diff --git a/package/CHANGELOG b/package/CHANGELOG index a069607334e..232c859ef08 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -10,7 +10,7 @@ The rules for this file: use tabs but use spaces for formatting ------------------------------------------------------------------------------ -??/??/15 manuel.nuno.melo, richardjgowers +03/27/15 manuel.nuno.melo, richardjgowers * 0.9.1 Enhancements diff --git a/package/MDAnalysis/__init__.py b/package/MDAnalysis/__init__.py index 98118dba723..e9c82208652 100644 --- a/package/MDAnalysis/__init__.py +++ b/package/MDAnalysis/__init__.py @@ -153,7 +153,7 @@ 394 (2009), 160--176, doi:10.1016/j.jmb.2009.09.009 """ -__version__ = "1.0.0-dev" # NOTE: keep in sync with RELEASE in setup.py +__version__ = "0.9.1" # NOTE: keep in sync with RELEASE in setup.py __all__ = ['Timeseries', 'Universe', 'asUniverse', 'Writer', 'collection'] diff --git a/package/doc/html/.buildinfo b/package/doc/html/.buildinfo index 6a60063a18f..0067366f065 100644 --- a/package/doc/html/.buildinfo +++ b/package/doc/html/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. 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Navigation

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    Source code for MDAnalysis

                     394 (2009), 160--176, doi:10.1016/j.jmb.2009.09.009
 """
 
-__version__ = "1.0.0-dev"  # NOTE: keep in sync with RELEASE in setup.py
+__version__ = "0.9.1"  # NOTE: keep in sync with RELEASE in setup.py
 
 __all__ = ['Timeseries', 'Universe', 'asUniverse', 'Writer', 'collection']
 
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    • @@ -421,7 +421,7 @@

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    • @@ -434,7 +434,7 @@

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    • @@ -241,19 +241,25 @@

    Source code for MDAnalysis.analysis.hbonds.hbond_autocorrel

    *universe* The MDA universe *hydrogens* - Hydrogens which can form hydrogen bonds + AtomGroup of Hydrogens which can form hydrogen bonds *acceptors* - Accepting atoms + AtomGroup of all Acceptor atoms *donors* - The atoms which are connected to the hydrogens + The atoms which are connected to the hydrogens. This group + must be identical in length to the hydrogen group and matched, + ie hydrogens[1] is bonded to donors[0]. + For many cases, this will mean a donor appears twice in this + group. *bond_type* Which definition of hydrogen bond lifetime to consider, either - 'continuous' or 'intermittent' + 'continuous' or 'intermittent'. :Keywords: *exclusions* - Indices of Hydrogen-Donor pairs to be excluded. Must be a tuple of - two arrays + Indices of Hydrogen-Acceptor pairs to be excluded. + With nH and nA Hydrogens and Acceptors, a (nH x nA) array of distances + is calculated, *exclusions* is used as a mask on this array to exclude + some pairs. *angle_crit* The angle (in degrees) which all bonds must be greater than [130.0] *dist_crit* @@ -279,8 +285,8 @@

    Source code for MDAnalysis.analysis.hbonds.hbond_autocorrel

    self.h = hydrogens self.a = acceptors self.d = donors - if not (len(self.h) == len(self.a)) and (len(self.a) == len(self.d)): - raise ValueError("All selections must have the same length") + if not len(self.h) == len(self.d): + raise ValueError("Donors and Hydrogen groups must be matched") self.exclusions = exclusions if self.exclusions: @@ -605,7 +611,7 @@

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    • @@ -145,35 +145,13 @@

    Source code for MDAnalysis.coordinates.XYZ

     import os
 import errno
 import numpy
-import bz2
-import gzip
 import itertools
 
 import base
 import MDAnalysis
 import MDAnalysis.core
 import MDAnalysis.core.util as util
-
-
-class Timestep(base.Timestep):
-    @property
-    def dimensions(self):
-        """unitcell dimensions (*A*, *B*, *C*, *alpha*, *beta*, *gamma*)
-
-        XYZ files do not contain unitcell information but in order to
-        allow interoperability (and give the use a chance to set the
-        simulation box themselves for e.g. writing out to different
-        formats) we add an empty unit cell, i.e. when reading a XYZ
-        file this will only contain zeros.
-
-        lengths *a*, *b*, *c* are in the MDAnalysis length unit (Ã…), and
-        angles are in degrees.
-        """
-        return self._unitcell
-
-    @dimensions.setter
-    def dimensions(self, box):
-        self._unitcell[:] = box
+from MDAnalysis import NoDataError
 
 
 
    [docs]class XYZWriter(base.Writer):
@@ -336,7 +314,7 @@ 
    Source code for MDAnalysis.coordinates.XYZ
         format = "XYZ"
     # these are assumed!
     units = {'time': 'ps', 'length': 'Angstrom'}
-    _Timestep = Timestep
+    _Timestep = base.Timestep
 
     def __init__(self, filename, **kwargs):
         self.filename = filename
@@ -518,7 +496,7 @@ 
    Navigation
    
         
  • 
           modules |
    • 
-        
  • MDAnalysis 1.0.0-dev documentation »
    • 
+        
  • MDAnalysis 0.9.1 documentation »
    • 
           
  • Module code »
    • 
           
  • MDAnalysis »
    •  
       
@@ -531,7 +509,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
   
 
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/coordinates/__init__.html b/package/doc/html/_modules/MDAnalysis/coordinates/__init__.html
index a9c0f115d9c..d58fe2557a1 100644
--- a/package/doc/html/_modules/MDAnalysis/coordinates/__init__.html
+++ b/package/doc/html/_modules/MDAnalysis/coordinates/__init__.html
@@ -6,7 +6,7 @@
   
     
     
-    MDAnalysis.coordinates.__init__ — MDAnalysis 1.0.0-dev documentation
+    MDAnalysis.coordinates.__init__ — MDAnalysis 0.9.1 documentation
     
     
     
@@ -14,7 +14,7 @@
     
     
     
     
-    
+    
      
   
   
@@ -41,7 +41,7 @@ 
    Navigation
    
         
  • 
           modules |
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-        
  • MDAnalysis 1.0.0-dev documentation »
    • 
+        
  • MDAnalysis 0.9.1 documentation »
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  • Module code »
    • 
           
  • MDAnalysis »
    •  
       
@@ -178,10 +178,11 @@ 
    Source code for MDAnalysis.coordinates.__init__
    <
    |               |           |       | correctly (requires testing). Module                 |
    |               |           |       | :mod:`MDAnalysis.coordinates.DCD`                    |
    +---------------+-----------+-------+------------------------------------------------------+
-   | LAMMPS        | dcd,      |  r/w  | CHARMM-style binary trajectory; endianness is        |
-   |               | data      |  r    | autodetected. Units are appropriate for LAMMPS.      |
+   | LAMMPS        | dcd       |  r/w  | CHARMM-style binary trajectory; endianness is        |
+   |               |           |       | autodetected. Units are appropriate for LAMMPS.      |
    |               |           |       | Module :mod:`MDAnalysis.coordinates.LAMMPS`          |
-   |               |           |       | Single frames can be read from .data files.          |
+   +---------------+-----------+-------+------------------------------------------------------+
+   | LAMMPS [#a]_  | data      |  r    | Single frame of coordinates read from .data files    |
    +---------------+-----------+-------+------------------------------------------------------+
    | Gromacs       | xtc       |  r/w  | Compressed (lossy) xtc trajectory format. Module     |
    |               |           |       | :mod:`MDAnalysis.coordinates.XTC`                    |
@@ -190,10 +191,14 @@ 
    Source code for MDAnalysis.coordinates.__init__
    <
    |               |           |       | velocities are processed. Module                     |
    |               |           |       | :mod:`MDAnalysis.coordinates.TRR`                    |
    +---------------+-----------+-------+------------------------------------------------------+
-   | XYZ           |  xyz      |  r/w  | Generic white-space separate XYZ format; can be      |
+   | XYZ [#a]_     |  xyz      |  r/w  | Generic white-space separate XYZ format; can be      |
    |               |           |       | compressed (gzip or bzip2). Module                   |
    |               |           |       | :mod:`MDAnalysis.coordinates.XYZ`                    |
    +---------------+-----------+-------+------------------------------------------------------+
+   | GAMESS        |  gms,     |  r    | Generic semi-formatted GAMESS output log; can be     |
+   |               |  log,     |       | compressed (gzip or bzip2). Module                   |
+   |               |  out      |       | :mod:`MDAnalysis.coordinates.GMS`                    |
+   +---------------+-----------+-------+------------------------------------------------------+
    | AMBER         | trj,      |  r    | formatted (ASCII) trajectories; the presence of a    |
    |               | mdcrd     |       | periodic box is autodetected (*experimental*).       |
    |               |           |       | Module :mod:`MDAnalysis.coordinates.TRJ`             |
@@ -701,6 +706,7 @@ 
    Source code for MDAnalysis.coordinates.__init__
    <
 import DMS
 import TRZ
 import MOL2
+import GMS
 import base
 from core import reader, writer
 
@@ -727,6 +733,7 @@ 
    Source code for MDAnalysis.coordinates.__init__
    <
     'DMS': DMS.DMSReader,
     'TRZ': TRZ.TRZReader,
     'DATA': LAMMPS.DATAReader,
+    'GMS': GMS.GMSReader,
 }
 
 #: formats of readers that can also handle gzip or bzip2 compressed files
@@ -744,6 +751,7 @@ 
    Source code for MDAnalysis.coordinates.__init__
    <
     'DMS': DMS.DMSReader,
     'MOL2': MOL2.MOL2Reader,
     'DATA': LAMMPS.DATAReader,
+    'GMS': GMS.GMSReader,
 }
 
 #: hack: readers that ignore most errors (permissive=True); at the moment
@@ -803,7 +811,7 @@ 
    Navigation
    
         
  • 
           modules |
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-        
  • MDAnalysis 1.0.0-dev documentation »
    • 
+        
  • MDAnalysis 0.9.1 documentation »
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  • Module code »
    • 
           
  • MDAnalysis »
    •  
       
@@ -816,7 +824,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
   
 
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/coordinates/base.html b/package/doc/html/_modules/MDAnalysis/coordinates/base.html
index dedadccf1a3..50a6c218e81 100644
--- a/package/doc/html/_modules/MDAnalysis/coordinates/base.html
+++ b/package/doc/html/_modules/MDAnalysis/coordinates/base.html
@@ -6,7 +6,7 @@
   
     
     
-    MDAnalysis.coordinates.base — MDAnalysis 1.0.0-dev documentation
+    MDAnalysis.coordinates.base — MDAnalysis 0.9.1 documentation
     
     
     
@@ -14,7 +14,7 @@
     
     
     
     
-    
+    
      
   
   
@@ -41,7 +41,7 @@ 
    Navigation
    
         
  • 
           modules |
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-        
  • MDAnalysis 1.0.0-dev documentation »
    • 
+        
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  • Module code »
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  • MDAnalysis »
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@@ -1075,7 +1075,7 @@ 
    Navigation
    
         
  • 
           modules |
    • 
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  • MDAnalysis 1.0.0-dev documentation »
    • 
+        
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@@ -1088,7 +1088,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
   
 
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/coordinates/core.html b/package/doc/html/_modules/MDAnalysis/coordinates/core.html
index e8642f67f0b..e52cf305058 100644
--- a/package/doc/html/_modules/MDAnalysis/coordinates/core.html
+++ b/package/doc/html/_modules/MDAnalysis/coordinates/core.html
@@ -6,7 +6,7 @@
   
     
     
-    MDAnalysis.coordinates.core — MDAnalysis 1.0.0-dev documentation
+    MDAnalysis.coordinates.core — MDAnalysis 0.9.1 documentation
     
     
     
@@ -14,7 +14,7 @@
     
     
     
     
-    
+    
      
   
   
@@ -41,7 +41,7 @@ 
    Navigation
    
         
  • 
           modules |
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-        
  • MDAnalysis 1.0.0-dev documentation »
    • 
+        
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  • Module code »
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  • MDAnalysis »
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@@ -460,7 +460,7 @@ 
    Navigation
    
         
  • 
           modules |
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-        
  • MDAnalysis 1.0.0-dev documentation »
    • 
+        
  • MDAnalysis 0.9.1 documentation »
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  • Module code »
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@@ -473,7 +473,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
   
 
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/coordinates/pdb/extensions.html b/package/doc/html/_modules/MDAnalysis/coordinates/pdb/extensions.html
index bac6e954232..4d0bc3e96bd 100644
--- a/package/doc/html/_modules/MDAnalysis/coordinates/pdb/extensions.html
+++ b/package/doc/html/_modules/MDAnalysis/coordinates/pdb/extensions.html
@@ -6,7 +6,7 @@
   
     
     
-    MDAnalysis.coordinates.pdb.extensions — MDAnalysis 1.0.0-dev documentation
+    MDAnalysis.coordinates.pdb.extensions — MDAnalysis 0.9.1 documentation
     
     
     
@@ -14,7 +14,7 @@
     
     
     
     
-    
+    
      
   
   
@@ -41,7 +41,7 @@ 
    Navigation
    
         
  • 
           modules |
    • 
-        
  • MDAnalysis 1.0.0-dev documentation »
    • 
+        
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  • Module code »
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  • MDAnalysis »
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@@ -274,7 +274,7 @@ 
    Navigation
    
         
  • 
           modules |
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-        
  • MDAnalysis 1.0.0-dev documentation »
    • 
+        
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  • Module code »
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  • MDAnalysis »
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@@ -287,7 +287,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
   
 
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/coordinates/xdrfile/TRR.html b/package/doc/html/_modules/MDAnalysis/coordinates/xdrfile/TRR.html
index 94c3cb4baac..ce52bc780b0 100644
--- a/package/doc/html/_modules/MDAnalysis/coordinates/xdrfile/TRR.html
+++ b/package/doc/html/_modules/MDAnalysis/coordinates/xdrfile/TRR.html
@@ -6,7 +6,7 @@
   
     
     
-    MDAnalysis.coordinates.xdrfile.TRR — MDAnalysis 1.0.0-dev documentation
+    MDAnalysis.coordinates.xdrfile.TRR — MDAnalysis 0.9.1 documentation
     
     
     
@@ -14,7 +14,7 @@
     
     
     
     
-    
+    
      
   
   
@@ -41,7 +41,7 @@ 
    Navigation
    
         
  • 
           modules |
    • 
-        
  • MDAnalysis 1.0.0-dev documentation »
    • 
+        
  • MDAnalysis 0.9.1 documentation »
    • 
           
  • Module code »
    • 
           
  • MDAnalysis »
    •  
       
@@ -350,19 +350,19 @@ 
    Source code for MDAnalysis.coordinates.xdrfile.TRR
    @property
     def _y(self):
-        return self._pos[:, 0]
+        return self._pos[:, 1]
 
     @_y.setter
     def _y(self, y):
-        self._tpos[:, 0] = y
+        self._tpos[:, 1] = y
 
     @property
     def _z(self):
-        return self._pos[:, 0]
+        return self._pos[:, 2]
 
     @_z.setter
     def _z(self, z):
-        self._tpos[:, 0] = z
+        self._tpos[:, 2] = z
 
     # VELOCITIES
     @property
@@ -444,7 +444,7 @@ 
    Navigation
    
         
  • 
           modules |
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  • MDAnalysis 1.0.0-dev documentation »
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+        
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@@ -457,7 +457,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
   
 
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/coordinates/xdrfile/XTC.html b/package/doc/html/_modules/MDAnalysis/coordinates/xdrfile/XTC.html
index c5072f27d35..6cdf3aab866 100644
--- a/package/doc/html/_modules/MDAnalysis/coordinates/xdrfile/XTC.html
+++ b/package/doc/html/_modules/MDAnalysis/coordinates/xdrfile/XTC.html
@@ -6,7 +6,7 @@
   
     
     
-    MDAnalysis.coordinates.xdrfile.XTC — MDAnalysis 1.0.0-dev documentation
+    MDAnalysis.coordinates.xdrfile.XTC — MDAnalysis 0.9.1 documentation
     
     
     
@@ -14,7 +14,7 @@
     
     
     
     
-    
+    
      
   
   
@@ -41,7 +41,7 @@ 
    Navigation
    
         
  • 
           modules |
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-        
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+        
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  • Module code »
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@@ -158,7 +158,7 @@ 
    Navigation
    
         
  • 
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+        
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@@ -171,7 +171,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
   
 
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/coordinates/xdrfile/core.html b/package/doc/html/_modules/MDAnalysis/coordinates/xdrfile/core.html
index 11e7b4a7667..e7059b415eb 100644
--- a/package/doc/html/_modules/MDAnalysis/coordinates/xdrfile/core.html
+++ b/package/doc/html/_modules/MDAnalysis/coordinates/xdrfile/core.html
@@ -6,7 +6,7 @@
   
     
     
-    MDAnalysis.coordinates.xdrfile.core — MDAnalysis 1.0.0-dev documentation
+    MDAnalysis.coordinates.xdrfile.core — MDAnalysis 0.9.1 documentation
     
     
     
@@ -14,7 +14,7 @@
     
     
     
     
-    
+    
      
   
   
@@ -41,7 +41,7 @@ 
    Navigation
    
         
  • 
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-        
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+        
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@@ -1048,7 +1048,7 @@ 
    Navigation
    
         
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+        
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@@ -1061,7 +1061,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
   
 
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/coordinates/xdrfile/libxdrfile2.html b/package/doc/html/_modules/MDAnalysis/coordinates/xdrfile/libxdrfile2.html
index 7fa2b6d7249..4bd415883cb 100644
--- a/package/doc/html/_modules/MDAnalysis/coordinates/xdrfile/libxdrfile2.html
+++ b/package/doc/html/_modules/MDAnalysis/coordinates/xdrfile/libxdrfile2.html
@@ -6,7 +6,7 @@
   
     
     
-    MDAnalysis.coordinates.xdrfile.libxdrfile2 — MDAnalysis 1.0.0-dev documentation
+    MDAnalysis.coordinates.xdrfile.libxdrfile2 — MDAnalysis 0.9.1 documentation
     
     
     
@@ -14,7 +14,7 @@
     
     
     
     
-    
+    
      
   
   
@@ -41,7 +41,7 @@ 
    Navigation
    
         
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+        
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  • Module code »
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@@ -641,7 +641,7 @@ 
    Navigation
    
         
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  • MDAnalysis 1.0.0-dev documentation »
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+        
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  • Module code »
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@@ -654,7 +654,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
    \ No newline at end of file diff --git a/package/doc/html/_modules/MDAnalysis/coordinates/xdrfile/statno.html b/package/doc/html/_modules/MDAnalysis/coordinates/xdrfile/statno.html index b31e5ac2236..4307c4d7207 100644 --- a/package/doc/html/_modules/MDAnalysis/coordinates/xdrfile/statno.html +++ b/package/doc/html/_modules/MDAnalysis/coordinates/xdrfile/statno.html @@ -6,7 +6,7 @@ - MDAnalysis.coordinates.xdrfile.statno — MDAnalysis 1.0.0-dev documentation + MDAnalysis.coordinates.xdrfile.statno — MDAnalysis 0.9.1 documentation @@ -14,7 +14,7 @@ - + @@ -41,7 +41,7 @@

    Navigation

  • modules |
    • -
  • MDAnalysis 1.0.0-dev documentation »
    • +
  • MDAnalysis 0.9.1 documentation »
  • Module code »
  • MDAnalysis »
    • @@ -131,7 +131,7 @@

    Navigation

  • modules |
    • -
  • MDAnalysis 1.0.0-dev documentation »
    • +
  • MDAnalysis 0.9.1 documentation »
  • Module code »
  • MDAnalysis »
    • @@ -144,7 +144,7 @@

    Navigation

    Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon, Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi, Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein. - Created using Sphinx 1.2.3. + Created using Sphinx 1.2. \ No newline at end of file diff --git a/package/doc/html/_modules/MDAnalysis/core/AtomGroup.html b/package/doc/html/_modules/MDAnalysis/core/AtomGroup.html index f93d79540fa..d5ad1c0cd9a 100644 --- a/package/doc/html/_modules/MDAnalysis/core/AtomGroup.html +++ b/package/doc/html/_modules/MDAnalysis/core/AtomGroup.html @@ -6,7 +6,7 @@ - MDAnalysis.core.AtomGroup — MDAnalysis 1.0.0-dev documentation + MDAnalysis.core.AtomGroup — MDAnalysis 0.9.1 documentation @@ -14,7 +14,7 @@ - + @@ -41,7 +41,7 @@

    Navigation

  • modules |
    • -
  • MDAnalysis 1.0.0-dev documentation »
    • +
  • MDAnalysis 0.9.1 documentation »
  • Module code »
  • MDAnalysis »
    • @@ -860,11 +860,11 @@

    Source code for MDAnalysis.core.AtomGroup

         def __getitem__(self, item):
         """Return element (index) or group (slicing).
 
-        .. versionchanged:: 0.8 
-           :class:`ResidueGroup` and :class:`SegmentGroup`: 
+        .. versionchanged:: 0.8
+           :class:`ResidueGroup` and :class:`SegmentGroup`:
            return groups themselves and allow advanced slicing
         .. versionchanged:: 0.9.0
-           This method now used by all subclasses.  These subclasses override 
+           This method now used by all subclasses.  These subclasses override
            :attr:`_cls` to define the returned class.
         """
         container = self._container
@@ -934,7 +934,7 @@ 
    Source code for MDAnalysis.core.AtomGroup
             return len(self.segments)
 
    
     @cached('indices')
-    def indices(self):
+
    [docs]    def indices(self):
         """Array of all :attr:`Atom.number` in the group.
 
         These indices are 0-based and can be used to directly index
@@ -942,7 +942,7 @@ 
    Source code for MDAnalysis.core.AtomGroup
             :attr:`MDAnalysis.coordinates.base.Timestep._pos`.
         """
         return numpy.array([atom.number for atom in self._atoms])
-
+
    
 
    [docs]    def names(self):
         """Returns a list of atom names.
 
@@ -960,7 +960,7 @@ 
    Source code for MDAnalysis.core.AtomGroup
     
    
     @property
     @cached('fragments')
-    def fragments(self):
+
    [docs]    def fragments(self):
         """Read-only list of fragments.
 
         Contains all fragments that any Atom in this AtomGroup is part of, the contents of
@@ -969,10 +969,10 @@ 
    Source code for MDAnalysis.core.AtomGroup
             .. versionadded 0.9.0
         """
         return tuple(set(a.fragment for a in self._atoms))
-
+
    
     @property
     @cached('residues')
-    def residues(self):
+
    [docs]    def residues(self):
         """Read-only list of :class:`Residue` objects.
 
         A :class:`ResidueGroup` of all residues that contain atoms in
@@ -991,7 +991,7 @@ 
    Source code for MDAnalysis.core.AtomGroup
                     seen_residues.add(atom.residue)
             current_residue = atom.residue
         return ResidueGroup(residues)
-
+
    
 
    [docs]    def resids(self):
         """Returns a list of residue numbers.
 
@@ -1109,7 +1109,7 @@ 
    Source code for MDAnalysis.core.AtomGroup
     
    
     @property
     @cached('segments')
-    def segments(self):
+
    [docs]    def segments(self):
         """Read-only list of :class:`Segment` objects.
 
         A :class:`SegmentGroup` of all segments that contain atoms in this group.
@@ -1128,7 +1128,7 @@ 
    Source code for MDAnalysis.core.AtomGroup
                     seen_segments.add(atom.segment)
             current_segment = atom.segment
         return SegmentGroup(segments)
-
+
    
 
    [docs]    def segids(self):
         """Returns a list of segment ids (=segment names).
 
@@ -1139,7 +1139,7 @@ 
    Source code for MDAnalysis.core.AtomGroup
     
    
     @property
     @cached('bonds')
-    def bonds(self):
+
    [docs]    def bonds(self):
         """All the bonds in this AtomGroup
 
         Note that these bonds might extend out of the AtomGroup, to select
@@ -1155,10 +1155,10 @@ 
    Source code for MDAnalysis.core.AtomGroup
                 return None
         else:
             return TopologyGroup(mybonds)
-
+
    
     @property
     @cached('angles')
-    def angles(self):
+
    [docs]    def angles(self):
         """All the angles in this AtomGroup
 
         Note that these angles might extend out of the AtomGroup, to select
@@ -1174,10 +1174,10 @@ 
    Source code for MDAnalysis.core.AtomGroup
                 return None
         else:
             return TopologyGroup(mybonds)
-
+
    
     @property
     @cached('torsions')
-    def torsions(self):
+
    [docs]    def torsions(self):
         """All the torsions in this AtomGroup
 
         Note that these torsions might extend out of the AtomGroup, to select
@@ -1193,10 +1193,10 @@ 
    Source code for MDAnalysis.core.AtomGroup
                 return None
         else:
             return TopologyGroup(mybonds)
-
+
    
     @property
     @cached('impropers')
-    def impropers(self):
+
    [docs]    def impropers(self):
         """All the improper torsions in this AtomGroup
 
         Note that these improper torsions might extend out of the AtomGroup,
@@ -1212,12 +1212,12 @@ 
    Source code for MDAnalysis.core.AtomGroup
                 return None
         else:
             return TopologyGroup(mybonds)
-
+
    
     @cached('masses')
-    def masses(self):
+
    [docs]    def masses(self):
         """Array of atomic masses (as defined in the topology)"""
         return numpy.array([atom.mass for atom in self._atoms])
-
+
    
 
    [docs]    def totalMass(self):
         """Total mass of the selection (masses are taken from the topology or guessed)."""
         return numpy.sum(self.masses(), axis=0)
@@ -1638,8 +1638,8 @@ 
    Source code for MDAnalysis.core.AtomGroup
             # Create the inertia tensor
         # m_i = mass of atom i
         # (x_i, y_i, z_i) = pos of atom i
-        # Ixx = sum(m_i*(y_i^2+z_i^2)); 
-        # Iyy = sum(m_i*(x_i^2+z_i^2)); 
+        # Ixx = sum(m_i*(y_i^2+z_i^2));
+        # Iyy = sum(m_i*(x_i^2+z_i^2));
         # Izz = sum(m_i*(x_i^2+y_i^2))
         # Ixy = Iyx = -1*sum(m_i*x_i*y_i)
         # Ixz = Izx = -1*sum(m_i*x_i*z_i)
@@ -2053,7 +2053,7 @@ 
    Source code for MDAnalysis.core.AtomGroup
     
         .. versionadded:: 0.7.7
         """
-        if ts == None:
+        if ts is None:
             ts = self.universe.trajectory.ts
         try:
             if hasattr(ts, 'has_f'):  # TRR handling must be told frame now holds valid force info.
@@ -3402,13 +3402,13 @@ 
    Source code for MDAnalysis.core.AtomGroup
     
     @property
     @cached('fragments')
-    def fragments(self):
+
    [docs]    def fragments(self):
         """Read only tuple of fragments in the Universe
 
         .. versionadded 0.9.0
         """
         return self._init_fragments()
-
+
    
     @property
     @cached('bondDict')
     def _bondDict(self):
@@ -3552,7 +3552,7 @@ 
    Source code for MDAnalysis.core.AtomGroup
             self._fill_cache('bonds', self._init_bonds())
 
     @bonds.deleter
-    def bonds(self):
+
    [docs]    def bonds(self):
         """Delete the bonds from Universe
 
         This must also remove the per atom record of bonds (bondDict)
@@ -3560,7 +3560,7 @@ 
    Source code for MDAnalysis.core.AtomGroup
             .. versionadded:: 0.9.0
         """
         self._clear_caches('bonds', 'bondDict')
-
+
    
     @property
     @cached('angles')
     def angles(self):
@@ -3581,9 +3581,9 @@ 
    Source code for MDAnalysis.core.AtomGroup
             self._fill_cache('angles', self._init_angles())
 
     @angles.deleter
-    def angles(self):
+
    [docs]    def angles(self):
         self._clear_caches('angles', 'angleDict')
-
+
    
     @property
     @cached('torsions')
     def torsions(self):
@@ -3604,9 +3604,9 @@ 
    Source code for MDAnalysis.core.AtomGroup
             self._fill_cache('torsions', self._init_torsions())
 
     @torsions.deleter
-    def torsions(self):
+
    [docs]    def torsions(self):
         self._clear_caches('torsions', 'torsionDict')
-
+
    
     @property
     @cached('impropers')
     def impropers(self):
@@ -3627,9 +3627,9 @@ 
    Source code for MDAnalysis.core.AtomGroup
             self._fill_cache('impropers', self._init_impropers())
 
     @impropers.deleter
-    def impropers(self):
+
    [docs]    def impropers(self):
         self._clear_caches('impropers', 'improperDict')
-
+
    
 
    [docs]    def load_new(self, filename, **kwargs):
         """Load coordinates from *filename*, using the suffix to detect file format.
 
@@ -4034,7 +4034,7 @@ 
    Navigation
    
         
  • 
           modules |
    • 
-        
  • MDAnalysis 1.0.0-dev documentation »
    • 
+        
  • MDAnalysis 0.9.1 documentation »
    • 
           
  • Module code »
    • 
           
  • MDAnalysis »
    •  
       
@@ -4047,7 +4047,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
   
 
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/core/Selection.html b/package/doc/html/_modules/MDAnalysis/core/Selection.html
index 5a855f9b226..be007e4d7c9 100644
--- a/package/doc/html/_modules/MDAnalysis/core/Selection.html
+++ b/package/doc/html/_modules/MDAnalysis/core/Selection.html
@@ -6,7 +6,7 @@
   
     
     
-    MDAnalysis.core.Selection — MDAnalysis 1.0.0-dev documentation
+    MDAnalysis.core.Selection — MDAnalysis 0.9.1 documentation
     
     
     
@@ -14,7 +14,7 @@
     
     
     
     
-    
+    
      
   
   
@@ -41,7 +41,7 @@ 
    Navigation
    
         
  • 
           modules |
    • 
-        
  • MDAnalysis 1.0.0-dev documentation »
    • 
+        
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    • 
           
  • Module code »
    • 
           
  • MDAnalysis »
    •  
       
@@ -1145,7 +1145,7 @@ 
    Navigation
    
         
  • 
           modules |
    • 
-        
  • MDAnalysis 1.0.0-dev documentation »
    • 
+        
  • MDAnalysis 0.9.1 documentation »
    • 
           
  • Module code »
    • 
           
  • MDAnalysis »
    •  
       
@@ -1158,7 +1158,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
   
 
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/core/Timeseries.html b/package/doc/html/_modules/MDAnalysis/core/Timeseries.html
index 4652cd2daf3..9043e63663c 100644
--- a/package/doc/html/_modules/MDAnalysis/core/Timeseries.html
+++ b/package/doc/html/_modules/MDAnalysis/core/Timeseries.html
@@ -6,7 +6,7 @@
   
     
     
-    MDAnalysis.core.Timeseries — MDAnalysis 1.0.0-dev documentation
+    MDAnalysis.core.Timeseries — MDAnalysis 0.9.1 documentation
     
     
     
@@ -14,7 +14,7 @@
     
     
     
     
-    
+    
      
   
   
@@ -41,7 +41,7 @@ 
    Navigation
    
         
  • 
           modules |
    • 
-        
  • MDAnalysis 1.0.0-dev documentation »
    • 
+        
  • MDAnalysis 0.9.1 documentation »
    • 
           
  • Module code »
    • 
           
  • MDAnalysis »
    •  
       
@@ -488,7 +488,7 @@ 
    Navigation
    
         
  • 
           modules |
    • 
-        
  • MDAnalysis 1.0.0-dev documentation »
    • 
+        
  • MDAnalysis 0.9.1 documentation »
    • 
           
  • Module code »
    • 
           
  • MDAnalysis »
    •  
       
@@ -501,7 +501,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
   
 
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/core/__init__.html b/package/doc/html/_modules/MDAnalysis/core/__init__.html
index 647b58b1dd7..64807ba9f14 100644
--- a/package/doc/html/_modules/MDAnalysis/core/__init__.html
+++ b/package/doc/html/_modules/MDAnalysis/core/__init__.html
@@ -6,7 +6,7 @@
   
     
     
-    MDAnalysis.core.__init__ — MDAnalysis 1.0.0-dev documentation
+    MDAnalysis.core.__init__ — MDAnalysis 0.9.1 documentation
     
     
     
@@ -14,7 +14,7 @@
     
     
     
     
-    
+    
      
   
   
@@ -41,7 +41,7 @@ 
    Navigation
    
         
  • 
           modules |
    • 
-        
  • MDAnalysis 1.0.0-dev documentation »
    • 
+        
  • MDAnalysis 0.9.1 documentation »
    • 
           
  • Module code »
    • 
           
  • MDAnalysis »
    •  
       
@@ -536,7 +536,7 @@ 
    Navigation
    
         
  • 
           modules |
    • 
-        
  • MDAnalysis 1.0.0-dev documentation »
    • 
+        
  • MDAnalysis 0.9.1 documentation »
    • 
           
  • Module code »
    • 
           
  • MDAnalysis »
    •  
       
@@ -549,7 +549,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
   
 
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/core/log.html b/package/doc/html/_modules/MDAnalysis/core/log.html
index e8c14f3e38f..54358ecf0a9 100644
--- a/package/doc/html/_modules/MDAnalysis/core/log.html
+++ b/package/doc/html/_modules/MDAnalysis/core/log.html
@@ -6,7 +6,7 @@
   
     
     
-    MDAnalysis.core.log — MDAnalysis 1.0.0-dev documentation
+    MDAnalysis.core.log — MDAnalysis 0.9.1 documentation
     
     
     
@@ -14,7 +14,7 @@
     
     
     
     
-    
+    
      
   
   
@@ -41,7 +41,7 @@ 
    Navigation
    
         
  • 
           modules |
    • 
-        
  • MDAnalysis 1.0.0-dev documentation »
    • 
+        
  • MDAnalysis 0.9.1 documentation »
    • 
           
  • Module code »
    • 
           
  • MDAnalysis »
    •  
       
@@ -369,7 +369,7 @@ 
    Navigation
    
         
  • 
           modules |
    • 
-        
  • MDAnalysis 1.0.0-dev documentation »
    • 
+        
  • MDAnalysis 0.9.1 documentation »
    • 
           
  • Module code »
    • 
           
  • MDAnalysis »
    •  
       
@@ -382,7 +382,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
   
 
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/core/transformations.html b/package/doc/html/_modules/MDAnalysis/core/transformations.html
index 0eb92ce0a4b..db9e51573b2 100644
--- a/package/doc/html/_modules/MDAnalysis/core/transformations.html
+++ b/package/doc/html/_modules/MDAnalysis/core/transformations.html
@@ -6,7 +6,7 @@
   
     
     
-    MDAnalysis.core.transformations — MDAnalysis 1.0.0-dev documentation
+    MDAnalysis.core.transformations — MDAnalysis 0.9.1 documentation
     
     
     
@@ -14,7 +14,7 @@
     
     
     
     
-    
+    
      
   
   
@@ -41,7 +41,7 @@ 
    Navigation
    
         
  • 
           modules |
    • 
-        
  • MDAnalysis 1.0.0-dev documentation »
    • 
+        
  • MDAnalysis 0.9.1 documentation »
    • 
           
  • Module code »
    • 
           
  • MDAnalysis »
    •  
       
@@ -1932,7 +1932,7 @@ 
    Navigation
    
         
  • 
           modules |
    • 
-        
  • MDAnalysis 1.0.0-dev documentation »
    • 
+        
  • MDAnalysis 0.9.1 documentation »
    • 
           
  • Module code »
    • 
           
  • MDAnalysis »
    •  
       
@@ -1945,7 +1945,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
   
 
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/core/units.html b/package/doc/html/_modules/MDAnalysis/core/units.html
index 226ed951f06..6d34e32fbbb 100644
--- a/package/doc/html/_modules/MDAnalysis/core/units.html
+++ b/package/doc/html/_modules/MDAnalysis/core/units.html
@@ -6,7 +6,7 @@
   
     
     
-    MDAnalysis.core.units — MDAnalysis 1.0.0-dev documentation
+    MDAnalysis.core.units — MDAnalysis 0.9.1 documentation
     
     
     
@@ -14,7 +14,7 @@
     
     
     
     
-    
+    
      
   
   
@@ -41,7 +41,7 @@ 
    Navigation
    
         
  • 
           modules |
    • 
-        
  • MDAnalysis 1.0.0-dev documentation »
    • 
+        
  • MDAnalysis 0.9.1 documentation »
    • 
           
  • Module code »
    • 
           
  • MDAnalysis »
    •  
       
@@ -446,7 +446,7 @@ 
    Navigation
    
         
  • 
           modules |
    • 
-        
  • MDAnalysis 1.0.0-dev documentation »
    • 
+        
  • MDAnalysis 0.9.1 documentation »
    • 
           
  • Module code »
    • 
           
  • MDAnalysis »
    •  
       
@@ -459,7 +459,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
   
 
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/core/util.html b/package/doc/html/_modules/MDAnalysis/core/util.html
index 448f72acfb6..0401e9e67c9 100644
--- a/package/doc/html/_modules/MDAnalysis/core/util.html
+++ b/package/doc/html/_modules/MDAnalysis/core/util.html
@@ -6,7 +6,7 @@
   
     
     
-    MDAnalysis.core.util — MDAnalysis 1.0.0-dev documentation
+    MDAnalysis.core.util — MDAnalysis 0.9.1 documentation
     
     
     
@@ -14,7 +14,7 @@
     
     
     
     
-    
+    
      
   
   
@@ -41,7 +41,7 @@ 
    Navigation
    
         
  • 
           modules |
    • 
-        
  • MDAnalysis 1.0.0-dev documentation »
    • 
+        
  • MDAnalysis 0.9.1 documentation »
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  • Module code »
    • 
           
  • MDAnalysis »
    •  
       
@@ -239,7 +239,7 @@ 
    Source code for MDAnalysis.core.util
     import re
 import io
 import warnings
-
+from functools import wraps
 import numpy
 
 
@@ -1231,6 +1231,7 @@ 
    Source code for MDAnalysis.core.util
         """
 
     def cached_lookup(func):
+        @wraps(func)
         def wrapper(self, *args, **kwargs):
             try:
                 return self._cache[key]
@@ -1257,7 +1258,7 @@ 
    Navigation
    
         
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           modules |
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    • 
           
  • MDAnalysis »
    •  
       
@@ -1270,7 +1271,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
   
 
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/selections/base.html b/package/doc/html/_modules/MDAnalysis/selections/base.html
index e8cb89571c2..70ae9b2c43d 100644
--- a/package/doc/html/_modules/MDAnalysis/selections/base.html
+++ b/package/doc/html/_modules/MDAnalysis/selections/base.html
@@ -6,7 +6,7 @@
   
     
     
-    MDAnalysis.selections.base — MDAnalysis 1.0.0-dev documentation
+    MDAnalysis.selections.base — MDAnalysis 0.9.1 documentation
     
     
     
@@ -14,7 +14,7 @@
     
     
     
     
-    
+    
      
   
   
@@ -41,7 +41,7 @@ 
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    •  
       
@@ -309,7 +309,7 @@ 
    Navigation
    
         
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    • 
           
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    •  
       
@@ -322,7 +322,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
   
 
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/selections/charmm.html b/package/doc/html/_modules/MDAnalysis/selections/charmm.html
index 09861600baa..7df1594a37d 100644
--- a/package/doc/html/_modules/MDAnalysis/selections/charmm.html
+++ b/package/doc/html/_modules/MDAnalysis/selections/charmm.html
@@ -6,7 +6,7 @@
   
     
     
-    MDAnalysis.selections.charmm — MDAnalysis 1.0.0-dev documentation
+    MDAnalysis.selections.charmm — MDAnalysis 0.9.1 documentation
     
     
     
@@ -14,7 +14,7 @@
     
     
     
     
-    
+    
      
   
   
@@ -41,7 +41,7 @@ 
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    •  
       
@@ -146,7 +146,7 @@ 
    Navigation
    
         
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    • 
           
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    •  
       
@@ -159,7 +159,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
   
 
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/selections/gromacs.html b/package/doc/html/_modules/MDAnalysis/selections/gromacs.html
index 190799fafc7..9fee49a78ce 100644
--- a/package/doc/html/_modules/MDAnalysis/selections/gromacs.html
+++ b/package/doc/html/_modules/MDAnalysis/selections/gromacs.html
@@ -6,7 +6,7 @@
   
     
     
-    MDAnalysis.selections.gromacs — MDAnalysis 1.0.0-dev documentation
+    MDAnalysis.selections.gromacs — MDAnalysis 0.9.1 documentation
     
     
     
@@ -14,7 +14,7 @@
     
     
     
     
-    
+    
      
   
   
@@ -41,7 +41,7 @@ 
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    •  
       
@@ -137,7 +137,7 @@ 
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    •  
       
@@ -150,7 +150,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
   
 
\ No newline at end of file
diff --git a/package/doc/html/_modules/MDAnalysis/selections/pymol.html b/package/doc/html/_modules/MDAnalysis/selections/pymol.html
index 275a6dda893..3c0387a4559 100644
--- a/package/doc/html/_modules/MDAnalysis/selections/pymol.html
+++ b/package/doc/html/_modules/MDAnalysis/selections/pymol.html
@@ -6,7 +6,7 @@
   
     
     
-    MDAnalysis.selections.pymol — MDAnalysis 1.0.0-dev documentation
+    MDAnalysis.selections.pymol — MDAnalysis 0.9.1 documentation
     
     
     
@@ -14,7 +14,7 @@
     
     
     
     
-    
+    
      
   
   
@@ -41,7 +41,7 @@ 
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    •  
       
@@ -145,7 +145,7 @@ 
    Navigation
    
         
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    •  
       
@@ -158,7 +158,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
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@@ -6,7 +6,7 @@
   
     
     
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@@ -6,7 +6,7 @@
   
     
     
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     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
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diff --git a/package/doc/html/_modules/MDAnalysis/topology/TPRParser.html b/package/doc/html/_modules/MDAnalysis/topology/TPRParser.html
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@@ -6,7 +6,7 @@
   
     
     
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     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
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diff --git a/package/doc/html/_modules/MDAnalysis/topology/core.html b/package/doc/html/_modules/MDAnalysis/topology/core.html
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@@ -6,7 +6,7 @@
   
     
     
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    Source code for MDAnalysis.topology.core
     
    
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+
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@@ -932,7 +932,7 @@ 
    Source code for MDAnalysis.topology.core
             .. versionadded 0.9.0
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+
    
 
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     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
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     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
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diff --git a/package/doc/html/_modules/MDAnalysis/visualization/streamlines.html b/package/doc/html/_modules/MDAnalysis/visualization/streamlines.html
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@@ -6,7 +6,7 @@
   
     
     
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     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
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diff --git a/package/doc/html/_static/basic.css b/package/doc/html/_static/basic.css
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\ No newline at end of file
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@@ -6,7 +6,7 @@
   
     
     
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\ No newline at end of file
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\ No newline at end of file
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\ No newline at end of file
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@@ -14,7 +14,7 @@
     
     
     
     
-    
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@@ -656,7 +656,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
   
 
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diff --git a/package/doc/html/documentation_pages/analysis/contacts.html b/package/doc/html/documentation_pages/analysis/contacts.html
index 772d751e669..4f9aaf6fe5d 100644
--- a/package/doc/html/documentation_pages/analysis/contacts.html
+++ b/package/doc/html/documentation_pages/analysis/contacts.html
@@ -6,7 +6,7 @@
   
     
     
-    3.1.2. Native contacts analysis — MDAnalysis.analysis.contacts — MDAnalysis 1.0.0-dev documentation
+    3.1.2. Native contacts analysis — MDAnalysis.analysis.contacts — MDAnalysis 0.9.1 documentation
     
     
     
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@@ -226,8 +226,7 @@ 
    3.1.2.2. ClassesContactAnalysis.timeseries. It is a numpy array which
 contains the frame number at index 0, q1 and q2 at index 1 and 2,
 and the total number of contacts in 3 and 4.
    
-
    frame  q1 q2  n1 n2
-
    
+
    frame  q1 q2  n1 n2
    
 
    
 
    The total number of contacts in the reference states 1 and 2 are
 stored in ContactAnalysis.nref (index 0 and 1).
    
@@ -599,7 +598,7 @@ 
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@@ -611,7 +610,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
   
 
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diff --git a/package/doc/html/documentation_pages/analysis/density.html b/package/doc/html/documentation_pages/analysis/density.html
index 61ca556b396..41b4a99c83a 100644
--- a/package/doc/html/documentation_pages/analysis/density.html
+++ b/package/doc/html/documentation_pages/analysis/density.html
@@ -6,7 +6,7 @@
   
     
     
-    3.6.1. Generating densities from trajectories — MDAnalysis.analysis.density — MDAnalysis 1.0.0-dev documentation
+    3.6.1. Generating densities from trajectories — MDAnalysis.analysis.density — MDAnalysis 0.9.1 documentation
     
     
     
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@@ -922,7 +922,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
   
 
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/analysis/distances.html b/package/doc/html/documentation_pages/analysis/distances.html
index eb82480c944..63f8b6300ea 100644
--- a/package/doc/html/documentation_pages/analysis/distances.html
+++ b/package/doc/html/documentation_pages/analysis/distances.html
@@ -6,7 +6,7 @@
   
     
     
-    3.1.3. Distance analysis — MDAnalysis.analysis.distances — MDAnalysis 1.0.0-dev documentation
+    3.1.3. Distance analysis — MDAnalysis.analysis.distances — MDAnalysis 0.9.1 documentation
     
     
     
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@@ -289,7 +289,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
   
 
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diff --git a/package/doc/html/documentation_pages/analysis/gnm.html b/package/doc/html/documentation_pages/analysis/gnm.html
index dbdcf78bd16..4ed8f4d2a2d 100644
--- a/package/doc/html/documentation_pages/analysis/gnm.html
+++ b/package/doc/html/documentation_pages/analysis/gnm.html
@@ -6,7 +6,7 @@
   
     
     
-    3.5.1. Elastic network analysis of MD trajectories — MDAnalysis.analysis.gnm — MDAnalysis 1.0.0-dev documentation
+    3.5.1. Elastic network analysis of MD trajectories — MDAnalysis.analysis.gnm — MDAnalysis 0.9.1 documentation
     
     
     
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@@ -175,8 +175,7 @@ 
    3.5.1.1. Analysis tasksrun(skip=1)[source]¶
 
    Analyze trajectory and produce timeseries.
    
 
    Returns GNM results per frame:
    
-
    results = [(time,eigenvalues[1],eigenvectors[1]),(time,eigenvalues[1],eigenvectors[1])... ]
-
    
+
    results = [(time,eigenvalues[1],eigenvectors[1]),(time,eigenvalues[1],eigenvectors[1])... ]
    
 
    
 
    
 
@@ -240,7 +239,7 @@ 
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@@ -252,7 +251,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
   
 
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diff --git a/package/doc/html/documentation_pages/analysis/hbond_analysis.html b/package/doc/html/documentation_pages/analysis/hbond_analysis.html
index 3de0e0155a7..63985881575 100644
--- a/package/doc/html/documentation_pages/analysis/hbond_analysis.html
+++ b/package/doc/html/documentation_pages/analysis/hbond_analysis.html
@@ -6,7 +6,7 @@
   
     
     
-    3.2.1. Hydrogen Bond analysis — MDAnalysis.analysis.hbonds.hbond_analysis — MDAnalysis 1.0.0-dev documentation
+    3.2.1. Hydrogen Bond analysis — MDAnalysis.analysis.hbonds.hbond_analysis — MDAnalysis 0.9.1 documentation
     
     
     
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@@ -147,7 +147,7 @@ 
    3.2.1. Hydrogen Bond analysis — HydrogenBondAnalysis.timeseries (In the following description, #
 indicates comments that are not part of the output.):
    
-
    results = [
+
    results = [
     [ # frame 1
        [ # hbond 1
           <donor index>, <acceptor index>, <donor string>, <acceptor string>, <distance>, <angle>
@@ -161,8 +161,7 @@ 
    3.2.1. Hydrogen Bond analysis — 
 
    Note
    
@@ -585,7 +584,7 @@ 
    3.2.1.4. Classes
    results = [
+
    results = [
     [ # frame 1
        [ # hbond 1
           <donor index>, <acceptor index>, <donor string>, <acceptor string>, <distance>, <angle>
@@ -599,8 +598,7 @@ 
    3.2.1.4. Classestimesteps.
    
@@ -809,7 +807,7 @@ 
    3.2.1.4. Classes
 
    
-r_cov = defaultdict(<function <lambda> at 0x7f32c5aaf2a8>, {'P': 1.58, 'S': 1.55, 'O': 1.31, 'N': 1.31})¶
    
+r_cov = defaultdict(<function <lambda> at 0x7fb8c0e93aa0>, {'P': 1.58, 'S': 1.55, 'O': 1.31, 'N': 1.31})¶
 
    A collections.defaultdict of covalent radii of common donors
 (used in :meth`_get_bonded_hydrogens_list` to check if a hydrogen is
 sufficiently close to its donor heavy atom). Values are stored for
@@ -896,7 +894,7 @@ 
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@@ -908,7 +906,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
   
 
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/analysis/hbond_autocorrel.html b/package/doc/html/documentation_pages/analysis/hbond_autocorrel.html
index 4cda8e2c31c..c7ddee958f7 100644
--- a/package/doc/html/documentation_pages/analysis/hbond_autocorrel.html
+++ b/package/doc/html/documentation_pages/analysis/hbond_autocorrel.html
@@ -6,7 +6,7 @@
   
     
     
-    3.2.2. Hydrogen bond autocorrelation — MDAnalysis.analysis.hbonds.hbond_autocorrel — MDAnalysis 1.0.0-dev documentation
+    3.2.2. Hydrogen bond autocorrelation — MDAnalysis.analysis.hbonds.hbond_autocorrel — MDAnalysis 0.9.1 documentation
     
     
     
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@@ -233,25 +233,31 @@ 
    3.2.2.4. ExamplesThe MDA universe
    
 
 
    hydrogens
    
-
    Hydrogens which can form hydrogen bonds
    
+
    AtomGroup of Hydrogens which can form hydrogen bonds
    
 
    
 
    acceptors
    
-
    Accepting atoms
    
+
    AtomGroup of all Acceptor atoms
    
 
    
 
    donors
    
-
    The atoms which are connected to the hydrogens
    
+
    The atoms which are connected to the hydrogens.  This group
+must be identical in length to the hydrogen group and matched,
+ie hydrogens[1] is bonded to donors[0].
+For many cases, this will mean a donor appears twice in this
+group.
    
 
    
 
    bond_type
    
 
    Which definition of hydrogen bond lifetime to consider, either
-‘continuous’ or ‘intermittent’
    
+‘continuous’ or ‘intermittent’.
    
 
    
 
 
 
 
    Keywords:
    
 
    exclusions
    
-
    Indices of Hydrogen-Donor pairs to be excluded.  Must be a tuple of
-two arrays
    
+
    Indices of Hydrogen-Acceptor pairs to be excluded.
+With nH and nA Hydrogens and Acceptors, a (nH x nA) array of distances
+is calculated, exclusions is used as a mask on this array to exclude
+some pairs.
    
 
    
 
    angle_crit
    
 
    The angle (in degrees) which all bonds must be greater than [130.0]
    
@@ -387,7 +393,7 @@ 
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@@ -399,7 +405,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
   
 
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/analysis/helanal.html b/package/doc/html/documentation_pages/analysis/helanal.html
index 4e80379164c..e45cb5c85b6 100644
--- a/package/doc/html/documentation_pages/analysis/helanal.html
+++ b/package/doc/html/documentation_pages/analysis/helanal.html
@@ -6,7 +6,7 @@
   
     
     
-    3.5.2. HELANAL — analysis of protein helices — MDAnalysis 1.0.0-dev documentation
+    3.5.2. HELANAL — analysis of protein helices — MDAnalysis 0.9.1 documentation
     
     
     
@@ -14,7 +14,7 @@
     
     
     
     
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@@ -324,7 +324,7 @@ 
    Navigation
    
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     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
   
 
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/analysis/hole.html b/package/doc/html/documentation_pages/analysis/hole.html
index 573d9227d7c..00f45a5366a 100644
--- a/package/doc/html/documentation_pages/analysis/hole.html
+++ b/package/doc/html/documentation_pages/analysis/hole.html
@@ -6,7 +6,7 @@
   
     
     
-    3.3.1. Generation and Analysis of HOLE pore profiles — MDAnalysis.analysis.hole — MDAnalysis 1.0.0-dev documentation
+    3.3.1. Generation and Analysis of HOLE pore profiles — MDAnalysis.analysis.hole — MDAnalysis 0.9.1 documentation
     
     
     
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@@ -205,8 +205,7 @@ 
    3.3.1.1.3. Trajectory with RMSD as order parameter
 
    3.3.1.2. Data structures¶
    
 
    A profile is stored as a numpy.recarray:
    
-
    frame   rxncoord   radius
-
    
+
    frame   rxncoord   radius
    
 
    
 
    
 
    frame
    
@@ -499,8 +498,7 @@ 
    3.3.1.3. Analysiscollect(**kwargs)[source]¶
 
    Parse the output from a HOLE run into numpy recarrays.
    
 
    Can deal with outputs containing multiple frames. Output format:
    
-
    frame  rxncoord   radius
-
    
+
    frame  rxncoord   radius
    
 
    
 
    The method saves the result as HOLE.profiles, a dictionary
 indexed by the frame number. Each entry is a
@@ -534,8 +532,7 @@ 
    3.3.1.3. Analysissos_triangle as described under Visualization of HOLE
 results.
    
 
    Load the output file filename into VMD by issuing in the tcl console
    
-
    source hole.vmd
-
    
+
    source hole.vmd
    
 
    
 
    The level of detail is determined by HOLE.dotden (which can be
 overriden by keyword dotden).
    
@@ -886,6 +883,7 @@ 
    3.3.1.4. Utilities
 
    New in version 0.7.7.
    
 
    
+
    x.__init__(...) initializes x; see help(type(x)) for signature
    
 
    
 
 
    
@@ -912,7 +910,7 @@ 
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@@ -924,7 +922,7 @@ 
    Navigation
    
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     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
   
 
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diff --git a/package/doc/html/documentation_pages/analysis/leaflet.html b/package/doc/html/documentation_pages/analysis/leaflet.html
index bd40e0997b4..208ca4f4e7c 100644
--- a/package/doc/html/documentation_pages/analysis/leaflet.html
+++ b/package/doc/html/documentation_pages/analysis/leaflet.html
@@ -6,7 +6,7 @@
   
     
     
-    3.3.2. Leaflet identification — MDAnalysis.analysis.leaflet — MDAnalysis 1.0.0-dev documentation
+    3.3.2. Leaflet identification — MDAnalysis.analysis.leaflet — MDAnalysis 0.9.1 documentation
     
     
     
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@@ -318,7 +318,7 @@ 
    Navigation
    
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     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
   
 
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diff --git a/package/doc/html/documentation_pages/analysis/nuclinfo.html b/package/doc/html/documentation_pages/analysis/nuclinfo.html
index e0dbf4d2c4d..e62a8327467 100644
--- a/package/doc/html/documentation_pages/analysis/nuclinfo.html
+++ b/package/doc/html/documentation_pages/analysis/nuclinfo.html
@@ -6,7 +6,7 @@
   
     
     
-    3.4.1. Nucleic acid analysis — MDAnalysis.analysis.nuclinfo — MDAnalysis 1.0.0-dev documentation
+    3.4.1. Nucleic acid analysis — MDAnalysis.analysis.nuclinfo — MDAnalysis 0.9.1 documentation
     
     
     
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@@ -676,7 +676,7 @@ 
    Navigation
    
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     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
   
 
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diff --git a/package/doc/html/documentation_pages/analysis/rms.html b/package/doc/html/documentation_pages/analysis/rms.html
index 36d565ec7ff..1772828a042 100644
--- a/package/doc/html/documentation_pages/analysis/rms.html
+++ b/package/doc/html/documentation_pages/analysis/rms.html
@@ -6,7 +6,7 @@
   
     
     
-    3.1.4. Calculating root mean square quantities — MDAnalysis.analysis.rms — MDAnalysis 1.0.0-dev documentation
+    3.1.4. Calculating root mean square quantities — MDAnalysis.analysis.rms — MDAnalysis 0.9.1 documentation
     
     
     
@@ -14,7 +14,7 @@
     
     
     
     
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@@ -232,8 +232,7 @@ 
    3.1.4.3. Analysis classes
    Class to perform RMSD analysis on a trajectory.
    
 
    Run the analysis with RMSD.run(), which stores the results
 in the array RMSD.rmsd:
    
-
    frame    time (ps)    RMSD (A)
-
    
+
    frame    time (ps)    RMSD (A)
    
 
    
 
    This class uses Douglas Theobald’s fast QCP algorithm
 [Theobald2005] to calculate the RMSD.
    
@@ -378,7 +377,7 @@ 
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@@ -390,7 +389,7 @@ 
    Navigation
    
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     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
   
 
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diff --git a/package/doc/html/documentation_pages/analysis/x3dna.html b/package/doc/html/documentation_pages/analysis/x3dna.html
index 69d92dc583c..dbd30a65e16 100644
--- a/package/doc/html/documentation_pages/analysis/x3dna.html
+++ b/package/doc/html/documentation_pages/analysis/x3dna.html
@@ -6,7 +6,7 @@
   
     
     
-    3.4.2. Generation and Analysis of X3DNA helicoidal parameter profiles — MDAnalysis.analysis.x3dna — MDAnalysis 1.0.0-dev documentation
+    3.4.2. Generation and Analysis of X3DNA helicoidal parameter profiles — MDAnalysis.analysis.x3dna — MDAnalysis 0.9.1 documentation
     
     
     
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@@ -460,6 +460,7 @@ 
    3.4.2.3. Utilities
 
    New in version 0.7.7.
    
 
+
    x.__init__(...) initializes x; see help(type(x)) for signature
    
 
    
 
 
@@ -486,7 +487,7 @@ 
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@@ -498,7 +499,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
   
 
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/analysis_modules.html b/package/doc/html/documentation_pages/analysis_modules.html
index 2e869f10ae7..bad30670d99 100644
--- a/package/doc/html/documentation_pages/analysis_modules.html
+++ b/package/doc/html/documentation_pages/analysis_modules.html
@@ -6,7 +6,7 @@
   
     
     
-    3. Analysis modules — MDAnalysis 1.0.0-dev documentation
+    3. Analysis modules — MDAnalysis 0.9.1 documentation
     
     
     
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+    
     
      
   
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    Table Of Contents
    
   
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    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
   
 
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/CRD.html b/package/doc/html/documentation_pages/coordinates/CRD.html
index 1457a9bca5b..5dc15b6f6d2 100644
--- a/package/doc/html/documentation_pages/coordinates/CRD.html
+++ b/package/doc/html/documentation_pages/coordinates/CRD.html
@@ -6,7 +6,7 @@
   
     
     
-    5.2. CRD structure files in MDAnalysis — MDAnalysis.coordinates.CRD — MDAnalysis 1.0.0-dev documentation
+    5.2. CRD structure files in MDAnalysis — MDAnalysis.coordinates.CRD — MDAnalysis 0.9.1 documentation
     
     
     
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@@ -174,7 +174,7 @@ 
    Navigation
    
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     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
   
 
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diff --git a/package/doc/html/documentation_pages/coordinates/DCD.html b/package/doc/html/documentation_pages/coordinates/DCD.html
index 324875d631a..657921af914 100644
--- a/package/doc/html/documentation_pages/coordinates/DCD.html
+++ b/package/doc/html/documentation_pages/coordinates/DCD.html
@@ -6,7 +6,7 @@
   
     
     
-    5.3. DCD trajectory I/O — MDAnalysis.coordinates.DCD — MDAnalysis 1.0.0-dev documentation
+    5.3. DCD trajectory I/O — MDAnalysis.coordinates.DCD — MDAnalysis 0.9.1 documentation
     
     
     
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@@ -536,10 +536,9 @@ 
    5.4. Classesclass MDAnalysis.coordinates.DCD.DCDWriter(filename, numatoms, start=0, step=1, delta=20.45482949774598, dt=None, remarks='Created by DCDWriter', convert_units=None)[source]¶
 
    Writes to a DCD file
    
 
    Typical usage:
    
-
    with DCDWriter("new.dcd", u.atoms.numberOfAtoms()) as w:
+
    with DCDWriter("new.dcd", u.atoms.numberOfAtoms()) as w:
     for ts in u.trajectory
-        w.write_next_timestep(ts)
-
    
+        w.write_next_timestep(ts)
    
 
    
 
    Keywords are available to set some of the low-level attributes of the DCD.
    
 
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    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/DMS.html b/package/doc/html/documentation_pages/coordinates/DMS.html
index 0bc03d73efc..046ea5cef0c 100644
--- a/package/doc/html/documentation_pages/coordinates/DMS.html
+++ b/package/doc/html/documentation_pages/coordinates/DMS.html
@@ -6,7 +6,7 @@
   
     
-    5.5. DESRES file format — MDAnalysis.coordinates.DMS — MDAnalysis 1.0.0-dev documentation
+    5.5. DESRES file format — MDAnalysis.coordinates.DMS — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
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@@ -135,7 +135,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/GRO.html b/package/doc/html/documentation_pages/coordinates/GRO.html
index e4296ddb122..690e2deae19 100644
--- a/package/doc/html/documentation_pages/coordinates/GRO.html
+++ b/package/doc/html/documentation_pages/coordinates/GRO.html
@@ -6,7 +6,7 @@
   
     
-    5.7. GRO file format — MDAnalysis.coordinates.GRO — MDAnalysis 1.0.0-dev documentation
+    5.7. GRO file format — MDAnalysis.coordinates.GRO — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
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    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/LAMMPS.html b/package/doc/html/documentation_pages/coordinates/LAMMPS.html
index e6c07456208..b2f0b639fa7 100644
--- a/package/doc/html/documentation_pages/coordinates/LAMMPS.html
+++ b/package/doc/html/documentation_pages/coordinates/LAMMPS.html
@@ -6,7 +6,7 @@
   
     
-    5.6. LAMMPS DCD trajectory I/O — MDAnalysis.coordinates.LAMMPS — MDAnalysis 1.0.0-dev documentation
+    5.6. LAMMPS DCD trajectory I/O — MDAnalysis.coordinates.LAMMPS — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
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    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/PDB.html b/package/doc/html/documentation_pages/coordinates/PDB.html
index 113aad76e38..c373a2a8d34 100644
--- a/package/doc/html/documentation_pages/coordinates/PDB.html
+++ b/package/doc/html/documentation_pages/coordinates/PDB.html
@@ -6,7 +6,7 @@
   
     
-    5.8. PDB structure files in MDAnalysis — MDAnalysis.coordinates.PDB — MDAnalysis 1.0.0-dev documentation
+    5.8. PDB structure files in MDAnalysis — MDAnalysis.coordinates.PDB — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
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     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
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diff --git a/package/doc/html/documentation_pages/coordinates/PDBQT.html b/package/doc/html/documentation_pages/coordinates/PDBQT.html
index b59291bf899..a946c8c2f97 100644
--- a/package/doc/html/documentation_pages/coordinates/PDBQT.html
+++ b/package/doc/html/documentation_pages/coordinates/PDBQT.html
@@ -6,7 +6,7 @@
   
     
-    5.9. PDBQT structure files in MDAnalysis — MDAnalysis.coordinates.PDBQT — MDAnalysis 1.0.0-dev documentation
+    5.9. PDBQT structure files in MDAnalysis — MDAnalysis.coordinates.PDBQT — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
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@@ -238,9 +238,9 @@ 
    5.9. PDBQT structure files in MDAnalysis — 
    COMPND    NSC7810
+
    COMPND    NSC7810
 REMARK  3 active torsions:
-REMARK  status: ('A' for Active; 'I' for Inactive)
+REMARK  status: ('A' for Active; 'I' for Inactive)
 REMARK    1  A    between atoms: A7_7  and  C22_23
 REMARK    2  A    between atoms: A9_9  and  A11_11
 REMARK    3  A    between atoms: A17_17  and  C21_21
@@ -280,8 +280,7 @@ 
    5.9. PDBQT structure files in MDAnalysis — 
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@@ -426,7 +425,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
   
 
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diff --git a/package/doc/html/documentation_pages/coordinates/PQR.html b/package/doc/html/documentation_pages/coordinates/PQR.html
index d611c7e711e..a82c31db8fc 100644
--- a/package/doc/html/documentation_pages/coordinates/PQR.html
+++ b/package/doc/html/documentation_pages/coordinates/PQR.html
@@ -6,7 +6,7 @@
   
     
     
-    5.10. PQR file format — MDAnalysis.coordinates.PQR — MDAnalysis 1.0.0-dev documentation
+    5.10. PQR file format — MDAnalysis.coordinates.PQR — MDAnalysis 0.9.1 documentation
     
     
     
@@ -14,7 +14,7 @@
     
     
     
     
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@@ -99,13 +99,11 @@ 
    5.10. PQR file format — PDB format. This more liberal formatting allows coordinates
 which are larger/smaller than ±999 Å.
    
 
    MDAnalysis reads data on a per-line basis from PQR files using the following format:
    
-
    recordName serial atomName residueName chainID residueNumber X Y Z charge radius
-
    
+
    recordName serial atomName residueName chainID residueNumber X Y Z charge radius
    
 
    
 
    If this fails it is assumed that the chainID was omitted and the shorter
 format is read:
    
-
    recordName serial atomName residueName residueNumber X Y Z charge radius
-
    
+
    recordName serial atomName residueName residueNumber X Y Z charge radius
    
 
    
 
    Anything else will raise a ValueError.
    
 
    The whitespace is the most important feature of this format: fields
@@ -145,8 +143,7 @@ 
    5.10. PQR file format — PDB2PQR and the –whitespace
 option are guaranteed to conform to the above format:
    
-
    pdb2pqr --ff=charmm --whitespace 4ake.pdb 4ake.pqr
-
    
+
    pdb2pqr --ff=charmm --whitespace 4ake.pdb 4ake.pqr
    
 
    
 
    
 
    
@@ -292,7 +289,7 @@ 
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@@ -304,7 +301,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
   
 
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/TRJ.html b/package/doc/html/documentation_pages/coordinates/TRJ.html
index 4257e3cf522..7f279fd4d86 100644
--- a/package/doc/html/documentation_pages/coordinates/TRJ.html
+++ b/package/doc/html/documentation_pages/coordinates/TRJ.html
@@ -6,7 +6,7 @@
   
     
     
-    5.11. AMBER trajectories — MDAnalysis.coordinates.TRJ — MDAnalysis 1.0.0-dev documentation
+    5.11. AMBER trajectories — MDAnalysis.coordinates.TRJ — MDAnalysis 0.9.1 documentation
     
     
     
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@@ -434,7 +434,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/TRR.html b/package/doc/html/documentation_pages/coordinates/TRR.html
index 37107fa2539..0fc4255e4b3 100644
--- a/package/doc/html/documentation_pages/coordinates/TRR.html
+++ b/package/doc/html/documentation_pages/coordinates/TRR.html
@@ -6,7 +6,7 @@
   
     
-    5.12. Gromacs TRR file IO — MDAnalysis.coordinates.TRR — MDAnalysis 1.0.0-dev documentation
+    5.12. Gromacs TRR file IO — MDAnalysis.coordinates.TRR — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
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@@ -149,19 +149,19 @@ 
    5.12.1.1. Filling a TRR with PCA modes_pos attribute of
 Timestep:
    
-
    # 'modes' is a mode object with M PCs, similar to a MxNx3 array
-# 'xav' the average coordinates, a Nx3 array for N atoms
+
    # 'modes' is a mode object with M PCs, similar to a MxNx3 array
+# 'xav' the average coordinates, a Nx3 array for N atoms
 
 N = len(xav)   # number of atoms, i.e. number of coordinates
 
-W = Writer('pca.trr', numatoms=N)            # TRR writer
+W = Writer('pca.trr', numatoms=N)            # TRR writer
 ts = MDAnalysis.coordinates.TRR.Timestep(N)  # TRR time step
-                                             #   TRR handling requires 'has_x' to be set
+                                             #   TRR handling requires 'has_x' to be set
                                              #   before low-level assignment to ts._pos.
-                                             #   (likewise for 'has_v' and 'has_f' for assignment
+                                             #   (likewise for 'has_v' and 'has_f' for assignment
                                              #   to ts._velocites and ts._forces). The default of
-                                             #   the Timestep constructor is to set 'has_x' to True
-                                             #   (but not 'has_v' or 'has_f') when only the number
+                                             #   the Timestep constructor is to set 'has_x' to True
+                                             #   (but not 'has_v' or 'has_f') when only the number
                                              #   of atoms is passed.
 for frame,mode in enumerate(modes[4:16]):
     ts.lmbda = -1
@@ -177,8 +177,7 @@ 
    5.12.1.1. Filling a TRR with PCA modes
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@@ -918,7 +917,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
   
 
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diff --git a/package/doc/html/documentation_pages/coordinates/TRZ.html b/package/doc/html/documentation_pages/coordinates/TRZ.html
index 27039389d49..b3163a0a6a7 100644
--- a/package/doc/html/documentation_pages/coordinates/TRZ.html
+++ b/package/doc/html/documentation_pages/coordinates/TRZ.html
@@ -6,7 +6,7 @@
   
     
     
-    5.15. TRZ trajectory I/O — MDAnalysis.coordinates.TRZ — MDAnalysis 1.0.0-dev documentation
+    5.15. TRZ trajectory I/O — MDAnalysis.coordinates.TRZ — MDAnalysis 0.9.1 documentation
     
     
     
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@@ -508,7 +508,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/XTC.html b/package/doc/html/documentation_pages/coordinates/XTC.html
index 78d1542959a..7cd88aae92d 100644
--- a/package/doc/html/documentation_pages/coordinates/XTC.html
+++ b/package/doc/html/documentation_pages/coordinates/XTC.html
@@ -6,7 +6,7 @@
   
     
-    5.13. Gromacs XTC file IO — MDAnalysis.coordinates.XTC — MDAnalysis 1.0.0-dev documentation
+    5.13. Gromacs XTC file IO — MDAnalysis.coordinates.XTC — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
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@@ -801,7 +801,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/XYZ.html b/package/doc/html/documentation_pages/coordinates/XYZ.html
index 42a930db798..ce8ef4a69fe 100644
--- a/package/doc/html/documentation_pages/coordinates/XYZ.html
+++ b/package/doc/html/documentation_pages/coordinates/XYZ.html
@@ -6,7 +6,7 @@
   
     
-    5.14. XYZ trajectory reader — MDAnalysis.coordinates.XYZ — MDAnalysis 1.0.0-dev documentation
+    5.14. XYZ trajectory reader — MDAnalysis.coordinates.XYZ — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
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+     
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    • 
@@ -126,14 +126,13 @@ 
    5.14. XYZ trajectory reader — 
    5.14.1. XYZ File format¶
    
 
    Definiton used by the XYZReader and XYZWriter (and
 the VMD xyzplugin from whence the definition was taken):
    
-
    [ comment line            ] !! NOT IMPLEMENTED !! DO NOT INCLUDE
+
    [ comment line            ] !! NOT IMPLEMENTED !! DO NOT INCLUDE
 [ N                       ] # of atoms, required by this xyz reader plugin  line 1
 [ molecule name           ] name of molecule (can be blank)                 line 2
 atom1 x y z [optional data] atom name followed by xyz coords                line 3
 atom2 x y z [ ...         ] and (optionally) other data.
 ...
-atomN x y z [ ...         ]                                                 line N+2
-
    
+atomN x y z [ ...         ]                                                 line N+2
    
 
    
 
     
    
@@ -343,7 +342,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/base.html b/package/doc/html/documentation_pages/coordinates/base.html
index 5106f8ef0a0..871d60a1a61 100644
--- a/package/doc/html/documentation_pages/coordinates/base.html
+++ b/package/doc/html/documentation_pages/coordinates/base.html
@@ -6,7 +6,7 @@
   
     
-    5.16. Base classes — MDAnalysis.coordinates.base — MDAnalysis 1.0.0-dev documentation
+    5.16. Base classes — MDAnalysis.coordinates.base — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
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+     
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  • 5. Coordinates modules »
    • 
@@ -234,6 +234,7 @@ 
    5.16. Base classes — 
 
    Changed in version 0.8: Added context manager protocol.
    
 
+
    x.__init__(...) initializes x; see help(type(x)) for signature
    
 
    
 
    
 close()[source]¶
    
@@ -365,6 +366,7 @@ 
    5.16. Base classes — Trajectory API definition in
 MDAnalysis.coordinates.__init__ for the required attributes and methods.
    
+
    x.__init__(...) initializes x; see help(type(x)) for signature
    
 
    
 
    
 OtherWriter(filename, **kwargs)[source]¶
    
@@ -515,6 +517,7 @@ 
    5.16. Base classes — MDAnalysis.coordinates.__init__ for
 the required attributes and methods.
    
+
    x.__init__(...) initializes x; see help(type(x)) for signature
    
 
    
 
    
 convert_dimensions_to_unitcell(ts)[source]¶
    
@@ -589,7 +592,7 @@ 
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@@ -601,7 +604,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
   
 
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/core.html b/package/doc/html/documentation_pages/coordinates/core.html
index d6e47cbe795..8fb131a66e4 100644
--- a/package/doc/html/documentation_pages/coordinates/core.html
+++ b/package/doc/html/documentation_pages/coordinates/core.html
@@ -6,7 +6,7 @@
   
     
     
-    5.17. Common functions for coordinate reading — MDAnalysis.coordinates.core — MDAnalysis 1.0.0-dev documentation
+    5.17. Common functions for coordinate reading — MDAnalysis.coordinates.core — MDAnalysis 0.9.1 documentation
     
     
     
@@ -14,7 +14,7 @@
     
     
     
     
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+    
     
     
      
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    •  
       
     
@@ -362,7 +362,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
   
 
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/init.html b/package/doc/html/documentation_pages/coordinates/init.html
index 3437550f2e5..aa23e29b403 100644
--- a/package/doc/html/documentation_pages/coordinates/init.html
+++ b/package/doc/html/documentation_pages/coordinates/init.html
@@ -6,7 +6,7 @@
   
     
     
-    5.1. Coordinate/Trajectory Readers and Writers — MDAnalysis.coordinates — MDAnalysis 1.0.0-dev documentation
+    5.1. Coordinate/Trajectory Readers and Writers — MDAnalysis.coordinates — MDAnalysis 0.9.1 documentation
     
     
     
@@ -14,7 +14,7 @@
     
     
     
     
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+    
     
     
      
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@@ -74,17 +74,17 @@ 
    Table Of Contents
    
 
 
 
  • 5.1.4.4. Trajectory Reader class
 
    • 
 
  • 5.1.4.5. Trajectory Writer class
 
    • 
 
  • 5.1.4.6. Single Frame Writer class
 
    • 
 
@@ -213,35 +213,46 @@ 
    5.1.3. Supported coordinate formatsMDAnalysis.coordinates.DCD
 
 
    
-
-
+
+
+Module MDAnalysis.coordinates.LAMMPS
-
+
+
+
+
+
+
-
+
-
+
+
+
+
+
+
@@ -258,7 +269,7 @@ 
    5.1.3. Supported coordinate formatsMDAnalysis.coordinates.TRJ
 
    
+[1]
-
+
-
+
+[1]
-
+
-
+
-
@@ -335,7 +346,7 @@ 
    5.1.3. Supported coordinate formats
-
    5.1.4. Trajectory API¶
    
+
    5.1.4. Trajectory API¶
    The Trajectory API defines how classes have to be structured that allow
 reading and writing of coordinate files. By following the API it is possible to
 seamlessly enhance the I/O capabilities of MDAnalysis. The actual underlying
@@ -482,8 +493,8 @@ 
    5.1.4.3.3. Private attributes¶
    Trajectory readers are derived from MDAnalysis.coordinates.base.Reader.
 Typically, many methods and attributes are overriden.
    
-
    
-
    5.1.4.4.1. Methods¶
    
+
    
+
    5.1.4.4.1. Methods¶
    
 
    The MDAnalysis.coordinates.DCD.DCDReader class is the primary
 implementation example.
    
 
    Mandatory methods
    
@@ -590,8 +601,8 @@ 
    5.1.4.4.1. Methods
-
    5.1.4.4.2. Attributes¶
    
+
    
+
    5.1.4.4.2. Attributes¶
    
 
    
 
    
 
    filename
    
@@ -663,8 +674,8 @@ 
    5.1.4.5. Trajectory Writer classW.write(Timestep)    # same as write_next_timestep()
 
    
 
    
-
    
-
    5.1.4.5.1. Methods¶
    
+
    
+
    5.1.4.5.1. Methods¶
    
 
    
 
    
 
    __init__(filename,numatoms[,start[,step[,delta[,remarks]]]])
    
@@ -683,8 +694,8 @@ 
    5.1.4.5.1. Methods
-
    5.1.4.5.2. Attributes¶
    
+
    
+
    5.1.4.5.2. Attributes¶
    
 
    
 
    
 
    filename
    
@@ -728,8 +739,8 @@ 
    5.1.4.6. Single Frame Writer classwriter()
 factory function can be used for all writers.
    
-
    
-
    5.1.4.6.1. Methods¶
    
+
    
+
    5.1.4.6.1. Methods¶
    
 
    
 
    
 
    __init__(filename, **kwargs)
    
@@ -762,20 +773,20 @@ 
    5.1.5. Reader/Writer registry
 
    
-MDAnalysis.coordinates.__init__._trajectory_readers = {'CHAIN': <class 'MDAnalysis.coordinates.base.ChainReader'>, 'XPDB': <class 'MDAnalysis.coordinates.PDB.ExtendedPDBReader'>, 'TRJ': <class 'MDAnalysis.coordinates.TRJ.TRJReader'>, 'TRZ': <class 'MDAnalysis.coordinates.TRZ.TRZReader'>, 'MDCRD': <class 'MDAnalysis.coordinates.TRJ.TRJReader'>, 'LAMMPS': <class 'MDAnalysis.coordinates.LAMMPS.DCDReader'>, 'DCD': <class 'MDAnalysis.coordinates.DCD.DCDReader'>, 'PDB': <class 'MDAnalysis.coordinates.PDB.PDBReader'>, 'PDBQT': <class 'MDAnalysis.coordinates.PDBQT.PDBQTReader'>, 'MOL2': <class 'MDAnalysis.coordinates.MOL2.MOL2Reader'>, 'PQR': <class 'MDAnalysis.coordinates.PQR.PQRReader'>, 'DMS': <class 'MDAnalysis.coordinates.DMS.DMSReader'>, 'XTC': <class 'MDAnalysis.coordinates.xdrfile.XTC.XTCReader'>, 'CRD': <class 'MDAnalysis.coordinates.CRD.CRDReader'>, 'GRO': <class 'MDAnalysis.coordinates.GRO.GROReader'>, 'TRR': <class 'MDAnalysis.coordinates.xdrfile.TRR.TRRReader'>, 'DATA': <class 'MDAnalysis.coordinates.LAMMPS.DATAReader'>, 'XYZ': <class 'MDAnalysis.coordinates.XYZ.XYZReader'>, 'NCDF': <class 'MDAnalysis.coordinates.TRJ.NCDFReader'>}¶
    
+MDAnalysis.coordinates.__init__._trajectory_readers = {'CHAIN': <class 'MDAnalysis.coordinates.base.ChainReader'>, 'XPDB': <class 'MDAnalysis.coordinates.PDB.ExtendedPDBReader'>, 'TRJ': <class 'MDAnalysis.coordinates.TRJ.TRJReader'>, 'TRZ': <class 'MDAnalysis.coordinates.TRZ.TRZReader'>, 'MDCRD': <class 'MDAnalysis.coordinates.TRJ.TRJReader'>, 'LAMMPS': <class 'MDAnalysis.coordinates.LAMMPS.DCDReader'>, 'DCD': <class 'MDAnalysis.coordinates.DCD.DCDReader'>, 'PDB': <class 'MDAnalysis.coordinates.PDB.PDBReader'>, 'PDBQT': <class 'MDAnalysis.coordinates.PDBQT.PDBQTReader'>, 'MOL2': <class 'MDAnalysis.coordinates.MOL2.MOL2Reader'>, 'PQR': <class 'MDAnalysis.coordinates.PQR.PQRReader'>, 'DMS': <class 'MDAnalysis.coordinates.DMS.DMSReader'>, 'XTC': <class 'MDAnalysis.coordinates.xdrfile.XTC.XTCReader'>, 'CRD': <class 'MDAnalysis.coordinates.CRD.CRDReader'>, 'GMS': <class 'MDAnalysis.coordinates.GMS.GMSReader'>, 'GRO': <class 'MDAnalysis.coordinates.GRO.GROReader'>, 'TRR': <class 'MDAnalysis.coordinates.xdrfile.TRR.TRRReader'>, 'DATA': <class 'MDAnalysis.coordinates.LAMMPS.DATAReader'>, 'XYZ': <class 'MDAnalysis.coordinates.XYZ.XYZReader'>, 'NCDF': <class 'MDAnalysis.coordinates.TRJ.NCDFReader'>}¶
 
    standard trajectory readers (dict with identifier as key and reader class as value)
    
 
    
 
 
    
 
    
-MDAnalysis.coordinates.__init__._topology_coordinates_readers = {'PDBQT': <class 'MDAnalysis.coordinates.PDBQT.PDBQTReader'>, 'XPDB': <class 'MDAnalysis.coordinates.PDB.ExtendedPDBReader'>, 'DMS': <class 'MDAnalysis.coordinates.DMS.DMSReader'>, 'PQR': <class 'MDAnalysis.coordinates.PQR.PQRReader'>, 'CRD': <class 'MDAnalysis.coordinates.CRD.CRDReader'>, 'GRO': <class 'MDAnalysis.coordinates.GRO.GROReader'>, 'MOL2': <class 'MDAnalysis.coordinates.MOL2.MOL2Reader'>, 'DATA': <class 'MDAnalysis.coordinates.LAMMPS.DATAReader'>, 'PDB': <class 'MDAnalysis.coordinates.PDB.PrimitivePDBReader'>}¶
    
+MDAnalysis.coordinates.__init__._topology_coordinates_readers = {'PDBQT': <class 'MDAnalysis.coordinates.PDBQT.PDBQTReader'>, 'XPDB': <class 'MDAnalysis.coordinates.PDB.ExtendedPDBReader'>, 'DMS': <class 'MDAnalysis.coordinates.DMS.DMSReader'>, 'PQR': <class 'MDAnalysis.coordinates.PQR.PQRReader'>, 'CRD': <class 'MDAnalysis.coordinates.CRD.CRDReader'>, 'GMS': <class 'MDAnalysis.coordinates.GMS.GMSReader'>, 'GRO': <class 'MDAnalysis.coordinates.GRO.GROReader'>, 'MOL2': <class 'MDAnalysis.coordinates.MOL2.MOL2Reader'>, 'DATA': <class 'MDAnalysis.coordinates.LAMMPS.DATAReader'>, 'PDB': <class 'MDAnalysis.coordinates.PDB.PrimitivePDBReader'>}¶
 
    readers of files that contain both topology/atom data and coordinates
 (currently only the keys are used)
    
 
    
 
 
    
 
    
-MDAnalysis.coordinates.__init__._trajectory_readers_permissive = {'TRJ': <class 'MDAnalysis.coordinates.TRJ.TRJReader'>, 'MDCRD': <class 'MDAnalysis.coordinates.TRJ.TRJReader'>, 'TRZ': <class 'MDAnalysis.coordinates.TRZ.TRZReader'>, 'XTC': <class 'MDAnalysis.coordinates.xdrfile.XTC.XTCReader'>, 'CRD': <class 'MDAnalysis.coordinates.CRD.CRDReader'>, 'GRO': <class 'MDAnalysis.coordinates.GRO.GROReader'>, 'TRR': <class 'MDAnalysis.coordinates.xdrfile.TRR.TRRReader'>, 'DATA': <class 'MDAnalysis.coordinates.LAMMPS.DATAReader'>, 'PDB': <class 'MDAnalysis.coordinates.PDB.PrimitivePDBReader'>, 'XPDB': <class 'MDAnalysis.coordinates.PDB.ExtendedPDBReader'>, 'LAMMPS': <class 'MDAnalysis.coordinates.LAMMPS.DCDReader'>, 'CHAIN': <class 'MDAnalysis.coordinates.base.ChainReader'>, 'DCD': <class 'MDAnalysis.coordinates.DCD.DCDReader'>, 'PDBQT': <class 'MDAnalysis.coordinates.PDBQT.PDBQTReader'>, 'PQR': <class 'MDAnalysis.coordinates.PQR.PQRReader'>, 'DMS': <class 'MDAnalysis.coordinates.DMS.DMSReader'>, 'XYZ': <class 'MDAnalysis.coordinates.XYZ.XYZReader'>, 'MOL2': <class 'MDAnalysis.coordinates.MOL2.MOL2Reader'>, 'NCDF': <class 'MDAnalysis.coordinates.TRJ.NCDFReader'>}¶
    
+MDAnalysis.coordinates.__init__._trajectory_readers_permissive = {'TRJ': <class 'MDAnalysis.coordinates.TRJ.TRJReader'>, 'MDCRD': <class 'MDAnalysis.coordinates.TRJ.TRJReader'>, 'TRZ': <class 'MDAnalysis.coordinates.TRZ.TRZReader'>, 'XTC': <class 'MDAnalysis.coordinates.xdrfile.XTC.XTCReader'>, 'CRD': <class 'MDAnalysis.coordinates.CRD.CRDReader'>, 'GMS': <class 'MDAnalysis.coordinates.GMS.GMSReader'>, 'GRO': <class 'MDAnalysis.coordinates.GRO.GROReader'>, 'TRR': <class 'MDAnalysis.coordinates.xdrfile.TRR.TRRReader'>, 'DATA': <class 'MDAnalysis.coordinates.LAMMPS.DATAReader'>, 'PDB': <class 'MDAnalysis.coordinates.PDB.PrimitivePDBReader'>, 'XPDB': <class 'MDAnalysis.coordinates.PDB.ExtendedPDBReader'>, 'LAMMPS': <class 'MDAnalysis.coordinates.LAMMPS.DCDReader'>, 'CHAIN': <class 'MDAnalysis.coordinates.base.ChainReader'>, 'DCD': <class 'MDAnalysis.coordinates.DCD.DCDReader'>, 'PDBQT': <class 'MDAnalysis.coordinates.PDBQT.PDBQTReader'>, 'PQR': <class 'MDAnalysis.coordinates.PQR.PQRReader'>, 'DMS': <class 'MDAnalysis.coordinates.DMS.DMSReader'>, 'XYZ': <class 'MDAnalysis.coordinates.XYZ.XYZReader'>, 'MOL2': <class 'MDAnalysis.coordinates.MOL2.MOL2Reader'>, 'NCDF': <class 'MDAnalysis.coordinates.TRJ.NCDFReader'>}¶
 
    hack: readers that ignore most errors (permissive=True); at the moment
 the same as _trajectory_readers with the exception of the
 the PDB reader (PDBReader is replaced by
    
@@ -836,7 +847,7 @@ 
    Navigation
    
         
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@@ -848,7 +859,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
   
 
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/pdbextensions.html b/package/doc/html/documentation_pages/coordinates/pdbextensions.html
index 84b4fa2e76c..80ddc7ce623 100644
--- a/package/doc/html/documentation_pages/coordinates/pdbextensions.html
+++ b/package/doc/html/documentation_pages/coordinates/pdbextensions.html
@@ -6,7 +6,7 @@
   
     
     
-    5.19. Extensions to Bio.PDB — pdb.extensions — MDAnalysis 1.0.0-dev documentation
+    5.19. Extensions to Bio.PDB — pdb.extensions — MDAnalysis 0.9.1 documentation
     
     
     
@@ -14,7 +14,7 @@
     
     
     
     
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@@ -214,7 +214,7 @@ 
    Navigation
    
         
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@@ -226,7 +226,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
   
 
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/xdrfile.html b/package/doc/html/documentation_pages/coordinates/xdrfile.html
index 0716194fd6f..d04297a5877 100644
--- a/package/doc/html/documentation_pages/coordinates/xdrfile.html
+++ b/package/doc/html/documentation_pages/coordinates/xdrfile.html
@@ -6,7 +6,7 @@
   
     
     
-    5.18. NumPy access to Gromacs XDR trajectories — MDAnalysis.coordinates.xdrfile — MDAnalysis 1.0.0-dev documentation
+    5.18. NumPy access to Gromacs XDR trajectories — MDAnalysis.coordinates.xdrfile — MDAnalysis 0.9.1 documentation
     
     
     
@@ -14,7 +14,7 @@
     
     
     
     
-    
+    
     
     
      
@@ -49,7 +49,7 @@ 
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@@ -135,7 +135,7 @@ 
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+        
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@@ -147,7 +147,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
   
 
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/xdrfile/TRR.html b/package/doc/html/documentation_pages/coordinates/xdrfile/TRR.html
index 234424ae534..26d96812a52 100644
--- a/package/doc/html/documentation_pages/coordinates/xdrfile/TRR.html
+++ b/package/doc/html/documentation_pages/coordinates/xdrfile/TRR.html
@@ -6,7 +6,7 @@
   
     
     
-    5.18.2. Gromacs TRR trajectory I/O — MDAnalysis.coordinates.xdrfile.TRR — MDAnalysis 1.0.0-dev documentation
+    5.18.2. Gromacs TRR trajectory I/O — MDAnalysis.coordinates.xdrfile.TRR — MDAnalysis 0.9.1 documentation
     
     
     
@@ -14,7 +14,7 @@
     
     
     
     
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  • MDAnalysis 1.0.0-dev documentation »
    • 
+        
  • MDAnalysis 0.9.1 documentation »
    • 
           
  • 5. Coordinates modules »
    • 
           
  • 5.18. NumPy access to Gromacs XDR trajectories — MDAnalysis.coordinates.xdrfile »
    •  
       
@@ -836,7 +836,7 @@ 
    Navigation
    
         
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           previous |
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  • MDAnalysis 1.0.0-dev documentation »
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+        
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    • 
           
  • 5. Coordinates modules »
    • 
           
  • 5.18. NumPy access to Gromacs XDR trajectories — MDAnalysis.coordinates.xdrfile »
    •  
       
@@ -849,7 +849,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
   
 
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/xdrfile/XTC.html b/package/doc/html/documentation_pages/coordinates/xdrfile/XTC.html
index 335514f8f14..ec853ce6b22 100644
--- a/package/doc/html/documentation_pages/coordinates/xdrfile/XTC.html
+++ b/package/doc/html/documentation_pages/coordinates/xdrfile/XTC.html
@@ -6,7 +6,7 @@
   
     
     
-    5.18.1. Gromacs XTC trajectory I/O — MDAnalysis.coordinates.xdrfile.XTC — MDAnalysis 1.0.0-dev documentation
+    5.18.1. Gromacs XTC trajectory I/O — MDAnalysis.coordinates.xdrfile.XTC — MDAnalysis 0.9.1 documentation
     
     
     
@@ -14,7 +14,7 @@
     
     
     
     
-    
+    
     
     
      
@@ -49,7 +49,7 @@ 
    Navigation
    
         
  • 
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  • MDAnalysis 1.0.0-dev documentation »
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+        
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  • 5. Coordinates modules »
    • 
           
  • 5.18. NumPy access to Gromacs XDR trajectories — MDAnalysis.coordinates.xdrfile »
    •  
       
@@ -771,7 +771,7 @@ 
    Navigation
    
         
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-        
  • MDAnalysis 1.0.0-dev documentation »
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+        
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  • 5. Coordinates modules »
    • 
           
  • 5.18. NumPy access to Gromacs XDR trajectories — MDAnalysis.coordinates.xdrfile »
    •  
       
@@ -784,7 +784,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/xdrfile/core.html b/package/doc/html/documentation_pages/coordinates/xdrfile/core.html
index 93d38452dc6..32b7f3e01a7 100644
--- a/package/doc/html/documentation_pages/coordinates/xdrfile/core.html
+++ b/package/doc/html/documentation_pages/coordinates/xdrfile/core.html
@@ -6,7 +6,7 @@
   
     
-    5.18.3. Common high-level Gromacs XDR functionality — MDAnalysis.coordinates.xdrfile.core — MDAnalysis 1.0.0-dev documentation
+    5.18.3. Common high-level Gromacs XDR functionality — MDAnalysis.coordinates.xdrfile.core — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
-    
+     
@@ -49,7 +49,7 @@ 
    Navigation
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  • MDAnalysis 1.0.0-dev documentation »
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+        
  • MDAnalysis 0.9.1 documentation »
  • 5. Coordinates modules »
  • 5.18. NumPy access to Gromacs XDR trajectories — MDAnalysis.coordinates.xdrfile »
    • 
@@ -496,7 +496,7 @@ 
    Navigation
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           previous |
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-        
  • MDAnalysis 1.0.0-dev documentation »
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+        
  • MDAnalysis 0.9.1 documentation »
  • 5. Coordinates modules »
  • 5.18. NumPy access to Gromacs XDR trajectories — MDAnalysis.coordinates.xdrfile »
    • 
@@ -509,7 +509,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/xdrfile/libxdrfile2.html b/package/doc/html/documentation_pages/coordinates/xdrfile/libxdrfile2.html
index d1198ab9f8f..8b48a06a63f 100644
--- a/package/doc/html/documentation_pages/coordinates/xdrfile/libxdrfile2.html
+++ b/package/doc/html/documentation_pages/coordinates/xdrfile/libxdrfile2.html
@@ -6,7 +6,7 @@
   
     
-    5.18.4. The Gromacs XTC/TRR library libxdrfile2 — MDAnalysis 1.0.0-dev documentation
+    5.18.4. The Gromacs XTC/TRR library libxdrfile2 — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
-    
+     
@@ -49,7 +49,7 @@ 
    Navigation
  • 
           previous |
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-        
  • MDAnalysis 1.0.0-dev documentation »
    • 
+        
  • MDAnalysis 0.9.1 documentation »
  • 5. Coordinates modules »
  • 5.18. NumPy access to Gromacs XDR trajectories — MDAnalysis.coordinates.xdrfile »
    • 
@@ -684,7 +684,7 @@ 
    Navigation
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  • MDAnalysis 1.0.0-dev documentation »
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+        
  • MDAnalysis 0.9.1 documentation »
  • 5. Coordinates modules »
  • 5.18. NumPy access to Gromacs XDR trajectories — MDAnalysis.coordinates.xdrfile »
    • 
@@ -697,7 +697,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates/xdrfile/statno.html b/package/doc/html/documentation_pages/coordinates/xdrfile/statno.html
index a74cb5622e5..69e70bd8d41 100644
--- a/package/doc/html/documentation_pages/coordinates/xdrfile/statno.html
+++ b/package/doc/html/documentation_pages/coordinates/xdrfile/statno.html
@@ -6,7 +6,7 @@
   
     
-    5.18.5. Status codes and symbols — statno — MDAnalysis 1.0.0-dev documentation
+    5.18.5. Status codes and symbols — statno — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
-    
+     
@@ -49,7 +49,7 @@ 
    Navigation
  • 
           previous |
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-        
  • MDAnalysis 1.0.0-dev documentation »
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+        
  • MDAnalysis 0.9.1 documentation »
  • 5. Coordinates modules »
  • 5.18. NumPy access to Gromacs XDR trajectories — MDAnalysis.coordinates.xdrfile »
    • 
@@ -132,7 +132,7 @@ 
    Navigation
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+        
  • MDAnalysis 0.9.1 documentation »
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  • 5.18. NumPy access to Gromacs XDR trajectories — MDAnalysis.coordinates.xdrfile »
    • 
@@ -145,7 +145,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/coordinates_modules.html b/package/doc/html/documentation_pages/coordinates_modules.html
index da850a77aed..7ab909f90c6 100644
--- a/package/doc/html/documentation_pages/coordinates_modules.html
+++ b/package/doc/html/documentation_pages/coordinates_modules.html
@@ -6,7 +6,7 @@
   
     
-    5. Coordinates modules — MDAnalysis 1.0.0-dev documentation
+    5. Coordinates modules — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
-    
+    
@@ -48,7 +48,7 @@ 
    Navigation
  • 
           previous |
    • 
-        
  • MDAnalysis 1.0.0-dev documentation »
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+        
  • MDAnalysis 0.9.1 documentation »
    • 
@@ -151,7 +151,7 @@ 
    Navigation
    
         
  • 
           previous |
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-        
  • MDAnalysis 1.0.0-dev documentation »
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+        
  • MDAnalysis 0.9.1 documentation »
    •  
       
     
    
@@ -162,7 +162,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/core/AtomGroup.html b/package/doc/html/documentation_pages/core/AtomGroup.html
index fad52f48d67..a832510c938 100644
--- a/package/doc/html/documentation_pages/core/AtomGroup.html
+++ b/package/doc/html/documentation_pages/core/AtomGroup.html
@@ -6,7 +6,7 @@
   
     
-    7.2. Fundamental building blocks — MDAnalysis.core.AtomGroup — MDAnalysis 1.0.0-dev documentation
+    7.2. Fundamental building blocks — MDAnalysis.core.AtomGroup — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
-    
+     
@@ -49,7 +49,7 @@ 
    Navigation
  • 
           previous |
    • 
-        
  • MDAnalysis 1.0.0-dev documentation »
    • 
+        
  • MDAnalysis 0.9.1 documentation »
  • 7. Core modules »
    • 
@@ -133,7 +133,7 @@ 
    7.2.1. Class Hierarchyatoms,
-residues or residue, segments or
+residues or residue, segments or
 segment) that give access to the tiers in the hierarchy
 that the object belongs to.
    
 
@@ -240,33 +240,32 @@ 
    7.2.3.2. Replicating
    import MDAnalysis; from MDAnalysis.tests.datafiles import *
+
    import MDAnalysis; from MDAnalysis.tests.datafiles import *
 u = MDAnalysis.Universe(PSF, DCD)
-p = u.selectAtoms("protein")
+p = u.selectAtoms("protein")
 m = MDAnalysis.Merge(p,p)
 
 # now renumber resids and segids for each copy
 
-# first copy of the protein (need to use atom indices because currently that's the only reliable property in the
+# first copy of the protein (need to use atom indices because currently that's the only reliable property in the
 merged universe)
-p1 = m.selectAtoms("bynum 1:3341")
+p1 = m.selectAtoms("bynum 1:3341")
 # second copy
-p2 = m.selectAtoms("bynum 3342:6682")
+p2 = m.selectAtoms("bynum 3342:6682")
 
-p1.set_segid("A")
-p2.set_segid("B")
+p1.set_segid("A")
+p2.set_segid("B")
 p2.residues.set_resid(p2.residues.resids() + p1.residues.resids()[-1])  # increment resids for p2 with the last
 resid from p1
 
 # you must regenerate the selections after modifying them (see notes in the docs!)
 # because the changed resids are not reflected in the selection (due to how residues are referenced internally)
-p1 = m.selectAtoms("segid A")       # or as before:  m.selectAtoms("bynum 1:3341")
-p2 = m.selectAtoms("segid B")
+p1 = m.selectAtoms("segid A")       # or as before:  m.selectAtoms("bynum 1:3341")
+p2 = m.selectAtoms("segid B")
 
 # rotate and translate
 p2.rotateby(180, [0,0,1])
-p2.translate([50,0,0])
-
    
+p2.translate([50,0,0])
    
 
    
 
    Note that we have to manually set the residue numbers (resids) and
 segment identifies because Merge() simply concatenates the
@@ -429,6 +428,22 @@ 
    7.2.4. Classes and functionsChanged in version 0.7.4: New topology_format and format parameters to override the file
 format detection.
    
 
+
    
+
    
+angles[source]¶
    
+
    Returns a TopologyGroup
+of all angles in the Universe
    
+
    If none are found, returns None
    
+
    
+
+
    
+
    
+bonds[source]¶
    
+
    Returns a TopologyGroup of all
+bonds in the Universe.
+If none are found, returns None
    
+
    
+
 
    
 
    
 build_topology()[source]¶
    
@@ -461,6 +476,20 @@ 
    7.2.4. Classes and functions
+
    
+fragments[source]¶
    
+
    Read only tuple of fragments in the Universe
    
+
    
+
+
    
+
    
+impropers[source]¶
    
+
    Returns a TopologyGroup
+of all improper torsions in the Universe
    
+
    If none are found, returns None
    
+
    
+
 
    
 
    
 load_new(filename, **kwargs)[source]¶
    
@@ -663,6 +692,14 @@ 
    7.2.4. Classes and functions
+
    
+torsions[source]¶
    
+
    Returns a TopologyGroup
+of all torsions in the Universe
    
+
    If none are found, returns None
    
+
    
+
 
    
 
    
 trajectory[source]¶
    
@@ -806,14 +843,14 @@ 
    7.2.4. Classes and functions
 
  • atoms (for “in” lookup); cache is only built for large systems with
 > 10,000 atoms
    • 
-
  • indices (AtomGroup.indices())
    • 
-
  • masses (AtomGroup.masses())
    • 
-
  • residues (AtomGroup.residues)
    • 
-
  • segments (AtomGroup.segments)
    • 
-
  • bonds (AtomGroup.bonds)
    • 
-
  • angles (AtomGroup.angles)
    • 
-
  • torsions (AtomGroup.torsions)
    • 
-
  • improper torsions (AtomGroup.impropers)
    • 
+
  • indices (AtomGroup.indices())
    • 
+
  • masses (AtomGroup.masses())
    • 
+
  • residues (AtomGroup.residues)
    • 
+
  • segments (AtomGroup.segments)
    • 
+
  • bonds (AtomGroup.bonds)
    • 
+
  • angles (AtomGroup.angles)
    • 
+
  • torsions (AtomGroup.torsions)
    • 
+
  • improper torsions (AtomGroup.impropers)
    • 
 
 
    
 
    See also
    
@@ -886,11 +923,10 @@ 
    7.2.4. Classes and functionsangle()[source]¶
 
    Returns the angle in degrees between atoms 0, 1, 2.
    
 
    Angle between atoms 0 and 2 with apex at 1:
    
-
       2
+
       2
   /
  /
-1------0
-
    
+1------0
    
 
    
 
    
 
    Note
    
@@ -902,6 +938,15 @@ 
    7.2.4. Classes and functions
+
    
+angles[source]¶
    
+
    All the angles in this AtomGroup
    
+
    Note that these angles might extend out of the AtomGroup, to select
+only angles which are entirely contained by the AtomGroup use
+u.angles.atomgroup_intersection(ag, strict=True)
    
+
    
+
 
    
 
    
 asphericity(**kwargs)[source]¶
    
@@ -1028,6 +1073,15 @@ 
    7.2.4. Classes and functions
+
    
+bonds[source]¶
    
+
    All the bonds in this AtomGroup
    
+
    Note that these bonds might extend out of the AtomGroup, to select
+only bonds which are entirely contained by the AtomGroup use
+u.bonds.atomgroup_intersection(ag, strict=True)
    
+
    
+
 
    
 
    
 bsphere(**kwargs)[source]¶
    
@@ -1173,12 +1227,11 @@ 
    7.2.4. Classes and functions
            3
+
            3
         |
   1-----2
  /
-0
-
    
+0
    
 
    
 
    
 
    Note
    
@@ -1211,6 +1264,14 @@ 
    7.2.4. Classes and functions
+
    
+fragments[source]¶
    
+
    Read-only list of fragments.
    
+
    Contains all fragments that any Atom in this AtomGroup is part of, the contents of
+the fragments may extend beyond the contents of this AtomGroup.
    
+
    
+
 
    
 
    
 get_forces(ts=None, copy=False, dtype=<type 'numpy.float32'>)[source]¶
    
@@ -1226,7 +1287,7 @@ 
    7.2.4. Classes and functionsTimestep instead of
 the one from the current trajectory belonging to this universe.
 The ts is indexed with the indices returned by
-indices() and it is the user’s responsibility
+indices() and it is the user’s responsibility
 to provide a time step that has the appropriate dimensions.
    
 
 
    copy
    
@@ -1268,7 +1329,7 @@ 
    7.2.4. Classes and functionsTimestep instead of
 the one from the current trajectory belonging to this universe.
 The ts is indexed with the indices returned by
-indices() and it is the user’s responsibility
+indices() and it is the user’s responsibility
 to provide a time step that has the appropriate dimensions.
    
 
 
    copy
    
@@ -1331,6 +1392,30 @@ 
    7.2.4. Classes and functions
+
    
+impropers[source]¶
    
+
    All the improper torsions in this AtomGroup
    
+
    Note that these improper torsions might extend out of the AtomGroup,
+to select only torsions which are entirely contained by the AtomGroup use
+u.impropers.atomgroup_intersection(ag, strict=True)
    
+
    
+
+
    
+
    
+indices(*args, **kwargs)[source]¶
    
+
    Array of all Atom.number in the group.
    
+
    These indices are 0-based and can be used to directly index
+Universe.atoms or the coordinate array
+MDAnalysis.coordinates.base.Timestep._pos.
    
+
    
+
+
    
+
    
+masses(*args, **kwargs)[source]¶
    
+
    Array of atomic masses (as defined in the topology)
    
+
    
+
 
    
 
    
 momentOfInertia(**kwargs)[source]¶
    
@@ -1520,6 +1605,18 @@ 
    7.2.4. Classes and functions
+
    
+residues[source]¶
    
+
    Read-only list of Residue objects.
    
+
    A ResidueGroup of all residues that contain atoms in
+this group.
    
+
    
+
    Changed in version 0.9.0: Now returns strictly a ResidueGroup of the unique Residues that Atoms in this group
+belong to.
    
+
    
+
    
+
 
    
 
    
 resnames()[source]¶
    
@@ -1603,6 +1700,17 @@ 
    7.2.4. Classes and functions
+
    
+segments[source]¶
    
+
    Read-only list of Segment objects.
    
+
    A SegmentGroup of all segments that contain atoms in this group.
    
+
    
+
    Changed in version 0.9.0: Now strictly returns a SegmentGroup of a set of
+the Segment instances from this AtomGroup
    
+
    
+
    
+
 
    
 
    
 selectAtoms(sel, *othersel, **selgroups)[source]¶
    
@@ -2050,6 +2158,15 @@ 
    7.2.4. Classes and functions
+
    
+torsions[source]¶
    
+
    All the torsions in this AtomGroup
    
+
    Note that these torsions might extend out of the AtomGroup, to select
+only torsions which are entirely contained by the AtomGroup use
+u.torsions.atomgroup_intersection(ag, strict=True)
    
+
    
+
 
    
 
    
 totalCharge()[source]¶
    
@@ -2621,7 +2738,7 @@ 
    7.2.4. Classes and functionsset(name, value, **kwargs)¶
 
    Set attribute name to value for all residues in the ResidueGroup.
    
 
    If value is a sequence of the same length as the
-ResidueGroup (AtomGroup.residues) then each
+ResidueGroup (AtomGroup.residues) then each
 Residue‘s property name is set to the corresponding
 value. If value is neither of length 1 (or a scalar) nor of the
 length of the ResidueGroup then a ValueError is raised.
    
@@ -2797,7 +2914,7 @@ 
    7.2.4. Classes and functionsset(name, value, **kwargs)¶
 
    Set attribute name to value for all Segment in this AtomGroup.
    
 
    If value is a sequence of the same length as the
-SegmentGroup (AtomGroup.residues) then each
+SegmentGroup (AtomGroup.residues) then each
 Segment‘s property name is set to the corresponding
 value. If value is neither of length 1 (or a scalar) nor of the
 length of the SegmentGroup then a ValueError is raised.
    
@@ -2853,16 +2970,14 @@ 
    7.2.4. Classes and functions
 
  • If the first argument is a universe, just return it:
    
-
    as_universe(universe) --> universe
-
    
+
    as_universe(universe) --> universe
    
 
    
 
    • 
 
  • Otherwise try to build a universe from the first or the first
 and second argument:
    
-
    asUniverse(PDB, **kwargs) --> Universe(PDB, **kwargs)
+
    asUniverse(PDB, **kwargs) --> Universe(PDB, **kwargs)
 asUniverse(PSF, DCD, **kwargs) --> Universe(PSF, DCD, **kwargs)
-asUniverse(*args, **kwargs) --> Universe(*args, **kwargs)
-
    
+asUniverse(*args, **kwargs) --> Universe(*args, **kwargs)
    
 
    
 
    • 
 
@@ -2880,18 +2995,21 @@ 
    7.2.4. Classes and functions
 exception MDAnalysis.core.AtomGroup.SelectionError¶
 
    Raised when a atom selection failed.
    
+
    x.__init__(...) initializes x; see help(type(x)) for signature
    
 
    
 
 
    
 
    
 exception MDAnalysis.core.AtomGroup.SelectionWarning¶
    
 
    Warning indicating a possible problem with a selection.
    
+
    x.__init__(...) initializes x; see help(type(x)) for signature
    
 
    
 
 
    
 
    
 exception MDAnalysis.core.AtomGroup.NoDataError¶
    
 
    Raised when empty input is not allowed or required data are missing.
    
+
    x.__init__(...) initializes x; see help(type(x)) for signature
    
 
    
 
 
@@ -2918,7 +3036,7 @@ 
    Navigation
  • 
           previous |
    • 
-        
  • MDAnalysis 1.0.0-dev documentation »
    • 
+        
  • MDAnalysis 0.9.1 documentation »
  • 7. Core modules »
    • 
@@ -2930,7 +3048,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/core/Selection.html b/package/doc/html/documentation_pages/core/Selection.html
index 820ed43deae..26b9344e9ef 100644
--- a/package/doc/html/documentation_pages/core/Selection.html
+++ b/package/doc/html/documentation_pages/core/Selection.html
@@ -6,7 +6,7 @@
   
     
-    7.3. Atom selection Hierarchy — MDAnalysis.core.Selection — MDAnalysis 1.0.0-dev documentation
+    7.3. Atom selection Hierarchy — MDAnalysis.core.Selection — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
-    
+     
@@ -49,7 +49,7 @@ 
    Navigation
  • 
           previous |
    • 
-        
  • MDAnalysis 1.0.0-dev documentation »
    • 
+        
  • MDAnalysis 0.9.1 documentation »
  • 7. Core modules »
    • 
@@ -199,17 +199,16 @@ 
    7.3. Atom selection Hierarchy — http://www.engr.mun.ca/~theo/Misc/exp_parsing.htm).  Transforms
 expressions into nested Selection tree.
    
 
    For reference, the grammar that we parse is
    
-
    E(xpression)--> Exp(0)
+
    E(xpression)--> Exp(0)
 Exp(p) -->      P {B Exp(q)}
-P -->           U Exp(q) | "(" E ")" | v
-B(inary) -->    "and" | "or"
-U(nary) -->     "not"
+P -->           U Exp(q) | "(" E ")" | v
+B(inary) -->    "and" | "or"
+U(nary) -->     "not"
 T(erms) -->     segid [value]
                 | resname [value]
                 | resid [value]
                 | name [value]
-                | type [value]
-
    
+                | type [value]
    
 
    
 
 
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@@ -248,7 +247,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/core/Timeseries.html b/package/doc/html/documentation_pages/core/Timeseries.html
index db8fbb62ca1..807d3465d4e 100644
--- a/package/doc/html/documentation_pages/core/Timeseries.html
+++ b/package/doc/html/documentation_pages/core/Timeseries.html
@@ -6,7 +6,7 @@
   
     
-    7.4. Compute observable timeseries from trajectories — MDAnalysis.core.Timeseries — MDAnalysis 1.0.0-dev documentation
+    7.4. Compute observable timeseries from trajectories — MDAnalysis.core.Timeseries — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
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@@ -132,13 +132,12 @@ 
    7.4.1. Basic classes
    collection = TimeseriesCollection()
+
    collection = TimeseriesCollection()
 collection.addTimeseries(Timeseries.Atom(...)) - add a new Timeseries object
 collection.compute(...)                        - compute the collection of timeseries from the trajectory
 collection.clear()                             - clear the collection
-collection[i]                                  - access the i'th timeseries
-len(collection)                                - return the number of Timeseries added to the collection
-
    
+collection[i]                                  - access the i'th timeseries
+len(collection)                                - return the number of Timeseries added to the collection
    
 
    
 
    
 
    
@@ -307,7 +306,7 @@ 
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@@ -319,7 +318,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
   
 
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/core/distances.html b/package/doc/html/documentation_pages/core/distances.html
index 3771be48cba..5d7f229cfe3 100644
--- a/package/doc/html/documentation_pages/core/distances.html
+++ b/package/doc/html/documentation_pages/core/distances.html
@@ -6,7 +6,7 @@
   
     
     
-    7.5. Fast distance array computation — MDAnalysis.core.distances — MDAnalysis 1.0.0-dev documentation
+    7.5. Fast distance array computation — MDAnalysis.core.distances — MDAnalysis 0.9.1 documentation
     
     
     
@@ -14,7 +14,7 @@
     
     
     
     
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+    
     
     
      
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@@ -166,8 +166,7 @@ 
    7.5.2. Functions
    numpy.linalg.norm(a - b) for a, b in zip(coords1, coords2)
-
    
+
    numpy.linalg.norm(a - b) for a, b in zip(coords1, coords2)
    
 
    
 
    The optional argument box applies minimum image convention if supplied.
 box can be either orthogonal or triclinic
    
@@ -273,12 +272,11 @@ 
    7.5.2. Functions
            3
+
            3
         |
   1-----2
  /
-0
-
    
+0
    
 
    
 
    If a 1D numpy array of dtype numpy.float64 with len(atom1) elements is
 provided in result then this preallocated array is filled. This can speed
@@ -452,7 +450,7 @@ 
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@@ -464,7 +462,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
   
 
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/core/init.html b/package/doc/html/documentation_pages/core/init.html
index 0017a0f5fc3..87e75c5b0ce 100644
--- a/package/doc/html/documentation_pages/core/init.html
+++ b/package/doc/html/documentation_pages/core/init.html
@@ -6,7 +6,7 @@
   
     
     
-    7.1. Core functions of MDAnalysis — MDAnalysis 1.0.0-dev documentation
+    7.1. Core functions of MDAnalysis — MDAnalysis 0.9.1 documentation
     
     
     
@@ -14,7 +14,7 @@
     
     
     
     
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+    
     
     
      
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@@ -279,6 +279,7 @@ 
    7.1.1.1. List of MDAnalysis flags with default values
 
 
+
    x.__init__(...) initializes x; see help(type(x)) for signature
    
 
    
 
 
@@ -350,11 +351,10 @@ 
    7.1.1.2. Classesdoc string; may contain string interpolation mappings for:
    
-
    %%(name)s        name of the flag
+
    %%(name)s        name of the flag
 %%(default)r     default value
 %%(value)r       current value
-%%(mapping)r     mapping
-
    
+%%(mapping)r     mapping
    
 
    
 
    Doc strings are generated dynamically and reflect the current state.
    
 
@@ -396,7 +396,7 @@ 
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@@ -408,7 +408,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
   
 
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/core/log.html b/package/doc/html/documentation_pages/core/log.html
index d9a564b5f3c..5f54114b812 100644
--- a/package/doc/html/documentation_pages/core/log.html
+++ b/package/doc/html/documentation_pages/core/log.html
@@ -6,7 +6,7 @@
   
     
     
-    7.10. Setting up logging — MDAnalysis.core.log — MDAnalysis 1.0.0-dev documentation
+    7.10. Setting up logging — MDAnalysis.core.log — MDAnalysis 0.9.1 documentation
     
     
     
@@ -14,7 +14,7 @@
     
     
     
     
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+    
     
     
      
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@@ -181,10 +181,9 @@ 
    7.10.2. Other functions and classes for logging purposes
    Step   100/10000 [  1.0%]
+
    Step   100/10000 [  1.0%]
 Step   200/10000 [  2.0%]
-...
-
    
+...
    
 
    
 
    Because the default format string
    
 
    "Step %(step)5d/%(numsteps)d [%(percentage)5.1f%%]\r"
@@ -342,7 +341,7 @@ 
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@@ -354,7 +353,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
   
 
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/core/parallel.html b/package/doc/html/documentation_pages/core/parallel.html
index 4bba3c424e8..aabc243a968 100644
--- a/package/doc/html/documentation_pages/core/parallel.html
+++ b/package/doc/html/documentation_pages/core/parallel.html
@@ -6,7 +6,7 @@
   
     
     
-    7.11. Parallel algorithms for MDAnalysis — MDAnalysis 1.0.0-dev documentation
+    7.11. Parallel algorithms for MDAnalysis — MDAnalysis 0.9.1 documentation
     
     
     
@@ -14,7 +14,7 @@
     
     
     
     
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+    
     
     
      
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@@ -210,7 +210,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/core/qcprot.html b/package/doc/html/documentation_pages/core/qcprot.html
index fc7ba9a2b9b..e4cb3a1e5e2 100644
--- a/package/doc/html/documentation_pages/core/qcprot.html
+++ b/package/doc/html/documentation_pages/core/qcprot.html
@@ -6,7 +6,7 @@
   
     
-    7.7. Fast QCP RMSD structure alignment — MDAnalysis.core.qcprot — MDAnalysis 1.0.0-dev documentation
+    7.7. Fast QCP RMSD structure alignment — MDAnalysis.core.qcprot — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
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@@ -230,9 +230,8 @@ 
    7.7.2. FunctionsPlease note how the structure coordinates are stored as 3xN arrays,
 not Nx3 arrays as is also commonly used. The difference is
 something like this for storage of a structure with 8 atoms:
    
-
    Nx3: xyzxyzxyzxyzxyzxyzxyzxyz
-3xN: xxxxxxxxyyyyyyyyzzzzzzzz
-
    
+
    Nx3: xyzxyzxyzxyzxyzxyzxyzxyz
+3xN: xxxxxxxxyyyyyyyyzzzzzzzz
    
 
    
 
 
@@ -299,7 +298,7 @@ 
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@@ -311,7 +310,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/core/transformations.html b/package/doc/html/documentation_pages/core/transformations.html
index f0bef931bd6..44d34985020 100644
--- a/package/doc/html/documentation_pages/core/transformations.html
+++ b/package/doc/html/documentation_pages/core/transformations.html
@@ -6,7 +6,7 @@
   
     
-    7.6. Homogeneous Transformation Matrices and Quaternions — MDAnalysis.core.transformations — MDAnalysis 1.0.0-dev documentation
+    7.6. Homogeneous Transformation Matrices and Quaternions — MDAnalysis.core.transformations — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
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+     
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@@ -602,7 +602,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/core/units.html b/package/doc/html/documentation_pages/core/units.html
index 41842732e5f..c26e427f339 100644
--- a/package/doc/html/documentation_pages/core/units.html
+++ b/package/doc/html/documentation_pages/core/units.html
@@ -6,7 +6,7 @@
   
     
-    7.8. Constants and unit conversion — MDAnalysis.core.units — MDAnalysis 1.0.0-dev documentation
+    7.8. Constants and unit conversion — MDAnalysis.core.units — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
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@@ -170,10 +170,9 @@ 
    7.8.1. Implementation notes\(f_{b,b'}\).
    
 
    Conversion between different units is always carried out via the base unit as
 an intermediate step:
    
-
    x is in u1: from u1 to b:  x'  = x  / factor[u1]
-            from b  to u2: x'' = x' * factor[u2]
-so f[u1,u2] = factor[u2]/factor[u1]
-
    
+
    x is in u1: from u1 to b:  x'  = x  / factor[u1]
+            from b  to u2: x'' = x' * factor[u2]
+so f[u1,u2] = factor[u2]/factor[u1]
    
 
    
 
    
 
    7.8.1.1. Conversions¶
    
@@ -196,14 +195,12 @@ 
    7.8.1.1. ConversionsExample for how to convert the conversion factor to Molar (mol/l):
    
-
    factor = 1 A**-3 / (N_Avogadro * (10**-9 dm)**-3)
-
    
+
    factor = 1 A**-3 / (N_Avogadro * (10**-9 dm)**-3)
    
 
    
 
    relative to a density rho0 in g/cm^3:
    
-
    M(H2O) = 18 g/mol   Molar mass of water
+
    M(H2O) = 18 g/mol   Molar mass of water
 
-factor = 1/(1e-24 * N_Avogadro / M(H2O))
-
    
+factor = 1/(1e-24 * N_Avogadro / M(H2O))
    
 
    
 
    from rho/rho0 = n/(N_A * M**-1) / rho0  where [n] = 1/Volume, [rho] = mass/Volume
    
 
@@ -419,7 +416,7 @@ 
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@@ -431,7 +428,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
   
 
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diff --git a/package/doc/html/documentation_pages/core/util.html b/package/doc/html/documentation_pages/core/util.html
index 3fb486dc5f8..2cf9540d85b 100644
--- a/package/doc/html/documentation_pages/core/util.html
+++ b/package/doc/html/documentation_pages/core/util.html
@@ -6,7 +6,7 @@
   
     
     
-    7.9. Helper functions — MDAnalysis.core.util — MDAnalysis 1.0.0-dev documentation
+    7.9. Helper functions — MDAnalysis.core.util — MDAnalysis 0.9.1 documentation
     
     
     
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@@ -685,13 +685,12 @@ 
    7.9.7. Mathematics and GeometryMDAnalysis.core.util.dihedral(ab, bc, cd)[source]¶
 
    Returns the dihedral angle in radians between vectors connecting A,B,C,D.
    
 
    The dihedral measures the rotation around bc:
    
-
      ab
+
      ab
 A---->B
        \ bc
-       _\'
+       _\'
          C---->D
-           cd
-
    
+           cd
    
 
    
 
    The dihedral angle is restricted to the range -π <= x <= π.
    
 
    
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@@ -791,7 +790,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
   
 
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diff --git a/package/doc/html/documentation_pages/core_modules.html b/package/doc/html/documentation_pages/core_modules.html
index 922c7a0f468..2c2514225a1 100644
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+++ b/package/doc/html/documentation_pages/core_modules.html
@@ -6,7 +6,7 @@
   
     
     
-    7. Core modules — MDAnalysis 1.0.0-dev documentation
+    7. Core modules — MDAnalysis 0.9.1 documentation
     
     
     
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    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
   
 
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diff --git a/package/doc/html/documentation_pages/overview.html b/package/doc/html/documentation_pages/overview.html
index 3c803a58a42..2be497750a6 100644
--- a/package/doc/html/documentation_pages/overview.html
+++ b/package/doc/html/documentation_pages/overview.html
@@ -6,7 +6,7 @@
   
     
     
-    1. Overview over MDAnalysis — MDAnalysis 1.0.0-dev documentation
+    1. Overview over MDAnalysis — MDAnalysis 0.9.1 documentation
     
     
     
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@@ -112,7 +112,7 @@ 
    1. Overview over MDAnalysisAtomGroup object has a
 centerOfMass() method that
 returns the center of mass of the group of atoms. It also contains an
-attribute called residues
+attribute called residues
 that lists all the residues that belong to the group. Using methods
 such as selectAtoms()
 (which uses CHARMM-style atom Selection Commands) one
@@ -287,7 +287,7 @@ 
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@@ -298,7 +298,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/selections.html b/package/doc/html/documentation_pages/selections.html
index f0fc8260172..44c17b63421 100644
--- a/package/doc/html/documentation_pages/selections.html
+++ b/package/doc/html/documentation_pages/selections.html
@@ -6,7 +6,7 @@
   
     
-    2. Selection Commands — MDAnalysis 1.0.0-dev documentation
+    2. Selection Commands — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
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@@ -434,11 +434,10 @@ 
    2.2.4. Atom name selector
 
    Just for comparison to show that a single selection string does not work as one
 might expect:
    
-
    # WRONG!
->>> print list(universe.selectAtoms("segid DMPC and ( resid 3 or resid 2 ) and name P"))
-[< Atom 452: name 'P' of type '180' of resid 'DMPC', 2 and 'DMPC'>,
-< Atom 570: name 'P' of type '180' of resid 'DMPC', 3 and 'DMPC'>]
-
    
+
    # WRONG!
+>>> print list(universe.selectAtoms("segid DMPC and ( resid 3 or resid 2 ) and name P"))
+[< Atom 452: name 'P' of type '180' of resid 'DMPC', 2 and 'DMPC'>,
+< Atom 570: name 'P' of type '180' of resid 'DMPC', 3 and 'DMPC'>]
    
 
    
 
    
 
    
@@ -464,7 +463,7 @@ 
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  • MDAnalysis 1.0.0-dev documentation »
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@@ -475,7 +474,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/selections/base.html b/package/doc/html/documentation_pages/selections/base.html
index 2b736389f5f..1916682dd73 100644
--- a/package/doc/html/documentation_pages/selections/base.html
+++ b/package/doc/html/documentation_pages/selections/base.html
@@ -6,7 +6,7 @@
   
     
-    6.5. Base classes for the selection writers — MDAnalysis 1.0.0-dev documentation
+    6.5. Base classes for the selection writers — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
-    
+     
@@ -49,7 +49,7 @@ 
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    • 
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    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/selections/charmm.html b/package/doc/html/documentation_pages/selections/charmm.html
index 3ab525fec05..20ec2c750e7 100644
--- a/package/doc/html/documentation_pages/selections/charmm.html
+++ b/package/doc/html/documentation_pages/selections/charmm.html
@@ -6,7 +6,7 @@
   
     
-    6.4. CHARMM selections — MDAnalysis 1.0.0-dev documentation
+    6.4. CHARMM selections — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
-    
+     
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    • 
@@ -94,8 +94,7 @@ 
    Quick search
    6.4. CHARMM selections¶
    Write MDAnalysis.core.AtomGroup.AtomGroup selection to a str file
 that defines a CHARMM selection. To be used in CHARMM like this:
    
-
    stream macro.str
-
    
+
    stream macro.str
    
 
    
 
    The selection is named mdanalysis001.
    
 
    
@@ -203,7 +202,7 @@ 
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  • 6. Selection exporters »
    •  
       
     
    
@@ -215,7 +214,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/selections/gromacs.html b/package/doc/html/documentation_pages/selections/gromacs.html
index e0c22827b15..f0d75a8ae26 100644
--- a/package/doc/html/documentation_pages/selections/gromacs.html
+++ b/package/doc/html/documentation_pages/selections/gromacs.html
@@ -6,7 +6,7 @@
   
     
-    6.3. Gromacs selections — MDAnalysis 1.0.0-dev documentation
+    6.3. Gromacs selections — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
-    
+     
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  • 6. Selection exporters »
    • 
@@ -94,8 +94,7 @@ 
    Quick search
    6.3. Gromacs selections¶
    Write MDAnalysis.core.AtomGroup.AtomGroup selection to a ndx file
 that defines a Gromacs index group. To be used in Gromacs like this:
    
-
    <GROMACS_COMMAND> -n macro.ndx
-
    
+
    <GROMACS_COMMAND> -n macro.ndx
    
 
    
 
    The index groups are named mdanalysis001, mdanalysis002, etc.
    
 
    
@@ -203,7 +202,7 @@ 
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    •  
       
     
    
@@ -215,7 +214,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/selections/pymol.html b/package/doc/html/documentation_pages/selections/pymol.html
index 1eeee92af1f..168d571c951 100644
--- a/package/doc/html/documentation_pages/selections/pymol.html
+++ b/package/doc/html/documentation_pages/selections/pymol.html
@@ -6,7 +6,7 @@
   
     
-    6.2. PyMOL selections — MDAnalysis 1.0.0-dev documentation
+    6.2. PyMOL selections — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
-    
+     
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    • 
@@ -95,8 +95,7 @@ 
    6.2. PyMOL selectionsMDAnalysis.core.AtomGroup.AtomGroup selection to a
 script pml file that defines PyMOL atomselect macros. To be used
 in PyMOL like this:
    
-
    @macros.pml
-
    
+
    @macros.pml
    
 
    
 
    The selections should appear in the user interface.
    
 
    
@@ -204,7 +203,7 @@ 
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  • 6. Selection exporters »
    •  
       
     
    
@@ -216,7 +215,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/selections/vmd.html b/package/doc/html/documentation_pages/selections/vmd.html
index c943273b054..258b70abae5 100644
--- a/package/doc/html/documentation_pages/selections/vmd.html
+++ b/package/doc/html/documentation_pages/selections/vmd.html
@@ -6,7 +6,7 @@
   
     
-    6.1. VMD selections — MDAnalysis 1.0.0-dev documentation
+    6.1. VMD selections — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
-    
+     
@@ -49,7 +49,7 @@ 
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  • 6. Selection exporters »
    • 
@@ -94,9 +94,8 @@ 
    Quick search
    6.1. VMD selections¶
    Write MDAnalysis.core.AtomGroup.AtomGroup selection to a VMD tcl file
 that defines atomselect macros. To be used in VMD like this:
    
-
    source macros.vmd
-set sel [atomselect top mdanalysis001]  # use macro 001
-
    
+
    source macros.vmd
+set sel [atomselect top mdanalysis001]  # use macro 001
    
 
    
 
    
 
    
@@ -203,7 +202,7 @@ 
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+        
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    • 
           
  • 6. Selection exporters »
    •  
       
     
    
@@ -215,7 +214,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/selections_modules.html b/package/doc/html/documentation_pages/selections_modules.html
index 0ae92c8466a..7e821e4cdae 100644
--- a/package/doc/html/documentation_pages/selections_modules.html
+++ b/package/doc/html/documentation_pages/selections_modules.html
@@ -6,7 +6,7 @@
   
     
-    6. Selection exporters — MDAnalysis 1.0.0-dev documentation
+    6. Selection exporters — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
-    
+    
@@ -48,7 +48,7 @@ 
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@@ -185,7 +185,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/topology/CRDParser.html b/package/doc/html/documentation_pages/topology/CRDParser.html
index 7dfa0dbb3fe..67e9663da9d 100644
--- a/package/doc/html/documentation_pages/topology/CRDParser.html
+++ b/package/doc/html/documentation_pages/topology/CRDParser.html
@@ -6,7 +6,7 @@
   
     
-    4.6. CRD topology parser — MDAnalysis 1.0.0-dev documentation
+    4.6. CRD topology parser — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
-    
+     
@@ -49,7 +49,7 @@ 
    Navigation
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    • 
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    • 
@@ -129,7 +129,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/topology/DMSParser.html b/package/doc/html/documentation_pages/topology/DMSParser.html
index 85cd7c9726d..cc61df87d80 100644
--- a/package/doc/html/documentation_pages/topology/DMSParser.html
+++ b/package/doc/html/documentation_pages/topology/DMSParser.html
@@ -6,7 +6,7 @@
   
     
-    4.13. DESRES Molecular Structure file format topology parser — MDAnalysis 1.0.0-dev documentation
+    4.13. DESRES Molecular Structure file format topology parser — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
-    
+     
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    • 
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  • MDAnalysis 0.9.1 documentation »
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    • 
@@ -129,7 +129,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/topology/ExtendedPDBParser.html b/package/doc/html/documentation_pages/topology/ExtendedPDBParser.html
index 7780d3a2664..f188eab7a9c 100644
--- a/package/doc/html/documentation_pages/topology/ExtendedPDBParser.html
+++ b/package/doc/html/documentation_pages/topology/ExtendedPDBParser.html
@@ -6,7 +6,7 @@
   
     
-    4.10. Extended PDB topology parser — MDAnalysis 1.0.0-dev documentation
+    4.10. Extended PDB topology parser — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
-    
+     
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    • 
@@ -170,7 +170,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/topology/GROParser.html b/package/doc/html/documentation_pages/topology/GROParser.html
index 4a094678a32..4d838001b6b 100644
--- a/package/doc/html/documentation_pages/topology/GROParser.html
+++ b/package/doc/html/documentation_pages/topology/GROParser.html
@@ -6,7 +6,7 @@
   
     
-    4.7. GRO topology parser — MDAnalysis 1.0.0-dev documentation
+    4.7. GRO topology parser — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
-    
+     
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    • 
@@ -129,7 +129,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/topology/PDBParser.html b/package/doc/html/documentation_pages/topology/PDBParser.html
index d8bc9d5b96b..88a144d9f00 100644
--- a/package/doc/html/documentation_pages/topology/PDBParser.html
+++ b/package/doc/html/documentation_pages/topology/PDBParser.html
@@ -6,7 +6,7 @@
   
     
-    4.8. PDB topology parser — MDAnalysis 1.0.0-dev documentation
+    4.8. PDB topology parser — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
-    
+     
@@ -49,7 +49,7 @@ 
    Navigation
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    • 
@@ -134,7 +134,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/topology/PDBQTParser.html b/package/doc/html/documentation_pages/topology/PDBQTParser.html
index 6c2d159b8bb..dd5989f3af6 100644
--- a/package/doc/html/documentation_pages/topology/PDBQTParser.html
+++ b/package/doc/html/documentation_pages/topology/PDBQTParser.html
@@ -6,7 +6,7 @@
   
     
-    4.11. PDBQT topology parser — MDAnalysis 1.0.0-dev documentation
+    4.11. PDBQT topology parser — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
-    
+     
@@ -49,7 +49,7 @@ 
    Navigation
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  • 4. Topology modules »
    • 
@@ -137,7 +137,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/topology/PQRParser.html b/package/doc/html/documentation_pages/topology/PQRParser.html
index 755096e17c1..92d70bc75b9 100644
--- a/package/doc/html/documentation_pages/topology/PQRParser.html
+++ b/package/doc/html/documentation_pages/topology/PQRParser.html
@@ -6,7 +6,7 @@
   
     
-    4.12. PQR topology parser — MDAnalysis 1.0.0-dev documentation
+    4.12. PQR topology parser — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
-    
+     
@@ -49,7 +49,7 @@ 
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  • 4. Topology modules »
    • 
@@ -176,7 +176,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/topology/PSFParser.html b/package/doc/html/documentation_pages/topology/PSFParser.html
index b960559c73a..58b13e49df9 100644
--- a/package/doc/html/documentation_pages/topology/PSFParser.html
+++ b/package/doc/html/documentation_pages/topology/PSFParser.html
@@ -6,7 +6,7 @@
   
     
-    4.4. PSF topology parser — MDAnalysis 1.0.0-dev documentation
+    4.4. PSF topology parser — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
-    
+     
@@ -49,7 +49,7 @@ 
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    • 
@@ -132,7 +132,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/topology/PrimitivePDBParser.html b/package/doc/html/documentation_pages/topology/PrimitivePDBParser.html
index ec6717ff357..7693186f9b7 100644
--- a/package/doc/html/documentation_pages/topology/PrimitivePDBParser.html
+++ b/package/doc/html/documentation_pages/topology/PrimitivePDBParser.html
@@ -6,7 +6,7 @@
   
     
-    4.9. Primitive PDB topology parser — MDAnalysis 1.0.0-dev documentation
+    4.9. Primitive PDB topology parser — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
-    
+     
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@@ -180,7 +180,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/topology/TOPParser.html b/package/doc/html/documentation_pages/topology/TOPParser.html
index 7a7c20a5e64..be4f15ca4d1 100644
--- a/package/doc/html/documentation_pages/topology/TOPParser.html
+++ b/package/doc/html/documentation_pages/topology/TOPParser.html
@@ -6,7 +6,7 @@
   
     
-    4.5. AMBER PRMTOP topology parser — MDAnalysis 1.0.0-dev documentation
+    4.5. AMBER PRMTOP topology parser — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
-    
+     
@@ -49,7 +49,7 @@ 
    Navigation
  • 
           previous |
    • 
-        
  • MDAnalysis 1.0.0-dev documentation »
    • 
+        
  • MDAnalysis 0.9.1 documentation »
  • 4. Topology modules »
    • 
@@ -129,7 +129,7 @@ 
    Navigation
  • 
           previous |
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-        
  • MDAnalysis 1.0.0-dev documentation »
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+        
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  • 4. Topology modules »
    • 
@@ -141,7 +141,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/topology/TPRParser.html b/package/doc/html/documentation_pages/topology/TPRParser.html
index 402b1e97873..8f325460828 100644
--- a/package/doc/html/documentation_pages/topology/TPRParser.html
+++ b/package/doc/html/documentation_pages/topology/TPRParser.html
@@ -6,7 +6,7 @@
   
     
-    4.14. Gromacs portable run input TPR format parser — MDAnalysis 1.0.0-dev documentation
+    4.14. Gromacs portable run input TPR format parser — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
-    
+     
@@ -49,7 +49,7 @@ 
    Navigation
  • 
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  • MDAnalysis 1.0.0-dev documentation »
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+        
  • MDAnalysis 0.9.1 documentation »
  • 4. Topology modules »
    • 
@@ -213,7 +213,7 @@ 
    Navigation
  • 
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    • 
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  • MDAnalysis 1.0.0-dev documentation »
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+        
  • MDAnalysis 0.9.1 documentation »
  • 4. Topology modules »
    • 
@@ -225,7 +225,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/topology/core.html b/package/doc/html/documentation_pages/topology/core.html
index 37993acda2a..685c64a5a0b 100644
--- a/package/doc/html/documentation_pages/topology/core.html
+++ b/package/doc/html/documentation_pages/topology/core.html
@@ -6,7 +6,7 @@
   
     
-    4.2. Common functions for topology building — MDAnalysis.topology.core — MDAnalysis 1.0.0-dev documentation
+    4.2. Common functions for topology building — MDAnalysis.topology.core — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
-    
+     
@@ -49,7 +49,7 @@ 
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  • MDAnalysis 1.0.0-dev documentation »
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  • 4. Topology modules »
    • 
@@ -118,11 +118,10 @@ 
    4.2. Common functions for topology building — angle()[source]¶
 
    Returns the angle in degrees of this Angle.
    
 
    Angle between atoms 0 and 2 with apex at 1:
    
-
       2
+
       2
   /
  /
-1------0
-
    
+1------0
    
 
    
 
    
 
    New in version 0.9.0.
    
@@ -235,7 +234,7 @@ 
    4.2. Common functions for topology building — TopologyGroup.topDict
+
    TopologyDicts are also built lazily from a TopologyGroup.topDict
 attribute.
    
 
    The TopologyDict collects all the selected topology type from the
 atoms and categorises them according to the types of the atoms within.
@@ -420,6 +419,16 @@ 
    4.2. Common functions for topology building — 
+
    
+topDict[source]¶
    
+
    Returns the TopologyDict for this topology group.
    
+
    This is used for the selectBonds method when fetching a certain type
+of bond.
    
+
    This is a cached property so will be generated the first time it is
+accessed.
    
+
    
+
 
    
 
    
 torsions(result=None, pbc=False)[source]¶
    
@@ -503,12 +512,11 @@ 
    4.2. Common functions for topology building — 
            3
+
            3
         |
   1-----2
  /
-0
-
    
+0
    
 
    
 
    
 
    New in version 0.9.0.
    
@@ -783,7 +791,7 @@ 
    Navigation
    
         
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-        
  • MDAnalysis 1.0.0-dev documentation »
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+        
  • MDAnalysis 0.9.1 documentation »
    • 
           
  • 4. Topology modules »
    •  
       
     
    
@@ -795,7 +803,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
   
 
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/topology/init.html b/package/doc/html/documentation_pages/topology/init.html
index 3087c9d7f05..7e07f4eb3f5 100644
--- a/package/doc/html/documentation_pages/topology/init.html
+++ b/package/doc/html/documentation_pages/topology/init.html
@@ -6,7 +6,7 @@
   
     
     
-    4.1. Topology readers — MDAnalysis.topology — MDAnalysis 1.0.0-dev documentation
+    4.1. Topology readers — MDAnalysis.topology — MDAnalysis 0.9.1 documentation
     
     
     
@@ -14,7 +14,7 @@
     
     
     
     
-    
+    
     
     
      
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    • 
           
  • 4. Topology modules »
    •  
       
     
    
@@ -119,8 +119,8 @@ 
    4.1. Topology readers — Table of Supported topology formats
 
    --++
@@ -205,12 +205,25 @@ 
    4.1. Topology readers — LAMMPS Data file parser
 MDAnalysis.topology.LAMMPSParser
 
    
+
+
+
+
+
+
+
+
    
         
            
       
     
   
 
     
     
     
     
     
     
     
     
     
     
         
            
       
     
         
            
       
     
   
 
     
     
     
     
     
     
     
     
     
     
         
            
       
     
         
            
       
     
   
 
     
     
     
     
     
     
     
     
     
     
         
            
       
     
         
            
       
     
   
 
     
     
     
     
     
     
     
     
     
     
         
            
       
     
         
            
       
     
   
 
     
     
     
     
     
     
     
     
     
     
         
            
       
     
         
            
       
     
         
            
       
     
   
 
     
     
     
     
     
     
     
     
     
     
         
            
       
     
         
            
       
     
   
 
     
     
     
     
     
     
     
     
     
     
         
            
       
     
         
            
       
     
   
 
     
     
     
     
     
     
     
     
     
     
         
            
       
     
   
 
     
     
     
     
     
     
     
     
     
     
         
            
       
     
    LAMMPSdcd,
-datar/w
-rdcdr/w
 CHARMM-style binary trajectory; endianness is
 autodetected. Units are appropriate for LAMMPS.
-Module MDAnalysis.coordinates.LAMMPS
-Single frames can be read from .data files.
 
    Gromacs
    LAMMPS [1]datarSingle frame of coordinates read from .data files
    Gromacs
 xtc
 r/w
 Compressed (lossy) xtc trajectory format. Module
 MDAnalysis.coordinates.XTC
 
    Gromacs
    Gromacs
 trr
 r/w
 Full precision trr trajectory. Coordinates and
 velocities are processed. Module
 MDAnalysis.coordinates.TRR
 
    XYZ
    XYZ [1]
 xyz
 r/w
 Generic white-space separate XYZ format; can be
 compressed (gzip or bzip2). Module
 MDAnalysis.coordinates.XYZ
 
    GAMESSgms,
+log,
+outrGeneric semi-formatted GAMESS output log; can be
+compressed (gzip or bzip2). Module
+MDAnalysis.coordinates.GMS
    
 
    AMBER
 trj,
 mdcrd
    
 
    Brookhaven
-[1]
 pdb
 r/w
 a simplified PDB format (as used in MD simulations)
@@ -276,14 +287,14 @@ 
    5.1.3. Supported coordinate formatsUniverse(..., format="XPDB").
 Module :MDAnalysis.coordinates.PDB`
    		
 
    PDBQT [1]
    PDBQT [1]
 pdbqt
 r/w
 file format used by AutoDock with atom types t
 and partial charges q. Module:
 MDAnalysis.coordinates.PDBQT
 
    PQR [1]
    PQR [1]
 pqr
 r/w
 PDB-like but whitespace-separated files with charge
@@ -291,20 +302,20 @@ 
    5.1.3. Supported coordinate formatsMDAnalysis.coordinates.PQR
    		
 
    
 
    GROMOS96
-[1]
 gro
 r/w
 basic GROMOS96 format (velocities as well). Module
 MDAnalysis.coordinates.GRO
 
    CHARMM [1]
    CHARMM [1]
 crd
 r/w
 “CARD” coordinate output from CHARMM; deals with
 either standard or EXTended format. Module
 MDAnalysis.coordinates.CRD
 
    DESRES [1]
    DESRES [1]
 dms
 r
 DESRES Molecular Structure file format reader.
@@ -327,7 +338,7 @@ 
    5.1.3. Supported coordinate formats
 
    
 
    [1](1, 2, 3, 4, 5, 6) This format can also be used to provide basic topology
+
    [1](1, 2, 3, 4, 5, 6, 7, 8) This format can also be used to provide basic topology
 information (i.e. the list of atoms); it is possible to create a
 full Universe by simply
 providing a file of this format: u = Universe(filename)
    
 
 
   
 
     
     
     
     
     
     
     
     
     
     
         
           
            
       
         
           
            
       
   
 
     
     
     
     
     
     
     
     
     
     
         
           
            
       
         
           
            
       
   
 
     
     
     
     
     
     
     
     
     
     
         
           
            
       
         
           
            
       
   
 
     
     
     
     
     
     
     
     
      
   
          
       
     
       
     
   
 
     
     
     
     
     
     
     
     
     
     
         
            
       
     
         
            
       
     
   
 
     
     
     
     
     
     
     
     
     
     
         
            
       
     
   
 
     
     
     
     
     
     
     
     
     
     
         
            
       
     
         
            
       
     
         
            
       
     
         
            
       
     
   
 
     
     
     
     
     
     
     
     
     
     
         
            
       
     
   
 
     
     
     
     
     
     
     
     
     
     
         
            
       
     
         
            
       
     
   
 
     
     
     
     
     
     
     
     
     
     
         
            
       
     
          
       
     
       
     
   
 
     
     
     
     
     
     
     
     
      
   
          
       
     
        
       
     
     
   
 
     
     
     
     
     
     
     
     
     
     
         
            
       
     
         
            
       
     
   
 
     
     
     
     
     
     
     
     
     
     
         
            
       
     
 
 
   
 
     
     
     
     
     
     
     
     
     
     
         
            
       
     
 
 
   
 
     
     
     
     
     
     
     
     
     
     
         
            
       
     
   
 
     
     
     
     
     
     
     
     
     
     
         
            
       
     
 
 
   
 
     
     
     
     
     
     
     
     
      
   
          
       
     
       
     
   
 
     
     
     
     
     
     
     
     
     
     
         
            
       
     
         
            
       
     
   
 
     
     
     
     
     
     
     
     
     
     
         
            
       
     
         
            
       
     
   
 
     
     
     
     
     
     
     
     
     
     
         
            
       
     
         
            
       
     
   
 
     
     
     
     
     
     
     
     
     
     
         
            
       
     
         
            
       
     
   
 
     
     
     
     
     
     
     
     
     
     
         
            
       
     
         
            
       
     
   
 
     
     
     
     
     
     
     
     
     
     
         
            
       
     
         
            
       
     
   
 
     
     
     
     
     
     
     
     
     
     
         
            
       
     
         
            
       
     
   
 
     
     
     
     
     
     
     
     
     
     
         
            
       
     
         
            
       
     
   
 
     
     
     
     
     
     
     
     
     
     
         
            
       
     
         
            
       
     
   
 
     
     
     
     
     
     
     
     
     
     
         
            
       
     
         
            
       
     
   
 
     
     
     
     
     
     
     
     
     
     
         
            
       
     
         
            
       
     
   
 
     
     
     
     
     
     
     
     
     
     
         
            
       
         
 




 
 
 
    Name
    XYZ [1]xyzXYZ File Parser.  Reads only the labels from atoms and
+constructs minimal topology data.
+MDAnalysis.topology.XYZParser
    GMSgms,
+logGAMESS output parser. Read only atoms of assembly
+section (atom, elems and coords) and construct topology.
+MDAnalysis.topology.GMSParser
    
 
 
    
 
-
    
 
 
    [1](1, 2, 3, 4, 5, 6) This format can also be used to provide coordinates so that
+
    [1](1, 2, 3, 4, 5, 6, 7) This format can also be used to provide coordinates so that
 it is possible to create a full
 Universe by simply providing a
 file of this format as the sole argument to
@@ -341,7 +354,7 @@ 
    Navigation
    
         
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  • MDAnalysis 1.0.0-dev documentation »
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+        
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  • 4. Topology modules »
    •  
       
     
@@ -353,7 +366,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
   
 
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/topology/tables.html b/package/doc/html/documentation_pages/topology/tables.html
index 1604c1178eb..6678d297e01 100644
--- a/package/doc/html/documentation_pages/topology/tables.html
+++ b/package/doc/html/documentation_pages/topology/tables.html
@@ -6,7 +6,7 @@
   
     
     
-    4.3. MDAnalysis topology tables — MDAnalysis 1.0.0-dev documentation
+    4.3. MDAnalysis topology tables — MDAnalysis 0.9.1 documentation
     
     
     
@@ -14,7 +14,7 @@
     
     
     
     
-    
+    
     
     
      
@@ -49,7 +49,7 @@ 
    Navigation
    
         
  • 
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  • MDAnalysis 1.0.0-dev documentation »
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    •  
       
     
@@ -167,7 +167,7 @@ 
    Navigation
    
         
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+        
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@@ -179,7 +179,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
   
 
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/topology_modules.html b/package/doc/html/documentation_pages/topology_modules.html
index 07bf0fea323..54872de7b8c 100644
--- a/package/doc/html/documentation_pages/topology_modules.html
+++ b/package/doc/html/documentation_pages/topology_modules.html
@@ -6,7 +6,7 @@
   
     
     
-    4. Topology modules — MDAnalysis 1.0.0-dev documentation
+    4. Topology modules — MDAnalysis 0.9.1 documentation
     
     
     
@@ -14,7 +14,7 @@
     
     
     
     
-    
+    
     
      
   
@@ -48,7 +48,7 @@ 
    Navigation
    
         
  • 
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-        
  • MDAnalysis 1.0.0-dev documentation »
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+        
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    •  
       
     
       
    
@@ -144,7 +144,7 @@ 
    Navigation
    
         
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-        
  • MDAnalysis 1.0.0-dev documentation »
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+        
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@@ -155,7 +155,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
   
 
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/visualization/streamlines.html b/package/doc/html/documentation_pages/visualization/streamlines.html
index 4e5514e08d7..b7b5bcda933 100644
--- a/package/doc/html/documentation_pages/visualization/streamlines.html
+++ b/package/doc/html/documentation_pages/visualization/streamlines.html
@@ -6,7 +6,7 @@
   
     
     
-    9.1.1. 2D Streamplot — MDAnalysis 1.0.0-dev documentation
+    9.1.1. 2D Streamplot — MDAnalysis 0.9.1 documentation
     
     
     
@@ -14,7 +14,7 @@
     
     
     
     
-    
+    
     
     
      
@@ -49,7 +49,7 @@ 
    Navigation
    
         
  • 
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  • MDAnalysis 1.0.0-dev documentation »
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+        
  • MDAnalysis 0.9.1 documentation »
    • 
           
  • 9. Visualization modules »
    •  
       
     
@@ -180,22 +180,21 @@ 
    9.1.1. Multicore 2D streamplot Python library for MDAnalysis — 
 
    
 
    
-
    import matplotlib, matplotlib.pyplot, numpy
+
    import matplotlib, matplotlib.pyplot, numpy
 import MDAnalysis, MDAnalysis.visualization.streamlines
 u1, v1, average_displacement,standard_deviation_of_displacement =
-MDAnalysis.visualization.streamlines.generate_streamlines('testing.gro','testing_filtered.xtc',grid_spacing =
-20, MDA_selection = 'name PO4',start_frame=2,end_frame=3,xmin=-8.73000049591,xmax= 1225.96008301,
+MDAnalysis.visualization.streamlines.generate_streamlines('testing.gro','testing_filtered.xtc',grid_spacing =
+20, MDA_selection = 'name PO4',start_frame=2,end_frame=3,xmin=-8.73000049591,xmax= 1225.96008301,
 ymin= -12.5799999237, ymax=1224.34008789,maximum_delta_magnitude = 1.0,num_cores=16)
 x = numpy.linspace(0,1200,61)
 y = numpy.linspace(0,1200,61)
 speed = numpy.sqrt(u1*u1 + v1*v1)
 fig = matplotlib.pyplot.figure()
-ax = fig.add_subplot(111,aspect='equal')
-ax.set_xlabel('x ($\AA$)')
-ax.set_ylabel('y ($\AA$)')
+ax = fig.add_subplot(111,aspect='equal')
+ax.set_xlabel('x ($\AA$)')
+ax.set_ylabel('y ($\AA$)')
 ax.streamplot(x,y,u1,v1,density=(10,10),color=speed,linewidth=3*speed/speed.max())
-fig.savefig('testing_streamline.png',dpi=300)
-
    
+fig.savefig('testing_streamline.png',dpi=300)
    
 
    
 ../../_images/testing_streamline.png
 
@@ -233,7 +232,7 @@ 
    Navigation
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  • MDAnalysis 1.0.0-dev documentation »
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+        
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@@ -245,7 +244,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/visualization/streamlines_3D.html b/package/doc/html/documentation_pages/visualization/streamlines_3D.html
index 6a5b2f936f6..5801e41fe98 100644
--- a/package/doc/html/documentation_pages/visualization/streamlines_3D.html
+++ b/package/doc/html/documentation_pages/visualization/streamlines_3D.html
@@ -6,7 +6,7 @@
   
     
-    9.1.2. 3D Streamplot — MDAnalysis 1.0.0-dev documentation
+    9.1.2. 3D Streamplot — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
-    
+    
@@ -45,7 +45,7 @@ 
    Navigation
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           previous |
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+        
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    • 
@@ -235,7 +235,7 @@ 
    Navigation
  • 
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  • MDAnalysis 1.0.0-dev documentation »
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+        
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    • 
@@ -247,7 +247,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
\ No newline at end of file
diff --git a/package/doc/html/documentation_pages/visualization_modules.html b/package/doc/html/documentation_pages/visualization_modules.html
index ced754269f6..29a9529ccc2 100644
--- a/package/doc/html/documentation_pages/visualization_modules.html
+++ b/package/doc/html/documentation_pages/visualization_modules.html
@@ -6,7 +6,7 @@
   
     
-    9. Visualization modules — MDAnalysis 1.0.0-dev documentation
+    9. Visualization modules — MDAnalysis 0.9.1 documentation
@@ -14,7 +14,7 @@
     
-    
+    
@@ -48,7 +48,7 @@ 
    Navigation
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@@ -59,7 +59,9 @@ 
    Navigation
    
   
    Table Of Contents
    
   
@@ -140,7 +142,7 @@ 
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+        
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@@ -151,7 +153,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
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diff --git a/package/doc/html/genindex.html b/package/doc/html/genindex.html
index 238df92870d..959b699d4f0 100644
--- a/package/doc/html/genindex.html
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-    Index — MDAnalysis 1.0.0-dev documentation
+    Index — MDAnalysis 0.9.1 documentation
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@@ -287,6 +287,16 @@ 
    A
    
   
    angles (MDAnalysis.core.AtomGroup.Atom attribute), [1]
   
    
 
+      
    
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+  
    
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@@ -429,6 +439,16 @@ 
    B
    
   
    bonds (MDAnalysis.core.AtomGroup.Atom attribute), [1]
   
    
 
+      
    
+        
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    F
    
   
    flagsDocs (class in MDAnalysis.core.__init__)
   
    
 
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@@ -1893,6 +1913,16 @@ 
    F
    
   
 
       
+  
    fragments (MDAnalysis.core.AtomGroup.AtomGroup attribute)
+  
    
+
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+        
+  
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@@ -2246,10 +2276,26 @@ 
    I
    
   
    impropers (MDAnalysis.core.AtomGroup.Atom attribute)
   
    
 
+      
    
+        
+  
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+  
    
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+  
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+  
    
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+  
    indices() (MDAnalysis.core.AtomGroup.AtomGroup method)
+  
    
+
       
   
    InnerProduct() (in module MDAnalysis.core.qcprot)
   
    
 
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    IObase (class in MDAnalysis.coordinates.base)
   
    
@@ -2407,6 +2451,10 @@ 
    M
    
   
 
       
+  
    masses() (MDAnalysis.core.AtomGroup.AtomGroup method)
+  
    
+
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    matrix() (MDAnalysis.core.transformations.Arcball method)
   
    
 
@@ -2554,12 +2602,12 @@ 
    M
    
   
    MDAnalysis.core.__init__ (module)
   
    
 
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    reset() (MDAnalysis.core.util.NamedStream method)
   
    
 
-  
    
       
   
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    resids() (MDAnalysis.core.AtomGroup.AtomGroup method)
   
    
@@ -3413,6 +3461,10 @@ 
    R
    
   
 
       
+  
    residues (MDAnalysis.core.AtomGroup.AtomGroup attribute)
+  
    
+
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    resname (MDAnalysis.core.AtomGroup.Atom attribute)
   
    
 
@@ -3699,6 +3751,10 @@ 
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+  
    segments (MDAnalysis.core.AtomGroup.AtomGroup attribute)
+  
    
+
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    selectAtoms() (MDAnalysis.core.AtomGroup.AtomGroup method)
   
    
 
@@ -4111,6 +4167,10 @@ 
    T
    
 
       
    
       
+  
    topDict (MDAnalysis.topology.core.TopologyGroup attribute)
+  
    
+
+      
   
    TopologyDict (class in MDAnalysis.topology.core)
   
    
 
@@ -4168,6 +4228,16 @@ 
    T
    
   
    torsions (MDAnalysis.core.AtomGroup.Atom attribute), [1]
   
    
 
+      
    
+        
+  
    (MDAnalysis.core.AtomGroup.AtomGroup attribute)
+  
    
+
+        
+  
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+  
    
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    torsions() (MDAnalysis.topology.core.TopologyGroup method)
   
    
@@ -4775,7 +4845,7 @@ 
    Navigation
    
         
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           modules |
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-        
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    •  
+        
  • MDAnalysis 0.9.1 documentation »
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@@ -4786,7 +4856,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
   
 
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diff --git a/package/doc/html/index.html b/package/doc/html/index.html
index b22963ff378..ea897ac3f6d 100644
--- a/package/doc/html/index.html
+++ b/package/doc/html/index.html
@@ -6,7 +6,7 @@
   
     
     
-    MDAnalysis documentation — MDAnalysis 1.0.0-dev documentation
+    MDAnalysis documentation — MDAnalysis 0.9.1 documentation
     
     
     
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+    
      
   
   
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@@ -56,7 +56,9 @@ 
    Table Of Contents
    
   
    
 
    Release:1.0.0-dev
    Release:0.9.1
 
    Date:March 17, 2015
    Date:March 27, 2015
 
    
     
 
    
@@ -201,7 +203,7 @@ 
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@@ -212,7 +214,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
   
 
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diff --git a/package/doc/html/objects.inv b/package/doc/html/objects.inv
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diff --git a/package/doc/html/py-modindex.html b/package/doc/html/py-modindex.html
index 7eef2045e44..91525d09821 100644
--- a/package/doc/html/py-modindex.html
+++ b/package/doc/html/py-modindex.html
@@ -6,7 +6,7 @@
   
     
     
-    Python Module Index — MDAnalysis 1.0.0-dev documentation
+    Python Module Index — MDAnalysis 0.9.1 documentation
     
     
     
@@ -14,7 +14,7 @@
     
     
     
     
-    
+    
  
 
 
@@ -43,7 +43,7 @@ 
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@@ -456,7 +456,7 @@ 
    Navigation
    
         
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           modules |
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-        
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+        
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@@ -467,7 +467,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
   
 
\ No newline at end of file
diff --git a/package/doc/html/search.html b/package/doc/html/search.html
index 5099a6040eb..43a649e7c2f 100644
--- a/package/doc/html/search.html
+++ b/package/doc/html/search.html
@@ -6,7 +6,7 @@
   
     
     
-    Search — MDAnalysis 1.0.0-dev documentation
+    Search — MDAnalysis 0.9.1 documentation
     
     
     
@@ -14,7 +14,7 @@
     
     
     
     
-    
+    
   
@@ -48,7 +48,7 @@ 
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@@ -113,7 +113,7 @@ 
    Navigation
    
     Benjamin Hall, Joe Jordan, Jinju Lu, Robert McGibbon,
     Manuel Nuno Melo, Danny Parton, Joshua L. Phillips, Tyler Reddy, Paul Rigor, Andy Somogyi,
     Lukas Stelzl, Zhuyi Xue, and Oliver Beckstein.
-      Created using Sphinx 1.2.3.
+      Created using Sphinx 1.2.
     
    
   
 
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diff --git a/package/doc/html/searchindex.js b/package/doc/html/searchindex.js
index 7eb7654ccdc..ddbc56c10cf 100644
--- a/package/doc/html/searchindex.js
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@@ -1 +1 @@
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,32,35,36,38,39,41,43,44,46,47,48,49,50,79,53,54,20,56,57,58,59,60,62,64,65,66,67,68,69,70,71,72,34,1,76,78],cal:77,run_x3dna:26,purpos:[9,2,56],qsalt:49,major_pair:21,nremark:2,favourit:25,nclal:77,stream:4,slightli:[38,35],search_list:56,biopolym:53,sph:2,tabl:[72,36],surround:36,spc:[48,9,72,47,15],shoemak:60,verlag:3,orthorhomb:[65,7,48,64,68,38],alwai:[3,4,47,51,9,15,18,23,1,32,58,41,44,46,48,64,79,55,35,62,49,66,69,72,76],differenti:53,selection_1_typ:72,multipl:[14,9,2,49],tilt:[53,26],clustalw2:36,pathwai:49,endmdl:35,write:[0,1,2,4,7,10,11,12,15,16,18,19,22,23,25,27,32,33,35,36,39,40,41,44,46,48,49,50,79,31,58,59,62,64,66,67,69,76],cmap:2,criterion:[55,72],dcdreader:[41,76,4,55,66,35],pure:[71,36,42,38,35],lower_bound:71,nyb:77,parameter:72,map:[8,36,2,79,69],remap:9,max:[18,23,44,1,69,32,66,61,76],chi1:48,rmax:2,usabl:[32,12],mac:49,"4th":65,fit_tilt:53,divx:49,mai:[18,2,23,32,5,47,69,48,9,50,79,41,56],unit_twist:53,nobl:77,data:[53,3,49,78,43,9,72],x3dna_param:26,array_lik:60,explicit:[71,4],inform:[28,2,70,51,13,18,23,1,32,41,42,44,48,64,50,7,20,31,35,59,65,66,71,72,76,34],"switch":[68,72,79],preced:[9,53,73],combin:[2,44,26,49,36,66,76],fasta2select:[36,39],thirumalai:48,ordinari:69,epydoc:60,zmax:[48,54,47],mol2pars:20,cutoff:[78,47,7,48,9,72,68],record2:48,exdrmag:58,record1:48,classifi:[53,2],nitrogen:21,still:[18,59,2,23,32,1,76,73,35],pointer:[18,59,23,32,1,48,58],mobile_on_ref:36,dynam:[19,41,60,9,79,2,55],entiti:[56,35],velavan:[19,53],overhaul:71,monitor:[14,78],apex:[48,65,72,71],window:[60,53],requir:[41,23,65,32,48,9,50,44,14,35,36,34,58],"_get_bonded_hydrogens_dist":72,mail:19,main:[9,72,23],basenam:49,all_get_radii:3,errorsymbol:8,non:[60,22,71,4,5,47,27,69,48,64,72,11,12,33],"float":[60,77,3,46,69,48,9,54,61,36,56,31,58],jame:60,initi:[2,4,47,7,9,12,14,18,23,26,32,41,44,60,64,50,79,20,35,59,48,62,69],bound:[48,72],tilt_filenam:53,half:[65,6],now:[18,59,2,23,49,65,32,1,48,9,10,72,71,66,35,76,58],hall:[19,53,78],nor:[48,50,17,35],introduct:55,current_rmsd:62,term:[71,49,53,12],amino_acid_cod:69,rmsf:[9,39],name:[9,49,36,56,78],rmsd:36,rmsfit:36,revers:[71,67],oliv:[2,3,49,67,7,9,72,53,36,39],linspac:61,separ:[77,41,46,26,47,48,49,69,30,2,20,35],akma:[66,15,41,76],attributeerror:[44,41],helanal_:53,"602176565e":15,citat:[54,13,61,34],replac:[41,71,78,2,69,48,62,35],individu:[2,4,11,12,13,20,22,25,26,27,55,78,33,36,43,44,48,68,58,53,71,34],table_mass:77,box_orthorhomb:10,intermitt:14,hb_ac:14,order_list:78,xyzwrit:[50,41],significantli:[18,59,23,32,1,79,58],year:[53,21,3,43,78,67,26,7,9,49,72,38,14,2,54,61,36,57,39],happen:[48,32,47,23,35],sel_acid:49,shown:[62,2,26],selection1:72,selection2:72,space:[53,61,2,50,23,64,65,44,46,47,72,69,48,9,77,30,54,41,35,58],storag:[2,57,58],formula:15,correct:[41,71,6,69,48,49,72,79,76],integr:[40,41,76,26,14,66],state:[19,62,60,78,48,49,79,55],variant:30,water_oxygen:48,orn:73,california:60,argn:73,dcdfilenam:[66,76,79],org:[67,49,4,31,35],"byte":[69,58],nucleicxstalselect:73,card:[55,41,45,2,20,16],care:[2,46,48,24,17,58],funki:9,kaufmann:60,wai:[41,60,2,22,11,49,78,47,27,69,48,9,72,7,12,33,55,36,79],groupselect:39,question:[19,69,21,49],prescrib:9,frequenc:[19,68,72,78,32],insert:[49,5,79,31,35],get_radii:[46,3],recov:60,turn:[53,2],place:[18,60,2,23,44,1,69,48,9,10,32,66,41,76,57],nist:15,residuenam:46,principl:64,crystallographica:[19,57],first:[0,2,3,4,6,7,77,54,21,23,26,32,61,36,39,41,44,46,47,48,49,50,20,31,35,60,64,71,66,69,72,76],oper:[73,65,47,48,9,35,71,55,58,39],totallength:69,directli:[41,64,44,47,48,49,72,79,78,20,58],carri:[60,48,15,13,56,34],onc:[62,71,47,69,9,72,35],arrai:[3,4,6,9,14,18,23,1,32,58,36,39,40,41,44,46,48,49,68,56,31,35,59,66,75,76,73],"_check_pdb_coordin":35,yourself:[48,49],"long":[18,59,53,23,32,1,48],symmetri:48,modulo:67,ring:21,open:[18,40,2,23,64,44,59,1,26,72,49,50,32,41,76,78,39],predefin:[48,71],intermolecular:14,size:[2,4,7,9,54,18,23,1,78,36,39,41,44,60,56,57,58,59,48,66,69,32,76],given:[18,59,2,3,23,43,71,32,1,47,69,48,9,49,72,14,56],rightmost:60,silent:62,workaround:76,fmt:[10,69],imshow:49,eachoth:71,cumul:44,draft:41,averag:[2,32,49,14,55,36,39],circl:53,"66053892103219e":15,desmond:[63,52],white:[77,46,41,69],conveni:[41,44,48,9,79,2,76],cite:[53,19,36,39],prettier:49,alad:73,especi:[76,48,49,72,15,66],pittsburgh:57,copi:[18,2,23,44,1,48,64,32,66,41,68,76],histogramdd:9,artifact:9,broadcast:48,arbitrari:[2,49,26,48,9,62,36,58],"short":[18,2,23,44,1,48,32,66,55,76],enclos:48,mostli:[48,71],sugeta:53,attempt:[18,2,32,69,48,66,15,76],savetxt:39,than:[2,3,47,9,10,14,16,23,36,38,39,42,32,46,48,64,50,79,68,35,53,49,71,69,72],png:[54,49,61],molfil:[76,50],serv:35,wide:2,update_select:72,follw:67,u_eq_adk:55,timesteps_by_typ:72,s4ake:[48,55,47],radiusofgyr:[48,55,7],balanc:7,were:[18,3,32,47,48,50,79,66,72,35,76,58],posit:[2,6,9,15,18,55,21,23,1,32,36,41,44,47,48,64,68,56,58,59,66,69,72,75,76,78],set_ylabel:[61,39],seri:[60,49,55,6],sai:[48,41],san:[3,43],angel:42,pro:73,argument:[0,28,2,4,47,7,9,10,11,12,14,1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diff --git a/package/setup.py b/package/setup.py
index 9f23fd503de..0bc6d652c43 100755
--- a/package/setup.py
+++ b/package/setup.py
@@ -172,7 +172,7 @@ def detect_openmp():
 
 
 if __name__ == '__main__':
-    RELEASE = "1.0.0-dev"  # NOTE: keep in sync with MDAnalysis.version in __init__.py
+    RELEASE = "0.9.1"  # NOTE: keep in sync with MDAnalysis.version in __init__.py
     with open("SUMMARY.txt") as summary:
         LONG_DESCRIPTION = summary.read()
     CLASSIFIERS = [
diff --git a/testsuite/MDAnalysisTests/__init__.py b/testsuite/MDAnalysisTests/__init__.py
index 39ce8cb6379..cb9dd691b62 100644
--- a/testsuite/MDAnalysisTests/__init__.py
+++ b/testsuite/MDAnalysisTests/__init__.py
@@ -101,7 +101,7 @@
 .. _Gromacs: http://www.gromacs.org
 """
 
-__version__ = "1.0.0-dev"  # keep in sync with RELEASE in setup.py
+__version__ = "0.9.1"  # keep in sync with RELEASE in setup.py
 
 try:
     from numpy.testing import Tester
diff --git a/testsuite/setup.py b/testsuite/setup.py
index 954bdbe2cdf..5ee989482ba 100755
--- a/testsuite/setup.py
+++ b/testsuite/setup.py
@@ -63,7 +63,7 @@
 
 
 if __name__ == '__main__':
-    RELEASE = "1.0.0-dev"  # this must be in-sync with MDAnalysis
+    RELEASE = "0.9.1"  # this must be in-sync with MDAnalysis
     LONG_DESCRIPTION = \
         """MDAnalysis is a tool for analyzing molecular dynamics trajectories.