Releases: biojava/biojava
Releases · biojava/biojava
BioJava 6.0.1
BioJava 6.0.0
Removed
- All code related to All-vs-All structural alignments db calculation and access
- JFatCatClient and all code depending on it
- PDP domain providers (depended on JFatCatClient)
- Support for retrieving structure data with prefix "PDP:" (AtomCache, StructureIO)
- RemoteScopInstallation consuming data provided by source.rcsb.org
- The whole
org.biojava.nbio.structure.rcsb
package, a client for the legacy RCSB PDB APIs (disappearing in Nov 2020) - The whole
org.biojava.nbio.structure.validation
package - The
org.biojava.nbio.structure.domain.PDBDomainProvider
class to pull domain definitions from legacy RCSB PDB APIs - Support for automatically fetching dssp files from RCSB (
org.biojava.nbio.structure.secstruc.DSSPParser.fetch()
) org.biojava.nbio.structure.PDBStatus
: simplifiedStatus
enum to 3 states, with OBSOLETE now called REMOVEDorg.biojava.nbio.structure.PDBStatus
: removedgetReplacement
andgetReplaces
- Removed
org.biojava.nbio.structure.io.mmcif
package - Removed functionality to write isolated CIF headers from
FileConvert
- Removed
org.biojava.nbio.structure.io.mmtf.MmtfUtils.setUpBioJava()
- Removed from
org.biojava.nbio.structure.Chain
interface:getParent()
,setParent()
,getAtomLigands()
,getSwissprotId()
,setSwissprotId()
,getInternalChainID()
,setInternalChainID()
,getChainID()
,setChainID()
- Removed from
org.biojava.nbio.structure.Structure
interface:findChain()
,getId()
,setId()
,getChainByPDB()
,getCompoundById()
,getResidueRanges()
,getRanges()
- Removed from
org.biojava.nbio.structure.StructureTools
:isNucleicAcid()
,isProtein()
,getPredominantGroupType()
,isChainWaterOnly()
,isChainPureNonPolymer()
,getReducedStructure()
- Removed
org.biojava.nbio.structure.io.SandboxStyleStructureProvider
- In
org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser
made all methods private exceptparseXMLfile
Breaking API changes
- Extracted
StructureIO.StructureFiletype
enum toorg.biojava.nbio.structure.io.StructureFiletype
(supportsPDB
,MMTF
,CIF
, andBCIF
) org.biojava.nbio.structure.align.util.AtomCache
: removedsetUseMmCif
,setUseMmtf
,isUseMmCif
, andisUseMmtf
- replaced bysetFiletype
andgetFiletype
that controls parsed content via theStructureFiletype
org.biojava.nbio.structure.io.MMCIFFileReader
is now effectivelyorg.biojava.nbio.structure.io.CifFileReader
- Moved
org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord
toorg.biojava.nbio.structure.DatabasePDBRevRecord.java
- Moved all chem-comp model classes from
org.biojava.nbio.structure.io.mmcif.chem
toorg.biojava.nbio.structure.chem
- Moved all chem-comp parsing classes from
org.biojava.nbio.structure.io.mmcif.chem
toorg.biojava.nbio.structure.io.cif
- Moved classes in
org.biojava.nbio.structure.io.mmcif
toorg.biojava.nbio.structure.chem
- Fixed
CRC64Checksum#public void update(byte[] b, int offset, int length)
to use thelength
argument correctly as specified injava.util.zip.Checksum
interface. - In
SubstructureIdentifier
,StructureName
,EcodDomain
,ScopDomain
:getPdbId()
returnsPdbId
object instead ofString
. - Removed
DownloadChemCompProvider.useDefaultUrlLayout
with a more flexible system to provide templated URLsDownloadChemCompProvider.setChemCompPathUrlTemplate()
andDownloadChemCompProvider.setServerBaseUrl()
- In
Structure
(andStructureImple
), the accessor methodsString getPdbId()
andsetPdbId(String)
were previously depricated. They were revived in BioJava 6.0.0 but asPdbId getPdbId()
andsetPdbId(PdbId)
instead.n
Added
- New
keywords
field inPDBHeader
class, populated by PDB and mmCIF parsers #946 - OBO parsing now supports multiple altids, #960
- New class
PdbId
that wrapps a PDB Identifier and handles conversion between current short PDBID format and upcoming extended PDBID format #930
Fixed
BioJava 5.4.0
New features
- Minimal read support for mmCIF files with branched entities (upcoming PDB release July 2020). The new entity type is understood now but branched entities are still treated as non-polymers within BioJava. #868
- InterfaceFinder class to find interfaces of a given PDB assembly #867
- New switch in Subunit clusterer
useEntityIdForSeqIdentityDetermination
#857 #859
Changed
- Now genbank parser will allow 5'<3' for circular DNA #855
Bug fixes
- Issue in bonds between atoms of different alt locs (rcsb/mmtf#44) #854
- Upgrade ciftools-java dependency to latest java-8 compatible release 0.7.1
BioJava 5.3.0
New features
- Support for reading structures from binary cif format in structure module, thanks to CIFTools-java library. Thanks @JonStargaryen
- Reading structures from mmCIF via new parser from CIFTools-java library. Much better read performance than existing parser. Both parsers still live alongside in BioJava 5.3.0, with default still being the BioJava native one.
Bug fixes
- 8x performance increase in reading (non-gzipped) MMTF files thanks to mmtf-java dependency upgrade to 1.0.9
- Bug fixes in MMTF file reading, #671 #850
- Bug fix in OBO reading, where only one synonym was saved, #836
- Bug fix in Genbank LOCUS line parsing #833
- Bug fix in PDB file reading of MTRIX records #845
- Bug fix in GenbankReader #800 #829
- Dependencies and maven plugin upgrades
BioJava 5.2.1
Bug fixes
- 2 bugfixes in ASA calculation introduced in 5.2.0: calculation would fail when an atom had no neighbors or when supplying a 0-length atom array, #824
- Fixes in bioassembly creation, where EntityInfo objects weren't correctly cloned and wired #825
- More efficient interface ASA calculation in NCS cases #823
- Add EntityInfo to reduced structure #822
BioJava 5.2.0
BioJava 5.2.0 runs on Java 8 or later.
New Feature
- improved algorithm for ASA computation. It is much faster on large molecules. #820
Bug fixes
BioJava 5.1.1
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.
Bug fixes
- #801 - Chain identifiers for generated bioassemblies now more explicit
- #804 - Adapted BioJava to run under 9, 10 and 111 JREs
Manual Download
BioJava 5.1.0
This release contains 55 commits from 7 contributors.
New feature
Bug fixes
- Performance improvement for secondary structure calculation, #789
- #731
- Improved alt locs docs and some fixes, #778
- Jmol dep updated to 14.29.17
- #712
- #791
- #797
- #784
Manual Download
BioJava 4.2.12
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:
- Fix #703: Recover from empty structure files in PDB_CACHE_DIR
- Reflect changes in external resources (#780, 0c10a2e)
- CE-Symm bug fixes (#92)
This release is associated with CE-Symm 2.0.0.
BioJava 5.0.2
This release contains 5 commits from 2 contributors.
Requires Java 8 or newer.
Bug fixes
- Fixed issue #770
- Upgraded to latest mmtf-java 1.0.8