diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml index 3b5fec63596..5ae17001de5 100644 --- a/.github/workflows/gh-ci.yaml +++ b/.github/workflows/gh-ci.yaml @@ -217,7 +217,7 @@ jobs: - name: install_deps run: | conda_deps="${{ env.MDA_CONDA_MIN_DEPS }} ${{ env.MDA_CONDA_EXTRA_DEPS}}" - pip_deps="${{ env.MDA_PIP_MIN_DEPS}} ${{ env.MDA_PIP_EXTRA_DEPS }} sphinx==1.8.5 sphinx-sitemap sphinx_rtd_theme msmb_theme==1.2.0" + pip_deps="${{ env.MDA_PIP_MIN_DEPS}} ${{ env.MDA_PIP_EXTRA_DEPS }} sphinx sphinx-sitemap sphinx_rtd_theme msmb_theme==1.2.0" mamba install ${conda_deps} pip install ${pip_deps} @@ -227,7 +227,7 @@ jobs: - name: build_docs run: | - cd package && python setup.py build_sphinx -E + cd package && python setup.py build_sphinx -E --keep-going - name: deploy_docs if: github.event_name != 'pull_request' diff --git a/package/CHANGELOG b/package/CHANGELOG index 7a286db998f..341d2c8dad5 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -13,7 +13,7 @@ The rules for this file: * release numbers follow "Semantic Versioning" http://semver.org ------------------------------------------------------------------------------ -??/??/?? IAlibay, melomcr, mdd31, ianmkenney, richardjgowers, hmacdope +??/??/?? IAlibay, melomcr, mdd31, ianmkenney, richardjgowers, hmacdope, orbeckst * 2.1.0 @@ -22,6 +22,7 @@ Fixes * TRRWriter preserves timestep data (Issue #3350). * Fixed Universe creation from a custom object which only provided a topology, previously raised a TypeError. (Issue #3443) + * Documentation fixes (Issues #3224, #2667) Enhancements * Add option for custom compiler flags for C/C++ on build and remove march diff --git a/package/MDAnalysis/analysis/density.py b/package/MDAnalysis/analysis/density.py index dda724726d9..aad7cfcb40f 100644 --- a/package/MDAnalysis/analysis/density.py +++ b/package/MDAnalysis/analysis/density.py @@ -102,13 +102,6 @@ :members: :inherited-members: run - .. attribute:: results.density - - After the analysis (see the :meth:`~DensityAnalysis.run` method), the - resulting density is stored in the :attr:`results.density` attribute as - a :class:`Density` instance. Note: this replaces the now deprecated - :attr:`density` attribute. - .. automethod:: _set_user_grid @@ -217,6 +210,11 @@ class DensityAnalysis(AnalysisBase): A :class:`Density` instance containing a physical density of units :math:`Angstrom^{-3}`. + After the analysis (see the :meth:`~DensityAnalysis.run` method), + the resulting density is stored in the :attr:`results.density` + attribute as a :class:`Density` instance. Note: this replaces the + now deprecated :attr:`density` attribute. + density : :class:`Density` Alias to the :attr:`results.density`. @@ -396,6 +394,7 @@ class DensityAnalysis(AnalysisBase): :func:`_set_user_grid` is now a method of :class:`DensityAnalysis`. :class:`Density` results are now stored in a :class:`MDAnalysis.analysis.base.Results` instance. + """ def __init__(self, atomgroup, delta=1.0, diff --git a/package/MDAnalysis/analysis/encore/similarity.py b/package/MDAnalysis/analysis/encore/similarity.py index c338ba28ee3..1b8b1df098d 100644 --- a/package/MDAnalysis/analysis/encore/similarity.py +++ b/package/MDAnalysis/analysis/encore/similarity.py @@ -20,7 +20,8 @@ # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 # -"""================================================================================= +""" +================================================================================= Ensemble Similarity Calculations --- :mod:`MDAnalysis.analysis.encore.similarity` ================================================================================= @@ -157,11 +158,13 @@ ================================== .. autofunction:: hes + :noindex: .. autofunction:: ces + :noindex: .. autofunction:: dres - + :noindex: Function reference ================== diff --git a/package/MDAnalysis/analysis/hole2/hole.py b/package/MDAnalysis/analysis/hole2/hole.py index 0063c39aea1..7536aa613c7 100644 --- a/package/MDAnalysis/analysis/hole2/hole.py +++ b/package/MDAnalysis/analysis/hole2/hole.py @@ -560,7 +560,7 @@ class HoleAnalysis(AnalysisBase): .. versionchanged:: 2.0.0 :attr:`sphpdbs`, :attr:`outfiles` and :attr:`profiles ` - are now stored in a :class:`MDAnalysis.analysis.base.Results` + are now stored in a :class:`MDAnalysis.analysis.base.Results` instance. """ @@ -1300,14 +1300,14 @@ def bin_radii(self, frames=None, bins=100, range=None): Profiles to include by frame. If ``None``, includes all frames. bins : int or iterable of edges, optional - If bins is an int, it defines the number of equal-width bins in the given - range. If bins is a sequence, it defines a monotonically increasing array of + If bins is an int, it defines the number of equal-width bins in the given + range. If bins is a sequence, it defines a monotonically increasing array of bin edges, including the rightmost edge, allowing for non-uniform bin widths. range : (float, float), optional The lower and upper range of the bins. If not provided, ``range`` is simply ``(a.min(), a.max())``, where ``a`` is the array of reaction coordinates. - Values outside the range are ignored. The first element of the range must be + Values outside the range are ignored. The first element of the range must be less than or equal to the second. @@ -1358,14 +1358,14 @@ def histogram_radii(self, aggregator=np.mean, frames=None, Profiles to include by frame. If ``None``, includes all frames. bins : int or iterable of edges, optional - If bins is an int, it defines the number of equal-width bins in the given - range. If bins is a sequence, it defines a monotonically increasing array of + If bins is an int, it defines the number of equal-width bins in the given + range. If bins is a sequence, it defines a monotonically increasing array of bin edges, including the rightmost edge, allowing for non-uniform bin widths. range : (float, float), optional The lower and upper range of the bins. If not provided, ``range`` is simply ``(a.min(), a.max())``, where ``a`` is the array of reaction coordinates. - Values outside the range are ignored. The first element of the range must be + Values outside the range are ignored. The first element of the range must be less than or equal to the second. @@ -1394,14 +1394,14 @@ def plot_mean_profile(self, bins=100, range=None, Profiles to include by frame. If ``None``, includes all frames. bins : int or iterable of edges, optional - If bins is an int, it defines the number of equal-width bins in the given - range. If bins is a sequence, it defines a monotonically increasing array of + If bins is an int, it defines the number of equal-width bins in the given + range. If bins is a sequence, it defines a monotonically increasing array of bin edges, including the rightmost edge, allowing for non-uniform bin widths. range : (float, float), optional The lower and upper range of the bins. If not provided, ``range`` is simply ``(a.min(), a.max())``, where ``a`` is the array of reaction coordinates. - Values outside the range are ignored. The first element of the range must be + Values outside the range are ignored. The first element of the range must be less than or equal to the second. color : str or array-like, optional Color for the plot. diff --git a/package/MDAnalysis/analysis/pca.py b/package/MDAnalysis/analysis/pca.py index c12d79e347c..a4066ed78be 100644 --- a/package/MDAnalysis/analysis/pca.py +++ b/package/MDAnalysis/analysis/pca.py @@ -208,14 +208,6 @@ class PCA(AnalysisBase): Will be removed in MDAnalysis 3.0.0. Please use :attr:`results.cumulated_variance` instead. - - Methods - ------- - transform(atomgroup, n_components=None) - Take an atomgroup or universe with the same number of atoms as was - used for the calculation in :meth:`PCA.run`, and project it onto the - principal components. - Notes ----- Computation can be sped up by supplying precalculated mean positions. diff --git a/package/MDAnalysis/coordinates/FHIAIMS.py b/package/MDAnalysis/coordinates/FHIAIMS.py index 6809adc9490..9077f0b0117 100644 --- a/package/MDAnalysis/coordinates/FHIAIMS.py +++ b/package/MDAnalysis/coordinates/FHIAIMS.py @@ -63,10 +63,6 @@ Classes ------- -.. autoclass:: Timestep - :members: - :inherited-members: - .. autoclass:: FHIAIMSReader :members: :inherited-members: diff --git a/package/MDAnalysis/coordinates/GRO.py b/package/MDAnalysis/coordinates/GRO.py index 9a4a12f95be..4775d2c6f8b 100644 --- a/package/MDAnalysis/coordinates/GRO.py +++ b/package/MDAnalysis/coordinates/GRO.py @@ -52,9 +52,6 @@ Classes ------- -.. autoclass:: Timestep - :members: - .. autoclass:: GROReader :members: diff --git a/package/MDAnalysis/coordinates/TRZ.py b/package/MDAnalysis/coordinates/TRZ.py index 0a14fc475c0..b4b67cb7e14 100644 --- a/package/MDAnalysis/coordinates/TRZ.py +++ b/package/MDAnalysis/coordinates/TRZ.py @@ -38,45 +38,6 @@ Classes ------- -.. autoclass:: MDAnalysis.coordinates.TRZ.Timestep - :members: - - .. attribute:: frame - - Index of current frame number (0 based) - - .. attribute:: time - - Current system time in ps - - .. attribute:: n_atoms - - Number of atoms in the frame (will be constant throughout trajectory) - - .. attribute:: pressure - - System pressure in pascals - - .. attribute:: pressure_tensor - - Array containing pressure tensors in order: xx, xy, yy, xz, yz, zz - - .. attribute:: total_energy - - Hamiltonian for the system in kJ/mol - - .. attribute:: potential_energy - - Potential energy of the system in kJ/mol - - .. attribute:: kinetic_energy - - Kinetic energy of the system in kJ/mol - - .. attribute:: temperature - - Temperature of the system in Kelvin - .. autoclass:: TRZReader :members: @@ -101,8 +62,8 @@ class TRZReader(base.ReaderBase): Attributes ---------- - ts : TRZ.Timestep - :class:`~MDAnalysis.coordinates.TRZ.Timestep` object containing + ts : base.Timestep + :class:`~MDAnalysis.coordinates.base.Timestep` object containing coordinates of current frame Note diff --git a/package/MDAnalysis/core/topology.py b/package/MDAnalysis/core/topology.py index b0d006407e5..6d94562d129 100644 --- a/package/MDAnalysis/core/topology.py +++ b/package/MDAnalysis/core/topology.py @@ -114,7 +114,7 @@ def make_downshift_arrays(upshift, nparents): """ if not len(upshift): return np.array([], dtype=object) - + order = np.argsort(upshift) upshift_sorted = upshift[order] @@ -178,30 +178,9 @@ class TransTable(object): number of residues in topology n_segments : int number of segments in topology - size - tuple describing the shape of the TransTable - - Methods - ------- - atoms2residues(aix) - Returns the residue index for many atom indices - residues2atoms_1d(rix) - All atoms in the residues represented by *rix* - residues2atoms_2d(rix) - List of atom indices for each residue in *rix* - residues2segments(rix) - Segment indices for each residue in *rix* - segments2residues_1d(six) - Similar to `residues2atoms_1d` - segments2residues_2d(six) - Similar to `residues2atoms_2d` - atoms2segments(aix) - Segment indices for each atom in *aix* - segments2atoms_1d(six) - Similar to `residues2atoms_1d` - segments2atoms_2d(six) - Similar to `residues2atoms_2d` - + size : tuple + tuple ``(n_atoms, n_residues, n_segments)`` describing the shape of + the TransTable """ def __init__(self, n_atoms, n_residues, n_segments, # Size of tables @@ -236,7 +215,10 @@ def copy(self): @property def size(self): - """The shape of the table, (n_atoms, n_residues, n_segments)""" + """The shape of the table, ``(n_atoms, n_residues, n_segments)``. + + :meta private: + """ return (self.n_atoms, self.n_residues, self.n_segments) def atoms2residues(self, aix): @@ -597,4 +579,4 @@ def add_Segment(self, **new_attrs): attr.values = np.concatenate([attr.values, np.array([newval])]) return segidx - + diff --git a/package/MDAnalysis/core/universe.py b/package/MDAnalysis/core/universe.py index de5b038216d..38b40ab9c1f 100644 --- a/package/MDAnalysis/core/universe.py +++ b/package/MDAnalysis/core/universe.py @@ -177,49 +177,33 @@ def _generate_from_topology(universe): class Universe(object): """The MDAnalysis Universe contains all the information describing the system. - The system always requires a *topology* file --- in the simplest case just + The system always requires a *topology file* --- in the simplest case just a list of atoms. This can be a CHARMM/NAMD PSF file or a simple coordinate - file with atom informations such as XYZ, PDB, Gromacs GRO, or CHARMM + file with atom informations such as XYZ, PDB, GROMACS GRO or TPR, or CHARMM CRD. See :ref:`Supported topology formats` for what kind of topologies can be read. - A trajectory provides coordinates; the coordinates have to be ordered in - the same way as the list of atoms in the topology. A trajectory can be a - single frame such as a PDB, CRD, or GRO file, or it can be a MD trajectory - (in CHARMM/NAMD/LAMMPS DCD, Gromacs XTC/TRR, or generic XYZ format). See - :ref:`Supported coordinate formats` for what can be read as a - "trajectory". + A *trajectory file* provides coordinates; the coordinates have to be + ordered in the same way as the list of atoms in the topology. A trajectory + can be a single frame such as a PDB, CRD, or GRO file, or it can be a MD + trajectory (in CHARMM/NAMD/LAMMPS DCD, GROMACS XTC/TRR, AMBER nc, generic + XYZ format, ...). See :ref:`Supported coordinate formats` for what can be + read as a "trajectory". As a special case, when the topology is a file that contains atom information *and* coordinates (such as XYZ, PDB, GRO or CRD, see :ref:`Supported coordinate formats`) then the coordinates are immediately loaded from the "topology" file unless a trajectory is supplied. - Examples for setting up a universe:: - - u = Universe(topology, trajectory) # read system from file(s) - u = Universe(pdbfile) # read atoms and coordinates from PDB or GRO - u = Universe(topology, [traj1, traj2, ...]) # read from a list of trajectories - u = Universe(topology, traj1, traj2, ...) # read from multiple trajectories - - Load new data into a universe (replaces old trajectory and does *not* append):: - - u.load_new(trajectory) # read from a new trajectory file - - Select atoms, with syntax similar to CHARMM (see - :class:`~Universe.select_atoms` for details):: - - u.select_atoms(...) - Parameters ---------- - topology: str, stream, `~MDAnalysis.core.topology.Topology`, `np.ndarray`, None + topology: str, stream, Topology, numpy.ndarray, None A CHARMM/XPLOR PSF topology file, PDB file or Gromacs GRO file; used to define the list of atoms. If the file includes bond information, partial charges, atom masses, ... then these data will be available to MDAnalysis. Alternatively, an existing :class:`MDAnalysis.core.topology.Topology` instance may be given, - numpy coordinates, or None for an empty universe. + numpy coordinates, or ``None`` for an empty universe. coordinates: str, stream, list of str, list of stream (optional) Coordinates can be provided as files of a single frame (eg a PDB, CRD, or GRO file); a list of single @@ -272,15 +256,53 @@ class Universe(object): Attributes ---------- - trajectory - currently loaded trajectory reader; - dimensions - current system dimensions (simulation unit cell, if set in the - trajectory) - atoms, residues, segments - principal Groups for each topology level - bonds, angles, dihedrals - principal ConnectivityGroups for each connectivity type + trajectory : base.ReaderBase or base.SingleFrameReaderBase + currently loaded trajectory reader; readers are described in + :ref:`Coordinates` + dimensions : numpy.ndarray + system dimensions (simulation unit cell, if set in the + trajectory) at the *current time step* + (see :attr:`MDAnalysis.coordinates.base.Timestep.dimensions`). + The unit cell can be set for the current time step (but the change is + not permanent unless written to a file). + atoms : AtomGroup + all particles (:class:`~MDAnalysis.core.groups.Atom`) in the system, + as read from the `topology` file + residues : ResidueGroup + all residues (:class:`~MDAnalysis.core.groups.Residue`) in the system + segments : SegmentGroup + all segments (:class:`~MDAnalysis.core.groups.Segment`) in the system + bonds : topologyattrs.Bonds + all bonds (if defined in the `topology`) as provided by + :attr:`Universe.atoms.bonds` + angles : topologyattrs.Angles + all angles (if defined in the `topology`), same as + :attr:`Universe.atoms.angles` + dihedrals : topologyattrs.Dihedrals + all dihedral angles (if defined in the `topology`), same as + :attr:`Universe.atoms.dihedrals` + impropers : topologyattrs.Impropers + all improper dihedral angles (if defined in the `topology`), same as + :attr:`Universe.atoms.impropers` + + Examples + -------- + Examples for setting up a :class:`Universe`:: + + u = Universe(topology, trajectory) # read system from file(s) + u = Universe(pdbfile) # read atoms and coordinates from PDB or GRO + u = Universe(topology, [traj1, traj2, ...]) # read from a list of trajectories + u = Universe(topology, traj1, traj2, ...) # read from multiple trajectories + + Load new data into a universe (replaces old trajectory and does *not* append):: + + u.load_new(trajectory) # read from a new trajectory file + + Selecting atoms with :meth:`~Universe.select_atoms` :: + + ag = u.select_atoms(...) + + returns an :class:`~MDAnalysis.core.groups.AtomGroup`. .. versionchanged:: 1.0.0 @@ -289,8 +311,8 @@ class Universe(object): .. versionchanged:: 2.0.0 Universe now can be (un)pickled. - ``topology`` and ``trajectory`` are reserved - upon unpickle. + ``topology`` and ``trajectory`` are reserved upon unpickle. + """ def __init__(self, topology=None, *coordinates, all_coordinates=False, format=None, topology_format=None, transformations=None, @@ -366,7 +388,7 @@ def empty(cls, n_atoms, n_residues=1, n_segments=1, Useful for building a Universe without requiring existing files, for example for system building. - If `trajectory` is set to True, a + If `trajectory` is set to ``True``, a :class:`MDAnalysis.coordinates.memory.MemoryReader` will be attached to the Universe. @@ -385,33 +407,39 @@ def empty(cls, n_atoms, n_residues=1, n_segments=1, residue_segindex: array like, optional mapping of residues to segments trajectory: bool, optional - if True, attaches a :class:`MDAnalysis.coordinates.memory.MemoryReader` - allowing coordinates to be set and written. Default is False + if ``True``, attaches a + :class:`MDAnalysis.coordinates.memory.MemoryReader` allowing + coordinates to be set and written. velocities: bool, optional - include velocities in the :class:`MDAnalysis.coordinates.memory.MemoryReader` + include velocities in the + :class:`MDAnalysis.coordinates.memory.MemoryReader` forces: bool, optional - include forces in the :class:`MDAnalysis.coordinates.memory.MemoryReader` + include forces in the + :class:`MDAnalysis.coordinates.memory.MemoryReader` Returns ------- - MDAnalysis.Universe object + Universe + :class:`~MDAnalysis.core.universe.Universe` instance with dummy + values for atoms and undefined coordinates/velocities/forces Examples -------- For example to create a new Universe with 6 atoms in 2 residues, with - positions for the atoms and a mass attribute: + positions for the atoms and a mass attribute:: - >>> u = mda.Universe.empty(6, 2, - atom_resindex=np.array([0, 0, 0, 1, 1, 1]), - trajectory=True, + u = mda.Universe.empty(6, 2, + atom_resindex=np.array([0, 0, 0, 1, 1, 1]), + trajectory=True, ) - >>> u.add_TopologyAttr('masses') + u.add_TopologyAttr('masses') .. versionadded:: 0.17.0 .. versionchanged:: 0.19.0 The attached Reader when trajectory=True is now a MemoryReader .. versionchanged:: 1.0.0 Universes can now be created with 0 atoms + """ if not n_atoms: n_residues = 0 @@ -496,8 +524,9 @@ def load_new(self, filename, format=None, in_memory=False, Raises ------ - TypeError if trajectory format can not be - determined or no appropriate trajectory reader found + TypeError + if trajectory format can not be determined or no appropriate + trajectory reader found .. versionchanged:: 0.8 @@ -512,6 +541,7 @@ def load_new(self, filename, format=None, in_memory=False, .. versionchanged:: 0.17.0 Now returns a :class:`Universe` instead of the tuple of file/array and detected file type. + """ # filename==None happens when only a topology is provided if filename is None: @@ -629,22 +659,34 @@ def select_atoms(self, *args, **kwargs): @property def bonds(self): - """Bonds between atoms""" + """Bonds between atoms. + + :meta private: + """ return self.atoms.bonds @property def angles(self): - """Angles between atoms""" + """Angles between atoms. + + :meta private: + """ return self.atoms.angles @property def dihedrals(self): - """Dihedral angles between atoms""" + """Dihedral angles between atoms. + + :meta private: + """ return self.atoms.dihedrals @property def impropers(self): - """Improper dihedral angles between atoms""" + """Improper dihedral angles between atoms. + + :meta private: + """ return self.atoms.impropers def __repr__(self): @@ -674,7 +716,10 @@ def __reduce__(self): # Properties @property def dimensions(self): - """Current dimensions of the unitcell""" + """Current dimensions of the unitcell. + + :meta private: + """ return self.coord.dimensions @dimensions.setter @@ -713,7 +758,10 @@ def kwargs(self): @property def trajectory(self): - """Reference to trajectory reader object containing trajectory data.""" + """Reference to trajectory reader object containing trajectory data. + + :meta private: + """ if self._trajectory is not None: return self._trajectory else: @@ -753,7 +801,7 @@ def add_TopologyAttr(self, topologyattr, values=None): attribute to add (eg 'charges'), can also supply initial values using values keyword. - .. versionchanged:: 1.1.0 + .. versionchanged:: 1.1.0 Now warns when adding bfactors to a Universe with existing tempfactors, or adding tempfactors to a Universe with existing bfactors. @@ -1321,19 +1369,25 @@ def from_smiles(cls, smiles, sanitize=True, addHs=True, addHs : bool (optional, default True) Add all necessary hydrogens to the molecule generate_coordinates : bool (optional, default True) - Generate 3D coordinates using RDKit's `AllChem.EmbedMultipleConfs` - function. Requires adding hydrogens with the `addHs` parameter + Generate 3D coordinates using RDKit's + :func:`AllChem.EmbedMultipleConfs` function. Requires adding + hydrogens with the `addHs` parameter numConfs : int (optional, default 1) Number of frames to generate coordinates for. Ignored if - `generate_coordinates=False` + ``generate_coordinates=False`` rdkit_kwargs : dict (optional) - Other arguments passed to the RDKit `EmbedMultipleConfs` function + Other arguments passed to the RDKit :func:`EmbedMultipleConfs` + function kwargs : dict Parameters passed on Universe creation Returns ------- - :class:`~MDAnalysis.core.Universe` + universe : Universe + contains atom names and topology information (bonds) derived from + the input SMILES string; coordinates are included if + `generate_coordinates` was set to ``True`` + Examples -------- @@ -1354,6 +1408,7 @@ def from_smiles(cls, smiles, sanitize=True, addHs=True, .. versionadded:: 2.0.0 + """ try: from rdkit import Chem diff --git a/package/MDAnalysis/lib/mdamath.py b/package/MDAnalysis/lib/mdamath.py index f65365cf244..349fbe8b9ba 100644 --- a/package/MDAnalysis/lib/mdamath.py +++ b/package/MDAnalysis/lib/mdamath.py @@ -25,10 +25,17 @@ Mathematical helper functions --- :mod:`MDAnalysis.lib.mdamath` =============================================================== -Helper functions for common mathematical operations + +Helper functions for common mathematical operations. Some of these functions +are written in C/cython for higher performance. + +Linear algebra +-------------- .. autofunction:: normal .. autofunction:: norm +.. autofunction:: pdot +.. autofunction:: pnorm .. autofunction:: angle .. autofunction:: dihedral .. autofunction:: stp @@ -36,12 +43,19 @@ .. autofunction:: triclinic_box .. autofunction:: triclinic_vectors .. autofunction:: box_volume + + +Connectivity +------------ + .. autofunction:: make_whole .. autofunction:: find_fragments + .. versionadded:: 0.11.0 .. versionchanged: 1.0.0 Unused function :func:`_angle()` has now been removed. + """ import numpy as np diff --git a/package/doc/sphinx/source/documentation_pages/analysis/hole2.rst b/package/doc/sphinx/source/documentation_pages/analysis/hole2.rst index 856f84ec21c..8c32a7f52b7 100644 --- a/package/doc/sphinx/source/documentation_pages/analysis/hole2.rst +++ b/package/doc/sphinx/source/documentation_pages/analysis/hole2.rst @@ -21,7 +21,7 @@ Module ------ .. automodule:: MDAnalysis.analysis.hole2.hole - :members: + Utility functions and templates @@ -32,4 +32,4 @@ Utility functions and templates .. automodule:: MDAnalysis.analysis.hole2.templates - :members: \ No newline at end of file + :members: diff --git a/package/doc/sphinx/source/documentation_pages/coordinates/TRZ.rst b/package/doc/sphinx/source/documentation_pages/coordinates/TRZ.rst index bcb5473dfd3..0fe61ad8992 100644 --- a/package/doc/sphinx/source/documentation_pages/coordinates/TRZ.rst +++ b/package/doc/sphinx/source/documentation_pages/coordinates/TRZ.rst @@ -1,2 +1,2 @@ .. automodule:: MDAnalysis.coordinates.TRZ - :members: + diff --git a/package/doc/sphinx/source/documentation_pages/lib/mdamath.rst b/package/doc/sphinx/source/documentation_pages/lib/mdamath.rst index d51c2eeb67a..22ef1f4fbee 100644 --- a/package/doc/sphinx/source/documentation_pages/lib/mdamath.rst +++ b/package/doc/sphinx/source/documentation_pages/lib/mdamath.rst @@ -1,2 +1 @@ .. automodule:: MDAnalysis.lib.mdamath - :members: diff --git a/package/doc/sphinx/source/documentation_pages/selections/charmm.rst b/package/doc/sphinx/source/documentation_pages/selections/charmm.rst index 7de34ab4503..673e74204aa 100644 --- a/package/doc/sphinx/source/documentation_pages/selections/charmm.rst +++ b/package/doc/sphinx/source/documentation_pages/selections/charmm.rst @@ -1,4 +1,2 @@ .. automodule:: MDAnalysis.selections.charmm - :members: - :inherited-members: diff --git a/package/doc/sphinx/source/documentation_pages/selections/gromacs.rst b/package/doc/sphinx/source/documentation_pages/selections/gromacs.rst index 794f0747997..accc0123ad7 100644 --- a/package/doc/sphinx/source/documentation_pages/selections/gromacs.rst +++ b/package/doc/sphinx/source/documentation_pages/selections/gromacs.rst @@ -1,3 +1 @@ .. automodule:: MDAnalysis.selections.gromacs - :members: - :inherited-members: diff --git a/package/doc/sphinx/source/documentation_pages/selections/jmol.rst b/package/doc/sphinx/source/documentation_pages/selections/jmol.rst index 394f42bede2..9fcce220207 100644 --- a/package/doc/sphinx/source/documentation_pages/selections/jmol.rst +++ b/package/doc/sphinx/source/documentation_pages/selections/jmol.rst @@ -1,3 +1 @@ .. automodule:: MDAnalysis.selections.jmol - :members: - :inherited-members: diff --git a/package/doc/sphinx/source/documentation_pages/selections/pymol.rst b/package/doc/sphinx/source/documentation_pages/selections/pymol.rst index b96e89daf36..390fcdd8381 100644 --- a/package/doc/sphinx/source/documentation_pages/selections/pymol.rst +++ b/package/doc/sphinx/source/documentation_pages/selections/pymol.rst @@ -1,4 +1,2 @@ .. automodule:: MDAnalysis.selections.pymol - :members: - :inherited-members: diff --git a/package/doc/sphinx/source/documentation_pages/selections/vmd.rst b/package/doc/sphinx/source/documentation_pages/selections/vmd.rst index 69e868b5f44..be547a4d390 100644 --- a/package/doc/sphinx/source/documentation_pages/selections/vmd.rst +++ b/package/doc/sphinx/source/documentation_pages/selections/vmd.rst @@ -1,4 +1,2 @@ .. automodule:: MDAnalysis.selections.vmd - :members: - :inherited-members: