From 2901cead289ae14b957b4454bb50efd94a52c734 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Thu, 27 Jul 2023 16:12:04 -0700 Subject: [PATCH] Doc fixes --- pyext/src/analysis.py | 4 ++-- pyext/src/output.py | 2 +- pyext/src/plotting/topology.py | 2 +- pyext/src/restraints/basic.py | 2 +- pyext/src/restraints/crosslinking.py | 2 +- pyext/src/restraints/em2d.py | 2 -- 6 files changed, 6 insertions(+), 8 deletions(-) diff --git a/pyext/src/analysis.py b/pyext/src/analysis.py index 212817e6..1735f39b 100644 --- a/pyext/src/analysis.py +++ b/pyext/src/analysis.py @@ -477,7 +477,7 @@ def __init__(self, hier0, hier1, molnames, label="None", dynamic0=True, """ @param hier0 first input hierarchy @param hier1 second input hierarchy - @param molname the names of the molecules used for the RMSD + @param molnames the names of the molecules used for the RMSD @dynamic0 if True stores the decorators XYZ and coordinates of hier0 can be update. If false coordinates are static (stored in Vector3Ds) and will never be updated @@ -1076,7 +1076,7 @@ def get_rmsd_wrt_reference_structure_with_alignment( self, structure_set_name, alignment_selection_key): """First align then calculate RMSD @param structure_set_name: the name of the structure set - @param alignment_selection: the key containing the selection tuples + @param alignment_selection_key: the key containing the selection tuples needed to make the alignment stored in self.selection_dictionary @return: for each structure in the structure set, returns the rmsd """ diff --git a/pyext/src/output.py b/pyext/src/output.py index 11a12f93..fefb0780 100644 --- a/pyext/src/output.py +++ b/pyext/src/output.py @@ -1773,7 +1773,7 @@ def plot_field_histogram(name, values_lists, valuename=None, bins=40, leg_names=None): '''Plot a list of histograms from a value list. @param name the name of the plot - @param value_lists the list of list of values eg: [[...],[...],[...]] + @param values_lists the list of list of values eg: [[...],[...],[...]] @param valuename the y-label @param bins the number of bins @param colors If None, will use rainbow. Else will use specific list diff --git a/pyext/src/plotting/topology.py b/pyext/src/plotting/topology.py index c8cf731d..1a73374b 100644 --- a/pyext/src/plotting/topology.py +++ b/pyext/src/plotting/topology.py @@ -16,7 +16,7 @@ def __init__(self, model, selections, cutoff, frequency_cutoff, quantitative_proteomic_data=None): """Set up a new graphXL object @param model The IMP model - @param selection_dict A dictionary containing component names. + @param selections A dictionary containing component names. Keys are labels values are either moleculename or start,stop,moleculename diff --git a/pyext/src/restraints/basic.py b/pyext/src/restraints/basic.py index c91b9885..318a1d89 100644 --- a/pyext/src/restraints/basic.py +++ b/pyext/src/restraints/basic.py @@ -454,7 +454,7 @@ def __init__(self, hier, selection, cutoff=6., sigma=3., xi=0.01, """ Constructor @param hier Hierarchy of the system - @param section Selection of residues and target; + @param selection Selection of residues and target; syntax is (prot, r1, r2, target_prot) or (prot1, r1, r2, target_prot, target_r1, target_r2) @param cutoff Distance cutoff between selected segment and target diff --git a/pyext/src/restraints/crosslinking.py b/pyext/src/restraints/crosslinking.py index 2cc4d291..b5791f08 100644 --- a/pyext/src/restraints/crosslinking.py +++ b/pyext/src/restraints/crosslinking.py @@ -841,7 +841,7 @@ def plot_violations(self, out_prefix, max_prob_for_violation=0.1, is above this @param coarsen Use CA positions @param limit_to_chains Try to visualize just these chains - @param exclude_to_chains Try to NOT visualize these chains + @param exclude_chains Try to NOT visualize these chains """ print('going to calculate violations and plot CMM files') all_stats = self.get_best_stats() diff --git a/pyext/src/restraints/em2d.py b/pyext/src/restraints/em2d.py index f5798dba..c20291f2 100644 --- a/pyext/src/restraints/em2d.py +++ b/pyext/src/restraints/em2d.py @@ -131,8 +131,6 @@ def __init__(self, hier, images=None, pixel_size=None, registration) to estimate the registration parameters @param resolution Which level of [model representation](@ref pmi_resolution) to use in the fit - @param n_components Number of the largest components to be - considered for the EM image """ import IMP.em2d