implemented coor and updated version

Project.toml

@@ -1,7 +1,7 @@
 name = "PDBTools"
 uuid = "e29189f1-7114-4dbd-93d0-c5673a921a58"
 authors = ["Leandro Martinez <leandro@iqm.unicamp.br>"]
-version = "0.11.4"
+version = "0.12"
 
 [deps]
 InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"

docs/src/elements.md

@@ -13,13 +13,13 @@ julia> printatom(atoms[1])
 julia> mass(atoms[1])
 14.0067
 
-julia> name(atoms[1])
-"Nitrogen"
-
 julia> atomic_number(atoms[1])
 7
 
 julia> element(atoms[1])
 "N"
 
+julia> element_name(atoms[1])
+"Nitrogen"
+
 ```

src/coor.jl

@@ -34,6 +34,10 @@ function coor(atoms::Vector{Atom}; only=all, column_based::Bool=true)
   return x
 end
 
+#
 # Coordinates of the atoms of a residue/molecule
-coor(residue::Residue; column_based::Bool=true) = 
-  coor(residue.atoms, only = atom -> (atom.index in residue.range), column_based=column_based)
+#
+coor(residue::Residue; only=all, column_based::Bool=true) = 
+  coor(residue.atoms, only=only, column_based=column_based)
+coor(residue::Residue, selection::String; column_based::Bool=true) = 
+  coor(residue.atoms, selection, column_based=column_based)

test/properties.jl

@@ -19,10 +19,13 @@
   @test m.xmin ≈ [-14.18, -17.561, -15.369]
   @test m.xmax ≈ [18.694, 14.182, 15.909]
   @test m.xlength ≈ [32.873999999999995, 31.743000000000002, 31.278]
-  @test coor(select(atoms,"residue = 3")) ==
+  s = select(atoms,"residue = 3")
+  r = Residue(select(atoms,"residue = 3"))  
+  @test coor(s) ==
           [  -4.383   -4.51    -3.903   -3.731   -4.938  -4.417  -5.543   -5.867   -5.451   -6.974   -2.626   -1.94
             -11.903  -11.263  -11.262  -12.076  -10.279  -9.552  -9.911  -10.85   -10.837  -11.289  -10.48   -10.014
              -6.849   -6.096   -8.062   -8.767   -8.612  -9.06   -7.784   -9.684  -10.863   -9.3     -7.749   -8.658 ]
+  @test coor(s) == coor(r)
   @test coor(select(atoms,"residue = 3"),column_based=false)' == coor(select(atoms,"residue = 3"))
   @test PDBTools.same_residue(atoms[1],atoms[2]) == true
   @test PDBTools.same_residue(atoms[1],atoms[20]) == false