fixed multiple typos in python files

Author: jyothiswaroopch

package/MDAnalysis/analysis/align.py

@@ -1393,7 +1393,7 @@ def fasta2select(
         substitutes the suffix with '.aln'.
     treefilename: str (optional)
         filename of ClustalW guide tree (Newick format);
-        if default ``None``  the the filename is generated from *alnfilename*
+        if default ``None``  the filename is generated from *alnfilename*
         with the suffix '.dnd' instead of '.aln'
     clustalw : str (optional)
         path to the ClustalW (or ClustalW2) binary; only

package/MDAnalysis/analysis/dielectric.py

@@ -86,17 +86,17 @@ class DielectricConstant(AnalysisBase):
     Attributes
     ----------
     results.M : numpy.ndarray
-      Directional dependant dipole moment
+      Directional dependent dipole moment
       :math:`\langle \boldsymbol M \rangle` in :math:`eÅ`.
     results.M2 : numpy.ndarray
-      Directional dependant squared dipole moment
+      Directional dependent squared dipole moment
       :math:`\langle \boldsymbol M^2 \rangle` in :math:`(eÅ)^2`
     results.fluct : float
-      Directional dependant dipole moment fluctuation
+      Directional dependent dipole moment fluctuation
       :math:`\langle \boldsymbol M^2 \rangle - \langle \boldsymbol M \rangle^2`
       in :math:`(eÅ)^2`
     results.eps : numpy.ndarray
-      Directional dependant static dielectric constant
+      Directional dependent static dielectric constant
     results.eps_mean : float
       Static dielectric constant
 

package/MDAnalysis/analysis/encore/covariance.py

@@ -48,7 +48,7 @@ def ml_covariance_estimator(coordinates, reference_coordinates=None):
     ----------
 
     coordinates : numpy.array
-        Flattened array of coordiantes
+        Flattened array of coordinates
 
     reference_coordinates : numpy.array
         Optional reference to use instead of mean

package/MDAnalysis/analysis/encore/utils.py

@@ -332,7 +332,7 @@ def run(self):
 
 def trm_indices(a, b):
     """
-    Generate (i,j) indeces of a triangular matrix, between elements a and b.
+    Generate (i,j) indices of a triangular matrix, between elements a and b.
     The matrix size is automatically determined from the number of elements.
     For instance: trm_indices((0,0),(2,1)) yields (0,0) (1,0) (1,1) (2,0)
     (2,1).
@@ -361,7 +361,7 @@ def trm_indices(a, b):
 
 
 def trm_indices_nodiag(n):
-    """generate (i,j) indeces of a triangular matrix of n rows (or columns),
+    """generate (i,j) indices of a triangular matrix of n rows (or columns),
     without diagonal (e.g. no elements (0,0),(1,1),...,(n,n))
 
     Parameters
@@ -377,7 +377,7 @@ def trm_indices_nodiag(n):
 
 
 def trm_indices_diag(n):
-    """generate (i,j) indeces of a triangular matrix of n rows (or columns),
+    """generate (i,j) indices of a triangular matrix of n rows (or columns),
     with diagonal
 
     Parameters

package/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py

@@ -1583,7 +1583,7 @@ def add_route(result, route):
             if len(route) == 1:
                 result["start"][route[0]] = None
             else:
-                # exclude the the selection which goes back to itself
+                # exclude the selection which goes back to itself
                 if sorted(route[0][0:3:2]) == sorted(route[-1][0:3:2]):
                     return
 

package/MDAnalysis/analysis/legacy/x3dna.py

@@ -521,7 +521,7 @@ def std(self):
     def plot(self, **kwargs):
         """Plot time-averaged base parameters for each basse pair in a 1D graph.
 
-        One plot is produced for each parameter. It shows the the mean and
+        One plot is produced for each parameter. It shows the mean and
         standard deviation for each individual base pair. Each plot is saved to
         PNG file with name "<parameter_name>.png".
 

package/MDAnalysis/analysis/msd.py

@@ -174,7 +174,7 @@
 excluded along with poorly averaged data at long time-lags. We can select the
 "middle" of the MSD by indexing the MSD and the time-lags. Appropriately
 linear segments of the MSD can be confirmed with a log-log plot as is often
-reccomended :footcite:p:`Maginn2019` where the "middle" segment can be identified
+recommended :footcite:p:`Maginn2019` where the "middle" segment can be identified
 as having a slope of 1.
 
 .. code-block:: python

package/MDAnalysis/analysis/rdf.py

@@ -155,7 +155,7 @@ class InterRDF(AnalysisBase):
           For 'rdf' calculate :math:`g_{ab}(r)`. For
           'density' the :ref:`single particle density<equation-nab>`
           :math:`n_{ab}(r)` is computed. 'none' computes the number of
-          particles occurences in each spherical shell.
+          particles occurrences in each spherical shell.
 
           .. versionadded:: 2.3.0
 
@@ -476,7 +476,7 @@ class InterRDF_s(AnalysisBase):
         For 'rdf' calculate :math:`g_{ab}(r)`. For
         'density' the :ref:`single particle density<equation-nab>`
         :math:`n_{ab}(r)` is computed. 'none' computes the number of
-        particles occurences in each spherical shell.
+        particles occurrences in each spherical shell.
 
         .. versionadded:: 2.3.0
 

package/MDAnalysis/analysis/rms.py

@@ -859,7 +859,7 @@ def __init__(self, atomgroup, **kwargs):
         ------
         ValueError
              raised if negative values are calculated, which indicates that a
-             numerical overflow or underflow occured
+             numerical overflow or underflow occurred
 
 
         Notes

package/MDAnalysis/auxiliary/base.py

@@ -1033,7 +1033,7 @@ def data_selector(self):
 
         Type differs between auxiliary formats, depending how the data for each
         step is read in and stored - e.g. data from .xvg files is read in as
-        a list and `data_selector` must be a list of valid indicies. If data
+        a list and `data_selector` must be a list of valid indices. If data
         selection is not enabled by the reader, ``data_selector`` will default
         to ``None``.