export and clean up mmcifutils functions

MurrellGroup · Oct 17, 2024 · 7d34254 · 7d34254
1 parent a2f128a
commit 7d34254
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Showing 3 changed files with 2 additions and 11 deletions.
diff --git 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
@@ -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
@@ -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