From 7d342544c6410ed39a62246430b0171859e3afba Mon Sep 17 00:00:00 2001 From: anton083 Date: Thu, 17 Oct 2024 17:19:58 +0200 Subject: [PATCH] export and clean up mmcifutils functions --- src/ProteinChains.jl | 3 ++- src/io/io.jl | 2 -- src/io/mmcifutils.jl | 8 -------- 3 files changed, 2 insertions(+), 11 deletions(-) diff --git a/src/ProteinChains.jl b/src/ProteinChains.jl index c57c955..9249571 100644 --- a/src/ProteinChains.jl +++ b/src/ProteinChains.jl @@ -31,7 +31,8 @@ include("io/io.jl") export readcif, readpdb export writecif, writepdb export pdbentry, @pdb_str -export PDBFormat, MMCIFFormat +export getmmcif, mapmmcif +export BioStructures, MMCIFDict, PDBFormat, MMCIFFormat include("store/store.jl") export ProteinStructureStore diff --git a/src/io/io.jl b/src/io/io.jl index 5f606a8..a5cdb8c 100644 --- a/src/io/io.jl +++ b/src/io/io.jl @@ -1,7 +1,5 @@ using BioStructures: BioStructures, MMCIFDict, PDBFormat, MMCIFFormat -export BioStructures, MMCIFDict, PDBFormat, MMCIFFormat - const ProteinFileFormat = Union{PDBFormat, MMCIFFormat} const AMINOACIDS = Set("ACDEFGHIKLMNPQRSTVWY") const BACKBONE_ATOM_NAMES = ["N", "CA", "C"] diff --git a/src/io/mmcifutils.jl b/src/io/mmcifutils.jl index f95f8f6..7f06192 100644 --- a/src/io/mmcifutils.jl +++ b/src/io/mmcifutils.jl @@ -37,11 +37,3 @@ Dict{String, String} with 3 entries: """ mapmmcif(mmcifdict, pairs::Pair{String,String}...) = mapreduce(((from,to),) -> map_first_occurrence(getmmcif(mmcifdict, from), getmmcif(mmcifdict, to)), compose_map, pairs) - -get_auth_asym_to_entity(mmcifdict) = mapmmcif(mmcifdict, "_atom_site.auth_asym_id" => "_atom_site.label_entity_id") - -function get_auth_asym_to_taxid(mmcifdict) - mapmmcif(mmcifdict, - "_atom_site.auth_asym_id" => "_atom_site.label_entity_id", - "_entity_src_gen.entity_id" => "_entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id") -end