classification
```
    - depDate
```
Date depDate
```
    - modDate
```
Date modDate
```
    - techniques
```
Set<E> techniques
```
    - crystallographicInfo
```
PDBCrystallographicInfo crystallographicInfo
```
    - resolution
```
float resolution
```
    - rFree
```
float rFree
```
    - journalArticle
```
JournalArticle journalArticle
```
    - authors
```
String authors
```
    - id
```
Long id
```
    - dateFormat
```
DateFormat dateFormat
```
    - bioAssemblies
```
Map<K,V> bioAssemblies
```
    - revisionRecords
```
List<E> revisionRecords
```
- Class org.biojava.nbio.structure.ResidueNumber extends Object implements Serializable
  
  serialVersionUID:
  
  1773011704758536083L
  - Serialized Fields
    - chainId
```
String chainId
```
    - insCode
```
Character insCode
```
    - seqNum
```
Integer seqNum
```
- Class org.biojava.nbio.structure.SeqMisMatchImpl extends Object implements Serializable
  
  serialVersionUID:
  
  -3699285122925652562L
  - Serialized Fields
    - seqNum
```
Integer seqNum
```
    - origGroup
```
String origGroup
```
    - pdbGroup
```
String pdbGroup
```
    - details
```
String details
```
    - uniProtId
```
String uniProtId
```
    - insCode
```
String insCode
```
    - pdbResNum
```
String pdbResNum
```
- Class org.biojava.nbio.structure.Site extends Object implements Serializable
  
  serialVersionUID:
  
  -4577047072916341237L
  - Serialized Fields
    - siteID
```
String siteID
```
    - groups
```
List<E> groups
```
    - evCode
```
String evCode
```
    - description
```
String description
```
- Class org.biojava.nbio.structure.StructureException extends Exception implements Serializable
  
  serialVersionUID:
  
  62946250941673093L
- Class org.biojava.nbio.structure.StructureImpl extends Object implements Serializable
  
  serialVersionUID:
  
  -8344837138032851348L
  - Serialized Fields
    - pdb_id
```
String pdb_id
```
    - models
```
List<E> models
```
    - connections
```
List<E> connections
```
    - compounds
```
List<E> compounds
```
    - dbrefs
```
List<E> dbrefs
```
    - ssbonds
```
List<E> ssbonds
```
    - sites
```
List<E> sites
```
    - hetAtoms
```
List<E> hetAtoms
```
    - name
```
String name
```
    - structureIdentifier
```
StructureIdentifier structureIdentifier
```
    - pdbHeader
```
PDBHeader pdbHeader
```
    - id
```
Long id
```
    - biologicalAssembly
```
boolean biologicalAssembly
```
- Class org.biojava.nbio.structure.SubstructureIdentifier extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - pdbId
```
String pdbId
```
    - ranges
```
List<E> ranges
```
Package org.biojava.nbio.structure.align.client
- Class org.biojava.nbio.structure.align.client.JobKillException extends Exception implements Serializable
  
  serialVersionUID:
  
  1L
- Class org.biojava.nbio.structure.align.client.StructureName extends Object implements Serializable
  
  serialVersionUID:
  
  4021229518711762957L
  - Serialized Fields
    - name
```
String name
```
    - pdbId
```
String pdbId
```
    - chainId
```
String chainId
```
    - mySource
```
StructureName.Source mySource
```
    - base
```
StructureIdentifier base
```
Package org.biojava.nbio.structure.align.gui
- Class org.biojava.nbio.structure.align.gui.AlignmentGui extends JFrame implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - algorithm
```
StructureAlignment algorithm
```
    - abortB
```
JButton abortB
```
    - tab1
```
SelectPDBPanel tab1
```
    - tab2
```
PDBUploadPanel tab2
```
    - tab3
```
ScopSelectPanel tab3
```
    - thread
```
Thread thread
```
    - alicalc
```
AlignmentCalculationRunnable alicalc
```
    - masterPane
```
JTabbedPane masterPane
```
    - tabPane
```
JTabbedPane tabPane
```
    - progress
```
JProgressBar progress
```
    - dbsearch
```
DBSearchGUI dbsearch
```
- Class org.biojava.nbio.structure.align.gui.AlignmentTextPanel extends JPrintPanel implements Serializable
  
  serialVersionUID:
  
  5092386365924879073L
  - Serialized Fields
    - tp
```
JEditorPane tp
```
- Class org.biojava.nbio.structure.align.gui.ChooseDirAction extends AbstractAction implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - textField
```
JTextField textField
```
    - config
```
UserConfiguration config
```
- Class org.biojava.nbio.structure.align.gui.ConfigPDBInstallPanel extends JPanel implements Serializable
  
  serialVersionUID:
  
  -1055193854675583808L
  - Serialized Fields
    - fromFtp
```
JCheckBox fromFtp
```
    - fileType
```
JComboBox<E> fileType
```
    - pdbDir
```
JTextField pdbDir
```
- Class org.biojava.nbio.structure.align.gui.DBSearchGUI extends JPanel implements Serializable
  
  serialVersionUID:
  
  -5657960663049062301L
  - Serialized Fields
    - algorithm
```
StructureAlignment algorithm
```
    - tab1
```
SelectPDBPanel tab1
```
    - tabPane
```
JTabbedPane tabPane
```
    - tab2
```
PDBUploadPanel tab2
```
    - tab3
```
ScopSelectPanel tab3
```
    - listPane
```
JPanel listPane
```
    - abortB
```
JButton abortB
```
    - alicalc
```
AlignmentCalcDB alicalc
```
    - progress
```
JProgressBar progress
```
    - drawer
```
org.biojava.nbio.structure.align.gui.ProgressThreadDrawer drawer
```
    - outFileLocation
```
JTextField outFileLocation
```
    - useDomainSplit
```
Boolean useDomainSplit
```
- Class org.biojava.nbio.structure.align.gui.DotPlotPanel extends ScaleableMatrixPanel implements Serializable
  
  serialVersionUID:
  
  -7641953255857483895L
- Class org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener extends JPanel implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - alignmentsProcessed
```
int alignmentsProcessed
```
    - progressBar
```
JProgressBar progressBar
```
    - taskOutput
```
JTextArea taskOutput
```
    - stopButton
```
JButton stopButton
```
    - farmJob
```
FarmJob farmJob
```
- Class org.biojava.nbio.structure.align.gui.JPrintPanel extends JPanel implements Serializable
  
  serialVersionUID:
  
  -3337337068138131455L
- Class org.biojava.nbio.structure.align.gui.MemoryMonitor extends JPanel implements Serializable
  
  serialVersionUID:
  
  56289234782130L
  - Serialized Fields
    - surf
```
MemoryMonitor.Surface surf
```
    - controls
```
JPanel controls
```
    - doControls
```
boolean doControls
```
    - tf
```
JTextField tf
```
- Class org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface extends JPanel implements Serializable
  
  serialVersionUID:
  
  2387409854370432908L
  - Serialized Fields
    - thread
```
Thread thread
```
    - sleepAmount
```
long sleepAmount
```
    - w
```
int w
```
    - h
```
int h
```
    - bimg
```
BufferedImage bimg
```
    - big
```
Graphics2D big
```
    - font
```
Font font
```
    - r
```
Runtime r
```
    - columnInc
```
int columnInc
```
    - pts
```
int[] pts
```
    - ptNum
```
int ptNum
```
    - ascent
```
int ascent
```
    - descent
```
int descent
```
    - graphOutlineRect
```
Rectangle graphOutlineRect
```
    - mfRect
```
Rectangle2D mfRect
```
    - muRect
```
Rectangle2D muRect
```
    - graphLine
```
Line2D graphLine
```
    - graphColor
```
Color graphColor
```
    - mfColor
```
Color mfColor
```
    - usedStr
```
String usedStr
```
- Class org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI extends JFrame implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - multiple
```
MultipleStructureAligner multiple
```
    - pairwise
```
StructureAlignment pairwise
```
    - tab
```
SelectMultiplePanel tab
```
    - tabPane
```
JTabbedPane tabPane
```
    - thread
```
Thread thread
```
    - alicalc
```
AlignmentCalculationRunnable alicalc
```
    - progress
```
JProgressBar progress
```
    - abortB
```
JButton abortB
```
- Class org.biojava.nbio.structure.align.gui.ParameterGUI extends JFrame implements Serializable
  
  serialVersionUID:
  
  723386061184110161L
  - Serialized Fields
    - params
```
ConfigStrucAligParams params
```
    - textFields
```
List<E> textFields
```
- Class org.biojava.nbio.structure.align.gui.SelectPDBPanel extends JPanel implements Serializable
  
  serialVersionUID:
  
  4002475313717172193L
  - Serialized Fields
    - debug
```
boolean debug
```
    - f1
```
JTextField f1
```
    - f2
```
JTextField f2
```
    - c1
```
JTextField c1
```
    - c2
```
JTextField c2
```
    - r1
```
JTextField r1
```
    - r2
```
JTextField r2
```
    - config
```
UserConfiguration config
```
    - configPane
```
JTabbedPane configPane
```
Package org.biojava.nbio.structure.align.gui.aligpanel
- Class org.biojava.nbio.structure.align.gui.aligpanel.AligPanel extends JPrintPanel implements Serializable
  
  serialVersionUID:
  
  -6892229111166263764L
  - Serialized Fields
    - afpChain
```
AFPChain afpChain
```
    - coordManager
```
AFPChainCoordManager coordManager
```
    - seqFont
```
Font seqFont
```
    - eqFont
```
Font eqFont
```
    - jmol
```
AbstractAlignmentJmol jmol
```
    - mouseMoLi
```
AligPanelMouseMotionListener mouseMoLi
```
    - selection
```
BitSet selection
```
    - selectionLocked
```
boolean selectionLocked
```
    - ca1
```
Atom[] ca1
```
    - ca2
```
Atom[] ca2
```
    - colorBySimilarity
```
boolean colorBySimilarity
```
    - colorByAlignmentBlock
```
boolean colorByAlignmentBlock
```
- Class org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel extends JPrintPanel implements Serializable
  
  serialVersionUID:
  
  -6892229111166263764L
  - Serialized Fields
    - multAln
```
MultipleAlignment multAln
```
    - alnSeq
```
List<E> alnSeq
```
    - mapSeqToStruct
```
List<E> mapSeqToStruct
```
    - size
```
int size
```
    - length
```
int length
```
    - seqFont
```
Font seqFont
```
    - eqFont
```
Font eqFont
```
    - jmol
```
AbstractAlignmentJmol jmol
```
    - mouseMoLi
```
MultipleAligPanelMouseMotionListener mouseMoLi
```
    - coordManager
```
MultipleAlignmentCoordManager coordManager
```
    - selection
```
BitSet selection
```
    - selectionLocked
```
boolean selectionLocked
```
    - colorBySimilarity
```
boolean colorBySimilarity
```
    - colorByAlignmentBlock
```
boolean colorByAlignmentBlock
```
- Class org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay extends JTextField implements Serializable
  
  serialVersionUID:
  
  6939947266417830429L
  - Serialized Fields
    - panel
```
MultipleAligPanel panel
```
- Class org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay extends JTextField implements Serializable
  
  serialVersionUID:
  
  6939947266417830429L
  - Serialized Fields
    - afpChain
```
AFPChain afpChain
```
    - ca1
```
Atom[] ca1
```
    - ca2
```
Atom[] ca2
```
Package org.biojava.nbio.structure.align.gui.autosuggest
- Class org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest extends JTextField implements Serializable
  
  serialVersionUID:
  
  8591734727984365156L
  - Serialized Fields
    - defaultText
```
String defaultText
```
    - dialog
```
JDialog dialog
```
    - location
```
Point location
```
    - list
```
JList<E> list
```
    - suggestions
```
Vector<E> suggestions
```
    - lastWord
```
String lastWord
```
      last word that was entered by user
    - autoSuggestProvider
```
AutoSuggestProvider autoSuggestProvider
```
    - regular
```
Font regular
```
    - busy
```
Font busy
```
    - matcher
```
org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest.SuggestionFetcher matcher
```
Package org.biojava.nbio.structure.align.gui.jmol
- Class org.biojava.nbio.structure.align.gui.jmol.JmolPanel extends JPrintPanel implements Serializable
  
  serialVersionUID:
  
  -3661941083797644242L
  - Serialized Fields
    - viewer
```
org.jmol.api.JmolViewer viewer
```
    - adapter
```
org.jmol.api.JmolAdapter adapter
```
    - statusListener
```
org.jmol.api.JmolStatusListener statusListener
```
    - currentSize
```
Dimension currentSize
```
    - rectClip
```
Rectangle rectClip
```
    - structure
```
Structure structure
```
Package org.biojava.nbio.structure.align.helper
- Class org.biojava.nbio.structure.align.helper.AligMatEl extends IndexPair implements Serializable
  
  serialVersionUID:
  
  -4040926588803887471L
  - Serialized Fields
    - value
```
int value
```
    - contig
```
int contig
```
- Class org.biojava.nbio.structure.align.helper.IndexPair extends Object implements Serializable
  
  serialVersionUID:
  
  1832393751152650420L
  - Serialized Fields
    - row
```
short row
```
    - col
```
short col
```

Package org.biojava.nbio.structure.align.model

Class org.biojava.nbio.structure.align.model.AFP extends Object implements Serializable

serialVersionUID:

3901209995477111829L
- Serialized Fields
  - p1
```
int p1
```
  - p2
```
int p2
```
  - fragLen
```
int fragLen
```
  - rmsd
```
double rmsd
```
  - m
```
Matrix m
```
  - t
```
double[] t
```
  - score
```
double score
```
  - id
```
long id
```

Class org.biojava.nbio.structure.align.model.AFPChain extends Object implements Serializable

serialVersionUID:: -4474029015606617947L

Serialized Fields

algorithmName
```
String algorithmName
```
version
```
String version
```
name1
```
String name1
```
name2
```
String name2
```
ioTime
```
long ioTime
```
calculationTime
```
long calculationTime
```
id
```
long id
```
alignScore
```
double alignScore
```
alignScoreUpdate
```
double alignScoreUpdate
```
afpChainTwiNum
```
int afpChainTwiNum
```
tmScore
```
double tmScore
```
minLen
```
int minLen
```
afpSet
```
List<E> afpSet
```
afpIndex
```
int[][] afpIndex
```
afpAftIndex
```
int[][] afpAftIndex
```
afpBefIndex
```
int[][] afpBefIndex
```
disTable1
```
Matrix disTable1
```
disTable2
```
Matrix disTable2
```
twi
```
int[] twi
```
afpChainLen
```
int afpChainLen
```
afpChainList
```
int[] afpChainList
```
afpChainTwiBin
```
double[] afpChainTwiBin
```
afpChainTwiList
```
double[] afpChainTwiList
```
chainRmsd
```
double chainRmsd
```
chainLen
```
int chainLen
```
misLen
```
int misLen
```
gapLen
```
int gapLen
```
blockNum
```
int blockNum
```
blockNumIni
```
int blockNumIni
```
blockNumClu
```
int blockNumClu
```
blockNumSpt
```
int blockNumSpt
```
blockRmsd
```
double[] blockRmsd
```
block2Afp
```
int[] block2Afp
```
blockSize
```
int[] blockSize
```
blockScore
```
double[] blockScore
```
blockGap
```
int[] blockGap
```
blockResSize
```
int[] blockResSize
```
blockResList
```
int[][][] blockResList
```
blockRotationMatrix
```
Matrix[] blockRotationMatrix
```
blockShiftVector
```
Atom[] blockShiftVector
```
focusResn
```
int focusResn
```
focusRes1
```
int[] focusRes1
```
focusRes2
```
int[] focusRes2
```
focusAfpn
```
int focusAfpn
```
focusAfpList
```
int[] focusAfpList
```
shortAlign
```
boolean shortAlign
```
pdbAln
```
String[][][] pdbAln
```
optAln
```
int[][][] optAln
```
optLen
```
int[] optLen
```
optRmsd
```
double[] optRmsd
```
optLength
```
int optLength
```
alnsymb
```
char[] alnsymb
```
alnseq1
```
char[] alnseq1
```
alnseq2
```
char[] alnseq2
```
alnLength
```
int alnLength
```
alnbeg1
```
int alnbeg1
```
alnbeg2
```
int alnbeg2
```
totalLenIni
```
int totalLenIni
```
totalLenOpt
```
int totalLenOpt
```
totalRmsdIni
```
double totalRmsdIni
```
totalRmsdOpt
```
double totalRmsdOpt
```
ca1Length
```
int ca1Length
```
ca2Length
```
int ca2Length
```
maxTra
```
int maxTra
```
conn
```
Double conn
```
dvar
```
Double dvar
```
probability
```
double probability
```
identity
```
double identity
```
similarity
```
double similarity
```
normAlignScore
```
double normAlignScore
```
myResultsEQR
```
int myResultsEQR
```
myResultsSimilarity1
```
int myResultsSimilarity1
```
myResultsSimilarity2
```
int myResultsSimilarity2
```
sequentialAlignment
```
boolean sequentialAlignment
```
distanceMatrix
```
Matrix distanceMatrix
```
description2
```
String description2
```

Package org.biojava.nbio.structure.align.multiple
- Class org.biojava.nbio.structure.align.multiple.BlockImpl extends AbstractScoresCache implements Serializable
  
  serialVersionUID:
  
  -5804042669466177641L
  - Serialized Fields
    - parent
```
BlockSet parent
```
    - alignRes
```
List<E> alignRes
```
    - coreLength
```
int coreLength
```
    - alignResCounts
```
List<E> alignResCounts
```
- Class org.biojava.nbio.structure.align.multiple.BlockSetImpl extends AbstractScoresCache implements Serializable
  
  serialVersionUID:
  
  -1015791986000076089L
  - Serialized Fields
    - parent
```
MultipleAlignment parent
```
    - blocks
```
List<E> blocks
```
    - pose
```
List<E> pose
```
    - length
```
int length
```
    - coreLength
```
int coreLength
```
    - alignResCounts
```
List<E> alignResCounts
```
- Class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl extends AbstractScoresCache implements Serializable
  
  serialVersionUID:
  
  -5732485866623431898L
  - Serialized Fields
    - algorithmName
```
String algorithmName
```
    - version
```
String version
```
    - ioTime
```
Long ioTime
```
    - calculationTime
```
Long calculationTime
```
    - structureIdentifiers
```
List<E> structureIdentifiers
```
    - atomArrays
```
List<E> atomArrays
```
    - distanceMatrix
```
List<E> distanceMatrix
```
    - multipleAlignments
```
List<E> multipleAlignments
```
- Class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl extends AbstractScoresCache implements Serializable
  
  serialVersionUID:
  
  3432043794125805139L
  - Serialized Fields
    - parent
```
MultipleAlignmentEnsemble parent
```
    - blockSets
```
List<E> blockSets
```
    - length
```
int length
```
    - coreLength
```
int coreLength
```
    - alignResCounts
```
List<E> alignResCounts
```
    - coverages
```
List<E> coverages
```
Package org.biojava.nbio.structure.align.pairwise
- Class org.biojava.nbio.structure.align.pairwise.AlignmentResult extends Object implements Serializable
  
  serialVersionUID:
  
  -4132105905712445473L
  - Serialized Fields
    - alignments
```
AlternativeAlignment[] alignments
```
    - pdb1
```
String pdb1
```
    - pdb2
```
String pdb2
```
    - chain1
```
String chain1
```
    - chain2
```
String chain2
```
    - length1
```
int length1
```
    - length2
```
int length2
```
    - calculationTime
```
long calculationTime
```
    - ioTime
```
long ioTime
```
- Class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment extends Object implements Serializable
  
  serialVersionUID:
  
  -6226717654562221241L
  - Serialized Fields
    - idx1
```
int[] idx1
```
    - idx2
```
int[] idx2
```
    - pdbresnum1
```
String[] pdbresnum1
```
    - pdbresnum2
```
String[] pdbresnum2
```
    - nfrags
```
int nfrags
```
    - center
```
Atom center
```
    - rot
```
Matrix rot
```
    - tr
```
Atom tr
```
    - gaps0
```
int gaps0
```
    - eqr0
```
int eqr0
```
    - rms0
```
int rms0
```
    - joined
```
int joined
```
    - percId
```
int percId
```
    - cluster
```
int cluster
```
    - score
```
float score
```
    - aligpath
```
IndexPair[] aligpath
```
    - fromia
```
int fromia
```
    - currentRotMatrix
```
Matrix currentRotMatrix
```
    - currentTranMatrix
```
Atom currentTranMatrix
```
    - rms
```
double rms
```
    - distanceMatrix
```
Matrix distanceMatrix
```
Package org.biojava.nbio.structure.align.util
- Class org.biojava.nbio.structure.align.util.ConfigurationException extends Exception implements Serializable
  
  serialVersionUID:
  
  -8047100079715000276L
Package org.biojava.nbio.structure.asa
- Class org.biojava.nbio.structure.asa.GroupAsa extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - g
```
Group g
```
    - asaU
```
double asaU
```
      ASA of uncomplexed residue
    - asaC
```
double asaC
```
      ASA of complexed residue
    - atomAsaUs
```
List<E> atomAsaUs
```
      The individual atoms uncomplexed ASAs
    - atomAsaCs
```
List<E> atomAsaCs
```
      The individual atoms complexed ASAs
Package org.biojava.nbio.structure.cath
- Class org.biojava.nbio.structure.cath.CathDomain extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - domainName
```
String domainName
```
      The CATH domain code. Always 7 characters in length, combining the PDB and chain letter with the number of the domain within CATH. Example: 1aoiA00 If the chain letter '0', domain refers to an entire PDB entry.
    - classId
```
Integer classId
```
      The class number of this domain.
    - architectureId
```
Integer architectureId
```
      The architecture number of this domain.
    - topologyId
```
Integer topologyId
```
      The topology number of this domain.
    - homologyId
```
Integer homologyId
```
      The homologous superfamily number of this domain.
    - sequenceFamilyId
```
Integer sequenceFamilyId
```
      The sequence family (35% identity) number of this domain.
    - orthologousSequenceFamilyId
```
Integer orthologousSequenceFamilyId
```
      The "orthologous" sequence family (60% identity) number of this domain.
    - likeSequenceFamilyId
```
Integer likeSequenceFamilyId
```
      The "Like" sequence family (95% identity) number of this domain.
    - identicalSequenceFamilyId
```
Integer identicalSequenceFamilyId
```
      The identical sequence family (100% identity) number of this domain.
    - domainCounter
```
Integer domainCounter
```
      The count of this domain among the identical sequence family members.
    - length
```
Integer length
```
      The domain length..
    - resolution
```
Double resolution
```
      The resolution of the domain structure. Nominally in Angstroms, the values 999.000 and 1000.000 signify NMR structures and obsolete structures, respectively.
    - format
```
String format
```
      The format and version of the CathDomainDescriptionFile.
    - version
```
String version
```
      The CATH version.
    - date
```
Date date
```
    - name
```
String name
```
      The so-called name field holds a potentially long description of the domain.
    - source
```
String source
```
      Complete source organism listing.
    - sequenceHeader
```
String sequenceHeader
```
      FASTA header.
    - sequence
```
String sequence
```
      FASTA sequence.
    - segments
```
List<E> segments
```
      List of all sub-domain segments.
    - comment
```
String comment
```
      A (potentially long) comment. Usually empty.
- Class org.biojava.nbio.structure.cath.CathFragment extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - fragmentId
```
Integer fragmentId
```
      The number of this segment within the domain.
    - start
```
String start
```
      The first residue in the segment. Refers to the complete residue specification (sequence number AND insertion code).
    - stop
```
String stop
```
      The last residue in the segment. Refers to the complete residue specification (sequence number AND insertion code).
    - length
```
Integer length
```
      Number of residues in the segment. This value is parsed, not calculated.
- Class org.biojava.nbio.structure.cath.CathNode extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - nodeId
```
String nodeId
```
      The CATH code of the node, e.g. "1.10.8.10".
    - parentId
```
String parentId
```
      The CATH code of the parent, e.g. "1.10.8". Calculated during parsing.
    - representative
```
String representative
```
      The representative domain for this node.
    - description
```
String description
```
      A name or description.
    - category
```
CathCategory category
```
      This node's level within the hierarchy. One of CATH, not CATHSOLID.
- Class org.biojava.nbio.structure.cath.CathSegment extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - segmentId
```
Integer segmentId
```
      The number of this segment within the domain.
    - start
```
String start
```
      The first residue in the segment. Refers to the complete residue specification (sequence number AND insertion code).
    - stop
```
String stop
```
      The last residue in the segment. Refers to the complete residue specification (sequence number AND insertion code).
    - length
```
Integer length
```
      Number of residues in the segment. This value is parsed, not calculated.
    - sequenceHeader
```
String sequenceHeader
```
      FASTA header.
    - sequence
```
String sequence
```
      FASTA sequence.
Package org.biojava.nbio.structure.contact
- Class org.biojava.nbio.structure.contact.AtomContact extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - pair
```
Pair<T> pair
```
    - distance
```
double distance
```
- Class org.biojava.nbio.structure.contact.AtomContactSet extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - contacts
```
HashMap<K,V> contacts
```
    - cutoff
```
double cutoff
```
- Class org.biojava.nbio.structure.contact.AtomIdentifier extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - pdbSerial
```
int pdbSerial
```
    - chainId
```
String chainId
```
- Class org.biojava.nbio.structure.contact.BoundingBox extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - xmin
```
double xmin
```
    - xmax
```
double xmax
```
    - ymin
```
double ymin
```
    - ymax
```
double ymax
```
    - zmin
```
double zmin
```
    - zmax
```
double zmax
```
- Class org.biojava.nbio.structure.contact.GroupContact extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - pair
```
Pair<T> pair
```
    - atomContacts
```
List<E> atomContacts
```
- Class org.biojava.nbio.structure.contact.GroupContactSet extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - contacts
```
HashMap<K,V> contacts
```
- Class org.biojava.nbio.structure.contact.Pair extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - first
```
Object first
```
    - second
```
Object second
```
- Class org.biojava.nbio.structure.contact.StructureInterface extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - id
```
int id
```
    - totalArea
```
double totalArea
```
    - contacts
```
AtomContactSet contacts
```
    - groupContacts
```
GroupContactSet groupContacts
```
    - molecules
```
Pair<T> molecules
```
    - moleculeIds
```
Pair<T> moleculeIds
```
      The identifier for each of the atom arrays (usually a chain identifier, i.e. a single capital letter) Serves to identify the molecules within the Asymmetric Unit of the crystal
    - transforms
```
Pair<T> transforms
```
      The transformations (crystal operators) applied to each molecule (if applicable)
    - groupAsas1
```
Map<K,V> groupAsas1
```
    - groupAsas2
```
Map<K,V> groupAsas2
```
    - cluster
```
StructureInterfaceCluster cluster
```
- Class org.biojava.nbio.structure.contact.StructureInterfaceCluster extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - id
```
int id
```
    - members
```
List<E> members
```
    - averageScore
```
double averageScore
```
      The average similarity score between all pairs of members in the cluster.
- Class org.biojava.nbio.structure.contact.StructureInterfaceList extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - list
```
List<E> list
```
    - clusters
```
List<E> clusters
```
Package org.biojava.nbio.structure.domain.pdp
- Class org.biojava.nbio.structure.domain.pdp.Domain extends Object implements Serializable
  
  serialVersionUID:
  
  -1293994033102271366L
  - Serialized Fields
    - id
```
String id
```
    - size
```
int size
```
    - nseg
```
int nseg
```
    - score
```
double score
```
    - segments
```
List<E> segments
```
- Class org.biojava.nbio.structure.domain.pdp.Segment extends Object implements Serializable
  
  serialVersionUID:
  
  1393487067559539657L
  - Serialized Fields
    - from
```
Integer from
```
    - to
```
Integer to
```
    - score
```
double score
```
Package org.biojava.nbio.structure.ecod
- Class org.biojava.nbio.structure.ecod.EcodDomain extends Object implements Serializable
  
  serialVersionUID:
  
  -7760082165560332048L
  - Serialized Fields
    - uid
```
Long uid
```
    - domainId
```
String domainId
```
    - manual
```
Boolean manual
```
    - xGroup
```
Integer xGroup
```
    - hGroup
```
Integer hGroup
```
    - tGroup
```
Integer tGroup
```
    - fGroup
```
Integer fGroup
```
    - pdbId
```
String pdbId
```
    - chainId
```
String chainId
```
    - range
```
String range
```
    - seqIdRange
```
String seqIdRange
```
    - architectureName
```
String architectureName
```
    - xGroupName
```
String xGroupName
```
    - hGroupName
```
String hGroupName
```
    - tGroupName
```
String tGroupName
```
    - fGroupName
```
String fGroupName
```
    - assemblyId
```
Long assemblyId
```
    - ligands
```
Set<E> ligands
```
Package org.biojava.nbio.structure.gui
- Class org.biojava.nbio.structure.gui.JMatrixPanel extends JPanel implements Serializable
  
  serialVersionUID:
  
  -1720879395453257846L
  - Serialized Fields
    - _bufImage
```
BufferedImage _bufImage
```
    - matrix
```
Matrix matrix
```
    - cellColor
```
ContinuousColorMapper cellColor
```
    - scale
```
float scale
```
    - fragmentPairs
```
FragmentPair[] fragmentPairs
```
    - aligs
```
AlternativeAlignment[] aligs
```
    - selectedAlignmentPos
```
int selectedAlignmentPos
```
    - params
```
StrucAligParameters params
```
- Class org.biojava.nbio.structure.gui.ScaleableMatrixPanel extends JPanel implements Serializable
  
  serialVersionUID:
  
  -8082261434322968652L
  - Serialized Fields
    - mPanel
```
JMatrixPanel mPanel
```
    - slider
```
JSlider slider
```
    - scroll
```
JScrollPane scroll
```
    - coloring
```
JComboBox<E> coloring
```
    - gradients
```
Map<K,V> gradients
```
- Class org.biojava.nbio.structure.gui.ScaleableMatrixPanel.GradientRenderer extends JPanel implements Serializable
  
  serialVersionUID:
  
  -2000575579184232365L
  - Serialized Fields
    - min
```
int min
```
    - max
```
int max
```
    - title
```
JLabel title
```
    - gradientContainer
```
JPanel gradientContainer
```
- Class org.biojava.nbio.structure.gui.SequenceDisplay extends JPanel implements Serializable
  
  serialVersionUID:
  
  -1829252532712454236L
  - Serialized Fields
    - structure1
```
Structure structure1
```
    - structure2
```
Structure structure2
```
    - alig
```
AlternativeAlignment alig
```
    - structurePairAligner
```
StructurePairAligner structurePairAligner
```
    - panel1
```
SequenceScalePanel panel1
```
    - panel2
```
SequenceScalePanel panel2
```
    - residueSizeSlider
```
JSlider residueSizeSlider
```
    - percentageDisplay
```
JLabel percentageDisplay
```
    - idx1
```
int[] idx1
```
    - idx2
```
int[] idx2
```
    - apos
```
List<E> apos
```
    - scale
```
float scale
```
    - mouseListener1
```
SequenceMouseListener mouseListener1
```
    - mouseListener2
```
SequenceMouseListener mouseListener2
```
    - label1
```
JLabel label1
```
    - label2
```
JLabel label2
```
- Class org.biojava.nbio.structure.gui.WrapLayout extends FlowLayout implements Serializable
  - Serialized Fields
    - preferredLayoutSize
```
Dimension preferredLayoutSize
```
Package org.biojava.nbio.structure.gui.util
- Class org.biojava.nbio.structure.gui.util.AlternativeAlignmentFrame extends JFrame implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - aligs
```
AlternativeAlignment[] aligs
```
    - panel
```
JPanel panel
```
    - structure1
```
Structure structure1
```
    - structure2
```
Structure structure2
```
    - structurePairAligner
```
StructurePairAligner structurePairAligner
```
- Class org.biojava.nbio.structure.gui.util.PDBDirPanel extends JPanel implements Serializable
  
  serialVersionUID:
  
  -5682120627824627408L
  - Serialized Fields
    - debug
```
boolean debug
```
    - pdbDir
```
JTextField pdbDir
```
    - f1
```
JTextField f1
```
    - f2
```
JTextField f2
```
    - c1
```
JTextField c1
```
    - c2
```
JTextField c2
```
- Class org.biojava.nbio.structure.gui.util.PDBServerPanel extends JPanel implements Serializable
  
  serialVersionUID:
  
  -5682120627824627408L
  - Serialized Fields
    - debug
```
boolean debug
```
    - pdbDir
```
JTextField pdbDir
```
    - f1
```
JTextField f1
```
    - f2
```
JTextField f2
```
    - c1
```
JTextField c1
```
    - c2
```
JTextField c2
```
- Class org.biojava.nbio.structure.gui.util.PDBUploadPanel extends JPanel implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - fileType
```
JComboBox<E> fileType
```
    - filePath1
```
JTextField filePath1
```
    - filePath2
```
JTextField filePath2
```
    - chain1
```
JTextField chain1
```
    - chain2
```
JTextField chain2
```
- Class org.biojava.nbio.structure.gui.util.ScopSelectPanel extends JPanel implements Serializable
  
  serialVersionUID:
  
  757947454156959178L
  - Serialized Fields
    - dom1
```
JAutoSuggest dom1
```
    - dom2
```
JAutoSuggest dom2
```
- Class org.biojava.nbio.structure.gui.util.SelectMultiplePanel extends JPanel implements Serializable
  
  serialVersionUID:
  
  757947454156959178L
  - Serialized Fields
    - input
```
JTextField input
```
- Class org.biojava.nbio.structure.gui.util.SequenceScalePanel extends JPanel implements Serializable
  
  serialVersionUID:
  
  7893248902423L
  - Serialized Fields
    - chain
```
Chain chain
```
    - chainLength
```
int chainLength
```
    - scale
```
float scale
```
    - seqArr
```
Character[] seqArr
```
    - coordManager
```
CoordManager coordManager
```
    - position
```
int position
```
    - apos
```
List<E> apos
```
Package org.biojava.nbio.structure.gui.util.color
- Class org.biojava.nbio.structure.gui.util.color.GradientPanel extends JPanel implements Serializable
  
  serialVersionUID:
  
  -6387922432121206731L
  - Serialized Fields
    - mapper
```
ContinuousColorMapper mapper
```
    - min
```
double min
```
    - max
```
double max
```
- Class org.biojava.nbio.structure.gui.util.color.HSVColorSpace extends ColorSpace implements Serializable
  
  serialVersionUID:
  
  8324413992279510075L
Package org.biojava.nbio.structure.io
- Class org.biojava.nbio.structure.io.FileParsingParameters extends Object implements Serializable
  
  serialVersionUID:
  
  5878292315163939027L
  - Serialized Fields
    - parseSecStruc
```
boolean parseSecStruc
```
      Flag to detect if the secondary structure info should be read
    - alignSeqRes
```
boolean alignSeqRes
```
      Flag to control if SEQRES and ATOM records should be aligned
    - parseCAOnly
```
boolean parseCAOnly
```
      Flag to control reading in only Calpha atoms - this is useful for parsing large structures like 1htq.
    - headerOnly
```
boolean headerOnly
```
      Flag to parse header only
    - updateRemediatedFiles
```
boolean updateRemediatedFiles
```
      Update locally cached files to the latest version of remediated files
    - atomCaThreshold
```
int atomCaThreshold
```
    - parseBioAssembly
```
boolean parseBioAssembly
```
      Should we parse the biological assembly information from a file?
    - createAtomBonds
```
boolean createAtomBonds
```
      Should we create bonds between atoms when parsing a file?
    - createAtomCharges
```
boolean createAtomCharges
```
      Should we create charges on atoms when parsing a file?
    - useInternalChainId
```
boolean useInternalChainId
```
      Should we use internal (asym_id) or public facing (author) chain ids
    - maxAtoms
```
int maxAtoms
```
    - fullAtomNames
```
String[] fullAtomNames
```
- Class org.biojava.nbio.structure.io.PDBParseException extends Exception implements Serializable
  
  serialVersionUID:
  
  219047230178423923L
- Class org.biojava.nbio.structure.io.SSBondImpl extends Object implements Serializable
  
  serialVersionUID:
  
  -8663681100691188647L
  - Serialized Fields
    - serNum
```
int serNum
```
    - chainID1
```
String chainID1
```
    - chainID2
```
String chainID2
```
    - resnum1
```
String resnum1
```
    - resnum2
```
String resnum2
```
    - insCode1
```
String insCode1
```
    - insCode2
```
String insCode2
```
Package org.biojava.nbio.structure.io.mmcif.model
- Class org.biojava.nbio.structure.io.mmcif.model.ChemComp extends Object implements Serializable
  
  serialVersionUID:
  
  -4736341142030215915L
  - Serialized Fields
    - id
```
String id
```
    - name
```
String name
```
    - type
```
String type
```
    - pdbx_type
```
String pdbx_type
```
    - formula
```
String formula
```
    - mon_nstd_parent_comp_id
```
String mon_nstd_parent_comp_id
```
    - pdbx_synonyms
```
String pdbx_synonyms
```
    - pdbx_formal_charge
```
String pdbx_formal_charge
```
    - pdbx_initial_date
```
String pdbx_initial_date
```
    - pdbx_modified_date
```
String pdbx_modified_date
```
    - pdbx_ambiguous_flag
```
String pdbx_ambiguous_flag
```
    - pdbx_release_status
```
String pdbx_release_status
```
    - pdbx_replaced_by
```
String pdbx_replaced_by
```
    - pdbx_replaces
```
String pdbx_replaces
```
    - formula_weight
```
String formula_weight
```
    - one_letter_code
```
String one_letter_code
```
    - three_letter_code
```
String three_letter_code
```
    - pdbx_model_coordinates_details
```
String pdbx_model_coordinates_details
```
    - pdbx_model_coordinates_missing_flag
```
String pdbx_model_coordinates_missing_flag
```
    - pdbx_ideal_coordinates_details
```
String pdbx_ideal_coordinates_details
```
    - pdbx_ideal_coordinates_missing_flag
```
String pdbx_ideal_coordinates_missing_flag
```
    - pdbx_model_coordinates_db_code
```
String pdbx_model_coordinates_db_code
```
    - pdbx_subcomponent_list
```
String pdbx_subcomponent_list
```
    - pdbx_processing_site
```
String pdbx_processing_site
```
    - mon_nstd_flag
```
String mon_nstd_flag
```
    - descriptors
```
List<E> descriptors
```
    - bonds
```
List<E> bonds
```
    - atoms
```
List<E> atoms
```
    - residueType
```
ResidueType residueType
```
    - polymerType
```
PolymerType polymerType
```
    - standard
```
boolean standard
```
- Class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom extends Object implements Serializable
  
  serialVersionUID:
  
  4070599340294758941L
  - Serialized Fields
    - comp_id
```
String comp_id
```
    - atom_id
```
String atom_id
```
    - alt_atom_id
```
String alt_atom_id
```
    - type_symbol
```
String type_symbol
```
    - charge
```
String charge
```
    - pdbx_align
```
String pdbx_align
```
    - pdbx_aromatic_flag
```
String pdbx_aromatic_flag
```
    - pdbx_leaving_atom_flag
```
String pdbx_leaving_atom_flag
```
    - pdbx_stereo_config
```
String pdbx_stereo_config
```
    - model_Cartn_x
```
String model_Cartn_x
```
    - model_Cartn_y
```
String model_Cartn_y
```
    - model_Cartn_z
```
String model_Cartn_z
```
    - pdbx_model_Cartn_x_ideal
```
String pdbx_model_Cartn_x_ideal
```
    - pdbx_model_Cartn_y_ideal
```
String pdbx_model_Cartn_y_ideal
```
    - pdbx_model_Cartn_z_ideal
```
String pdbx_model_Cartn_z_ideal
```
    - pdbx_component_comp_id
```
String pdbx_component_comp_id
```
    - pdbx_residue_numbering
```
String pdbx_residue_numbering
```
    - pdbx_component_atom_id
```
String pdbx_component_atom_id
```
    - pdbx_polymer_type
```
String pdbx_polymer_type
```
    - pdbx_ref_id
```
String pdbx_ref_id
```
    - pdbx_component_id
```
String pdbx_component_id
```
    - pdbx_ordinal
```
String pdbx_ordinal
```
- Class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond extends Object implements Serializable
  
  serialVersionUID:
  
  5905371029161975421L
  - Serialized Fields
    - comp_id
```
String comp_id
```
    - atom_id_1
```
String atom_id_1
```
    - atom_id_2
```
String atom_id_2
```
    - value_order
```
String value_order
```
    - pdbx_aromatic_flag
```
String pdbx_aromatic_flag
```
    - pdbx_stereo_config
```
String pdbx_stereo_config
```
    - pdbx_ordinal
```
String pdbx_ordinal
```
- Class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor extends Object implements Serializable
  
  serialVersionUID:
  
  1078685833800736278L
  - Serialized Fields
    - comp_id
```
String comp_id
```
    - type
```
String type
```
    - program
```
String program
```
    - program_version
```
String program_version
```
    - descriptor
```
String descriptor
```
- Class org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - rev_num
```
String rev_num
```
    - type
```
String type
```
    - details
```
String details
```
- Class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly extends Object implements Serializable
  
  serialVersionUID:
  
  3104504686693887219L
  - Serialized Fields
    - id
```
String id
```
    - details
```
String details
```
    - method_details
```
String method_details
```
    - oligomeric_details
```
String oligomeric_details
```
    - oligomeric_count
```
String oligomeric_count
```
- Class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen extends Object implements Serializable
  
  serialVersionUID:
  
  6739568389242514332L
  - Serialized Fields
    - assembly_id
```
String assembly_id
```
    - oper_expression
```
String oper_expression
```
    - asym_id_list
```
String asym_id_list
```
- Class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList extends Object implements Serializable
  
  serialVersionUID:
  
  8933552854747969787L
  - Serialized Fields
    - id
```
String id
```
    - type
```
String type
```
    - symmetry_operation
```
String symmetry_operation
```
    - matrix11
```
String matrix11
```
    - matrix12
```
String matrix12
```
    - matrix13
```
String matrix13
```
    - vector1
```
String vector1
```
    - matrix21
```
String matrix21
```
    - matrix22
```
String matrix22
```
    - matrix23
```
String matrix23
```
    - vector2
```
String vector2
```
    - matrix31
```
String matrix31
```
    - matrix32
```
String matrix32
```
    - matrix33
```
String matrix33
```
    - vector3
```
String vector3
```
    - name
```
String name
```
    - matrix
```
Matrix matrix
```
    - vector
```
double[] vector
```
Package org.biojava.nbio.structure.io.sifts
- Class org.biojava.nbio.structure.io.sifts.SiftsEntity extends Object implements Serializable
  
  serialVersionUID:
  
  750353252427491487L
  - Serialized Fields
    - type
```
String type
```
    - entityId
```
String entityId
```
    - segments
```
List<E> segments
```
- Class org.biojava.nbio.structure.io.sifts.SiftsResidue extends Object implements Serializable
  
  serialVersionUID:
  
  3425769737629800828L
  - Serialized Fields
    - pdbResNum
```
String pdbResNum
```
    - pdbResName
```
String pdbResName
```
    - chainId
```
String chainId
```
    - uniProtResName
```
String uniProtResName
```
    - uniProtPos
```
Integer uniProtPos
```
    - naturalPos
```
Integer naturalPos
```
    - seqResName
```
String seqResName
```
    - pdbId
```
String pdbId
```
    - uniProtAccessionId
```
String uniProtAccessionId
```
    - notObserved
```
Boolean notObserved
```
- Class org.biojava.nbio.structure.io.sifts.SiftsSegment extends Object implements Serializable
  
  serialVersionUID:
  
  -8005129863256307153L
  - Serialized Fields
    - segId
```
String segId
```
    - start
```
String start
```
    - end
```
String end
```
    - residues
```
List<E> residues
```
Package org.biojava.nbio.structure.jama
- Class org.biojava.nbio.structure.jama.CholeskyDecomposition extends Object implements Serializable
  
  serialVersionUID:
  
  224348942390823L
  - Serialized Fields
    - L
```
double[][] L
```
      Array for internal storage of decomposition.
      
      internal array storage.
    - n
```
int n
```
      Row and column dimension (square matrix).
      
      matrix dimension.
    - isspd
```
boolean isspd
```
      Symmetric and positive definite flag.
      
      is symmetric and positive definite flag.
- Class org.biojava.nbio.structure.jama.EigenvalueDecomposition extends Object implements Serializable
  
  serialVersionUID:
  
  3557806515310435894L
  - Serialized Fields
    - n
```
int n
```
      Row and column dimension (square matrix).
      
      matrix dimension.
    - issymmetric
```
boolean issymmetric
```
      Symmetry flag.
      
      internal symmetry flag.
    - d
```
double[] d
```
      Arrays for internal storage of eigenvalues.
      
      internal storage of eigenvalues.
    - e
```
double[] e
```
      Arrays for internal storage of eigenvalues.
      
      internal storage of eigenvalues.
    - V
```
double[][] V
```
      Array for internal storage of eigenvectors.
      
      internal storage of eigenvectors.
    - H
```
double[][] H
```
      Array for internal storage of nonsymmetric Hessenberg form.
      
      internal storage of nonsymmetric Hessenberg form.
    - ort
```
double[] ort
```
      Working storage for nonsymmetric algorithm.
      
      working storage for nonsymmetric algorithm.
- Class org.biojava.nbio.structure.jama.LUDecomposition extends Object implements Serializable
  
  serialVersionUID:
  
  9271028462937843L
  - Serialized Fields
    - LU
```
double[][] LU
```
      Array for internal storage of decomposition.
      
      internal array storage.
    - m
```
int m
```
      Row and column dimensions, and pivot sign.
      
      column dimension.
    - n
```
int n
```
      Row and column dimensions, and pivot sign.
      
      column dimension.
    - pivsign
```
int pivsign
```
      Row and column dimensions, and pivot sign.
      
      column dimension.
    - piv
```
int[] piv
```
      Internal storage of pivot vector.
      
      pivot vector.
- Class org.biojava.nbio.structure.jama.Matrix extends Object implements Serializable
  
  serialVersionUID:
  
  8492558293015348719L
  - Serialized Fields
    - A
```
double[][] A
```
      Array for internal storage of elements.
      
      internal array storage.
    - m
```
int m
```
      Row and column dimensions.
      
      row dimension.
    - n
```
int n
```
      Row and column dimensions.
      
      row dimension.
- Class org.biojava.nbio.structure.jama.QRDecomposition extends Object implements Serializable
  
  serialVersionUID:
  
  10293720387423L
  - Serialized Fields
    - QR
```
double[][] QR
```
      Array for internal storage of decomposition.
      
      internal array storage.
    - m
```
int m
```
      Row and column dimensions.
      
      column dimension.
    - n
```
int n
```
      Row and column dimensions.
      
      column dimension.
    - Rdiag
```
double[] Rdiag
```
      Array for internal storage of diagonal of R.
      
      diagonal of R.
- Class org.biojava.nbio.structure.jama.SingularValueDecomposition extends Object implements Serializable
  
  serialVersionUID:
  
  640239472093534756L
  - Serialized Fields
    - U
```
double[][] U
```
      Arrays for internal storage of U and V.
      
      internal storage of U.
    - V
```
double[][] V
```
      Arrays for internal storage of U and V.
      
      internal storage of U.
    - s
```
double[] s
```
      Array for internal storage of singular values.
      
      internal storage of singular values.
    - m
```
int m
```
      Row and column dimensions.
      
      row dimension.
    - n
```
int n
```
      Row and column dimensions.
      
      row dimension.
Package org.biojava.nbio.structure.math
- Class org.biojava.nbio.structure.math.SparseSquareMatrix extends Object implements Serializable
  
  serialVersionUID:
  
  -5217767192992868955L
  - Serialized Fields
    - N
```
int N
```
    - rows
```
SparseVector[] rows
```
- Class org.biojava.nbio.structure.math.SparseVector extends Object implements Serializable
  
  serialVersionUID:
  
  1174668523213431927L
  - Serialized Fields
    - N
```
int N
```
    - symbolTable
```
SymbolTable<Key extends Comparable<Key>,Value> symbolTable
```
- Class org.biojava.nbio.structure.math.SymbolTable extends Object implements Serializable
  
  serialVersionUID:
  
  -4417561575046471931L
  - Serialized Fields
    - st
```
TreeMap<K,V> st
```
Package org.biojava.nbio.structure.quaternary
- Class org.biojava.nbio.structure.quaternary.BioAssemblyInfo extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - id
```
int id
```
    - transforms
```
List<E> transforms
```
    - macromolecularSize
```
int macromolecularSize
```
- Class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation extends Object implements Serializable
  
  serialVersionUID:
  
  -6388503076022480391L
  - Serialized Fields
    - id
```
String id
```
    - chainId
```
String chainId
```
    - transformation
```
javax.vecmath.Matrix4d transformation
```
Package org.biojava.nbio.structure.scop
- Class org.biojava.nbio.structure.scop.ScopDescription extends Object implements Serializable
  
  serialVersionUID:
  
  8579808155176839161L
  - Serialized Fields
    - sunID
```
int sunID
```
    - category
```
ScopCategory category
```
    - classificationId
```
String classificationId
```
    - name
```
String name
```
    - description
```
String description
```
- Class org.biojava.nbio.structure.scop.ScopDomain extends Object implements Serializable
  
  serialVersionUID:
  
  5890476209571654301L
  - Serialized Fields
    - scopId
```
String scopId
```
    - pdbId
```
String pdbId
```
    - ranges
```
List<E> ranges
```
    - classificationId
```
String classificationId
```
    - sunid
```
Integer sunid
```
    - classId
```
int classId
```
    - foldId
```
int foldId
```
    - superfamilyId
```
int superfamilyId
```
    - familyId
```
int familyId
```
    - domainId
```
int domainId
```
    - speciesId
```
int speciesId
```
    - px
```
int px
```
- Class org.biojava.nbio.structure.scop.ScopIOException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  1L
- Class org.biojava.nbio.structure.scop.ScopNode extends Object implements Serializable
  
  serialVersionUID:
  
  1187083944488580995L
  - Serialized Fields
    - sunid
```
int sunid
```
    - parentSunid
```
int parentSunid
```
    - children
```
List<E> children
```
Package org.biojava.nbio.structure.scop.server
- Class org.biojava.nbio.structure.scop.server.ListStringWrapper extends Object implements Serializable
  
  serialVersionUID:
  
  4193799052494327416L
  - Serialized Fields
    - data
```
List<E> data
```
- Class org.biojava.nbio.structure.scop.server.ScopDescriptions extends Object implements Serializable
  
  serialVersionUID:
  
  4924350548761431852L
  - Serialized Fields
    - scopDescriptions
```
List<E> scopDescriptions
```
- Class org.biojava.nbio.structure.scop.server.ScopDomains extends Object implements Serializable
  
  serialVersionUID:
  
  7693404355005856746L
  - Serialized Fields
    - domains
```
List<E> domains
```
- Class org.biojava.nbio.structure.scop.server.ScopNodes extends Object implements Serializable
  
  serialVersionUID:
  
  5327454882500340305L
  - Serialized Fields
    - scopNodes
```
List<E> scopNodes
```
- Class org.biojava.nbio.structure.scop.server.TreeSetStringWrapper extends Object implements Serializable
  
  serialVersionUID:
  
  4193799052494327416L
  - Serialized Fields
    - data
```
TreeSet<E> data
```
Package org.biojava.nbio.structure.symmetry.core
- Class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - minimumSequenceLength
```
int minimumSequenceLength
```
    - absoluteMinimumSequenceLength
```
int absoluteMinimumSequenceLength
```
    - minimumSequenceLengthFraction
```
double minimumSequenceLengthFraction
```
    - sequenceIdentityThresholds
```
double[] sequenceIdentityThresholds
```
    - sequencePseudoSymmetryThreshold
```
double sequencePseudoSymmetryThreshold
```
    - alignmentFractionThreshold
```
double alignmentFractionThreshold
```
    - rmsdThreshold
```
double rmsdThreshold
```
    - angleThreshold
```
double angleThreshold
```
    - helixRmsdThreshold
```
double helixRmsdThreshold
```
    - helixRmsdToRiseRatio
```
double helixRmsdToRiseRatio
```
    - minimumHelixRise
```
double minimumHelixRise
```
    - minimumHelixAngle
```
double minimumHelixAngle
```
    - maximumLocalCombinations
```
int maximumLocalCombinations
```
    - maximumLocalResults
```
int maximumLocalResults
```
    - maximumLocalSubunits
```
int maximumLocalSubunits
```
    - localSymmetry
```
boolean localSymmetry
```
    - localTimeLimit
```
double localTimeLimit
```
    - onTheFly
```
boolean onTheFly
```
    - verbose
```
boolean verbose
```
Package org.biojava.nbio.structure.symmetry.gui
- Class org.biojava.nbio.structure.symmetry.gui.SymmetryGui extends JFrame implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - params
```
CESymmParameters params
```
    - abortB
```
JButton abortB
```
    - tab1
```
SelectPDBPanel tab1
```
    - tab2
```
PDBUploadPanel tab2
```
    - tab3
```
ScopSelectPanel tab3
```
    - thread
```
Thread thread
```
    - alicalc
```
AlignmentCalculationRunnable alicalc
```
    - masterPane
```
JTabbedPane masterPane
```
    - tabPane
```
JTabbedPane tabPane
```
    - progress
```
JProgressBar progress
```
Package org.biojava.nbio.structure.symmetry.internal
- Class org.biojava.nbio.structure.symmetry.internal.RefinerFailedException extends Exception implements Serializable
  
  serialVersionUID:
  
  -3592155787060329421L
Package org.biojava.nbio.structure.symmetry.utils
- Class org.biojava.nbio.structure.symmetry.utils.BlastClustReader extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - sequenceIdentity
```
int sequenceIdentity
```
    - clusters
```
List<E> clusters
```
Package org.biojava.nbio.structure.validation
- Class org.biojava.nbio.structure.validation.WwPDBValidationInformation extends Object implements Serializable
  
  serialVersionUID:
  
  -996804963717482650L
  - Serialized Fields
    - entry
```
Entry entry
```
    - modelledSubgroup
```
List<E> modelledSubgroup
```
    - programs
```
Programs programs
```
Package org.biojava.nbio.structure.xtal
- Class org.biojava.nbio.structure.xtal.CrystalCell extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - a
```
double a
```
    - b
```
double b
```
    - c
```
double c
```
    - alpha
```
double alpha
```
    - beta
```
double beta
```
    - gamma
```
double gamma
```
    - alphaRad
```
double alphaRad
```
    - betaRad
```
double betaRad
```
    - gammaRad
```
double gammaRad
```
    - volume
```
double volume
```
    - maxDimension
```
double maxDimension
```
    - M
```
javax.vecmath.Matrix3d M
```
    - Minv
```
javax.vecmath.Matrix3d Minv
```
    - Mtransp
```
javax.vecmath.Matrix3d Mtransp
```
    - MtranspInv
```
javax.vecmath.Matrix3d MtranspInv
```
- Class org.biojava.nbio.structure.xtal.CrystalTransform extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - sg
```
SpaceGroup sg
```
      The space group to which this transform belongs
    - transformId
```
int transformId
```
      The transform id corresponding to the SpaceGroup's transform indices. From 0 (identity) to m (m=number of symmetry operations of the space group) It is unique within the unit cell but equivalent units of different crystal unit cells will have same id
    - matTransform
```
javax.vecmath.Matrix4d matTransform
```
      The 4-dimensional matrix transformation in crystal basis. Note that the translational component of this matrix is not necessarily identical to crystalTranslation since some operators have fractional translations within the cell
    - crystalTranslation
```
javax.vecmath.Point3i crystalTranslation
```
      The crystal translation (always integer)
- Class org.biojava.nbio.structure.xtal.SpaceGroup extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - id
```
int id
```
    - multiplicity
```
int multiplicity
```
    - primitiveMultiplicity
```
int primitiveMultiplicity
```
    - shortSymbol
```
String shortSymbol
```
    - altShortSymbol
```
String altShortSymbol
```
    - transformations
```
List<E> transformations
```
    - transfAlgebraic
```
List<E> transfAlgebraic
```
    - cellTranslations
```
javax.vecmath.Vector3d[] cellTranslations
```
    - axisAngles
```
javax.vecmath.AxisAngle4d[] axisAngles
```
    - axisTypes
```
int[] axisTypes
```
    - bravLattice
```
BravaisLattice bravLattice
```
Package org.biojava.nbio.structure.xtal.io
- Class org.biojava.nbio.structure.xtal.io.TreeMapSpaceGroupWrapper extends Object implements Serializable
  
  serialVersionUID:
  
  4193799052494327416L
  - Serialized Fields
    - data
```
TreeMap<K,V> data
```
Package org.biojava.nbio.survival.data
- Class org.biojava.nbio.survival.data.CompactCharSequence extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - offset
```
int offset
```
    - end
```
int end
```
    - data
```
byte[] data
```
    - nullstring
```
boolean nullstring
```
Package org.biojava.nbio.survival.kaplanmeier.figure
- Class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure extends JPanel implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - title
```
ArrayList<E> title
```
    - top
```
int top
```
    - bottom
```
int bottom
```
    - left
```
int left
```
    - right
```
int right
```
    - titleHeight
```
int titleHeight
```
    - xAxisLabelHeight
```
int xAxisLabelHeight
```
    - labelWidth
```
int labelWidth
```
    - maxTime
```
Double maxTime
```
    - minX
```
Double minX
```
    - maxX
```
Double maxX
```
    - minY
```
Double minY
```
    - maxY
```
Double maxY
```
    - mean
```
Double mean
```
    - fm
```
FontMetrics fm
```
    - kmfi
```
KMFigureInfo kmfi
```
    - lineInfoList
```
ArrayList<E> lineInfoList
```
    - siList
```
ArrayList<E> siList
```
    - variable
```
String variable
```
    - fileName
```
String fileName
```
    - df
```
DecimalFormat df
```
- Class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure extends JPanel implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - title
```
ArrayList<E> title
```
    - top
```
int top
```
    - bottom
```
int bottom
```
    - left
```
int left
```
    - yaxisLabel
```
int yaxisLabel
```
    - right
```
int right
```
    - titleHeight
```
int titleHeight
```
    - xAxisLabelHeight
```
int xAxisLabelHeight
```
    - labelWidth
```
int labelWidth
```
    - minTime
```
double minTime
```
    - maxTime
```
double maxTime
```
    - minPercentage
```
double minPercentage
```
    - maxPercentage
```
double maxPercentage
```
    - fm
```
FontMetrics fm
```
    - kmfi
```
KMFigureInfo kmfi
```
    - survivalData
```
LinkedHashMap<K,V> survivalData
```
    - lineInfoList
```
ArrayList<E> lineInfoList
```
    - sfi
```
SurvFitInfo sfi
```
    - fileName
```
String fileName
```
    - xAxisTimeValues
```
ArrayList<E> xAxisTimeValues
```
    - xAxisTimeCoordinates
```
ArrayList<E> xAxisTimeCoordinates
```
    - df
```
DecimalFormat df
```
    - adjustedPercentIncrement
```
Double adjustedPercentIncrement
```
- Class org.biojava.nbio.survival.kaplanmeier.figure.NumbersAtRiskPanel extends JPanel implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - kmf
```
KaplanMeierFigure kmf
```
    - timePercentage
```
Double timePercentage
```
Package org.biojava.nbio.ws.alignment
Package org.biojava.nbio.ws.alignment.qblast
- Class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties extends Object implements Serializable
  
  serialVersionUID:
  
  7158270364392309841L
  - Serialized Fields
    - param
```
Map<K,V> param
```
- Class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties extends Object implements Serializable
  
  serialVersionUID:
  
  -9202060390925345163L
  - Serialized Fields
    - param
```
Map<K,V> param
```
Package org.biojava.nbio.ws.hmmer
- Class org.biojava.nbio.ws.hmmer.HmmerDomain extends Object implements Serializable
  
  serialVersionUID:
  
  8004302800150892757L
  - Serialized Fields
    - sqFrom
```
Integer sqFrom
```
    - sqTo
```
Integer sqTo
```
    - aliLenth
```
Integer aliLenth
```
    - simCount
```
Integer simCount
```
    - hmmFrom
```
Integer hmmFrom
```
    - hmmTo
```
Integer hmmTo
```
    - hmmName
```
String hmmName
```
    - hmmDesc
```
String hmmDesc
```
    - hmmAcc
```
String hmmAcc
```
    - evalue
```
Float evalue
```
- Class org.biojava.nbio.ws.hmmer.HmmerResult extends Object implements Serializable
  
  serialVersionUID:
  
  -6016026193090737943L
  - Serialized Fields
    - desc
```
String desc
```
    - score
```
Float score
```
    - evalue
```
Float evalue
```
    - pvalue
```
Double pvalue
```
    - acc
```
String acc
```
    - dcl
```
Integer dcl
```
    - name
```
String name
```
    - ndom
```
Integer ndom
```
    - nreported
```
Integer nreported
```
    - domains
```
SortedSet<E> domains
```

Serialized Form

Package demo

Class demo.GetColorGradient extends JPanel implements Serializable

Serialized Fields

colors

Package org.biojava.nbio.alignment

Class org.biojava.nbio.alignment.SimpleGapPenalty extends Object implements Serializable

Serialized Fields

type

gop

gep

Package org.biojava.nbio.core.alignment

Class org.biojava.nbio.core.alignment.SimpleAlignedSequence extends Object implements Serializable

Serialized Fields

prev

original

length

numBefore

numAfter

location

numGaps

numGapPositions

alignmentFromSequence

sequenceFromAlignment

Class org.biojava.nbio.core.alignment.SimpleProfile extends Object implements Serializable

Serialized Fields

list

originals

length

Class org.biojava.nbio.core.alignment.SimpleProfilePair extends SimpleProfile<S extends Sequence<C>,C extends Compound> implements Serializable

Serialized Fields

query

target

Class org.biojava.nbio.core.alignment.SimpleSequencePair extends SimpleProfile<S extends Sequence<C>,C extends Compound> implements Serializable

Serialized Fields

identicals

similars

Package org.biojava.nbio.core.alignment.matrices

Class org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix extends Object implements Serializable

Serialized Fields

compoundSet

description

name

matrix

max

min

rows

cols

Class org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper extends Object implements Serializable

Package org.biojava.nbio.core.exceptions

Class org.biojava.nbio.core.exceptions.CompoundNotFoundException extends Exception implements Serializable

Class org.biojava.nbio.core.exceptions.ParserException extends RuntimeException implements Serializable

Class org.biojava.nbio.core.exceptions.TranslationException extends RuntimeException implements Serializable

Package org.biojava.nbio.core.sequence.compound

Class org.biojava.nbio.core.sequence.compound.AminoAcidCompound extends AbstractCompound implements Serializable

Serialized Fields

compoundSet

Class org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet extends Object implements Serializable

Serialized Fields

aminoAcidCompoundCache

aminoAcidCompoundCache3Letter

equivalentsCache

Package org.biojava.nbio.core.sequence.location

Class org.biojava.nbio.core.sequence.location.FuzzyPoint extends SimplePoint implements Serializable

Serialized Fields

min

max

resolver

Class org.biojava.nbio.core.sequence.location.InsdcLocations.BondLocation extends AbstractLocation implements Serializable

Class org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation extends SimpleLocation implements Serializable

Class org.biojava.nbio.core.sequence.location.InsdcLocations.OneOfLocation extends AbstractLocation implements Serializable

Class org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation extends SimpleLocation implements Serializable

Class org.biojava.nbio.core.sequence.location.SequenceLocation extends SimpleLocation implements Serializable

Serialized Fields

sequence

Class org.biojava.nbio.core.sequence.location.SimpleLocation extends AbstractLocation implements Serializable

Class org.biojava.nbio.core.sequence.location.SimplePoint extends Object implements Serializable

Serialized Fields

position

unknown