Merge pull request #8 from chrisiacovella/update_tests

updated doc strings and additional tests
chrisiacovella · Mar 22, 2023 · c0ed6db · c0ed6db
2 parents d2d4a12 + bfc8569
commit c0ed6db
Show file tree

Hide file tree

Showing 3 changed files with 292 additions and 104 deletions.
diff --git a/docs/index.rst b/docs/index.rst
@@ -13,7 +13,7 @@ hoomdxml_reader
 
 
 .. note::
-    `mdtraj <hhttps://www.mdtraj.org/1.9.7/api/generated/mdtraj.load_hoomdxml.html?highlight=hoomd%20xml#mdtraj.load_hoomdxml>`_  provides support for the HOOMD-blue XML file format, including automated grouping of particles by connectivity, similar to this Module. It also provides support for GSD files. However, masses, charges, angles and dihedrals are not parsed from the files by mdtraj. `mdanalysis <https://userguide.mdanalysis.org/1.0.0/formats/reference/xml.html>`_ also has an XML reader, but similarly, does not do a full parsing of the information in XML. This missing information may be necessary, especially for converting legacy XML files to the current `GSD <https://gsd.readthedocs.io>`_ file format used by HOOMD-blue or to convert to MoSDeF's `GMSO <https://github.com/mosdef-hub/gmso>`_ format.  This module provides a more complete parsing of the file and automated grouping into molecules.
+    `mdtraj <hhttps://www.mdtraj.org/1.9.7/api/generated/mdtraj.load_hoomdxml.html?highlight=hoomd%20xml#mdtraj.load_hoomdxml>`_  provides support for the HOOMD-blue XML file format, including automated grouping of particles by connectivity, similar to this Module. It also provides support for GSD files. However, masses, charges, angles and dihedrals are not parsed from the files by mdtraj. `mdanalysis <https://userguide.mdanalysis.org/1.0.0/formats/reference/xml.html>`_ also has an XML reader, but similarly, does not do a full parsing of the information in the XML. This missing information may be necessary, especially for converting legacy XML files to the current `GSD <https://gsd.readthedocs.io>`_ file format used by HOOMD-blue or to convert to MoSDeF's  `mBuild Compounds <https://github.com/mosdef-hub/mbuild>` or `GMSO <https://github.com/mosdef-hub/gmso>`_ format.  This module provides a more complete parsing of the file and automated grouping into molecules and code to convert to mBuild Compounds.
 
 =========================================================