Remove MDTraj mentions from docs

README.rst

@@ -21,7 +21,7 @@ This package bundles popular tasks in computational molecular biology
 into a uniform *Python* library.
 It can handle a major part of the typical workflow
 for sequence and biomolecular structure data:
-   
+
    - Searching and fetching data from biological databases
    - Reading and writing popular sequence/structure file formats
    - Analyzing and editing sequence/structure data
@@ -57,7 +57,6 @@ Installation
 
 Some functions require some extra packages:
 
-   - **mdtraj** - Required for trajetory file I/O operations.
    - **matplotlib** - Required for plotting purposes.
 
 *Biotite* can be installed via *Conda*...

doc/contribution/development.rst

@@ -79,9 +79,8 @@ The import statement for the dependency should be located directly inside the
 function or class, rather than module level, to ensure that the package is not
 required for any other functionality or for building the API documentation.
 
-An example for this approach is the support for trajectory files in
-:mod:`biotite.structure.io`, that require `MDTraj <http://mdtraj.org/>`_.
-The usage of these packages is not only allowed but even encouraged.
+An example for this approach are the plotting functions in
+:mod:`biotite.sequence.graphics`, that require *Matplotlib*.
 
 Code efficiency
 ---------------

doc/install.rst

@@ -20,7 +20,6 @@ dependencies if not already present.
 
 Some functionalities require extra packages:
 
-   - ``mdtraj`` - Required for trajectory file I/O operations.
    - ``matplotlib`` - Required for plotting purposes.
 
 

doc/tutorial/structure/trajectories.rst

@@ -10,11 +10,6 @@ If you like, you can even use the
 seamless interaction between *Biotite* and the
 `OpenMM <https://openmm.org/>`_ MD simulation toolkit.
 
-.. note::
-
-    Reading/writing trajectory files currently requires the
-    `MDtraj <https://www.mdtraj.org>`_ package.
-
 Reading trajectory files
 ------------------------
 

src/biotite/structure/io/__init__.py

@@ -18,8 +18,8 @@
 The recommended format for reading structure files is *BinaryCIF*.
 It has by far the shortest parsing time and file size.
 
-Besides the mentioned structure formats, Gromacs trajectory files can be
-loaded, if `mdtraj` is installed.
+Besides the mentioned structure formats, common trajectory formats can be
+loaded as well.
 """
 
 __name__ = "biotite.structure.io"

src/biotite/structure/io/trajfile.py

@@ -22,9 +22,6 @@ class TrajectoryFile(File, metaclass=abc.ABCMeta):
     frames. The file formats are usually binary and involve sometimes
     heavy compression, so that a large number of frames can be stored
     in relatively small space.
-    Since all :class:`TrajectoryFile` subclasses interface *MDtraj*
-    trajectory file classes, `MDtraj` must be installed to use any of
-    them.
 
     Notes
     -----