:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.
org.biojava.nbio.structure.rcsb
package, a client for the legacy RCSB PDB APIs (disappearing in Nov 2020)org.biojava.nbio.structure.validation
packageorg.biojava.nbio.structure.domain.PDBDomainProvider
class to pull domain definitions from legacy RCSB PDB APIsorg.biojava.nbio.structure.secstruc.DSSPParser.fetch()
)org.biojava.nbio.structure.PDBStatus
: simplified Status
enum to 3 states, with OBSOLETE now called REMOVEDorg.biojava.nbio.structure.PDBStatus
: removed getReplacement
and getReplaces
org.biojava.nbio.structure.io.mmcif
packageFileConvert
org.biojava.nbio.structure.io.mmtf.MmtfUtils.setUpBioJava()
org.biojava.nbio.structure.Chain
interface: getParent()
, setParent()
, getAtomLigands()
, getSwissprotId()
, setSwissprotId()
, getInternalChainID()
, setInternalChainID()
, getChainID()
, setChainID()
org.biojava.nbio.structure.Structure
interface: findChain()
, getId()
, setId()
, getChainByPDB()
, getCompoundById()
, getResidueRanges()
, getRanges()
org.biojava.nbio.structure.StructureTools
: isNucleicAcid()
, isProtein()
, getPredominantGroupType()
, isChainWaterOnly()
, isChainPureNonPolymer()
, getReducedStructure()
org.biojava.nbio.structure.io.SandboxStyleStructureProvider
org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser
made all methods private except parseXMLfile
StructureIO.StructureFiletype
enum to org.biojava.nbio.structure.io.StructureFiletype
(supports PDB
, MMTF
, CIF
, and BCIF
)org.biojava.nbio.structure.align.util.AtomCache
: removed setUseMmCif
, setUseMmtf
, isUseMmCif
, and isUseMmtf
- replaced by setFiletype
and getFiletype
that controls parsed content via the StructureFiletype
org.biojava.nbio.structure.io.MMCIFFileReader
is now effectively org.biojava.nbio.structure.io.CifFileReader
org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord
to org.biojava.nbio.structure.DatabasePDBRevRecord.java
org.biojava.nbio.structure.io.mmcif.chem
to org.biojava.nbio.structure.chem
org.biojava.nbio.structure.io.mmcif.chem
to org.biojava.nbio.structure.io.cif
org.biojava.nbio.structure.io.mmcif
to org.biojava.nbio.structure.chem
CRC64Checksum#public void update(byte[] b, int offset, int length)
to use the length
argument correctly as specified in java.util.zip.Checksum
interface.SubstructureIdentifier
, StructureName
, EcodDomain
, ScopDomain
: getPdbId()
returns PdbId
object instead of String
.DownloadChemCompProvider.useDefaultUrlLayout
with a more flexible system to provide templated URLs DownloadChemCompProvider.setChemCompPathUrlTemplate()
and DownloadChemCompProvider.setServerBaseUrl()
Structure
(and StructureImple
), the accessor methods String getPdbId()
and setPdbId(String)
were previously depricated. They were revived in BioJava 6.0.0 but as PdbId getPdbId()
and setPdbId(PdbId)
instead.nkeywords
field in PDBHeader
class, populated by PDB and mmCIF parsers #946PdbId
that wrapps a PDB Identifier and handles conversion between current short PDBID format and upcoming extended PDBID format #930useEntityIdForSeqIdentityDetermination
#857 #859BioJava 5.2.0 runs on Java 8 or later.
This release contains 22 commits from 3 contributors.
Note this is the first version of BioJava that will run under 9, 10 or 11 JREs. It is still fully compatible with Java 8.
This release contains 55 commits from 7 contributors.
This is a bugfix release in the 4.2 branch. This branch is being maintained for use with Java 7. Applications using more recent versions of Java are encouraged to migrate to BioJava 5.
Changes:
This release is associated with CE-Symm 2.0.0.
This release contains 5 commits from 2 contributors.
Requires Java 8 or newer.