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Releases: MurrellGroup/ProteinChains.jl

v0.5.3

23 Jan 23:12
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ProteinChains v0.5.3

Diff since v0.5.2

v0.5.2

22 Dec 20:18
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ProteinChains v0.5.2

Diff since v0.5.1

Merged pull requests:

v0.5.1

18 Nov 19:22
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ProteinChains v0.5.1

Diff since v0.5.0

v0.5.0

05 Nov 23:55
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ProteinChains v0.5.0

Diff since v0.4.0

  • Add ProteinChain ins_codes field.
  • Add ProteinStructure properties field.
  • More robust and consistent ProteinStructureStore IO.
  • Remove renumbering functions
  • Remove BackboneGeometry and IdealResidue types and prepend/append residue functions.
  • Make ProteinChain and ProteinStructure types mutable.
  • Add addproperties!, removeproperties!, and setproperties! functions.

v0.4.0

29 Oct 10:58
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ProteinChains v0.4.0

Diff since v0.3.3

  • Changed HDF5 file structure, meaning ProteinStructureStores that were serialized in v0.3 can not be opened in v0.4. Please open an issue if this presents a problem.
  • Add readattribute and writeattribute functions for structure metadata.
  • Add readproperty, writeproperty, and deleteproperty functions for lazy manipulation of ProteinStructureStore entries.
  • Rename PersistentProperty to StandardProperty.
  • Generalized property serialization to categorize properties in subgroups by the AbstractProperty wrapper types.
  • Add @mmcifdict_str macro for getting the MMCIFDict of a PDB entry.

v0.3.3

23 Oct 14:45
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ProteinChains v0.3.3

Diff since v0.3.2

  • Remove ProteinChain's Ps 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

17 Oct 13:45
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ProteinChains v0.3.2

Diff since v0.3.1

  • Add removeproperties function for removing properties from ProteinChains.
  • Add getmmcif and mapmmcif functions.
  • Fix ProteinChain numbering field getting renumbered to label_seq_id when available instead of always auth_seq_id. renumbering is now added as an indexable property when an MMCIFDict is passed to the ProteinStructure{T}(::BioStructures.MolecularStructure) constructor, which happens by default in the MMCIF file read method.

Merged pull requests:

v0.3.1

15 Oct 00:28
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ProteinChains v0.3.1

Diff since v0.3.0

  • Add ProteinStructureStore(f::Function, ::Type{ProteinStructureStore}, args...), enabling do syntax for ensuring closure.
  • Define Base.open(::Type{ProteinStructureStore}, args...) method, with do syntax supported.
  • Fix parsing of atom names with tags wider than 2 characters.
  • Avoid constructing MMCIF dictionary multiple times when reading.

v0.3.0

10 Oct 17:49
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ProteinChains v0.3.0

Diff since v0.2.0

  • Remove dynamic AnnotatedProteinChain type in favor of the immutable ProteinChain type, with properties now bound to the type with a type parameter.
  • Add PersistentProperty and IndexableProperty wrappers for properties of ProteinChains, defining indexing behavior.
  • Add addproperties function for adding properties to chains.
  • Add public (but not exported) serialize and deserialize functions for writing/reading vectors of ProteinStructures 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:

  • Feedback on package design. (#7)
  • Simplifying the chain type definition with named tuples (#8)

v0.2.0

11 Sep 15:18
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ProteinChains v0.2.0

Diff since v0.1.1

  • 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).