Description
-
Bond.__eq__
does not check bond order incore.topologyobjects
:
mdanalysis/package/MDAnalysis/core/topologyobjects.py
Lines 163 to 167 in e110108
mdanalysis/package/MDAnalysis/core/topologyobjects.py
Lines 135 to 140 in e110108
-
All the "Reads the following Attributes" and "Guesses the following Attributes" should be double-checked in
topology.__init__
-
__init__
does not include ITPParser -
PSFParser
:.. _PSF: http://www.charmm.org/documentation/c35b1/struct.html
link broken. -
MinimalParser
: Ends in the middle of a sentence:
-
TRJReader
outdated: Outdated documentation for AMBER TRJReader #2398
-
-
dist
is missing documentation of thebox
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 intobox
-
Add lines to initialise
k
anddist
indistances.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