fixed multiple typos in python files

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``.
 

package/MDAnalysis/converters/RDKitInferring.py

@@ -234,7 +234,7 @@ def _infer_bo_and_charges(cls, mol: "Chem.Mol") -> None:
 
         Notes
         -----
-        This algorithm is order dependant. For example, for a carboxylate group
+        This algorithm is order dependent. For example, for a carboxylate group
         ``R-C(-O)-O`` the first oxygen read will receive a double bond and the
         other one will be charged. It will also affect more complex conjugated
         systems.

package/MDAnalysis/coordinates/H5MD.py

@@ -765,7 +765,7 @@ def _read_dataset_into_ts(self, dataset, attribute):
             raise ValueError(
                 f"Frame {self._frame} of the {dataset} dataset"
                 f" has {n_atoms_now} atoms but the initial frame"
-                " of either the postion, velocity, or force"
+                " of either the position, velocity, or force"
                 f" dataset had {self.n_atoms} atoms."
                 " MDAnalysis is unable to deal"
                 " with variable topology!"

package/MDAnalysis/coordinates/PQR.py

@@ -64,7 +64,7 @@
 *residueNumber*
     An integer which provides the residue index.
 *X Y Z*
-    Three floats which provide the atomic coordiantes.
+    Three floats which provide the atomic coordinates.
 *charge*
     A float which provides the atomic charge (in electrons).
 *radius*

package/MDAnalysis/coordinates/TRC.py

@@ -261,7 +261,7 @@ def _read_traj_properties(self):
                         # writers do actually produce trailing whitespace.
                         # By default we try to assume a consistent size of the
                         # POSITIONRED block. We then try to skip reading subsequent
-                        # occurences of this block.
+                        # occurrences of this block.
                         # If we end up somewhere unexpected, we will throw
                         # a warning and fall back to iterating over the file.
 

package/MDAnalysis/coordinates/__init__.py

@@ -81,7 +81,7 @@ class that defines a common :ref:`Trajectory API` and allows other code to
 Normally, one does not explicitly need to select a reader. This is handled
 automatically when creating a :class:`~MDAnalysis.core.universe.Universe` and
 the appropriate reader for the file type is selected (typically by the file
-extension but this choice can be overriden with the ``format`` argument to
+extension but this choice can be overridden with the ``format`` argument to
 :class:`~MDAnalysis.core.universe.Universe`).
 
 If additional simulation data is available, it may be added to and read
@@ -475,7 +475,7 @@ class can choose an appropriate reader automatically.
 from a subclass of :class:`~MDAnalysis.coordinates.base.ProtoReader` named
 :class:`MDAnalysis.coordinates.base.SingleFrameReaderBase`.
 
-Typically, many methods and attributes are overriden but the ones listed below
+Typically, many methods and attributes are overridden but the ones listed below
 *must* be implemented.
 
 .. SeeAlso::
@@ -674,7 +674,7 @@ class can choose an appropriate reader automatically.
 :meth:`~MDAnalysis.coordinates.base.WriterBase.write` method is called,
 another frame is appended to the trajectory.
 
-Typically, many methods and attributes are overriden.
+Typically, many methods and attributes are overridden.
 
 Signature::
 

package/MDAnalysis/coordinates/base.py

@@ -1175,7 +1175,7 @@ def aux_list(self):
         return self._auxs.keys()
 
     def _check_for_aux(self, auxname):
-        """ Check for the existance of an auxiliary *auxname*. If present,
+        """ Check for the existence of an auxiliary *auxname*. If present,
         return the AuxReader; if not, raise ValueError
         """
         if auxname in self.aux_list:
@@ -1576,7 +1576,7 @@ def convert_dimensions_to_unitcell(self, ts, inplace=True):
         """Read dimensions from timestep *ts* and return appropriate unitcell.
 
         The default is to return ``[A,B,C,alpha,beta,gamma]``; if this
-        is not appropriate then this method has to be overriden.
+        is not appropriate then this method has to be overridden.
         """
         # override if the native trajectory format does NOT use
         # [A,B,C,alpha,beta,gamma]

package/MDAnalysis/coordinates/memory.py

@@ -318,7 +318,7 @@ def __init__(
         self._kwargs = kwargs
 
         # See Issue #1685. The block below checks if the coordinate array
-        # passed is of shape (N, 3) and if it is, the coordiante array is
+        # passed is of shape (N, 3) and if it is, the coordinate array is
         # reshaped to (1, N, 3)
         try:
             if coordinate_array.ndim == 2 and coordinate_array.shape[1] == 3:

package/MDAnalysis/core/groups.py

@@ -2344,7 +2344,7 @@ def subtract(self, other):
 
         The original order of this group is kept, as well as any duplicate
         elements. If an element of this Group is duplicated and appears in
-        the other Group or Component, then all the occurences of that element
+        the other Group or Component, then all the occurrences of that element
         are removed from the returned Group.
 
         Parameters

package/MDAnalysis/core/topologyattrs.py

@@ -706,7 +706,7 @@ def set_atoms(self, ag, values):
 
     def get_residues(self, rg):
         """By default, the values for each atom present in the set of residues
-        are returned in a single array. This behavior can be overriden in child
+        are returned in a single array. This behavior can be overridden in child
         attributes.
 
         """
@@ -718,7 +718,7 @@ def set_residues(self, rg, values):
 
     def get_segments(self, sg):
         """By default, the values for each atom present in the set of residues
-        are returned in a single array. This behavior can be overriden in child
+        are returned in a single array. This behavior can be overridden in child
         attributes.
 
         """
@@ -2636,7 +2636,7 @@ def quadrupole_moment(group, **kwargs):
         accordingly.
 
         Note that when there is an unsymmetrical plane in the molecule or 
-        group, the magnitude of the quadrupole moment is dependant on the 
+        group, the magnitude of the quadrupole moment is dependent on the 
         ``center`` chosen and cannot be translated.
 
         Parameters
@@ -2867,7 +2867,7 @@ def set_residues(self, rg, values):
 
     def get_segments(self, sg):
         """By default, the values for each residue present in the set of
-        segments are returned in a single array. This behavior can be overriden
+        segments are returned in a single array. This behavior can be overridden
         in child attributes.
 
         """

package/MDAnalysis/guesser/tables.py

@@ -62,7 +62,7 @@ def kv2dict(s, convertor: Any = str):
 
     * Leading whitespace is ignored.
 
-    The *convertor* is a function that converts its single argument to
+    The *converter* is a function that converts its single argument to
     a valid Python type. The default is :func:`str` but other
     possibilities are :func:`int` (for integers) or :func:`float` for
     floating point numbers.

package/MDAnalysis/lib/correlations.py

@@ -129,7 +129,7 @@ def autocorrelation(list_of_sets, tau_max, window_step=1):
         the autocorelation values for each of the tau values
     timeseries_data : list of list of int
         the raw data from which the autocorrelation is computed, i.e :math:`S(\tau)` at each window.
-        This allows the time dependant evolution of :math:`S(\tau)` to be investigated.
+        This allows the time dependent evolution of :math:`S(\tau)` to be investigated.
 
     .. versionadded:: 0.19.2
     """

package/MDAnalysis/lib/distances.py

@@ -1605,7 +1605,7 @@ def transform_RtoS(coords, box, backend="serial"):
     Returns
     -------
     newcoords : numpy.ndarray (``dtype=numpy.float32``, ``shape=coords.shape``)
-        An array containing fractional coordiantes.
+        An array containing fractional coordinates.
 
 
     .. versionchanged:: 0.13.0
@@ -1654,7 +1654,7 @@ def transform_StoR(coords, box, backend="serial"):
     Returns
     -------
     newcoords : numpy.ndarray (``dtype=numpy.float32``, ``shape=coords.shape``)
-        An array containing real space coordiantes.
+        An array containing real space coordinates.
 
 
     .. versionchanged:: 0.13.0

package/MDAnalysis/topology/ITPParser.py

@@ -543,7 +543,7 @@ def parse(
             Default: "/usr/local/gromacs/share/gromacs/top/"
 
         infer_system: bool, optional (default True)
-            If a ``[ molecules ]`` directive is not found within the the
+            If a ``[ molecules ]`` directive is not found within the
             topology file, create a Topology with one of every
             ``[ moleculetype ]`` defined. If a ``[ molecules ]`` directive is
             found, this keyword is ignored.

package/MDAnalysis/topology/PDBParser.py

@@ -454,7 +454,7 @@ def _parsebonds(self, serials):
                           " be parsed")
             raise AttributeError  # gets caught in parse
 
-        # Mapping between the atom array indicies a.index and atom ids
+        # Mapping between the atom array indices a.index and atom ids
         # (serial) in the original PDB file
         mapping = dict((s, i) for i, s in enumerate(serials))
 

package/MDAnalysis/topology/PSFParser.py

@@ -225,7 +225,7 @@ def _parseatoms(self, lines, atoms_per, numlines):
         http://www.ks.uiuc.edu/Research/vmd/current/devel.html :
 
         psfplugin: Added more logic to the PSF plugin to determine cases where the
-        CHARMM "EXTended" PSF format cannot accomodate long atom types, and we add
+        CHARMM "EXTended" PSF format cannot accommodate long atom types, and we add
         a "NAMD" keyword to the PSF file flags line at the top of the file. Upon
         reading, if we detect the "NAMD" flag there, we know that it is possible
         to parse the file correctly using a simple space-delimited scanf() format

package/MDAnalysis/visualization/streamlines.py

@@ -31,7 +31,7 @@
 
 The :func:`generate_streamlines` function can generate a 2D flow field from a
 MD trajectory, for instance, lipid molecules in a flat membrane. It can make
-use of multiple cores to perform the analyis in parallel (using
+use of multiple cores to perform the analysis in parallel (using
 :mod:`multiprocessing`).
 
 See Also

package/MDAnalysis/visualization/streamlines_3D.py

@@ -31,7 +31,7 @@
 
 The :func:`generate_streamlines_3d` function can generate a 3D flow field from
 a MD trajectory, for instance, lipid molecules in a virus capsid. It can make
-use of multiple cores to perform the analyis in parallel (using
+use of multiple cores to perform the analysis in parallel (using
 :mod:`multiprocessing`).
 
 .. rubric: References