format

Author: BradyAJohnston

src/bcif.jl

@@ -8,17 +8,14 @@ import MsgPack
 
 A function to read a binary CIF file from MolStar and extract the list of attributes and their compressed bytes.
 """
-
-# currently isn't implementing the dssp / stride. If using BCIF it seems strange to write
-# out a .pdb, run dssp / string, then read it back in again. 
 function Base.read(input::IO,
-    ::Type{BCIFFormat},
-    structure_name::AbstractString="",
-    remove_disorder::Bool=false,
-    read_std_atoms::Bool=true,
-    read_het_atoms::Bool=true,
-    run_dssp::Bool=false,
-    run_stride::Bool=false)
+            ::Type{BCIFFormat};
+            structure_name::AbstractString="",
+            remove_disorder::Bool=false,
+            read_std_atoms::Bool=true,
+            read_het_atoms::Bool=true,
+            run_dssp::Bool=false,
+            run_stride::Bool=false)
 
     file = MsgPack.unpack(read(input))
     categories = file["dataBlocks"][1]["categories"]

src/download.jl

@@ -163,7 +163,7 @@ Requires an internet connection.
 """
 function downloadpdb(pdbid::AbstractString;
                 dir::AbstractString=pwd(),
-                format::Type{<:Union{PDBFormat,PDBXMLFormat,MMCIFFormat,BCIFFormat}}=PDBFormat,
+                format::Type{<:Union{PDBFormat, PDBXMLFormat, MMCIFFormat, BCIFFormat}}=PDBFormat,
                 obsolete::Bool=false,
                 overwrite::Bool=false,
                 ba_number::Integer=0)
@@ -317,7 +317,7 @@ automatically updates the PDB files of the given `format` inside the local
 Requires an internet connection.
 """
 function updatelocalpdb(; dir::AbstractString=pwd(),
-                format::Type{<:Union{PDBFormat,PDBXMLFormat,MMCIFFormat,BCIFFormat}}=PDBFormat)
+                format::Type{<:Union{PDBFormat, PDBXMLFormat, MMCIFFormat, BCIFFormat}}=PDBFormat)
     addedlist, modifiedlist, obsoletelist = pdbrecentchanges()
     # Download the newly added and modified pdb files
     downloadpdb(vcat(addedlist, modifiedlist), dir=dir, overwrite=true, format=format)
@@ -359,7 +359,7 @@ Requires an internet connection.
     in `dir`; by default skips downloading the PDB file if it exists.
 """
 function downloadallobsoletepdb(; obsolete_dir::AbstractString=pwd(),
-                format::Type{<:Union{PDBFormat,PDBXMLFormat,MMCIFFormat,BCIFFormat}}=PDBFormat,
+                format::Type{<:Union{PDBFormat, PDBXMLFormat, MMCIFFormat, BCIFFormat}}=PDBFormat,
                 overwrite::Bool=false)
     obsoletelist = pdbobsoletelist()
     downloadpdb(obsoletelist, dir=obsolete_dir, format=format, overwrite=overwrite)
@@ -398,7 +398,7 @@ Requires an internet connection.
 """
 function retrievepdb(pdbid::AbstractString;
             dir::AbstractString=pwd(),
-            format::Type{<:Union{PDBFormat,PDBXMLFormat,MMCIFFormat,BCIFFormat}}=MMCIFFormat,
+            format::Type{<:Union{PDBFormat, PDBXMLFormat, MMCIFFormat, BCIFFormat}}=MMCIFFormat,
             obsolete::Bool=false,
             overwrite::Bool=false,
             ba_number::Integer=0,