mention extensions in docstrings

Author: jgreener64

docs/src/api.md

@@ -6,7 +6,7 @@ CurrentModule = BioStructures
 
 Package extensions are used in order to reduce the number of dependencies:
 - To use `LongAA`, call `using BioSequences`.
-- To use `pairalign` or [`Transformation`](@ref) on structural elements, call `using BioSequences, BioAlignments`.
+- To use `pairalign`, [`superimpose!`](@ref), [`rmsd`](@ref)/[`displacements`](@ref) with the `superimpose` option or [`Transformation`](@ref) on structural elements, call `using BioSequences, BioAlignments`.
 - To use `DataFrame`, call `using DataFrames`.
 - To use `MetaGraph`, call `using Graphs, MetaGraphs`.
 - To use [`MMTFDict`](@ref) or [`writemmtf`](@ref), call `import MMTF as MMTFPkg` (to avoid clashing with [`BioStructures.MMTF`](@ref)).

docs/src/documentation.md

@@ -483,6 +483,8 @@ To carry out superimposition, BioStructures.jl carries out a sequence alignment
 For example:
 
 ```julia
+using BioSequences, BioAlignments
+
 # Change the coordinates of element 1 to superimpose it onto element 2
 # Do sequence alignment with standard residues and calculate the transformation with Cα atoms (the default)
 superimpose!(el1, el2, standardselector)

src/model.jl

@@ -222,12 +222,12 @@ A `StructuralElement` or `Vector` of `StructuralElement`s up to
 a `Vector{Model}`.
 """
 const StructuralElementOrList = Union{
-        StructuralElement,
-        Vector{Model},
-        Vector{Chain},
-        Vector{<:AbstractResidue},
-        Vector{<:AbstractAtom},
-    }
+    StructuralElement,
+    Vector{Model},
+    Vector{Chain},
+    Vector{<:AbstractResidue},
+    Vector{<:AbstractAtom},
+}
 
 # Allow accessing sub elements contained in an element like a dictionary
 # e.g. allows you to do res[atom_name] rather than res.atoms[atom_name]
@@ -1792,49 +1792,49 @@ Base.show(io::IO, struc::MolecularStructure) = print(io,
     "with $(countmodels(struc)) models, ",
     countchains(struc) != 0 ? "$(countchains(struc)) chains ($(join(chainids(struc), ","))), " : "0 chains, ",
     "$(countresidues(struc, standardselector)) residues, ",
-    "$(countatoms(struc)) atoms"
+    "$(countatoms(struc)) atoms",
 )
 
 Base.show(io::IO, mo::Model) = print(io,
     "Model $(modelnumber(mo)) with ",
     countchains(mo) != 0 ? "$(countchains(mo)) chains ($(join(chainids(mo), ","))), " : "0 chains, ",
     "$(countresidues(mo, standardselector)) residues, ",
-    "$(countatoms(mo)) atoms"
+    "$(countatoms(mo)) atoms",
 )
 
 Base.show(io::IO, ch::Chain) = print(io,
     "Chain $(chainid(ch)) with ",
     "$(countresidues(ch, standardselector)) residues, ",
     "$(countresidues(ch, heteroselector)) other molecules, ",
-    "$(countatoms(ch)) atoms"
+    "$(countatoms(ch)) atoms",
 )
 
 Base.show(io::IO, res::Residue) = print(io,
     "Residue $(resid(res, full=true)) with ",
     "name $(resname(res)), ",
-    "$(countatoms(res)) atoms"
+    "$(countatoms(res)) atoms",
 )
 
 Base.show(io::IO, dis_res::DisorderedResidue) = print(io,
     "DisorderedResidue $(resid(dis_res, full=true)) with ",
-    "names $(join(resnames(dis_res), ","))"
+    "names $(join(resnames(dis_res), ","))",
 )
 
 Base.show(io::IO, at::Atom) = print(io,
     "Atom $(atomname(at)) with ",
     "serial $(serial(at)), ",
     "coordinates $(coords(at))",
-    altlocid(at) != ' ' ? ", alt loc ID $(altlocid(at))" : ""
+    altlocid(at) != ' ' ? ", alt loc ID $(altlocid(at))" : "",
 )
 
 Base.show(io::IO, dis_at::DisorderedAtom) = print(io,
     "DisorderedAtom $(atomname(dis_at)) with ",
-    "alt loc IDs $(join(altlocids(dis_at), ","))"
+    "alt loc IDs $(join(altlocids(dis_at), ","))",
 )
 
 Base.show(io::IO, at_rec::AtomRecord) = print(io,
     "AtomRecord $(strip(at_rec.atom_name)) with ",
     "serial $(at_rec.serial), ",
     "coordinates $(at_rec.coords)",
-    at_rec.alt_loc_id != ' ' ? ", alt loc ID $(at_rec.alt_loc_id)" : ""
+    at_rec.alt_loc_id != ' ' ? ", alt loc ID $(at_rec.alt_loc_id)" : "",
 )

src/spatial.jl

@@ -123,6 +123,7 @@ end
 Calculate the `Transformation` that maps the first element onto the second,
 and modify all coordinates in the first element according to the transformation.
 
+Requires the BioSequences.jl and BioAlignments.jl packages to be imported.
 See `Transformation` for keyword arguments.
 """
 function superimpose!(el1::StructuralElementOrList,
@@ -166,6 +167,7 @@ Get the root-mean-square deviation (RMSD) in Å between two
 
 If `superimpose` is `true` (the default), the elements are superimposed before
 RMSD calculation and the RMSD is calculated on the superimposed residues.
+In this case the BioSequences.jl and BioAlignments.jl packages should be imported.
 See `Transformation` for keyword arguments.
 If `superimpose` is `false` the elements are assumed to be superimposed and must
 be of the same length.
@@ -209,6 +211,7 @@ Get the displacements in Å between atomic coordinates from two
 
 If `superimpose` is `true` (the default), the elements are superimposed before
 calculation and the displacements are calculated on the superimposed residues.
+In this case the BioSequences.jl and BioAlignments.jl packages should be imported.
 See `Transformation` for keyword arguments.
 If `superimpose` is `false` the elements are assumed to be superimposed and must
 be of the same length.