Releases: BioJulia/BioStructures.jl
Releases · BioJulia/BioStructures.jl
v0.10.0
- Change keyword argument names
pdb_dir
todir
andfile_format
toformat
fordownloadpdb
,downloadentirepdb
,updatelocalpdb
,downloadallobsoletepdb
andretrievepdb
. - Remove
readpdb
, which has the same functionality asread
. - API reference section, more docstrings, links to related software and interactive Bio3DView.jl examples in documentation.
v0.9.4
- Change compatibility bounds for new RecipesBase.jl and CodecZlib.jl releases.
v0.9.3
- Change compatibility bounds for new RecipesBase.jl release.
v0.9.2
- Improvements to performance throughout the package. Some functions are made up to 5 times faster.
v0.9.1
- Fix documentation build.
v0.9.0
- A reader and writer are added for the MMTF file format, building on top of MMTF.jl. The interface is the same as for PDB and mmCIF files, with files either being read into the standard hierarchical structure or a
MMTFDict
. Gzipped files are supported. PDB, mmCIF and MMTF files can be interconverted. - The
expand_disordered
flag is added tocollectatoms
,collectresidues
,countatoms
,countresidues
,coordarray
,writepdb
,writemmcif
,writemmtf
andDataFrame
. It determines whether disordered atoms and residues are expanded to include all entries. By default it isfalse
except for the output functions, i.e. the last four above, where it istrue
by default. - The
pdbextension
dictionary is changed to remove leading dots in the values. - Improved file writing of empty elements.
- Examples are split off into a separate section in the documentation.
- A benchmark suite is added to track performance.
v0.8.0
- Superimposition of structural elements is supported using the Kabsch algorithm. New functions are
superimpose!
,Transformation
,applytransform!
andapplytransform
. rmsd
anddisplacements
carry out superimposition by default, with the relevant keyword arguments available. Settingsuperimpose
tofalse
prevents this.rmsdatoms
anddispatoms
respectively determine which atoms to calculate the property for.- The trivial
allselector
, which selects all atoms or residues, is added. - The backbone oxygen
"O"
is added tobackboneatomnames
. - Compatible bounds of package dependencies are added to Project.toml.
v0.7.0
MetaGraph
from MetaGraphs.jl is extended to create graphs of contacting elements in a molecular structure, giving access to all the graph analysis tools in LightGraphs.jl.DataFrame
from DataFrames.jl is extended to allow creation of data frames from lists of atoms or residues.pairalign
from BioAlignments.jl is extended to produce pairwise alignments from structural elements.AminoAcidSequence
now takes any element type and has thegaps
keyword argument.- Documentation example of interoperability with NearestNeighbors.jl.
- Parametric types used more extensively internally.
v0.6.0
collectatoms
,collectresidues
,collectchains
andcollectmodels
no longer runsort
before returning the final list. The user can run an explicitsort
themselves if desired. This change makes the functions faster and allows preservation of the element order.- Speed up residue iteration.
- Documentation improvements.
v0.5.1
- Fix
MMCIFDict
to always contain aDict{String, Vector{String}}
rather than aDict{String, Union{String, Vector{String}}}
, which includes making the"data_"
tag aVector{String}
. - More functions documented and documentation bugfixes.