Releases: MurrellGroup/ProteinChains.jl
Releases · MurrellGroup/ProteinChains.jl
v0.5.3
ProteinChains v0.5.3
v0.5.2
ProteinChains v0.5.2
Merged pull requests:
- Bump codecov/codecov-action from 4 to 5 (#16) (@dependabot[bot])
v0.5.1
ProteinChains v0.5.1
v0.5.0
ProteinChains v0.5.0
- Add
ProteinChain
ins_codes field. - Add
ProteinStructure
properties field. - More robust and consistent
ProteinStructureStore
IO. - Remove renumbering functions
- Remove
BackboneGeometry
andIdealResidue
types and prepend/append residue functions. - Make
ProteinChain
andProteinStructure
types mutable. - Add
addproperties!
,removeproperties!
, andsetproperties!
functions.
v0.4.0
ProteinChains v0.4.0
- Changed HDF5 file structure, meaning
ProteinStructureStore
s that were serialized in v0.3 can not be opened in v0.4. Please open an issue if this presents a problem. - Add
readattribute
andwriteattribute
functions for structure metadata. - Add
readproperty
,writeproperty
, anddeleteproperty
functions for lazy manipulation ofProteinStructureStore
entries. - Rename
PersistentProperty
toStandardProperty
. - Generalized property serialization to categorize properties in subgroups by the
AbstractProperty
wrapper types. - Add
@mmcifdict_str
macro for getting theMMCIFDict
of a PDB entry.
v0.3.3
ProteinChains v0.3.3
- Remove
ProteinChain
'sPs
type parameter to avoid unnecessary method specialization for new combinations of properties. - Fix
delete!(::ProteinStructureStore, key)
failing to delete the HDF5 group. - Fix atom parsing edge case where the atom element symbol is not in the periodic table.
v0.3.2
ProteinChains v0.3.2
- Add
removeproperties
function for removing properties fromProteinChain
s. - Add
getmmcif
andmapmmcif
functions. - Fix
ProteinChain
numbering field getting renumbered tolabel_seq_id
when available instead of alwaysauth_seq_id
.renumbering
is now added as an indexable property when an MMCIFDict is passed to theProteinStructure{T}(::BioStructures.MolecularStructure)
constructor, which happens by default in the MMCIF fileread
method.
Merged pull requests:
- MMCIF utilities (#14) (@AntonOresten)
v0.3.1
ProteinChains v0.3.1
- Add
ProteinStructureStore(f::Function, ::Type{ProteinStructureStore}, args...)
, enablingdo
syntax for ensuring closure. - Define
Base.open(::Type{ProteinStructureStore}, args...)
method, withdo
syntax supported. - Fix parsing of atom names with tags wider than 2 characters.
- Avoid constructing MMCIF dictionary multiple times when reading.
v0.3.0
ProteinChains v0.3.0
- Remove dynamic
AnnotatedProteinChain
type in favor of the immutableProteinChain
type, with properties now bound to the type with a type parameter. - Add
PersistentProperty
andIndexableProperty
wrappers for properties ofProteinChain
s, defining indexing behavior. - Add
addproperties
function for adding properties to chains. - Add public (but not exported)
serialize
anddeserialize
functions for writing/reading vectors ofProteinStructure
s to HDF5 files. - Add
ProteinStructureStore
type that acts as a dictionary to bring HDF5-serialized structures into memory and vice versa.
Merged pull requests:
- Simplify properties (#9) (@AntonOresten)
- Add ProteinStructureStore (#10) (@AntonOresten)
- CompatHelper: add new compat entry for AssigningSecondaryStructure at version 0.5, (keep existing compat) (#11) (@github-actions[bot])
- CompatHelper: add new compat entry for StaticArrays at version 1, (keep existing compat) (#12) (@github-actions[bot])
- Renaming and docstrings (#13) (@AntonOresten)
Closed issues:
v0.2.0
ProteinChains v0.2.0
- Add AnnotatedProteinChain
- Cache up to four PDB entries that have been fetched with the
pdbentry
function or@pdb_str
macro. - Disordered atoms/residues no longer get thrown away (collapses to default).