finished Amber loading docs

package/MDAnalysis/coordinates/INPCRD.py

@@ -24,10 +24,6 @@
 """INPCRD structure files in MDAnalysis --- :mod:`MDAnalysis.coordinates.INPCRD`
 ================================================================================
 
-Read coordinates in Amber_ coordinate/restart file (suffix "inpcrd").
-
-.. _Amber: http://ambermd.org/formats.html#restart
-
 
 Classes
 -------

package/MDAnalysis/coordinates/TRJ.py

@@ -68,16 +68,6 @@
 Binary NetCDF trajectories
 --------------------------
 
-The `AMBER netcdf`_ format make use of NetCDF_ (Network Common Data
-Form) format. Such binary trajectories are recognized in MDAnalysis by
-the '.ncdf' suffix and read by the :class:`NCDFReader`.
-
-Binary trajectories can also contain velocities and forces, and can record the
-exact time
-step. In principle, the trajectories can be in different units than the AMBER
-defaults of ångström and picoseconds but at the moment MDAnalysis only supports
-those and will raise a :exc:`NotImplementedError` if anything else is detected.
-
 .. autoclass:: NCDFReader
    :members:
 
@@ -90,45 +80,6 @@
 ASCII TRAJ trajectories
 -----------------------
 
-ASCII AMBER_ TRJ coordinate files (as defined in `AMBER TRJ format`_)
-are handled by the :class:`TRJReader`. It is also possible to directly
-read *bzip2* or *gzip* compressed files.
-
-AMBER ASCII trajectories are recognised by the suffix '.trj',
-'.mdcrd' or '.crdbox (possibly with an additional '.gz' or '.bz2').
-
-.. Note::
-
-   In the AMBER community, these trajectories are often saved with the
-   suffix '.crd' but this extension conflicts with the CHARMM CRD
-   format and MDAnalysis *will not correctly autodetect AMBER ".crd"
-   trajectories*. Instead, explicitly provide the ``format="TRJ"``
-   argument to :class:`~MDAnalysis.core.universe.Universe`::
-
-     u = MDAnalysis.Universe("top.prmtop", "traj.crd", format="TRJ")
-
-   In this way, the AMBER :class:`TRJReader` is used.
-
-
-.. rubric:: Limitations
-
-* Periodic boxes are only stored as box lengths A, B, C in an AMBER
-  trajectory; the reader always assumes that these are orthorhombic
-  boxes.
-
-* The trajectory does not contain time information so we simply set
-  the time step to 1 ps (or the user could provide it as kwarg *dt*)
-
-* **No direct access of frames is implemented, only iteration through
-  the trajectory.**
-
-* Trajectories with fewer than 4 atoms probably fail to be read (BUG).
-
-* If the trajectory contains exactly *one* atom then it is always
-  assumed to be non-periodic (for technical reasons).
-
-* Velocities are currently *not supported* as ASCII trajectories.
-
 .. autoclass:: TRJReader
    :members:
 
@@ -145,8 +96,7 @@
 ..    The formats page was archived as
 ..    http://www.webcitation.org/query?url=http%3A%2F%2Fambermd.org%2Fnetcdf%2Fnctraj.xhtml&date=2018-02-11
 ..    Use the archived version if the original disappears. [orbeckst]
-.. _AMBER netcdf: http://ambermd.org/netcdf/nctraj.xhtml
-.. _NetCDF: http://www.unidata.ucar.edu/software/netcdf
+
 .. _Issue Tracker: https://github.com/MDAnalysis/mdanalysis/issues
 .. _MDAnalysis mailinglist: https://groups.google.com/group/mdnalysis-discussion
 

package/doc/sphinx/source/documentation_pages/loading_files/amber.rst

@@ -4,13 +4,13 @@
 Loading Amber files with MDAnalysis
 ###################################
 
-MDAnalysis can read PRMTOP, NCDF and ascii coordinate and restart files from
-Amber_.
+MDAnalysis can read PRMTOP files as topologies and
+NCDF and ascii coordinate and restart files as trajectories from
+`Amber MD`_ simulations.
 Typically using NCDF as the trajectory format will give the best performance
 as all other trajectory formats are ascii based.
 
-.. _Amber: http://ambermd.org
-
+.. _Amber MD: http://ambermd.org
 
 .. _load_amber_top:
 
@@ -63,19 +63,75 @@ For implementation details, see
 Loading Amber NCDF files
 ------------------------
 
-Pecularities of Amber NCDF files
+The `AMBER netcdf`_ format make use of NetCDF_ (Network Common Data
+Form) format. Such binary trajectories are recognized in MDAnalysis by
+the '.ncdf' or '.nc' suffix.
+
+Binary trajectories can also contain velocities and forces, and can record the
+exact time
+step. In principle, the trajectories can be in different units than the AMBER
+defaults of ångström and picoseconds but at the moment MDAnalysis only supports
+those and will raise a :exc:`NotImplementedError` if anything else is detected.
+
+For implementation details see :class:`MDAnalysis.coordinates.TRJ.NCDFReader`.
+
+.. _AMBER netcdf: http://ambermd.org/netcdf/nctraj.xhtml
+.. _NetCDF: http://www.unidata.ucar.edu/software/netcdf
 
 
 .. _load_amber_trj:
 
 Loading TRJ files
 -----------------
 
-All about loading Amber ascii TRJ files
+ASCII `AMBER TRJ coordinate files`_
+are handled by the :class:`TRJReader`. It is also possible to directly
+read *bzip2* or *gzip* compressed files.
+
+AMBER ASCII trajectories are recognised by the suffix '.trj',
+'.mdcrd' or '.crdbox (possibly with an additional '.gz' or '.bz2').
+
+.. Note::
+
+   In the AMBER community, these trajectories are often saved with the
+   suffix '.crd' but this extension conflicts with the CHARMM CRD
+   format and MDAnalysis *will not correctly autodetect AMBER ".crd"
+   trajectories*. Instead, explicitly provide the ``format="TRJ"``
+   argument to :class:`~MDAnalysis.core.universe.Universe`::
+
+     u = MDAnalysis.Universe("top.prmtop", "traj.crd", format="TRJ")
+
+   In this way, the format is correct set.
+
+.. rubric:: Limitations
+
+* Periodic boxes are only stored as box lengths A, B, C in an AMBER
+  trajectory; the reader always assumes that these are orthorhombic
+  boxes.
+
+* The trajectory does not contain time information so we simply set
+  the time step to 1 ps (or the user could provide it as kwarg *dt*)
+
+* Trajectories with fewer than 4 atoms probably fail to be read (BUG).
+
+* If the trajectory contains exactly *one* atom then it is always
+  assumed to be non-periodic (for technical reasons).
+
+* Velocities are currently *not supported* as ASCII trajectories.
+
+For implementation details see
+:class:`MDAnalysis.coordinates.TRJ.TRJReader`.
+
+.. _AMBER TRJ coordinate files: http://ambermd.org/formats.html#trajectory
 
 .. _load_amber_restart:
 
 Loading Amber restart files
 ---------------------------
 
-All about loading Amber restart files
+A single frame of positions can be read from `Amber restart files`_,
+which require a file suffix of ``.inpcrd`` or ``.restrt``.
+See :mod:`MDAnalysis.coordinates.INPCRD` for implementation details.
+
+.. _Amber restart files: http://ambermd.org/formats.html#restart
+