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rebuilt html docs for version 2.10.0-dev0 from branch develop with sphinx at 8fb40ad 
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‎2.10.0-dev0/_modules/MDAnalysis/coordinates/DLPoly.html‎

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<span class="sd">Read DL Poly_ format coordinate files</span>
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<span class="sd">.. _Poly: http://www.stfc.ac.uk/SCD/research/app/ccg/software/DL_POLY/44516.aspx</span>
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<span class="sd">.. _Poly: https://www.sc.stfc.ac.uk/software/type/computational-materials-and-molecular-science/?searchquery=dl_poly</span>
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<span class="sd">&quot;&quot;&quot;</span>
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<span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
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‎2.10.0-dev0/_modules/MDAnalysis/coordinates/GRO.html‎

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<span class="sd">.. _Gromacs: http://www.gromacs.org</span>
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<span class="sd">.. _GRO: http://manual.gromacs.org/current/online/gro.html</span>
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<span class="sd">.. _GRO: https://manual.gromacs.org/current/reference-manual/file-formats.html#gro</span>
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<span class="sd">.. _GRO format: http://chembytes.wikidot.com/g-grofile</span>
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<span class="sd">&quot;&quot;&quot;</span>

‎2.10.0-dev0/_modules/MDAnalysis/coordinates/GSD.html‎

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<span class="sd">to be different to the one that was set at the first time step. No check on</span>
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<span class="sd">changes in particle identity or topology is currently implemented.</span>
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<span class="sd">.. _`HOOMD-blue`: http://codeblue.umich.edu/hoomd-blue/index.html</span>
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<span class="sd">.. _`HOOMD-blue`: https://glotzerlab.engin.umich.edu/hoomd-blue/</span>
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<span class="sd">Classes</span>
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<span class="sd">-------</span>

‎2.10.0-dev0/_modules/MDAnalysis/coordinates/H5MD.html‎

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@@ -322,8 +322,8 @@ <h1>Source code for MDAnalysis.coordinates.H5MD</h1><div class="highlight"><pre>
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<span class="sd">.. _`H5PY`: http://docs.h5py.org/</span>
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<span class="sd">.. _`parallel h5py docs`: https://docs.h5py.org/en/stable/mpi.html</span>
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<span class="sd">.. _`mpi4py`: https://mpi4py.readthedocs.io/en/stable/index.html</span>
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<span class="sd">.. _`Build MPI from sources`: https://mpi4py.readthedocs.io/en/stable/appendix.html#building-mpi-from-sources</span>
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<span class="sd">.. _`Build HDF5 from sources`: https://support.hdfgroup.org/ftp/HDF5/current/src/unpacked/release_docs/INSTALL_parallel</span>
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<span class="sd">.. _`Build MPI from sources`: https://docs.open-mpi.org/en/v5.0.x/installing-open-mpi/downloading.html</span>
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<span class="sd">.. _`Build HDF5 from sources`: https://docs.h5py.org/en/latest/mpi.html</span>
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<span class="sd">.. _`Install mpi4py`: https://mpi4py.readthedocs.io/en/stable/install.html#requirements</span>
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<span class="sd">.. _`Build h5py from sources`: https://docs.h5py.org/en/stable/mpi.html#building-against-parallel-hdf5</span>
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<span class="sd">.. _`H5MD notation`: https://nongnu.org/h5md/modules/units.html</span>

‎2.10.0-dev0/_modules/MDAnalysis/coordinates/INPCRD.html‎

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<span class="sd">Read coordinates in Amber_ coordinate/restart file (suffix &quot;inpcrd&quot;).</span>
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<span class="sd">.. _Amber: http://ambermd.org/formats.html#restart</span>
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<span class="sd">.. _Amber: https://ambermd.org/FileFormats.php</span>
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<span class="sd">Classes</span>

‎2.10.0-dev0/_modules/MDAnalysis/coordinates/MMTF.html‎

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<span class="sd">.. autoclass:: MMTFReader</span>
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<span class="sd"> :members:</span>
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<span class="sd">.. _MMTF: https://mmtf.rcsb.org/</span>
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<span class="sd">.. _MMTF: https://www.rcsb.org/news/feature/65a1af31c76ca3abcc925d0c</span>
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<span class="sd">&quot;&quot;&quot;</span>
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<span class="kn">import</span><span class="w"> </span><span class="nn">warnings</span>

‎2.10.0-dev0/_modules/MDAnalysis/coordinates/PDBQT.html‎

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<span class="sd">available in this case).</span>
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<span class="sd">.. _PDBQT:</span>
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<span class="sd"> http://autodock.scripps.edu/faqs-help/faq/what-is-the-format-of-a-pdbqt-file</span>
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<span class="sd"> https://autodock.scripps.edu/wp-content/uploads/sites/56/2021/10/AutoDock4.2.6_UserGuide.pdf</span>
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<span class="sd">.. _AutoDock:</span>
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<span class="sd"> http://autodock.scripps.edu/</span>
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<span class="sd">&quot;&quot;&quot;</span>
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<span class="w"> </span><span class="sd">&quot;&quot;&quot;PDBQT writer that implements a subset of the PDB_ 3.2 standard and the PDBQT_ spec.</span>
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<span class="sd"> .. _PDB: http://www.wwpdb.org/documentation/file-format-content/format32/v3.2.html</span>
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<span class="sd"> .. _PDBQT: http://autodock.scripps.edu/faqs-help/faq/what-is-the-format-of-a-pdbqt-file</span>
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<span class="sd"> .. _PDBQT: https://autodock.scripps.edu/wp-content/uploads/sites/56/2021/10/AutoDock4.2.6_UserGuide.pdf</span>
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<span class="sd"> .. versionchanged:: 2.6.0</span>
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<span class="sd"> Files are now written in `wt` mode, and keep extensions, allowing</span>

‎2.10.0-dev0/_modules/MDAnalysis/coordinates/PQR.html‎

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<span class="sd">In all cases the `dimensions` attribute will be set to `None`.</span>
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<span class="sd">.. _PQR: https://apbs-pdb2pqr.readthedocs.io/en/latest/formats/pqr.html</span>
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<span class="sd">.. _APBS: https://apbs-pdb2pqr.readthedocs.io/en/latest/apbs/index.html</span>
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<span class="sd">.. _PDB2PQR: https://apbs-pdb2pqr.readthedocs.io/en/latest/pdb2pqr/index.html</span>
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<span class="sd">.. _PQR: https://apbs.readthedocs.io/en/latest/formats/pqr.html</span>
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<span class="sd">.. _APBS: https://apbs.readthedocs.io/en/latest/</span>
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<span class="sd">.. _PDB2PQR: https://pdb2pqr.readthedocs.io/en/latest/</span>
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<span class="sd">.. _PDB: http://www.wwpdb.org/documentation/file-format</span>
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<span class="kn">import</span><span class="w"> </span><span class="nn">itertools</span>
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<span class="w"> </span><span class="sd">&quot;&quot;&quot;Read a PQR_ file into MDAnalysis.</span>
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<span class="sd"> .. _PQR:</span>
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<span class="sd"> https://apbs-pdb2pqr.readthedocs.io/en/latest/formats/pqr.html</span>
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<span class="sd"> https://apbs.readthedocs.io/en/latest/formats/pqr.html</span>
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<span class="sd"> .. versionchanged:: 0.11.0</span>
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‎2.10.0-dev0/_modules/MDAnalysis/coordinates/TRJ.html‎

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<span class="sd">.. Links</span>
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<span class="sd">.. _AMBER: http://ambermd.org</span>
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<span class="sd">.. _AMBER TRJ format: http://ambermd.org/formats.html#trajectory</span>
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<span class="sd">.. _AMBER TRJ format: https://ambermd.org/FileFormats.php#trajectory</span>
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<span class="sd">.. The formats page was archived as</span>
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<span class="sd">.. http://www.webcitation.org/query?url=http%3A%2F%2Fambermd.org%2Fformats.html&amp;date=2018-02-11</span>
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<span class="sd">.. Use the archived version if the original disappears. [orbeckst]</span>
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<span class="sd">.. Use the archived version if the original (https://ambermd.org/FileFormats.php#trajectory) disappears. [orbeckst]</span>
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<span class="sd">.. _AMBER netcdf format: http://ambermd.org/netcdf/nctraj.xhtml</span>
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<span class="sd">.. The formats page was archived as</span>
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<span class="sd">.. http://www.webcitation.org/query?url=http%3A%2F%2Fambermd.org%2Fnetcdf%2Fnctraj.xhtml&amp;date=2018-02-11</span>
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<span class="sd"> .. _AMBER TRJ format: http://ambermd.org/formats.html#trajectory</span>
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<span class="sd"> .. _AMBER TRJ format: https://ambermd.org/FileFormats.php#trajectory</span>
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<span class="sd"> .. versionchanged:: 0.11.0</span>
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‎2.10.0-dev0/_modules/MDAnalysis/coordinates/TRZ.html‎

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<span class="sd">the machine hardware architecture, MDAnalysis *always* reads and writes TRZ</span>
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<span class="sd">.. _IBIsCO: http://www.theo.chemie.tu-darmstadt.de/ibisco/IBISCO.html</span>
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<span class="sd">.. _YASP: http://www.theo.chemie.tu-darmstadt.de/group/services/yaspdoc/yaspdoc.html</span>
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<span class="sd">.. _IBIsCO: https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.21717</span>
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<span class="sd">.. _YASP: https://www.sciencedirect.com/science/article/abs/pii/0010465593901442</span>
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<span class="sd">Classes</span>
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<span class="sd">-------</span>

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