Squashed 'modules/pmi/' changes from f7bcfd722d..198598f5c8

198598f5c8 Remove Python 2 workaround for TestCase.assertWarns
54b555a73b More Python 2 cleanups
9c20cd1755 Use no-argument form of super()
bc6ab67368 Drop Python 2 compatibility
75c8a62ff7 Squashed 'tools/dev_tools/' changes from 3ad5e0d8..c2d08a83

git-subtree-dir: modules/pmi
git-subtree-split: 198598f5c85a35bb01ccd0798d22f25456fe4008

modules/pmi/benchmark/benchmark_loop_reconstruction.py

@@ -7,10 +7,7 @@
 import time
 import sys
 import os
-try:
-    from time import process_time  # needs python 3.3 or later
-except ImportError:
-    from time import clock as process_time
+from time import process_time
 
 import IMP.pmi.restraints.stereochemistry
 import IMP.pmi.topology
@@ -26,7 +23,7 @@
 # Redirect chatty PMI output so we can see benchmark output
 old_stdout = sys.stdout
 
-class DummyFile(object):
+class DummyFile:
     def flush(self):
         pass
     def write(self, txt):

modules/pmi/benchmark/benchmark_replica_exchange.py

@@ -9,16 +9,13 @@
 import time
 import sys
 import shutil
-try:
-    from time import process_time  # needs python 3.3 or later
-except ImportError:
-    from time import clock as process_time
+from time import process_time
 
 
 IMP.setup_from_argv(sys.argv, "Replica exchange benchmark.")
 IMP.set_log_level(IMP.SILENT)
 old_stdout = sys.stdout
-class DummyFile(object):
+class DummyFile:
     def flush(self):
         pass
     def write(self, txt):

modules/pmi/pyext/src/alphabets.py

@@ -5,7 +5,7 @@
 import IMP.atom
 
 
-class ResidueAlphabet(object):
+class ResidueAlphabet:
     """Map between FASTA codes and residue types.
        Typically one would use the `amino_acid`, `rna`, or `dna` objects."""
     def __init__(self, charmm_to_one, chain_type=IMP.atom.UnknownChainType):

modules/pmi/pyext/src/analysis.py

@@ -18,7 +18,7 @@
 import numpy as np
 
 
-class Alignment(object):
+class Alignment:
     """Performs alignment and RMSD calculation for two sets of coordinates
 
     The class also takes into account non-equal stoichiometry of the proteins.
@@ -151,7 +151,7 @@ def align(self):
 
 
 # ----------------------------------
-class Violations(object):
+class Violations:
 
     def __init__(self, filename):
 
@@ -180,7 +180,7 @@ def get_number_violated_restraints(self, rsts_dict):
         return num_violated
 
 
-class Clustering(object):
+class Clustering:
     """A class to cluster structures.
     Uses scipy's cdist function to compute distance matrices
     and sklearn's kmeans clustering module.
@@ -458,7 +458,7 @@ def matrix_calculation(self, all_coords, template_coords, list_of_pairs):
         return raw_distance_dict, transformation_distance_dict
 
 
-class RMSD(object):
+class RMSD:
     """Compute the RMSD (without alignment) taking into account the copy
        ambiguity.
     To be used with pmi2 hierarchies. Can be used for instance as follows:
@@ -592,7 +592,7 @@ def get_output(self):
                 "RMSD_assignments_" + self.label: str(assignments_out)}
 
 
-class Precision(object):
+class Precision:
     """A class to evaluate the precision of an ensemble.
 
     Also can evaluate the cross-precision of multiple ensembles.
@@ -1151,7 +1151,7 @@ def set_precision_style(self, style):
             raise ValueError("No such style")
 
 
-class GetModelDensity(object):
+class GetModelDensity:
     """Compute mean density maps from structures.
 
     Keeps a dictionary of density maps,
@@ -1275,7 +1275,7 @@ def write_mrc(self, path="./", suffix=None):
                              IMP.em.MRCReaderWriter())
 
 
-class GetContactMap(object):
+class GetContactMap:
 
     def __init__(self, distance=15.):
         self.distance = distance
@@ -1627,7 +1627,7 @@ def get_particles_at_resolution_ten(prot):
     return particle_dict
 
 
-class CrossLinkTable(object):
+class CrossLinkTable:
     """Visualization of cross-links"""
     def __init__(self):
         self.crosslinks = []

modules/pmi/pyext/src/dof/__init__.py

@@ -22,7 +22,7 @@ def create_rigid_body_movers(dof, maxtrans, maxrot):
     return mvs
 
 
-class DegreesOfFreedom(object):
+class DegreesOfFreedom:
     """Simplify creation of constraints and movers for an IMP Hierarchy.
 
        * The various "create X" functions make movers for system components

modules/pmi/pyext/src/io/__init__.py

@@ -243,7 +243,7 @@ def save_best_models(model, out_dir, stat_files,
         print('wrote rmfs to', out_rmf_fn)
 
 
-class _TempProvenance(object):
+class _TempProvenance:
     """Placeholder to track provenance information added to the IMP model.
        This is since we typically don't preserve the IMP::Model object
        throughout a PMI protocol."""
@@ -541,7 +541,7 @@ def get_bead_sizes(model, rmf_tuple, rmsd_calculation_components=None,
     return rmsd_bead_size_dict
 
 
-class TotalScoreOutput(object):
+class TotalScoreOutput:
     """A helper output for model evaluation"""
     def __init__(self, model):
         self.model = model

modules/pmi/pyext/src/io/crosslink.py

@@ -39,7 +39,7 @@ def _handle_string_input(inp):
     return inp
 
 
-class _CrossLinkDataBaseStandardKeys(object):
+class _CrossLinkDataBaseStandardKeys:
     '''
     This class setup all the standard keys needed to
     identify the cross-link features from the data sets
@@ -197,7 +197,7 @@ def __str__(self):
         return outstr
 
 
-class FilterOperator(object):
+class FilterOperator:
     '''
     This class allows to create filter functions that can be passed to
     the CrossLinkDataBase in this way:
@@ -1397,7 +1397,7 @@ def get_number_of_unique_crosslinked_sites(self):
         return len(list(praset))
 
 
-class JaccardDistanceMatrix(object):
+class JaccardDistanceMatrix:
     """This class allows to compute and plot the distance between datasets"""
 
     def __init__(self, cldb_dictionary):
@@ -1480,7 +1480,7 @@ def plot_matrix(self, figurename="clustermatrix.pdf"):
         pl.close(fig)
 
 
-class MapCrossLinkDataBaseOnStructure(object):
+class MapCrossLinkDataBaseOnStructure:
     '''
     This class maps a CrossLinkDataBase on a given structure
     and save an rmf file with color-coded cross-links
@@ -1684,7 +1684,7 @@ def get_crosslink_violations(self, threshold):
         return violations
 
 
-class CrossLinkDataBaseFromStructure(object):
+class CrossLinkDataBaseFromStructure:
     '''
     This class generates a CrossLinkDataBase from a given structure
     '''

modules/pmi/pyext/src/macros.py

@@ -25,13 +25,13 @@
 import pickle
 
 
-class _MockMPIValues(object):
+class _MockMPIValues:
     """Replace samplers.MPI_values when in test mode"""
     def get_percentile(self, name):
         return 0.
 
 
-class _RMFRestraints(object):
+class _RMFRestraints:
     """All restraints that are written out to the RMF file"""
     def __init__(self, model, user_restraints):
         self._rmf_rs = IMP.pmi.tools.get_restraint_set(model, rmf=True)
@@ -43,10 +43,9 @@ def __len__(self):
 
     def __bool__(self):
         return len(self) > 0
-    __nonzero__ = __bool__  # Python 2 compatibility
 
     def __getitem__(self, i):
-        class FakePMIWrapper(object):
+        class FakePMIWrapper:
             def __init__(self, r):
                 self.r = IMP.RestraintSet.get_from(r)
 
@@ -63,7 +62,7 @@ def get_restraint(self):
             raise IndexError("Out of range")
 
 
-class ReplicaExchange(object):
+class ReplicaExchange:
     """A macro to help setup and run replica exchange.
     Supports Monte Carlo and molecular dynamics.
     Produces trajectory RMF files, best PDB structures,
@@ -628,7 +627,7 @@ def execute_macro(self):
             output.close_rmf(rmfname)
 
 
-class BuildSystem(object):
+class BuildSystem:
     """A macro to build a IMP::pmi::topology::System based on a
        TopologyReader object.
 
@@ -935,7 +934,7 @@ def execute_macro(self, max_rb_trans=4.0, max_rb_rot=0.04,
 
 
 @IMP.deprecated_object("2.8", "Use AnalysisReplicaExchange instead")
-class AnalysisReplicaExchange0(object):
+class AnalysisReplicaExchange0:
     """A macro for running all the basic operations of analysis.
     Includes clustering, precision analysis, and making ensemble density maps.
     A number of plots are also supported.
@@ -1621,7 +1620,7 @@ def load_objects(self, file_name):
         return objects
 
 
-class AnalysisReplicaExchange(object):
+class AnalysisReplicaExchange:
 
     """
     This class contains analysis utilities to investigate ReplicaExchange