diff --git a/package/MDAnalysis/analysis/align.py b/package/MDAnalysis/analysis/align.py index 3dc4f84fb1d..1ae5875b4ab 100644 --- a/package/MDAnalysis/analysis/align.py +++ b/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 diff --git a/package/MDAnalysis/analysis/dielectric.py b/package/MDAnalysis/analysis/dielectric.py index 28a22b5116b..77ffd160255 100644 --- a/package/MDAnalysis/analysis/dielectric.py +++ b/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 diff --git a/package/MDAnalysis/analysis/encore/covariance.py b/package/MDAnalysis/analysis/encore/covariance.py index 08e014e315c..ddd76627802 100644 --- a/package/MDAnalysis/analysis/encore/covariance.py +++ b/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 diff --git a/package/MDAnalysis/analysis/encore/utils.py b/package/MDAnalysis/analysis/encore/utils.py index ae6407ddd19..a01681dab53 100644 --- a/package/MDAnalysis/analysis/encore/utils.py +++ b/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 diff --git a/package/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py b/package/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py index 027c0b71255..ec68e5fd9ec 100644 --- a/package/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py +++ b/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 diff --git a/package/MDAnalysis/analysis/legacy/x3dna.py b/package/MDAnalysis/analysis/legacy/x3dna.py index 2365c181133..df2fe7a9e52 100644 --- a/package/MDAnalysis/analysis/legacy/x3dna.py +++ b/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 ".png". diff --git a/package/MDAnalysis/analysis/msd.py b/package/MDAnalysis/analysis/msd.py index 814ea37bed3..50fbb45422e 100644 --- a/package/MDAnalysis/analysis/msd.py +++ b/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 diff --git a/package/MDAnalysis/analysis/rdf.py b/package/MDAnalysis/analysis/rdf.py index eef8a6a86ea..8c3b5cf8680 100644 --- a/package/MDAnalysis/analysis/rdf.py +++ b/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` :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` :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 diff --git a/package/MDAnalysis/analysis/rms.py b/package/MDAnalysis/analysis/rms.py index f589a597d0a..11c696efe8f 100644 --- a/package/MDAnalysis/analysis/rms.py +++ b/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 diff --git a/package/MDAnalysis/auxiliary/base.py b/package/MDAnalysis/auxiliary/base.py index 29fbaf999a2..bf65845cffe 100644 --- a/package/MDAnalysis/auxiliary/base.py +++ b/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``. diff --git a/package/MDAnalysis/converters/RDKitInferring.py b/package/MDAnalysis/converters/RDKitInferring.py index 843986371af..33bd8267cca 100644 --- a/package/MDAnalysis/converters/RDKitInferring.py +++ b/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. diff --git a/package/MDAnalysis/coordinates/H5MD.py b/package/MDAnalysis/coordinates/H5MD.py index c597c36e4a4..eee2ffad02d 100644 --- a/package/MDAnalysis/coordinates/H5MD.py +++ b/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!" diff --git a/package/MDAnalysis/coordinates/PQR.py b/package/MDAnalysis/coordinates/PQR.py index a2f5a119f72..3f6ece49656 100644 --- a/package/MDAnalysis/coordinates/PQR.py +++ b/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* diff --git a/package/MDAnalysis/coordinates/TRC.py b/package/MDAnalysis/coordinates/TRC.py index 4c7c4009ec7..1010773ae3a 100644 --- a/package/MDAnalysis/coordinates/TRC.py +++ b/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. diff --git a/package/MDAnalysis/coordinates/__init__.py b/package/MDAnalysis/coordinates/__init__.py index f81c4915514..d844d4a2002 100644 --- a/package/MDAnalysis/coordinates/__init__.py +++ b/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:: diff --git a/package/MDAnalysis/coordinates/base.py b/package/MDAnalysis/coordinates/base.py index d2bfbe63d2c..3df8f1569d2 100644 --- a/package/MDAnalysis/coordinates/base.py +++ b/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] diff --git a/package/MDAnalysis/coordinates/memory.py b/package/MDAnalysis/coordinates/memory.py index 07c31fa2258..73a56488977 100644 --- a/package/MDAnalysis/coordinates/memory.py +++ b/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: diff --git a/package/MDAnalysis/core/groups.py b/package/MDAnalysis/core/groups.py index aad2fb02f34..fad4b2fda97 100644 --- a/package/MDAnalysis/core/groups.py +++ b/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 diff --git a/package/MDAnalysis/core/topologyattrs.py b/package/MDAnalysis/core/topologyattrs.py index 359bd20c9c1..c0fbd6e2e73 100644 --- a/package/MDAnalysis/core/topologyattrs.py +++ b/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. """ diff --git a/package/MDAnalysis/guesser/tables.py b/package/MDAnalysis/guesser/tables.py index fb66ce6c133..28b9ba2c55c 100644 --- a/package/MDAnalysis/guesser/tables.py +++ b/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. diff --git a/package/MDAnalysis/lib/correlations.py b/package/MDAnalysis/lib/correlations.py index af14df99fd7..4b3ef41d05c 100644 --- a/package/MDAnalysis/lib/correlations.py +++ b/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 """ diff --git a/package/MDAnalysis/lib/distances.py b/package/MDAnalysis/lib/distances.py index b3f862e005b..bac99365496 100644 --- a/package/MDAnalysis/lib/distances.py +++ b/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 diff --git a/package/MDAnalysis/topology/ITPParser.py b/package/MDAnalysis/topology/ITPParser.py index 1aa87b3864b..a88b50b4739 100644 --- a/package/MDAnalysis/topology/ITPParser.py +++ b/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. diff --git a/package/MDAnalysis/topology/PDBParser.py b/package/MDAnalysis/topology/PDBParser.py index b168b0a67ae..a02646dc5c0 100644 --- a/package/MDAnalysis/topology/PDBParser.py +++ b/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)) diff --git a/package/MDAnalysis/topology/PSFParser.py b/package/MDAnalysis/topology/PSFParser.py index 531c2ae592d..7494646fea3 100644 --- a/package/MDAnalysis/topology/PSFParser.py +++ b/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 diff --git a/package/MDAnalysis/visualization/streamlines.py b/package/MDAnalysis/visualization/streamlines.py index 12534a2e77c..328a1b4a3cd 100644 --- a/package/MDAnalysis/visualization/streamlines.py +++ b/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 diff --git a/package/MDAnalysis/visualization/streamlines_3D.py b/package/MDAnalysis/visualization/streamlines_3D.py index 4d2dace77bb..ad19d26d104 100644 --- a/package/MDAnalysis/visualization/streamlines_3D.py +++ b/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