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API typos, outdated info, broken links, etc (ongoing) #2401

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@lilyminium

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@lilyminium
  • Bond.__eq__ does not check bond order in core.topologyobjects:

    Two :class:`Bond` instances can be compared with the ``==`` and
    ``!=`` operators. A bond is equal to another if the same atom
    numbers are connected and they have the same bond order. The
    ordering of the two atom numbers is ignored as is the fact that a
    bond was guessed.

    def __eq__(self, other):
    """Check whether two bonds have identical contents"""
    if not self.universe == other.universe:
    return False
    return (np.array_equal(self.indices, other.indices) or
    np.array_equal(self.indices[::-1], other.indices))

  • All the "Reads the following Attributes" and "Guesses the following Attributes" should be double-checked in topology.__init__

  • dist is missing documentation of the box parameter (analysis.distances.dist). Note that AtomGroups can be (usually are?) from different Universes. Note that even if the Universe has dimensions associated, dist does not use them unless explicitly passed into box

  • Add lines to initialise k and dist in distances.self_distance_array returns example

  • Update Molnums documentation, which is identical to Moltypes

  • All of the helanal documentation. Best to leave this after update helanal to AnalysisBase #2452 is addressed

  • AtomGroup.guess_bonds misleading documentation, could pass in fudge_factor #2395 fix up guess_bonds documentation

  • All of the PSA documentation. Perhaps it will get AnalysisBased?

  • encore.hes returns unreadable details which are not documented

  • encore.ClusteringMethod.KMeans documents precompute_distances without actually having it as a kwarg

  • encore.DimensionalityReductionMethod.StochasticProximityEmbeddingNative documents the default number of dimensions as 3, but it's actually 2

  • for encore.hes, ces, dres: document that the method returns averages and standard deviations if estimate_error=True

  • for encore.ces_convergence document the output. The shape does not include preference_values.

  • for rdf.InterRDF_s document density kwarg

  • fix base.AnalysisFromFunction raises ValueError

  • document kwargs in Ramachandran.plot

  • PCA.mean_atoms is not the mean positions, PCA.mean is

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