From cbdb7df2fd33eb6d24a1aba75b5d71defe3ef1e3 Mon Sep 17 00:00:00 2001 From: Joe Greener Date: Tue, 29 Sep 2020 18:12:34 +0100 Subject: [PATCH] bump version --- NEWS.md | 5 +++++ Project.toml | 2 +- docs/src/documentation.md | 16 ++++++++-------- 3 files changed, 14 insertions(+), 9 deletions(-) diff --git a/NEWS.md b/NEWS.md index cee1c7e..d41a692 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,11 @@ BioStructures.jl release notes ============================== +## v0.11.4 - Sep 2020 + +* A `ProteinStructure` can now be obtained from a `MMCIFDict` or `MMTFDict` by passing them to the `ProteinStructure` constructor. This saves having to read the file twice when both the dictionary and the structure object are required. +* Add `get` method for `MMTFDict`. + ## v0.11.3 - Sep 2020 * Gzip support is added for reading and writing mmCIF files via the `gzip` keyword argument. diff --git a/Project.toml b/Project.toml index 627e10a..5d9f43f 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "BioStructures" uuid = "de9282ab-8554-53be-b2d6-f6c222edabfc" authors = ["Joe G Greener "] -version = "0.11.3" +version = "0.11.4" [deps] BioAlignments = "00701ae9-d1dc-5365-b64a-a3a3ebf5695e" diff --git a/docs/src/documentation.md b/docs/src/documentation.md index e474163..f01f7e2 100644 --- a/docs/src/documentation.md +++ b/docs/src/documentation.md @@ -45,7 +45,7 @@ MMTF files can be read into the same data structure with `read("/path/to/mmtf/fi The keyword argument `gzip`, default `false`, determines if the file is gzipped. In a similar manner to mmCIF dictionaries, a MMTF file can be read into a dictionary with [`MMTFDict`](@ref). The values of the dictionary are a variety of types depending on the [MMTF specification](https://github.com/rcsb/mmtf/blob/master/spec.md). -To convert a [`MMCIFDict`](@ref) or [`MMTFDict`](@ref) to the Structure-Model-Chain-Residue-Atom framework, use the `ProteinStructure` constructor, e.g. `ProteinStructure(mmcif_dict)`. +To convert a [`MMCIFDict`](@ref) or [`MMTFDict`](@ref) to the Structure-Model-Chain-Residue-Atom framework, use the [`ProteinStructure`](@ref) constructor, e.g. `ProteinStructure(mmcif_dict)`. The elements of `struc` can be accessed as follows: @@ -456,13 +456,13 @@ ProteinStructure 1EN2.pdb with 1 models, 1 chains (A), 85 residues, 754 atoms Read a mmCIF/MMTF file instead by replacing [`PDB`](@ref) with [`MMCIF`](@ref)/[`MMTF`](@ref). Various options can be set through optional keyword arguments when parsing PDB/mmCIF/MMTF files: -| Keyword Argument | Description | -| :------------------------------- | :--------------------------------------------------------------------------- | -| `structure_name::AbstractString` | The name given to the returned `ProteinStructure`; defaults to the file name | -| `remove_disorder::Bool=false` | Whether to remove atoms with alt loc ID not ' ' or 'A' | -| `read_std_atoms::Bool=true` | Whether to read standard ATOM records | -| `read_het_atoms::Bool=true` | Whether to read HETATOM records | -| `gzip::Bool=false` | Whether the file is gzipped (MMTF and mmCIF files only) | +| Keyword Argument | Description | +| :------------------------------- | :----------------------------------------------------------------------------------- | +| `structure_name::AbstractString` | The name given to the returned [`ProteinStructure`](@ref); defaults to the file name | +| `remove_disorder::Bool=false` | Whether to remove atoms with alt loc ID not ' ' or 'A' | +| `read_std_atoms::Bool=true` | Whether to read standard ATOM records | +| `read_het_atoms::Bool=true` | Whether to read HETATOM records | +| `gzip::Bool=false` | Whether the file is gzipped (MMTF and mmCIF files only) | Use [`retrievepdb`](@ref) to download and parse a PDB file into a Structure-Model-Chain-Residue-Atom framework in a single line: