move Trajectory to minor menu

docs/make.jl

@@ -22,7 +22,6 @@ makedocs(
         " ◦ POPC membrane in water/ethanol" => "example3.md",
         " ◦ Water/Glycerol mixture" => "example4.md",
         "Set solute and solvent" => "selection.md",
-        "Loading the trajectory" => "trajectory.md",
         "Computing the MDDF" => "mddf.md",
         "Results" => "results.md",
         "Atomic and group contributions" => "contributions.md",

docs/src/options.md

@@ -146,5 +146,45 @@ Modules = [ComplexMixtures]
 Pages = ["Options.jl"]
 ```
 
+## [Loading trajectories](@id trajectories)
+
+!!! note 
+    This explicit export of the `Trajectory` object is kept mostly
+    for legacy compatibility (previous to v2.9.0).
+
+To initialize a trajectory file for computation before calling the
+`mddf` or `coordination_number` functions, use the command
+```julia
+trajectory = Trajectory("trajectory.xtc",solute,solvent)
+```
+where `solute` and `solvent` are defined with the `AtomSelection` function 
+described [before](@ref selections). This function opens the stream for
+reading frames, which are read once a time when the coordinates are
+required for computing the MDDF.
+
+This object can be used to feed `mddf` and `coordination_number` with:
+```
+mddf(trajectory, options)
+coordination_number(trajectory, options)
+```
+
+The `Trajectory` function uses
+[Chemfiles](http://chemfiles.org/Chemfiles.jl/latest/) in background,
+and thus the most common trajectory formats are supported, as the ones
+produced with NAMD, Gromacs, LAMMPS, Amber, etc.  
+
+!!! tip
+    The format of the trajectory file is automatically determined by
+    Chemfiles from the extension of the file. However, it can be
+    provided by the user with the `format` keyword, for example:
+    ```julia
+    trajectory = Trajectory("trajectory.xtc",solute,solvent,format="xtc")
+    ```
+
+```@autodocs
+Modules = [ComplexMixtures]
+Pages = ["Trajectory.jl"]
+```
+