Merge pull request #20 from m3g/remove_AtomsBase

Remove atoms base

Project.toml

@@ -4,7 +4,6 @@ authors = ["Leandro Martinez <lmartine@unicamp.br> and contributors"]
 version = "1.22.2-DEV"
 
 [deps]
-AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"
 CellListMap = "69e1c6dd-3888-40e6-b3c8-31ac5f578864"
 Chemfiles = "46823bd8-5fb3-5f92-9aa0-96921f3dd015"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
@@ -30,7 +29,6 @@ Plotting = "Plots"
 
 [compat]
 Aqua = "0.8"
-AtomsBase = "0.3.4, 0.4"
 BenchmarkTools = "1.3"
 CellListMap = "0.9.6"
 Chemfiles = "0.10.31"

src/MolSimToolkit.jl

@@ -6,7 +6,6 @@ import OffsetArrays
 import LaTeXStrings # only because Aqua complains: used in the Plotting extensions
 
 using TestItems: @testitem
-using AtomsBase: atomic_mass
 using StaticArrays: FieldVector, SMatrix, MVector
 using LinearAlgebra: norm
 using Reexport: @reexport
@@ -33,6 +32,9 @@ export center_of_mass
 # Version of the package: used for printing in some places
 const version = pkgversion(@__MODULE__)
 
+# Minimal AtomType interface
+atomic_mass(atom::PDBTools.Atom) = PDBTools.mass(atom)
+
 # Testing module
 include("../test/Testing.jl")
 

src/datastructures/Simulation.jl

@@ -22,18 +22,19 @@ export get_frame
 
 Creates a new `Simulation` object. 
 
-The first constructor creates a `Simulation` object from a PDB file and a trajectory file. It will use the
+The first constructor creates a `Simulation` object from a PDB or mmCIF file and a trajectory file. It will use the
 `PDBTools.Atom` for the atom type, which will populate the `atoms` vector of the `Simulation` object.
+Currently, other atom types are supported, if the `MolSimToolkit.atomic_mass(::AtomType)` function is defined
+for the atom type.
 
 With the second constructor, the `atoms` vector is passed as an argument. This is useful when the atoms
-are provided by a different source than the PDB file. If the `AtomType` of the `atoms` vector conforms
-the `AtomsBase` interface, most functions in the `MolSimToolkit` will work with the `Simulation` object.
+are provided by a different source than the PDB file. 
 
 If `first`, `last`, and `step` are not specified, the `Simulation` will iterate over all frames in the file. 
 
 A `Simulation` object contains a trajectory file and a PDB data of the atoms. It can be iterated over to
 obtain the frames in the trajectory. The `Simulation` object is a mutable struct
-that contains the following data, that can be retrived by the corresponding
+that contains the following data, that can be retrieved by the corresponding
 functions:
 
 - `frame_range(::Simulation)`: the range of frames to be iterated over