Converters API

package/CHANGELOG

@@ -23,6 +23,8 @@ The rules for this file:
   * 2.0.0
 
 Fixes
+  * Fixed OpenMM converter documentation not showing up in the Converters
+    section (Issue #3262, PR #2882)
   * WaterBridgeAnalysis double counts the water (Issue #3119, PR #3120)
   * NCDFReader now defaults to a dt value of 1.0 ps when it cannot estimate
     it from the first two frames of the file (Issue #3166)
@@ -175,6 +177,12 @@ Enhancements
     checking if it can be used in parallel analysis. (Issue #2996, PR #2950)
 
 Changes
+  * Introduces a new converter API with all converters in MDAnalysis.converters
+    (Issue #2790, PR #2882)
+  * The ParmEd classes were moved to the `converters` module (PR #2882)
+  * The `convert_to` method of the AtomGroup is now case-insensitive and
+    passes keyword arguments to the underlying converter. It can also be used
+    as `convert_to.lowercase_pkg_name()` for tab-completion (PR #2882)
   * `analysis.polymer.PersistenceLength` class now stores `lb`,
     `lp` and `fit` using the `analysis.base.Results` class 
     (Issues #3289, #3291)
@@ -250,6 +258,8 @@ Changes
   * Added OpenMM coordinate and topology converters (Issue #2863, PR #2917)
 
 Deprecations
+  * In 3.0.0 the ParmEd classes will only be accessible from the
+    `MDAnalysis.converters` module.
   * The `analysis.polymer.PersistenceLength.lb`,
     `analysis.polymer.PersistenceLength.lp` and 
     `analysis.polymer.PersistenceLength.fit` attributes are now deprecated in

package/MDAnalysis/__init__.py

@@ -208,6 +208,7 @@
 
 # After Universe import
 from .coordinates.MMTF import fetch_mmtf
+from . import converters
 
 from .due import due, Doi, BibTeX
 

package/MDAnalysis/coordinates/OpenMM.py → package/MDAnalysis/converters/OpenMM.py

@@ -21,7 +21,7 @@
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
 
-"""OpenMM structure I/O --- :mod:`MDAnalysis.coordinates.OpenMM`
+"""OpenMM structure I/O --- :mod:`MDAnalysis.converters.OpenMM`
 ================================================================
 
 
@@ -66,8 +66,7 @@
 
 import numpy as np
 
-from . import base
-from .. import units
+from ..coordinates import base
 
 
 class OpenMMSimulationReader(base.SingleFrameReaderBase):

package/MDAnalysis/topology/OpenMMParser.py → package/MDAnalysis/converters/OpenMMParser.py

@@ -21,14 +21,14 @@
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
 
-"""OpenMM topology parser
-=========================
+"""OpenMM topology parser :mod:`MDAnalysis.converters.OpenMMParser`
+===================================================================
 
 .. versionadded:: 2.0.0
 
 
 Converts an
-`OpenMM <http://docs.openmm.org/latest/api-python/generated/simtk.openmm.app.topology.Topology.html#simtk.openmm.app.topology.Topology>`_
+`OpenMM topology <http://docs.openmm.org/latest/api-python/generated/simtk.openmm.app.topology.Topology.html#simtk.openmm.app.topology.Topology>`_
 :class:`simtk.openmm.app.topology.Topology` into a :class:`MDAnalysis.core.Topology`.
 
 Also converts some objects within the
@@ -57,8 +57,7 @@
 
 import numpy as np
 
-from .base import TopologyReaderBase
-from .guessers import guess_types
+from ..topology.base import TopologyReaderBase
 from ..core.topology import Topology
 from ..core.topologyattrs import (
     Atomids,