Doc fixes

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
         """

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

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

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

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()

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