Serialized Form (biojava-structure 5.4.0 API)

Package org.biojava.nbio.structure
- Class org.biojava.nbio.structure.AminoAcidImpl extends HetatomImpl implements Serializable
  
  serialVersionUID:
  
  -6018854413829044230L
  - Serialized Fields
    - amino_char
```
java.lang.Character amino_char
```
      IUPAC amino acid residue names
    - recordType
```
java.lang.String recordType
```
- Class org.biojava.nbio.structure.AtomImpl extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -2258364127420562883L
  - Serialized Fields
    - name
```
java.lang.String name
```
    - element
```
Element element
```
    - coords
```
javax.vecmath.Point3d coords
```
    - pdbserial
```
int pdbserial
```
    - charge
```
short charge
```
    - occupancy
```
float occupancy
```
    - tempfactor
```
float tempfactor
```
    - altLoc
```
char altLoc
```
    - parent
```
Group parent
```
    - bonds
```
java.util.List<E> bonds
```
- Class org.biojava.nbio.structure.Author extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  4840370515056666418L
  - Serialized Fields
    - surname
```
java.lang.String surname
```
    - initials
```
java.lang.String initials
```
- Class org.biojava.nbio.structure.BioAssemblyIdentifier extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -356206725119993449L
  - Serialized Fields
    - pdbCode
```
java.lang.String pdbCode
```
    - biolNr
```
int biolNr
```
- Class org.biojava.nbio.structure.BondImpl extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  8836120946858134380L
  - Serialized Fields
    - atomA
```
Atom atomA
```
    - atomB
```
Atom atomB
```
    - bondOrder
```
int bondOrder
```
- Class org.biojava.nbio.structure.ChainImpl extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1990171805277911840L
  - Serialized Fields
    - swissprot_id
```
java.lang.String swissprot_id
```
    - authId
```
java.lang.String authId
```
    - groups
```
java.util.List<E> groups
```
    - seqResGroups
```
java.util.List<E> seqResGroups
```
    - entity
```
EntityInfo entity
```
    - parent
```
Structure parent
```
    - pdbResnumMap
```
java.util.Map<K,V> pdbResnumMap
```
    - asymId
```
java.lang.String asymId
```
    - seqMisMatches
```
java.util.List<E> seqMisMatches
```
- Class org.biojava.nbio.structure.DBRef extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -1050178577542224379L
  - Serialized Fields
    - parent
```
Structure parent
```
    - idCode
```
java.lang.String idCode
```
    - chainName
```
java.lang.String chainName
```
    - seqbegin
```
int seqbegin
```
    - insertBegin
```
char insertBegin
```
    - seqEnd
```
int seqEnd
```
    - insertEnd
```
char insertEnd
```
    - database
```
java.lang.String database
```
    - dbAccession
```
java.lang.String dbAccession
```
    - dbIdCode
```
java.lang.String dbIdCode
```
    - dbSeqBegin
```
int dbSeqBegin
```
    - idbnsBegin
```
char idbnsBegin
```
    - dbSeqEnd
```
int dbSeqEnd
```
    - idbnsEnd
```
char idbnsEnd
```
    - id
```
java.lang.Long id
```
- Class org.biojava.nbio.structure.EntityInfo extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  2991897825657586356L
  - Serialized Fields
    - chains
```
java.util.List<E> chains
```
      The list of chains that are described by this EntityInfo
    - molId
```
int molId
```
      The Molecule identifier, called entity_id in mmCIF dictionary
    - chains2pdbResNums2ResSerials
```
java.util.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 EntityInfo.getAlignedResIndex(Group, Chain) Keys are asym_ids of chains, values maps of residue numbers to indices.
    - refChainId
```
java.lang.String refChainId
```
    - description
```
java.lang.String description
```
    - title
```
java.lang.String title
```
    - type
```
EntityType type
```
      The type of entity (polymer, non-polymer, water)
    - synonyms
```
java.util.List<E> synonyms
```
    - ecNums
```
java.util.List<E> ecNums
```
    - engineered
```
java.lang.String engineered
```
    - mutation
```
java.lang.String mutation
```
    - biologicalUnit
```
java.lang.String biologicalUnit
```
    - details
```
java.lang.String details
```
    - numRes
```
java.lang.String numRes
```
    - resNames
```
java.lang.String resNames
```
    - headerVars
```
java.lang.String headerVars
```
    - synthetic
```
java.lang.String synthetic
```
    - fragment
```
java.lang.String fragment
```
    - organismScientific
```
java.lang.String organismScientific
```
    - organismTaxId
```
java.lang.String organismTaxId
```
    - organismCommon
```
java.lang.String organismCommon
```
    - strain
```
java.lang.String strain
```
    - variant
```
java.lang.String variant
```
    - cellLine
```
java.lang.String cellLine
```
    - atcc
```
java.lang.String atcc
```
    - organ
```
java.lang.String organ
```
    - tissue
```
java.lang.String tissue
```
    - cell
```
java.lang.String cell
```
    - organelle
```
java.lang.String organelle
```
    - secretion
```
java.lang.String secretion
```
    - gene
```
java.lang.String gene
```
    - cellularLocation
```
java.lang.String cellularLocation
```
    - expressionSystem
```
java.lang.String expressionSystem
```
    - expressionSystemTaxId
```
java.lang.String expressionSystemTaxId
```
    - expressionSystemStrain
```
java.lang.String expressionSystemStrain
```
    - expressionSystemVariant
```
java.lang.String expressionSystemVariant
```
    - expressionSystemCellLine
```
java.lang.String expressionSystemCellLine
```
    - expressionSystemAtccNumber
```
java.lang.String expressionSystemAtccNumber
```
    - expressionSystemOrgan
```
java.lang.String expressionSystemOrgan
```
    - expressionSystemTissue
```
java.lang.String expressionSystemTissue
```
    - expressionSystemCell
```
java.lang.String expressionSystemCell
```
    - expressionSystemOrganelle
```
java.lang.String expressionSystemOrganelle
```
    - expressionSystemCellularLocation
```
java.lang.String expressionSystemCellularLocation
```
    - expressionSystemVectorType
```
java.lang.String expressionSystemVectorType
```
    - expressionSystemVector
```
java.lang.String expressionSystemVector
```
    - expressionSystemPlasmid
```
java.lang.String expressionSystemPlasmid
```
    - expressionSystemGene
```
java.lang.String expressionSystemGene
```
    - expressionSystemOtherDetails
```
java.lang.String expressionSystemOtherDetails
```
    - id
```
java.lang.Long id
```
- Class org.biojava.nbio.structure.HetatomImpl extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  4491470432023820382L
  - Serialized Fields
    - properties
```
java.util.Map<K,V> properties
```
    - id
```
long id
```
    - pdb_flag
```
boolean pdb_flag
```
      stores if 3d coordinates are available.
    - pdb_name
```
java.lang.String pdb_name
```
      3 letter name of amino acid in pdb file.
    - residueNumber
```
ResidueNumber residueNumber
```
    - atoms
```
java.util.List<E> atoms
```
    - parent
```
Chain parent
```
    - isHetAtomInFile
```
boolean isHetAtomInFile
```
    - atomNameLookup
```
java.util.Map<K,V> atomNameLookup
```
    - chemComp
```
ChemComp chemComp
```
    - altLocs
```
java.util.List<E> altLocs
```
- Class org.biojava.nbio.structure.JournalArticle extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  5062668226159515468L
  - Serialized Fields
    - authorList
```
java.util.List<E> authorList
```
    - editorList
```
java.util.List<E> editorList
```
    - title
```
java.lang.String title
```
    - ref
```
java.lang.String ref
```
    - journalName
```
java.lang.String journalName
```
    - volume
```
java.lang.String volume
```
    - startPage
```
java.lang.String startPage
```
    - publicationDate
```
int publicationDate
```
    - publisher
```
java.lang.String publisher
```
    - refn
```
java.lang.String refn
```
    - pmid
```
java.lang.String pmid
```
    - doi
```
java.lang.String doi
```
    - published
```
boolean published
```
- Class org.biojava.nbio.structure.Model extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  5320613424668781882L
  - Serialized Fields
    - polyChains
```
java.util.List<E> polyChains
```
    - nonPolyChains
```
java.util.List<E> nonPolyChains
```
    - waterChains
```
java.util.List<E> waterChains
```
- Class org.biojava.nbio.structure.NucleotideImpl extends HetatomImpl implements Serializable
  
  serialVersionUID:
  
  -7467726932980288712L
- Class org.biojava.nbio.structure.PassthroughIdentifier extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -2773111624414448950L
  - Serialized Fields
    - identifier
```
java.lang.String identifier
```
- Class org.biojava.nbio.structure.PDBCrystallographicInfo extends java.lang.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 java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -5834326174085429508L
  - Serialized Fields
    - title
```
java.lang.String title
```
    - description
```
java.lang.String description
```
    - idCode
```
java.lang.String idCode
```
    - classification
```
java.lang.String classification
```
    - depDate
```
java.util.Date depDate
```
    - relDate
```
java.util.Date relDate
```
    - modDate
```
java.util.Date modDate
```
    - techniques
```
java.util.Set<E> techniques
```
    - crystallographicInfo
```
PDBCrystallographicInfo crystallographicInfo
```
    - resolution
```
float resolution
```
    - rFree
```
float rFree
```
    - rWork
```
float rWork
```
    - journalArticle
```
JournalArticle journalArticle
```
    - authors
```
java.lang.String authors
```
    - id
```
java.lang.Long id
```
    - dateFormat
```
java.text.DateFormat dateFormat
```
    - bioAssemblies
```
java.util.Map<K,V> bioAssemblies
```
    - revisionRecords
```
java.util.List<E> revisionRecords
```
- Class org.biojava.nbio.structure.ResidueNumber extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1773011704758536083L
  - Serialized Fields
    - chainName
```
java.lang.String chainName
```
    - insCode
```
java.lang.Character insCode
```
    - seqNum
```
java.lang.Integer seqNum
```
- Class org.biojava.nbio.structure.SeqMisMatchImpl extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -3699285122925652562L
  - Serialized Fields
    - seqNum
```
java.lang.Integer seqNum
```
    - origGroup
```
java.lang.String origGroup
```
    - pdbGroup
```
java.lang.String pdbGroup
```
    - details
```
java.lang.String details
```
    - uniProtId
```
java.lang.String uniProtId
```
    - insCode
```
java.lang.String insCode
```
    - pdbResNum
```
java.lang.String pdbResNum
```
- Class org.biojava.nbio.structure.Site extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -4577047072916341237L
  - Serialized Fields
    - siteID
```
java.lang.String siteID
```
    - groups
```
java.util.List<E> groups
```
    - evCode
```
java.lang.String evCode
```
    - description
```
java.lang.String description
```
- Class org.biojava.nbio.structure.StructureException extends java.lang.Exception implements Serializable
  
  serialVersionUID:
  
  62946250941673093L
- Class org.biojava.nbio.structure.StructureImpl extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -8344837138032851348L
  - Serialized Fields
    - pdb_id
```
java.lang.String pdb_id
```
    - models
```
java.util.List<E> models
```
    - entityInfos
```
java.util.List<E> entityInfos
```
    - dbrefs
```
java.util.List<E> dbrefs
```
    - ssbonds
```
java.util.List<E> ssbonds
```
    - sites
```
java.util.List<E> sites
```
    - name
```
java.lang.String name
```
    - structureIdentifier
```
StructureIdentifier structureIdentifier
```
    - pdbHeader
```
PDBHeader pdbHeader
```
    - id
```
java.lang.Long id
```
    - biologicalAssembly
```
boolean biologicalAssembly
```
- Class org.biojava.nbio.structure.SubstructureIdentifier extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - pdbId
```
java.lang.String pdbId
```
    - ranges
```
java.util.List<E> ranges
```
- Class org.biojava.nbio.structure.URLIdentifier extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -5161230822868926035L
  - Serialized Fields
    - url
```
java.net.URL url
```
Package org.biojava.nbio.structure.align.client
- Class org.biojava.nbio.structure.align.client.JobKillException extends java.lang.Exception implements Serializable
  
  serialVersionUID:
  
  1L
- Class org.biojava.nbio.structure.align.client.StructureName extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  4021229518711762957L
  - Serialized Fields
    - name
```
java.lang.String name
```
    - pdbId
```
java.lang.String pdbId
```
    - chainName
```
java.lang.String chainName
```
    - mySource
```
StructureName.Source mySource
```
    - base
```
StructureIdentifier base
```
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.IdxComparator extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
- Class org.biojava.nbio.structure.align.helper.IndexPair extends java.lang.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 java.lang.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 java.lang.Object implements Serializable

serialVersionUID:: -4474029015606617947L

Serialized Fields

algorithmName
```
java.lang.String algorithmName
```
version
```
java.lang.String version
```
name1
```
java.lang.String name1
```
name2
```
java.lang.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
```
java.util.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
```
java.lang.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
```
java.lang.Double conn
```
dvar
```
java.lang.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
```
java.lang.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
```
java.util.List<E> alignRes
```
    - coreLength
```
int coreLength
```
    - alignResCounts
```
java.util.List<E> alignResCounts
```
- Class org.biojava.nbio.structure.align.multiple.BlockSetImpl extends AbstractScoresCache implements Serializable
  
  serialVersionUID:
  
  -1015791986000076089L
  - Serialized Fields
    - parent
```
MultipleAlignment parent
```
    - blocks
```
java.util.List<E> blocks
```
    - pose
```
java.util.List<E> pose
```
    - length
```
int length
```
    - coreLength
```
int coreLength
```
    - alignResCounts
```
java.util.List<E> alignResCounts
```
- Class org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl extends AbstractScoresCache implements Serializable
  
  serialVersionUID:
  
  -5732485866623431898L
  - Serialized Fields
    - algorithmName
```
java.lang.String algorithmName
```
    - version
```
java.lang.String version
```
    - ioTime
```
java.lang.Long ioTime
```
    - calculationTime
```
java.lang.Long calculationTime
```
    - structureIdentifiers
```
java.util.List<E> structureIdentifiers
```
    - atomArrays
```
java.util.List<E> atomArrays
```
    - distanceMatrix
```
java.util.List<E> distanceMatrix
```
    - multipleAlignments
```
java.util.List<E> multipleAlignments
```
- Class org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl extends AbstractScoresCache implements Serializable
  
  serialVersionUID:
  
  3432043794125805139L
  - Serialized Fields
    - parent
```
MultipleAlignmentEnsemble parent
```
    - blockSets
```
java.util.List<E> blockSets
```
    - length
```
int length
```
    - coreLength
```
int coreLength
```
    - alignResCounts
```
java.util.List<E> alignResCounts
```
    - coverages
```
java.util.List<E> coverages
```
Package org.biojava.nbio.structure.align.pairwise
- Class org.biojava.nbio.structure.align.pairwise.AlignmentResult extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -4132105905712445473L
  - Serialized Fields
    - alignments
```
AlternativeAlignment[] alignments
```
    - pdb1
```
java.lang.String pdb1
```
    - pdb2
```
java.lang.String pdb2
```
    - chain1
```
java.lang.String chain1
```
    - chain2
```
java.lang.String chain2
```
    - length1
```
int length1
```
    - length2
```
int length2
```
    - calculationTime
```
long calculationTime
```
    - ioTime
```
long ioTime
```
- Class org.biojava.nbio.structure.align.pairwise.AltAligComparator extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
- Class org.biojava.nbio.structure.align.pairwise.AlternativeAlignment extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -6226717654562221241L
  - Serialized Fields
    - idx1
```
int[] idx1
```
    - idx2
```
int[] idx2
```
    - pdbresnum1
```
java.lang.String[] pdbresnum1
```
    - pdbresnum2
```
java.lang.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 java.lang.Exception implements Serializable
  
  serialVersionUID:
  
  -8047100079715000276L
Package org.biojava.nbio.structure.asa
- Class org.biojava.nbio.structure.asa.GroupAsa extends java.lang.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
```
java.util.List<E> atomAsaUs
```
      The individual atoms uncomplexed ASAs
    - atomAsaCs
```
java.util.List<E> atomAsaCs
```
      The individual atoms complexed ASAs
Package org.biojava.nbio.structure.basepairs
- Class org.biojava.nbio.structure.basepairs.BasePairParameters extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  6214502385L
  - Serialized Fields
    - structure
```
Structure structure
```
    - canonical
```
boolean canonical
```
    - useRNA
```
boolean useRNA
```
    - nonredundant
```
boolean nonredundant
```
    - pairParameters
```
double[] pairParameters
```
    - pairSequence
```
java.lang.String pairSequence
```
    - pairingParameters
```
double[][] pairingParameters
```
    - stepParameters
```
double[][] stepParameters
```
    - pairingNames
```
java.util.List<E> pairingNames
```
    - referenceFrames
```
java.util.List<E> referenceFrames
```
- Class org.biojava.nbio.structure.basepairs.MismatchedBasePairParameters extends BasePairParameters implements Serializable
  
  serialVersionUID:
  
  2837124340169886674L
  - Serialized Fields
    - maxStagger
```
double maxStagger
```
    - maxShear
```
double maxShear
```
    - maxStretch
```
double maxStretch
```
    - maxPropeller
```
double maxPropeller
```
- Class org.biojava.nbio.structure.basepairs.TertiaryBasePairParameters extends BasePairParameters implements Serializable
  
  serialVersionUID:
  
  2556427111533466577L
  - Serialized Fields
    - maxStagger
```
double maxStagger
```
    - maxPropeller
```
double maxPropeller
```
Package org.biojava.nbio.structure.cath
- Class org.biojava.nbio.structure.cath.CathDomain extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - domainName
```
java.lang.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
```
java.lang.Integer classId
```
      The class number of this domain.
    - architectureId
```
java.lang.Integer architectureId
```
      The architecture number of this domain.
    - topologyId
```
java.lang.Integer topologyId
```
      The topology number of this domain.
    - homologyId
```
java.lang.Integer homologyId
```
      The homologous superfamily number of this domain.
    - sequenceFamilyId
```
java.lang.Integer sequenceFamilyId
```
      The sequence family (35% identity) number of this domain.
    - orthologousSequenceFamilyId
```
java.lang.Integer orthologousSequenceFamilyId
```
      The "orthologous" sequence family (60% identity) number of this domain.
    - likeSequenceFamilyId
```
java.lang.Integer likeSequenceFamilyId
```
      The "Like" sequence family (95% identity) number of this domain.
    - identicalSequenceFamilyId
```
java.lang.Integer identicalSequenceFamilyId
```
      The identical sequence family (100% identity) number of this domain.
    - domainCounter
```
java.lang.Integer domainCounter
```
      The count of this domain among the identical sequence family members.
    - length
```
java.lang.Integer length
```
      The domain length..
    - resolution
```
java.lang.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
```
java.lang.String format
```
      The format and version of the CathDomainDescriptionFile.
    - version
```
java.lang.String version
```
      The CATH version.
    - date
```
java.util.Date date
```
    - name
```
java.lang.String name
```
      The so-called name field holds a potentially long description of the domain.
    - source
```
java.lang.String source
```
      Complete source organism listing.
    - sequenceHeader
```
java.lang.String sequenceHeader
```
      FASTA header.
    - sequence
```
java.lang.String sequence
```
      FASTA sequence.
    - segments
```
java.util.List<E> segments
```
      List of all sub-domain segments.
    - comment
```
java.lang.String comment
```
      A (potentially long) comment. Usually empty.
- Class org.biojava.nbio.structure.cath.CathFragment extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - fragmentId
```
java.lang.Integer fragmentId
```
      The number of this segment within the domain.
    - start
```
java.lang.String start
```
      The first residue in the segment. Refers to the complete residue specification (sequence number AND insertion code).
    - stop
```
java.lang.String stop
```
      The last residue in the segment. Refers to the complete residue specification (sequence number AND insertion code).
    - length
```
java.lang.Integer length
```
      Number of residues in the segment. This value is parsed, not calculated.
- Class org.biojava.nbio.structure.cath.CathNode extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - nodeId
```
java.lang.String nodeId
```
      The CATH code of the node, e.g. "1.10.8.10".
    - parentId
```
java.lang.String parentId
```
      The CATH code of the parent, e.g. "1.10.8". Calculated during parsing.
    - representative
```
java.lang.String representative
```
      The representative domain for this node.
    - description
```
java.lang.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 java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - segmentId
```
java.lang.Integer segmentId
```
      The number of this segment within the domain.
    - start
```
java.lang.String start
```
      The first residue in the segment. Refers to the complete residue specification (sequence number AND insertion code).
    - stop
```
java.lang.String stop
```
      The last residue in the segment. Refers to the complete residue specification (sequence number AND insertion code).
    - length
```
java.lang.Integer length
```
      Number of residues in the segment. This value is parsed, not calculated.
    - sequenceHeader
```
java.lang.String sequenceHeader
```
      FASTA header.
    - sequence
```
java.lang.String sequence
```
      FASTA sequence.
Package org.biojava.nbio.structure.cluster
- Class org.biojava.nbio.structure.cluster.SubunitClustererParameters extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - minimumSequenceLength
```
int minimumSequenceLength
```
    - absoluteMinimumSequenceLength
```
int absoluteMinimumSequenceLength
```
    - minimumSequenceLengthFraction
```
double minimumSequenceLengthFraction
```
    - useGlobalMetrics
```
boolean useGlobalMetrics
```
    - sequenceIdentityThreshold
```
double sequenceIdentityThreshold
```
    - sequenceCoverageThreshold
```
double sequenceCoverageThreshold
```
    - useEntityIdForSeqIdentityDetermination
```
boolean useEntityIdForSeqIdentityDetermination
```
    - rmsdThreshold
```
double rmsdThreshold
```
    - structureCoverageThreshold
```
double structureCoverageThreshold
```
    - tmThreshold
```
double tmThreshold
```
    - clustererMethod
```
SubunitClustererMethod clustererMethod
```
    - superpositionAlgorithm
```
java.lang.String superpositionAlgorithm
```
    - optimizeAlignment
```
boolean optimizeAlignment
```
    - useSequenceCoverage
```
boolean useSequenceCoverage
```
    - useRMSD
```
boolean useRMSD
```
    - useStructureCoverage
```
boolean useStructureCoverage
```
    - useTMScore
```
boolean useTMScore
```
    - internalSymmetry
```
boolean internalSymmetry
```
Package org.biojava.nbio.structure.contact
- Class org.biojava.nbio.structure.contact.AtomContact extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - pair
```
Pair<T> pair
```
    - distance
```
double distance
```
- Class org.biojava.nbio.structure.contact.AtomContactSet extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - contacts
```
java.util.HashMap<K,V> contacts
```
    - cutoff
```
double cutoff
```
- Class org.biojava.nbio.structure.contact.AtomIdentifier extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - pdbSerial
```
int pdbSerial
```
    - chainId
```
java.lang.String chainId
```
- Class org.biojava.nbio.structure.contact.BoundingBox extends java.lang.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.Contact extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  5059569852079048728L
  - Serialized Fields
    - i
```
int i
```
    - j
```
int j
```
    - distance
```
double distance
```
- Class org.biojava.nbio.structure.contact.GroupContact extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - pair
```
Pair<T> pair
```
    - atomContacts
```
java.util.List<E> atomContacts
```
- Class org.biojava.nbio.structure.contact.GroupContactSet extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - contacts
```
java.util.HashMap<K,V> contacts
```
- Class org.biojava.nbio.structure.contact.Pair extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - first
```
java.lang.Object first
```
    - second
```
java.lang.Object second
```
- Class org.biojava.nbio.structure.contact.StructureInterface extends java.lang.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
```
java.util.Map<K,V> groupAsas1
```
    - groupAsas2
```
java.util.Map<K,V> groupAsas2
```
    - cluster
```
StructureInterfaceCluster cluster
```
- Class org.biojava.nbio.structure.contact.StructureInterfaceCluster extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - id
```
int id
```
    - members
```
java.util.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 java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - list
```
java.util.List<E> list
```
    - clusters
```
java.util.List<E> clusters
```
    - clustersNcs
```
java.util.List<E> clustersNcs
```
    - chainOrigNamesMap
```
java.util.Map<K,V> chainOrigNamesMap
```
Package org.biojava.nbio.structure.domain
- Class org.biojava.nbio.structure.domain.PDPDomain extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  6894463080739943026L
  - Serialized Fields
    - identifier
```
java.lang.String identifier
```
    - canonical
```
SubstructureIdentifier canonical
```
Package org.biojava.nbio.structure.domain.pdp
- Class org.biojava.nbio.structure.domain.pdp.Domain extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -1293994033102271366L
  - Serialized Fields
    - id
```
java.lang.String id
```
    - size
```
int size
```
    - nseg
```
int nseg
```
    - score
```
double score
```
    - segments
```
java.util.List<E> segments
```
- Class org.biojava.nbio.structure.domain.pdp.Segment extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1393487067559539657L
  - Serialized Fields
    - from
```
java.lang.Integer from
```
    - to
```
java.lang.Integer to
```
    - score
```
double score
```
- Class org.biojava.nbio.structure.domain.pdp.SegmentComparator extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L

Package org.biojava.nbio.structure.ecod

Class org.biojava.nbio.structure.ecod.EcodDomain extends java.lang.Object implements Serializable

serialVersionUID:: -7760082165560332048L

Serialized Fields

uid
```
java.lang.Long uid
```
domainId
```
java.lang.String domainId
```
manual
```
java.lang.Boolean manual
```
xGroup
```
java.lang.Integer xGroup
```
hGroup
```
java.lang.Integer hGroup
```
tGroup
```
java.lang.Integer tGroup
```
fGroup
```
java.lang.Integer fGroup
```
pdbId
```
java.lang.String pdbId
```
chainId
```
java.lang.String chainId
```
range
```
java.lang.String range
```
seqIdRange
```
java.lang.String seqIdRange
```
architectureName
```
java.lang.String architectureName
```
xGroupName
```
java.lang.String xGroupName
```
hGroupName
```
java.lang.String hGroupName
```
tGroupName
```
java.lang.String tGroupName
```
fGroupName
```
java.lang.String fGroupName
```
assemblyId
```
java.lang.Long assemblyId
```
ligands
```
java.util.Set<E> ligands
```

Package org.biojava.nbio.structure.io
- Class org.biojava.nbio.structure.io.FileParsingParameters extends java.lang.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
    - 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?
    - maxAtoms
```
int maxAtoms
```
    - fullAtomNames
```
java.lang.String[] fullAtomNames
```
- Class org.biojava.nbio.structure.io.PDBParseException extends java.lang.Exception implements Serializable
  
  serialVersionUID:
  
  219047230178423923L
- Class org.biojava.nbio.structure.io.SSBondImpl extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -8663681100691188647L
  - Serialized Fields
    - serNum
```
int serNum
```
    - chainID1
```
java.lang.String chainID1
```
    - chainID2
```
java.lang.String chainID2
```
    - resnum1
```
java.lang.String resnum1
```
    - resnum2
```
java.lang.String resnum2
```
    - insCode1
```
java.lang.String insCode1
```
    - insCode2
```
java.lang.String insCode2
```

Package org.biojava.nbio.structure.io.mmcif.model

Class org.biojava.nbio.structure.io.mmcif.model.ChemComp extends java.lang.Object implements Serializable

serialVersionUID:: -4736341142030215915L

Serialized Fields

id
```
java.lang.String id
```
name
```
java.lang.String name
```
type
```
java.lang.String type
```
pdbx_type
```
java.lang.String pdbx_type
```
formula
```
java.lang.String formula
```

mon_nstd_parent_comp_id

java.lang.String mon_nstd_parent_comp_id

pdbx_synonyms
```
java.lang.String pdbx_synonyms
```
pdbx_formal_charge
```
java.lang.String pdbx_formal_charge
```
pdbx_initial_date
```
java.lang.String pdbx_initial_date
```
pdbx_modified_date
```
java.lang.String pdbx_modified_date
```
pdbx_ambiguous_flag
```
java.lang.String pdbx_ambiguous_flag
```
pdbx_release_status
```
java.lang.String pdbx_release_status
```
pdbx_replaced_by
```
java.lang.String pdbx_replaced_by
```
pdbx_replaces
```
java.lang.String pdbx_replaces
```
formula_weight
```
java.lang.String formula_weight
```
one_letter_code
```
java.lang.String one_letter_code
```
three_letter_code
```
java.lang.String three_letter_code
```

pdbx_model_coordinates_details

java.lang.String pdbx_model_coordinates_details

pdbx_model_coordinates_missing_flag

java.lang.String pdbx_model_coordinates_missing_flag

pdbx_ideal_coordinates_details

java.lang.String pdbx_ideal_coordinates_details

pdbx_ideal_coordinates_missing_flag

java.lang.String pdbx_ideal_coordinates_missing_flag

pdbx_model_coordinates_db_code

java.lang.String pdbx_model_coordinates_db_code

pdbx_subcomponent_list
```
java.lang.String pdbx_subcomponent_list
```
pdbx_processing_site
```
java.lang.String pdbx_processing_site
```
mon_nstd_flag
```
java.lang.String mon_nstd_flag
```
descriptors
```
java.util.List<E> descriptors
```
bonds
```
java.util.List<E> bonds
```
atoms
```
java.util.List<E> atoms
```
residueType
```
ResidueType residueType
```
polymerType
```
PolymerType polymerType
```
standard
```
boolean standard
```

Class org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom extends java.lang.Object implements Serializable

serialVersionUID:: 4070599340294758941L

Serialized Fields

comp_id
```
java.lang.String comp_id
```
atom_id
```
java.lang.String atom_id
```
alt_atom_id
```
java.lang.String alt_atom_id
```
type_symbol
```
java.lang.String type_symbol
```
charge
```
java.lang.String charge
```
pdbx_align
```
java.lang.String pdbx_align
```
pdbx_aromatic_flag
```
java.lang.String pdbx_aromatic_flag
```
pdbx_leaving_atom_flag
```
java.lang.String pdbx_leaving_atom_flag
```
pdbx_stereo_config
```
java.lang.String pdbx_stereo_config
```
model_Cartn_x
```
java.lang.String model_Cartn_x
```
model_Cartn_y
```
java.lang.String model_Cartn_y
```
model_Cartn_z
```
java.lang.String model_Cartn_z
```

pdbx_model_Cartn_x_ideal

java.lang.String pdbx_model_Cartn_x_ideal

pdbx_model_Cartn_y_ideal

java.lang.String pdbx_model_Cartn_y_ideal

pdbx_model_Cartn_z_ideal

java.lang.String pdbx_model_Cartn_z_ideal

pdbx_component_comp_id
```
java.lang.String pdbx_component_comp_id
```
pdbx_residue_numbering
```
java.lang.String pdbx_residue_numbering
```
pdbx_component_atom_id
```
java.lang.String pdbx_component_atom_id
```
pdbx_polymer_type
```
java.lang.String pdbx_polymer_type
```
pdbx_ref_id
```
java.lang.String pdbx_ref_id
```
pdbx_component_id
```
java.lang.String pdbx_component_id
```
pdbx_ordinal
```
java.lang.String pdbx_ordinal
```

Class org.biojava.nbio.structure.io.mmcif.model.ChemCompBond extends java.lang.Object implements Serializable

serialVersionUID:

5905371029161975421L
- Serialized Fields
  - comp_id
```
java.lang.String comp_id
```
  - atom_id_1
```
java.lang.String atom_id_1
```
  - atom_id_2
```
java.lang.String atom_id_2
```
  - value_order
```
java.lang.String value_order
```
  - pdbx_aromatic_flag
```
java.lang.String pdbx_aromatic_flag
```
  - pdbx_stereo_config
```
java.lang.String pdbx_stereo_config
```
  - pdbx_ordinal
```
java.lang.String pdbx_ordinal
```
Class org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor extends java.lang.Object implements Serializable

serialVersionUID:

1078685833800736278L
- Serialized Fields
  - comp_id
```
java.lang.String comp_id
```
  - type
```
java.lang.String type
```
  - program
```
java.lang.String program
```
  - program_version
```
java.lang.String program_version
```
  - descriptor
```
java.lang.String descriptor
```
Class org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord extends java.lang.Object implements Serializable

serialVersionUID:

1L
- Serialized Fields
  - rev_num
```
java.lang.String rev_num
```
  - type
```
java.lang.String type
```
  - details
```
java.lang.String details
```
Class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly extends java.lang.Object implements Serializable

serialVersionUID:

3104504686693887219L
- Serialized Fields
  - id
```
java.lang.String id
```
  - details
```
java.lang.String details
```
  - method_details
```
java.lang.String method_details
```
  - oligomeric_details
```
java.lang.String oligomeric_details
```
  - oligomeric_count
```
java.lang.String oligomeric_count
```
Class org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen extends java.lang.Object implements Serializable

serialVersionUID:

6739568389242514332L
- Serialized Fields
  - assembly_id
```
java.lang.String assembly_id
```
  - oper_expression
```
java.lang.String oper_expression
```
  - asym_id_list
```
java.lang.String asym_id_list
```

Class org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList extends java.lang.Object implements Serializable

serialVersionUID:: 8933552854747969787L

Serialized Fields

id
```
java.lang.String id
```
type
```
java.lang.String type
```
symmetry_operation
```
java.lang.String symmetry_operation
```
matrix11
```
java.lang.String matrix11
```
matrix12
```
java.lang.String matrix12
```
matrix13
```
java.lang.String matrix13
```
vector1
```
java.lang.String vector1
```
matrix21
```
java.lang.String matrix21
```
matrix22
```
java.lang.String matrix22
```
matrix23
```
java.lang.String matrix23
```
vector2
```
java.lang.String vector2
```
matrix31
```
java.lang.String matrix31
```
matrix32
```
java.lang.String matrix32
```
matrix33
```
java.lang.String matrix33
```
vector3
```
java.lang.String vector3
```
name
```
java.lang.String name
```

Package org.biojava.nbio.structure.io.mmtf
- Class org.biojava.nbio.structure.io.mmtf.MmtfStructureReader extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  6772030485225130853L
  - Serialized Fields
    - structure
```
Structure structure
```
      The structure.
    - modelNumber
```
int modelNumber
```
      The model number.
    - chain
```
Chain chain
```
      The chain.
    - group
```
Group group
```
      The group.
    - atomsInGroup
```
java.util.List<E> atomsInGroup
```
      The atoms in a group.
    - allAtoms
```
Atom[] allAtoms
```
      All the atoms.
    - atomCounter
```
int atomCounter
```
    - entityInfoList
```
java.util.List<E> entityInfoList
```
      The list of EntityInformation
    - chainList
```
java.util.List<E> chainList
```
      All the chains
    - chainMap
```
java.util.List<E> chainMap
```
      All the chains as a list of maps
    - transformList
```
java.util.List<E> transformList
```
    - bioassIndex
```
int bioassIndex
```
    - chainSequenceMap
```
java.util.Map<K,V> chainSequenceMap
```
Package org.biojava.nbio.structure.io.sifts
- Class org.biojava.nbio.structure.io.sifts.SiftsEntity extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  750353252427491487L
  - Serialized Fields
    - type
```
java.lang.String type
```
    - entityId
```
java.lang.String entityId
```
    - segments
```
java.util.List<E> segments
```
- Class org.biojava.nbio.structure.io.sifts.SiftsResidue extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  3425769737629800828L
  - Serialized Fields
    - pdbResNum
```
java.lang.String pdbResNum
```
    - pdbResName
```
java.lang.String pdbResName
```
    - chainId
```
java.lang.String chainId
```
    - uniProtResName
```
java.lang.String uniProtResName
```
    - uniProtPos
```
java.lang.Integer uniProtPos
```
    - naturalPos
```
java.lang.Integer naturalPos
```
    - seqResName
```
java.lang.String seqResName
```
    - pdbId
```
java.lang.String pdbId
```
    - uniProtAccessionId
```
java.lang.String uniProtAccessionId
```
    - notObserved
```
java.lang.Boolean notObserved
```
- Class org.biojava.nbio.structure.io.sifts.SiftsSegment extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -8005129863256307153L
  - Serialized Fields
    - segId
```
java.lang.String segId
```
    - start
```
java.lang.String start
```
    - end
```
java.lang.String end
```
    - residues
```
java.util.List<E> residues
```
Package org.biojava.nbio.structure.jama
- Class org.biojava.nbio.structure.jama.CholeskyDecomposition extends java.lang.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 java.lang.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 java.lang.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 java.lang.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 java.lang.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 java.lang.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 java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -5217767192992868955L
  - Serialized Fields
    - N
```
int N
```
    - rows
```
SparseVector[] rows
```
- Class org.biojava.nbio.structure.math.SparseVector extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1174668523213431927L
  - Serialized Fields
    - N
```
int N
```
    - symbolTable
```
SymbolTable<Key extends java.lang.Comparable<Key>,Value> symbolTable
```
- Class org.biojava.nbio.structure.math.SymbolTable extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -4417561575046471931L
  - Serialized Fields
    - st
```
java.util.TreeMap<K,V> st
```
Package org.biojava.nbio.structure.quaternary
- Class org.biojava.nbio.structure.quaternary.BioAssemblyInfo extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - id
```
int id
```
    - transforms
```
java.util.List<E> transforms
```
    - macromolecularSize
```
int macromolecularSize
```
- Class org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -6388503076022480391L
  - Serialized Fields
    - id
```
java.lang.String id
```
    - chainId
```
java.lang.String chainId
```
    - transformation
```
javax.vecmath.Matrix4d transformation
```
Package org.biojava.nbio.structure.scop
- Class org.biojava.nbio.structure.scop.ScopDescription extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  8579808155176839161L
  - Serialized Fields
    - sunID
```
int sunID
```
    - category
```
ScopCategory category
```
    - classificationId
```
java.lang.String classificationId
```
    - name
```
java.lang.String name
```
    - description
```
java.lang.String description
```
- Class org.biojava.nbio.structure.scop.ScopDomain extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  5890476209571654301L
  - Serialized Fields
    - scopId
```
java.lang.String scopId
```
    - pdbId
```
java.lang.String pdbId
```
    - ranges
```
java.util.List<E> ranges
```
    - classificationId
```
java.lang.String classificationId
```
    - sunid
```
java.lang.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 java.lang.RuntimeException implements Serializable
  
  serialVersionUID:
  
  1L
- Class org.biojava.nbio.structure.scop.ScopNode extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1187083944488580995L
  - Serialized Fields
    - sunid
```
int sunid
```
    - parentSunid
```
int parentSunid
```
    - children
```
java.util.List<E> children
```
Package org.biojava.nbio.structure.scop.server
- Class org.biojava.nbio.structure.scop.server.ListStringWrapper extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  4193799052494327416L
  - Serialized Fields
    - data
```
java.util.List<E> data
```
- Class org.biojava.nbio.structure.scop.server.ScopDescriptions extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  4924350548761431852L
  - Serialized Fields
    - scopDescriptions
```
java.util.List<E> scopDescriptions
```
- Class org.biojava.nbio.structure.scop.server.ScopDomains extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  7693404355005856746L
  - Serialized Fields
    - domains
```
java.util.List<E> domains
```
- Class org.biojava.nbio.structure.scop.server.ScopNodes extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  5327454882500340305L
  - Serialized Fields
    - scopNodes
```
java.util.List<E> scopNodes
```
- Class org.biojava.nbio.structure.scop.server.TreeSetStringWrapper extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  4193799052494327416L
  - Serialized Fields
    - data
```
java.util.TreeSet<E> data
```
Package org.biojava.nbio.structure.secstruc
- Class org.biojava.nbio.structure.secstruc.BetaBridge extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -5097435425455958487L
  - Serialized Fields
    - type
```
BridgeType type
```
    - partner1
```
int partner1
```
    - partner2
```
int partner2
```
- Class org.biojava.nbio.structure.secstruc.HBond extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  8246764841329431337L
  - Serialized Fields
    - energy
```
double energy
```
    - partner
```
int partner
```
- Class org.biojava.nbio.structure.secstruc.Ladder extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -1658305503250364409L
  - Serialized Fields
    - from
```
int from
```
    - to
```
int to
```
    - lfrom
```
int lfrom
```
    - lto
```
int lto
```
    - btype
```
BridgeType btype
```
    - connectedTo
```
int connectedTo
```
    - connectedFrom
```
int connectedFrom
```
- Class org.biojava.nbio.structure.secstruc.SecStrucElement extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -8485685793171396131L
  - Serialized Fields
    - type
```
SecStrucType type
```
    - range
```
ResidueRangeAndLength range
```
    - index
```
int index
```
- Class org.biojava.nbio.structure.secstruc.SecStrucInfo extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  4516925175715607227L
  - Serialized Fields
    - type
```
SecStrucType type
```
    - assignment
```
java.lang.String assignment
```
    - parent
```
Group parent
```
- Class org.biojava.nbio.structure.secstruc.SecStrucState extends SecStrucInfo implements Serializable
  
  serialVersionUID:
  
  -5549430890272724340L
  - Serialized Fields
    - phi
```
double phi
```
    - psi
```
double psi
```
    - omega
```
double omega
```
    - kappa
```
float kappa
```
    - accept1
```
HBond accept1
```
    - accept2
```
HBond accept2
```
    - donor1
```
HBond donor1
```
    - donor2
```
HBond donor2
```
    - turn
```
char[] turn
```
    - bend
```
boolean bend
```
    - bridge1
```
BetaBridge bridge1
```
    - bridge2
```
BetaBridge bridge2
```
Package org.biojava.nbio.structure.symmetry.core
- Class org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - rmsdThreshold
```
double rmsdThreshold
```
    - angleThreshold
```
double angleThreshold
```
    - helixRmsdThreshold
```
double helixRmsdThreshold
```
    - helixRmsdToRiseRatio
```
double helixRmsdToRiseRatio
```
    - minimumHelixRise
```
double minimumHelixRise
```
    - minimumHelixAngle
```
double minimumHelixAngle
```
    - maximumLocalCombinations
```
int maximumLocalCombinations
```
    - localTimeLimit
```
double localTimeLimit
```
    - localTimeStart
```
double localTimeStart
```
    - onTheFly
```
boolean onTheFly
```
Package org.biojava.nbio.structure.symmetry.internal
- Class org.biojava.nbio.structure.symmetry.internal.RefinerFailedException extends java.lang.Exception implements Serializable
  
  serialVersionUID:
  
  -3592155787060329421L
Package org.biojava.nbio.structure.symmetry.utils
- Class org.biojava.nbio.structure.symmetry.utils.BlastClustReader extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - sequenceIdentity
```
int sequenceIdentity
```
    - clusters
```
java.util.List<E> clusters
```
Package org.biojava.nbio.structure.validation
- Class org.biojava.nbio.structure.validation.WwPDBValidationInformation extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -996804963717482650L
  - Serialized Fields
    - entry
```
Entry entry
```
    - modelledSubgroup
```
java.util.List<E> modelledSubgroup
```
    - programs
```
Programs programs
```
Package org.biojava.nbio.structure.xtal
- Class org.biojava.nbio.structure.xtal.CrystalCell extends java.lang.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 java.lang.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 java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - id
```
int id
```
    - multiplicity
```
int multiplicity
```
    - primitiveMultiplicity
```
int primitiveMultiplicity
```
    - shortSymbol
```
java.lang.String shortSymbol
```
    - altShortSymbol
```
java.lang.String altShortSymbol
```
    - transformations
```
java.util.List<E> transformations
```
    - transfAlgebraic
```
java.util.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 java.lang.Object implements Serializable
  
  serialVersionUID:
  
  4193799052494327416L
  - Serialized Fields
    - data
```
java.util.TreeMap<K,V> data
```

Serialized Form

Package org.biojava.nbio.structure

Class org.biojava.nbio.structure.AminoAcidImpl extends HetatomImpl implements Serializable

Serialized Fields

amino_char

recordType

Class org.biojava.nbio.structure.AtomImpl extends java.lang.Object implements Serializable

Serialized Fields

name

element

coords

pdbserial

charge

occupancy

tempfactor

altLoc

parent

bonds

Class org.biojava.nbio.structure.Author extends java.lang.Object implements Serializable

Serialized Fields

surname

initials

Class org.biojava.nbio.structure.BioAssemblyIdentifier extends java.lang.Object implements Serializable

Serialized Fields

pdbCode

biolNr

Class org.biojava.nbio.structure.BondImpl extends java.lang.Object implements Serializable

Serialized Fields

atomA

atomB

bondOrder

Class org.biojava.nbio.structure.ChainImpl extends java.lang.Object implements Serializable

Serialized Fields

swissprot_id

authId

groups

seqResGroups

entity

parent

pdbResnumMap

asymId

seqMisMatches

Class org.biojava.nbio.structure.DBRef extends java.lang.Object implements Serializable

Serialized Fields

parent

idCode

chainName

seqbegin

insertBegin

seqEnd

insertEnd

database

dbAccession

dbIdCode

dbSeqBegin

idbnsBegin

dbSeqEnd

idbnsEnd

id

Class org.biojava.nbio.structure.EntityInfo extends java.lang.Object implements Serializable

Serialized Fields

chains

molId

chains2pdbResNums2ResSerials

refChainId

description

title

type

synonyms

ecNums

engineered

mutation

biologicalUnit

details

numRes

resNames

headerVars

synthetic

fragment

organismScientific