molecule graph docs

Author: jgreener64

docs/src/documentation.md

@@ -527,7 +527,7 @@ The coordinate sets must be the same size and have the number of dimensions in t
 
 The contacting elements in a molecular structure form a graph, and this can be retrieved using `MetaGraph`.
 This extends `MetaGraph` from [MetaGraphs.jl](https://github.com/JuliaGraphs/MetaGraphs.jl), allowing you to use all the graph analysis tools in [Graphs.jl](https://github.com/JuliaGraphs/Graphs.jl).
-For example:
+For example to find the graph from a contact map of Cβ atoms closer than 8 Å:
 
 ```julia-repl
 julia> using Graphs, MetaGraphs
@@ -552,6 +552,9 @@ See the [Graphs docs](https://juliagraphs.org/Graphs.jl/dev) for details on how
 Similar to [`ContactMap`](@ref), contacts are found between any element type passed in.
 So if you wanted the graph of chain contacts in a protein complex you could give a [`Model`](@ref) as the first argument.
 
+Calling `MetaGraph` on a [`Chain`](@ref) without a contact distance does something different: it constructs a graph of atoms where edges are determined by the known bonds of standard amino acids in the chain.
+Hydrogens should be present and atom names should match those in OpenMM.
+
 ## Assigning secondary structure
 
 Any secondary structure assignment at a residue is accessed via [`sscode`](@ref):

ext/BioStructuresGraphsExt.jl

@@ -8,7 +8,8 @@ using BioStructures: findatombyname
 """
     MetaGraph(element, contact_distance)
 
-Construct a graph of atoms where edges are contacts separated by less than `contact_distance`.
+Construct a graph of elements where edges are contacts separated by less
+than `contact_distance`.
 
 See Graphs.jl and MetaGraphs.jl for more on how to use graphs.
 """
@@ -30,22 +31,24 @@ function MetaGraphs.MetaGraph(el::StructuralElementOrList, contact_dist::Real)
 end
 
 """
-    MetaGraph(chain::Chain; strict::Bool = true)
+    MetaGraph(chain::Chain; strict::Bool=true)
 
-Construct a graph of atoms where edges are determined by the known bonds of residues in the chain.
+Construct a graph of atoms where edges are determined by the known bonds
+of residues in the chain.
 
 By default, the graph is constructed in `strict` mode, which means that:
 
 - residue and atom names must be standard
 - all hydrogens are present
 - HIS must be disambiguated as HIE, HID, or HIP
 
-These constraints can be relaxed by setting `strict = false`, at some risk to accuracy.
+These constraints can be relaxed by setting `strict = false`, at some
+risk to accuracy.
 
 See Graphs.jl and MetaGraphs.jl for more on how to use graphs.
 """
-function MetaGraphs.MetaGraph(chain::Chain; strict::Bool = true)
-    el_list = collectatoms(chain; expand_disordered = true)
+function MetaGraphs.MetaGraph(chain::Chain; strict::Bool=true)
+    el_list = collectatoms(chain; expand_disordered=true)
     mg = MetaGraph(length(el_list))
     for (i, el) in enumerate(el_list)
         set_prop!(mg, i, :element, el)