* Package:    sci-chemistry/modeller-9.25
 * Repository: gentoo
 * Maintainer: alexxy@gentoo.org sci-chemistry@gentoo.org
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux python_targets_python3_8 userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox
>>> Unpacking source...
>>> Unpacking modeller-9.25.tar.gz to /var/tmp/portage/sci-chemistry/modeller-9.25/work
>>> Source unpacked in /var/tmp/portage/sci-chemistry/modeller-9.25/work
>>> Preparing source in /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25 ...
RefactoringTool: Skipping optional fixer: buffer
RefactoringTool: Skipping optional fixer: idioms
RefactoringTool: Skipping optional fixer: set_literal
RefactoringTool: Skipping optional fixer: ws_comma
RefactoringTool: Refactored modlib/modeller/__init__.py
--- modlib/modeller/__init__.py	(original)
+++ modlib/modeller/__init__.py	(refactored)
@@ -48,7 +48,7 @@
         return sys.maxsize > 2**32
     # This works on older Pythons, but not in Python 3
     else:
-        return type(sys.dllhandle) == long
+        return type(sys.dllhandle) == int
 
 # Special processing on Windows to find _modeller.pyd and Modeller DLLs:
 if hasattr(config, 'install_dir') and hasattr(sys, 'dllhandle'):
RefactoringTool: No changes to modlib/modeller/alignment.py
RefactoringTool: No changes to modlib/modeller/alnsequence.py
RefactoringTool: No changes to modlib/modeller/alnstructure.py
RefactoringTool: No changes to modlib/modeller/atom_type.py
RefactoringTool: Refactored modlib/modeller/coordinates.py
--- modlib/modeller/coordinates.py	(original)
+++ modlib/modeller/coordinates.py	(refactored)
@@ -147,7 +147,7 @@
         (startres, endres) = self._get_resind()
         (startatm, endatm) = get_residue_atom_indices(self.seq, startres,
                                                       endres)
-        return (range(startatm+1, endatm+1), self.seq)
+        return (list(range(startatm+1, endatm+1)), self.seq)
 
     atoms = property(__get_atoms, doc="List of all atoms in this chain")
 
@@ -158,7 +158,7 @@
     def get_atom_indices(self):
         (startind, endind) = get_residue_atom_indices(self.mdl, self._num,
                                                       self._num + 1)
-        return range(startind + 1, endind + 1), self.mdl
+        return list(range(startind + 1, endind + 1)), self.mdl
 
     def __repr__(self):
         # Get residue number before we do anything else. For alignment
@@ -252,7 +252,7 @@
     def get_atom_indices(self):
         (startind, endind) = get_residue_atom_indices(self.mdl, self.offset,
                                                       self.offset + len(self))
-        return range(startind + 1, endind + 1), self.mdl
+        return list(range(startind + 1, endind + 1)), self.mdl
 
     def __getitem__(self, indx):
         ret = modutil.handle_seq_indx(self, indx, self.mdl._indxres,
@@ -398,7 +398,7 @@
             return self.mdl.natm
 
     def get_atom_indices(self):
-        return range(self.offset + 1, self.offset + len(self) + 1), self.mdl
+        return list(range(self.offset + 1, self.offset + len(self) + 1)), self.mdl
 
     def __getitem__(self, indx):
         ret = modutil.handle_seq_indx(self, indx, self.mdl._indxatm,
RefactoringTool: No changes to modlib/modeller/density.py
RefactoringTool: No changes to modlib/modeller/energy_data.py
RefactoringTool: No changes to modlib/modeller/energy_profile.py
RefactoringTool: No changes to modlib/modeller/environ.py
RefactoringTool: No changes to modlib/modeller/excluded_pair.py
RefactoringTool: No changes to modlib/modeller/excluded_pair_list.py
RefactoringTool: No changes to modlib/modeller/features.py
RefactoringTool: No changes to modlib/modeller/forms.py
RefactoringTool: No changes to modlib/modeller/gbsa.py
RefactoringTool: No changes to modlib/modeller/group_restraints.py
RefactoringTool: Refactored modlib/modeller/id_table.py
--- modlib/modeller/id_table.py	(original)
+++ modlib/modeller/id_table.py	(refactored)
@@ -40,7 +40,7 @@
 def write_seqid_matrix(fh, coder, mat):
     """Write a sequence identity matrix to a file"""
     nseq = len(mat)
-    print(" " * 9 + "".join([ s[:8] for s in coder ]))
+    print((" " * 9 + "".join([ s[:8] for s in coder ])))
     for n1 in range(nseq):
         fh.write(coder[n1][:8] + " " + \
                  "".join(["%8d" % (mat[n1][n2]+0.5) for n2 in range(nseq)]))
RefactoringTool: No changes to modlib/modeller/information.py
RefactoringTool: No changes to modlib/modeller/io_data.py
RefactoringTool: Refactored modlib/modeller/libraries.py
--- modlib/modeller/libraries.py	(original)
+++ modlib/modeller/libraries.py	(refactored)
@@ -32,7 +32,7 @@
             return BytesIO(*args)
     else:
         def _make_bytes_io(self, *args):
-            from cStringIO import StringIO
+            from io import StringIO
             return StringIO(*args)
 
     def __getstate__(self):
RefactoringTool: Refactored modlib/modeller/model.py
--- modlib/modeller/model.py	(original)
+++ modlib/modeller/model.py	(refactored)
@@ -121,7 +121,7 @@
 
     def get_atom_indices(self):
         """Get the indices of all atoms in this model"""
-        return (range(1, self.natm+1), self)
+        return (list(range(1, self.natm+1)), self)
 
     def read(self, file, model_format='PDB',
              model_segment=('FIRST:@', 'LAST:'), io=None,
@@ -340,7 +340,7 @@
         dope_score = sel.assess_dope()
         scorer = normalized_dope.DOPEScorer(self)
         z_score = scorer.get_z_score(dope_score)
-        print(">> Normalized DOPE z score: %.3f" % z_score)
+        print((">> Normalized DOPE z score: %.3f" % z_score))
         return z_score
 
     def assess_normalized_dopehr(self):
@@ -351,7 +351,7 @@
         dope_score = sel.assess_dopehr()
         scorer = normalized_dope.DOPEHRScorer(self)
         z_score = scorer.get_z_score(dope_score)
-        print(">> Normalized DOPE-HR z score: %.3f" % z_score)
+        print((">> Normalized DOPE-HR z score: %.3f" % z_score))
         return z_score
 
     def get_normalized_dope_profile(self):
RefactoringTool: Refactored modlib/modeller/model_topology.py
--- modlib/modeller/model_topology.py	(original)
+++ modlib/modeller/model_topology.py	(refactored)
@@ -50,7 +50,7 @@
         self.check_args = args
     def __iter__(self):
         return self
-    def next(self):
+    def __next__(self):
         while True:
             atoms = self.__int_next()
             if self.check_func is None \
@@ -82,7 +82,7 @@
         self.check_args = args
     def __iter__(self):
         return self
-    def next(self):
+    def __next__(self):
         while True:
             atoms = self.__int_next()
             if self.check_func is None \
RefactoringTool: No changes to modlib/modeller/modfile.py
RefactoringTool: No changes to modlib/modeller/normalized_dope.py
RefactoringTool: No changes to modlib/modeller/orient.py
RefactoringTool: No changes to modlib/modeller/parameters.py
RefactoringTool: Refactored modlib/modeller/physical.py
--- modlib/modeller/physical.py	(original)
+++ modlib/modeller/physical.py	(refactored)
@@ -31,7 +31,7 @@
     def __init__(self, default=1.0, **keys):
         self._default = default
         self._dict = {}
-        for (term,val) in keys.items():
+        for (term,val) in list(keys.items()):
             term = eval("%s" % term)
             self[term] = val
 
RefactoringTool: No changes to modlib/modeller/profile.py
RefactoringTool: No changes to modlib/modeller/pseudo_atom.py
RefactoringTool: No changes to modlib/modeller/pseudo_atom_list.py
RefactoringTool: No changes to modlib/modeller/pssmdb.py
RefactoringTool: No changes to modlib/modeller/residue.py
RefactoringTool: No changes to modlib/modeller/restraints.py
RefactoringTool: No changes to modlib/modeller/rigid_body.py
RefactoringTool: No changes to modlib/modeller/rigid_body_list.py
RefactoringTool: Refactored modlib/modeller/salign.py
--- modlib/modeller/salign.py	(original)
+++ modlib/modeller/salign.py	(refactored)
@@ -38,8 +38,8 @@
             return aln.salign(auto_overhang=True, overhang_auto_limit=5,
                               overhang_factor=1, **keys)
         except modeller.ModellerError:
-            print("SALIGN with auto_overhang failed: %s" \
-                  % str(sys.exc_info()[1]))
+            print(("SALIGN with auto_overhang failed: %s" \
+                  % str(sys.exc_info()[1])))
             print("Retrying without auto_overhang")
             return aln.salign(**keys)
 
@@ -118,13 +118,13 @@
                 self.qscore = res.qscorepct
                 self.aln.write(file=output_aln_file, alignment_format='PIR')
                 better = True
-            print("Qlty scrs %g\t%g\t%g" % (open_penalty, extend_penalty,
-                                            res.qscorepct))
+            print(("Qlty scrs %g\t%g\t%g" % (open_penalty, extend_penalty,
+                                            res.qscorepct)))
         except modeller.ModellerError:
-            print("Set of parameters %s %g %g resulted in the "
+            print(("Set of parameters %s %g %g resulted in the "
                   "following error\t%s" % (str(weights), open_penalty,
                                            extend_penalty,
-                                           str(sys.exc_info()[1])))
+                                           str(sys.exc_info()[1]))))
         return better
 
 
@@ -181,7 +181,7 @@
                 best.try_struc_align(opfile, opfile2, fw2, ogp3d, egp3d,
                                      align_block)
 
-    print("final max quality = %g" % best.qscore)
+    print(("final max quality = %g" % best.qscore))
 
     if best.found_struc_align:
         aln.clear()
RefactoringTool: Refactored modlib/modeller/saxsdata.py
--- modlib/modeller/saxsdata.py	(original)
+++ modlib/modeller/saxsdata.py	(refactored)
@@ -206,7 +206,7 @@
         try:
             fh = open(saxsfilename,'r')
         except:
-            print("file "+saxsfilename+" not found :(")
+            print(("file "+saxsfilename+" not found :("))
             return
         fh.close()
         ns = 0
@@ -225,8 +225,8 @@
             s_low = s_min - .001
         if (not s_hi):
             s_hi = s_max + .001
-        print("s_min=%s, s_max=%s" % (str(s_min), str(s_max)))
-        print("s_low=%s, s_hi=%s" % (str(s_low), str(s_hi)))
+        print(("s_min=%s, s_max=%s" % (str(s_min), str(s_max))))
+        print(("s_low=%s, s_hi=%s" % (str(s_low), str(s_hi))))
         self.ini_saxs(atmsel,
                  filename=formfacfilename,
                  s_min=s_min, s_max=s_max, maxs=ns, nmesh=ns, natomtyp=natomtyp,
RefactoringTool: No changes to modlib/modeller/schedule.py
RefactoringTool: No changes to modlib/modeller/secondary_structure.py
RefactoringTool: Refactored modlib/modeller/selection.py
--- modlib/modeller/selection.py	(original)
+++ modlib/modeller/selection.py	(refactored)
@@ -23,7 +23,7 @@
             return self.mdl.atoms[obj - 1]
     else:
         def next(self):
-            obj = self.seliter.next()
+            obj = next(self.seliter)
             return self.mdl.atoms[obj - 1]
 
 class selection(object):
@@ -52,7 +52,7 @@
            :rtype: list of ints
         """
         if sys.version_info[:2] == (2,3):
-            keys = self.__selection.keys()
+            keys = list(self.__selection.keys())
             keys.sort()
         else:
             keys = sorted(self.__selection.keys())
@@ -722,9 +722,9 @@
     def assess(self, assessor, output='SHORT NO_REPORT', **vars):
         """Assess with the given assessor object
            (e.g. :class:`soap_loop.Scorer`)."""
-        print(">> Model assessment by %s" % assessor.name)
+        print((">> Model assessment by %s" % assessor.name))
         molpdf, terms = assessor._assess(self, output=output, **vars)
-        print("%s                     : %12.6f" % (assessor.name, molpdf))
+        print(("%s                     : %12.6f" % (assessor.name, molpdf)))
         return molpdf
 
     def _dope_energy(self, gprsr, name, output='SHORT NO_REPORT',
@@ -733,7 +733,7 @@
                                                     nonbond_spline=1.), **vars):
         """Internal function to do DOPE or DOPE-HR assessment"""
         mdl = self.__mdl
-        print(">> Model assessment by %s potential" % name)
+        print((">> Model assessment by %s potential" % name))
         edat = self.get_dope_energy_data()
         old_gprsr = mdl.group_restraints
         mdl.group_restraints = gprsr
@@ -744,7 +744,7 @@
                             **vars)
         finally:
             mdl.group_restraints = old_gprsr
-        print("%s score               : %12.6f" % (name, molpdf))
+        print(("%s score               : %12.6f" % (name, molpdf)))
         return molpdf
 
     def debug_function(self, residue_span_range=(0, 99999),
RefactoringTool: No changes to modlib/modeller/sequence.py
RefactoringTool: No changes to modlib/modeller/sequence_db.py
RefactoringTool: No changes to modlib/modeller/soap_loop.py
RefactoringTool: No changes to modlib/modeller/soap_peptide.py
RefactoringTool: No changes to modlib/modeller/soap_pp.py
RefactoringTool: No changes to modlib/modeller/soap_protein_od.py
RefactoringTool: No changes to modlib/modeller/superpose.py
RefactoringTool: No changes to modlib/modeller/symmetry.py
RefactoringTool: No changes to modlib/modeller/symmetry_list.py
RefactoringTool: No changes to modlib/modeller/terms.py
RefactoringTool: Refactored modlib/modeller/test.py
--- modlib/modeller/test.py	(original)
+++ modlib/modeller/test.py	(refactored)
@@ -2,7 +2,7 @@
 import modeller
 import math
 try:
-    from cStringIO import StringIO
+    from io import StringIO
 except ImportError:
     from io import StringIO
 import sys
@@ -150,7 +150,7 @@
         diff = abs(num1 - num2)
         if msg is None:
             msg = "%f != %f within %g" % (num1, num2, tolerance)
-        self.assert_(diff < tolerance, msg)
+        self.assertTrue(diff < tolerance, msg)
 
     def run_capture_stdout(self, method, *args, **keys):
         """Run a method and capture its standard output. Returns both the
RefactoringTool: No changes to modlib/modeller/topology.py
RefactoringTool: No changes to modlib/modeller/virtual_atom.py
RefactoringTool: No changes to modlib/modeller/automodel/__init__.py
RefactoringTool: No changes to modlib/modeller/automodel/allhmodel.py
RefactoringTool: No changes to modlib/modeller/automodel/assess.py
RefactoringTool: Refactored modlib/modeller/automodel/automodel.py
--- modlib/modeller/automodel/automodel.py	(original)
+++ modlib/modeller/automodel/automodel.py	(refactored)
@@ -203,13 +203,13 @@
 
     def write_ok_summary(self, all, modeltyp):
         """Print out a summary of all successfully generated models"""
-        print("\n>> Summary of successfully produced %s:" % modeltyp)
-        fields = [x for x in all[0].keys() if x.endswith(' score')]
+        print(("\n>> Summary of successfully produced %s:" % modeltyp))
+        fields = [x for x in list(all[0].keys()) if x.endswith(' score')]
         fields.sort()
         fields = ['molpdf'] + fields
         header = '%-25s ' % 'Filename' + " ".join(['%14s' % x for x in fields])
         print(header)
-        print('-' * len(header))
+        print(('-' * len(header)))
         for mdl in all:
             text = '%-25s' % mdl['name']
             for field in fields:
@@ -222,9 +222,9 @@
 
     def write_failure_summary(self, all, modeltyp):
         """Print out a summary of all failed models"""
-        print("\n>> Summary of failed %s:" % modeltyp)
+        print(("\n>> Summary of failed %s:" % modeltyp))
         for mdl in all:
-            print("%-25s %s" % (mdl['name'], mdl['failure']))
+            print(("%-25s %s" % (mdl['name'], mdl['failure'])))
         print('')
 
     def rd_restraints(self):
@@ -692,8 +692,8 @@
         elif atmsel.get_model() is not self:
             raise ModellerError("selection is defined on the wrong model")
         elif len(atmsel) < len(self.atoms):
-            print("%d (of %d total) atoms selected for optimization" \
-                  % (len(atmsel), len(self.atoms)))
+            print(("%d (of %d total) atoms selected for optimization" \
+                  % (len(atmsel), len(self.atoms))))
         return atmsel
 
     def mkhomcsr(self, atmsel, aln):
@@ -774,9 +774,9 @@
         selstd = selection(self).only_std_residues()
         selca = selstd.only_atom_types('CA')
 
-        print("%d atoms in HETATM/BLK residues constrained\n" % len(selhet) \
+        print(("%d atoms in HETATM/BLK residues constrained\n" % len(selhet) \
               + "to protein atoms within %.2f angstroms\n" % bond_distance \
-              + "and protein CA atoms within %.2f angstroms" % ca_distance)
+              + "and protein CA atoms within %.2f angstroms" % ca_distance))
         # Build the bonds first; this avoids duplicated CA-ligand bonds since
         # make_distance() will not build restraints that are already on the
         # nonbond exclusion list
@@ -823,8 +823,8 @@
         selhet = selhet.only_no_topology()
 
         # Intra-residue:
-        print("%d atoms in residues without defined topology\n" % len(selhet) \
-              + "constrained to be rigid bodies")
+        print(("%d atoms in residues without defined topology\n" % len(selhet) \
+              + "constrained to be rigid bodies"))
         rsr = self.restraints
         rsr.make_distance(selhet, selhet, aln=aln,
                           distance_rsr_model=7, maximal_distance=10.0,
@@ -898,8 +898,8 @@
             print("\nThe following CHARMM atom type assignments were made:")
             print("      Atom                 Old type        New type")
             for atom, old_type, new_type in zip(sel, old_types, new_types):
-                print("      %-20s %-15s %-15s"
-                      % (str(atom), fmt_typ(old_type), fmt_typ(new_type)))
+                print(("      %-20s %-15s %-15s"
+                      % (str(atom), fmt_typ(old_type), fmt_typ(new_type))))
 
     def select_atoms(self):
         """Select atoms to be optimized in the model building procedure. By
RefactoringTool: No changes to modlib/modeller/automodel/autosched.py
RefactoringTool: No changes to modlib/modeller/automodel/dope_loopmodel.py
RefactoringTool: No changes to modlib/modeller/automodel/dopehr_loopmodel.py
RefactoringTool: Refactored modlib/modeller/automodel/generate.py
--- modlib/modeller/automodel/generate.py	(original)
+++ modlib/modeller/automodel/generate.py	(refactored)
@@ -88,11 +88,11 @@
                 to_rebuild.append(r)
                 _unbuild_ring(r, ring_atoms + extra_atoms)
     if len(to_rebuild) > 0:
-        print("The following %d residues contain 6-membered rings with "
+        print(("The following %d residues contain 6-membered rings with "
               "poor geometries\nafter transfer from templates. Rebuilding "
               "rings from internal coordinates:\n   %s" \
               % (len(to_rebuild),
-                 "\n   ".join([str(r) for r in to_rebuild])))
+                 "\n   ".join([str(r) for r in to_rebuild]))))
         mdl.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES')
 
 def read_xyz(mdl, aln):
RefactoringTool: Refactored modlib/modeller/automodel/loopmodel.py
--- modlib/modeller/automodel/loopmodel.py	(original)
+++ modlib/modeller/automodel/loopmodel.py	(refactored)
@@ -105,7 +105,7 @@
         lendef = len(self._defined_indices)
         if lenall > lendef:
             s = selection(self) - s
-            print("""
+            print(("""
 The following %d atoms were not found in the input model's non-loop region,
 and were added automatically by Modeller in order to determine correct
 interactions between the loop and the rest of the protein:
@@ -115,7 +115,7 @@
 rest of the protein may exist (note, however, that the score of the loop does
 not include protein-protein internal interactions, so will not be adversely
 affected by any clashes).""" \
-% (lenall - lendef, ", ".join([repr(a) for a in s])))
+% (lenall - lendef, ", ".join([repr(a) for a in s]))))
 
             if self.loop.write_defined_only:
                 print("""
@@ -406,7 +406,7 @@
         elif len(atmsel.only_no_topology()) > 0:
             raise ModellerError("some selected residues have no topology")
         else:
-            print("%d atoms selected for loop refinement" % len(atmsel))
+            print(("%d atoms selected for loop refinement" % len(atmsel)))
         return atmsel
 
     def optimize_loop(self, atmsel, sched, actions):
RefactoringTool: No changes to modlib/modeller/automodel/parallel.py
RefactoringTool: No changes to modlib/modeller/automodel/randomize.py
RefactoringTool: No changes to modlib/modeller/automodel/refine.py
RefactoringTool: No changes to modlib/modeller/library_restraints/angles.py
RefactoringTool: No changes to modlib/modeller/library_restraints/bonds.py
RefactoringTool: No changes to modlib/modeller/library_restraints/chi1.py
RefactoringTool: No changes to modlib/modeller/library_restraints/chi2.py
RefactoringTool: No changes to modlib/modeller/library_restraints/chi3.py
RefactoringTool: No changes to modlib/modeller/library_restraints/chi4.py
RefactoringTool: No changes to modlib/modeller/library_restraints/impropers.py
RefactoringTool: No changes to modlib/modeller/library_restraints/omega_dihedrals.py
RefactoringTool: No changes to modlib/modeller/library_restraints/phi_psi.py
RefactoringTool: No changes to modlib/modeller/mmcif/data.py
RefactoringTool: Refactored modlib/modeller/mmcif/writer.py
--- modlib/modeller/mmcif/writer.py	(original)
+++ modlib/modeller/mmcif/writer.py	(refactored)
@@ -4,7 +4,7 @@
 # which works as far back as 2.3, so imports need to be protected by a
 # version check
 
-from __future__ import print_function
+
 import sys
 import textwrap
 
@@ -12,7 +12,7 @@
 if sys.version_info[0] >= 3:
     _long_type = int
 else:
-    _long_type = long
+    _long_type = int
 
 class _LineWriter(object):
     def __init__(self, writer, line_len=80):
RefactoringTool: No changes to modlib/modeller/optimizers/actions.py
RefactoringTool: Refactored modlib/modeller/optimizers/builtin_optimizer.py
--- modlib/modeller/optimizers/builtin_optimizer.py	(original)
+++ modlib/modeller/optimizers/builtin_optimizer.py	(refactored)
@@ -9,7 +9,7 @@
         # delete the key entirely, as __getstate__ must return a non-empty
         # dict in order for our __setstate__ method to be called).
         d = self.__dict__.copy()
-        for key in self.__dict__.keys():
+        for key in list(self.__dict__.keys()):
             if key.endswith("_modpt") or key.endswith("__optpt"):
                 d[key] = None
         return d
@@ -21,7 +21,7 @@
         vars = params.copy()
         self._update_params(vars, ok_keys, extravars)
         for key in ok_keys:
-            if key not in vars.keys() \
+            if key not in list(vars.keys()) \
                and key not in ("edat", "libs", "actions", "schedule_scale"):
                 raise ValueError("a value must be given for %s" % key)
 
RefactoringTool: No changes to modlib/modeller/optimizers/conjugate_gradients.py
RefactoringTool: No changes to modlib/modeller/optimizers/molecular_dynamics.py
RefactoringTool: Refactored modlib/modeller/optimizers/optimizer.py
--- modlib/modeller/optimizers/optimizer.py	(original)
+++ modlib/modeller/optimizers/optimizer.py	(refactored)
@@ -10,7 +10,7 @@
         return self.atmsel
 
     def _update_params(self, params, ok_keys, vars):
-        for key in vars.keys():
+        for key in list(vars.keys()):
             if key in ok_keys:
                 params[key] = vars[key]
             else:
RefactoringTool: No changes to modlib/modeller/optimizers/quasi_newton.py
RefactoringTool: No changes to modlib/modeller/optimizers/state_optimizer.py
RefactoringTool: No changes to modlib/modeller/parallel/communicator.py
RefactoringTool: Refactored modlib/modeller/parallel/data_types.py
--- modlib/modeller/parallel/data_types.py	(original)
+++ modlib/modeller/parallel/data_types.py	(refactored)
@@ -3,7 +3,7 @@
 import sys
 
 try:
-    import cPickle as pickle
+    import pickle as pickle
 except ImportError:
     import pickle
 
RefactoringTool: Refactored modlib/modeller/parallel/job.py
--- modlib/modeller/parallel/job.py	(original)
+++ modlib/modeller/parallel/job.py	(refactored)
@@ -106,7 +106,7 @@
         if id and id in pending_slaves:
             slave = pending_slaves.pop(id)
             connected_slaves[id] = slave
-            print("Identified slave %s " % str(slave))
+            print(("Identified slave %s " % str(slave)))
             slave.accept_connection(sock)
             slave.set_directory(self.cwd)
             if sys.path[0] != '':
@@ -117,7 +117,7 @@
             return slave
         elif id and id in connected_slaves:
             slave = connected_slaves[id]
-            print("Reconnect from slave %s " % str(slave))
+            print(("Reconnect from slave %s " % str(slave)))
             slave.accept_connection(sock)
         else:
             print("Ignoring request from unknown slave")
@@ -159,7 +159,7 @@
         """Run all tasks and return all the results, in the same order that they
            were submitted, when all the jobs have completed."""
         tasks = self.tasks[:]
-        print("Running %d tasks on %d slaves" % (len(tasks), len(self)))
+        print(("Running %d tasks on %d slaves" % (len(tasks), len(self))))
         self.push_tasks_to_slaves()
         while True:
             try:
@@ -174,7 +174,7 @@
     def yield_tasks_unordered(self):
         """Run all tasks and return their results (as a generator), in
            whatever order they complete."""
-        print("Running %d tasks on %d slaves" % (len(self.tasks), len(self)))
+        print(("Running %d tasks on %d slaves" % (len(self.tasks), len(self))))
         self.push_tasks_to_slaves()
         while True:
             try:
@@ -215,7 +215,7 @@
                 task = obj.task_results()
                 if task:
                     # The slave completed its task
-                    print("%s on %s completed" % (str(task), str(obj)))
+                    print(("%s on %s completed" % (str(task), str(obj))))
                     if len(self.tasks) > 0:
                         obj.run_task(self.tasks.pop(0))
                     return task
@@ -225,14 +225,14 @@
             except (NetworkError, TaskSetupError):
                 self.kill_slaves((obj,), sys.exc_info()[1])
         else:
-            print("Warning: slave %s reports data, but is not running a task" \
-                  % str(obj))
+            print(("Warning: slave %s reports data, but is not running a task" \
+                  % str(obj)))
 
     def kill_slaves(self, slaves, err=""):
         if err != "":
             err = "(%s) " % err
         for s in slaves:
-            print("%s failed %s- removing from %s" % (s, err, self))
+            print(("%s failed %s- removing from %s" % (s, err, self)))
             task = s.kill()
             if task:
                 self.tasks.append(task)
@@ -248,8 +248,8 @@
         timedout = [a for a in self if a.running_task() and \
                                     a.contact_timeout(self.heartbeat_timeout)]
         if len(timedout) > 0:
-            print("Did not hear from slaves %s in %d seconds" % \
-                  (str(timedout), self.heartbeat_timeout))
+            print(("Did not hear from slaves %s in %d seconds" % \
+                  (str(timedout), self.heartbeat_timeout)))
             self.kill_slaves(timedout)
 
     def push_tasks_to_slaves(self):
@@ -264,8 +264,8 @@
                 slave.run_task(t)
             # If a network error occurred, kill the slave and requeue the task
             except socket.error:
-                print("slave %s failed on run task with %s; removing from job" \
-                      % (slave, sys.exc_info()[1]))
+                print(("slave %s failed on run task with %s; removing from job" \
+                      % (slave, sys.exc_info()[1])))
                 slave.kill()
                 self.tasks.insert(0, t)
         self.expand_for_tasks()
RefactoringTool: No changes to modlib/modeller/parallel/local_slave.py
RefactoringTool: No changes to modlib/modeller/parallel/mypopen4.py
RefactoringTool: Refactored modlib/modeller/parallel/myspawn.py
--- modlib/modeller/parallel/myspawn.py	(original)
+++ modlib/modeller/parallel/myspawn.py	(refactored)
@@ -10,7 +10,7 @@
        ``output``."""
 
     fp = open(output, "w")
-    print("%s >& %s" % (cmd, output))
+    print(("%s >& %s" % (cmd, output)))
     if sys.platform == 'win32':
         _myspawn_win32(cmd, fp)
     else:
@@ -27,4 +27,4 @@
     # Ignore Windows "file not found" errors, so that behavior is consistent
     # between Unix and Windows
     except WindowsError:
-        print("WindowsError: %s (ignored)" % sys.exc_info()[1])
+        print(("WindowsError: %s (ignored)" % sys.exc_info()[1]))
RefactoringTool: No changes to modlib/modeller/parallel/sge_pe_job.py
RefactoringTool: No changes to modlib/modeller/parallel/sge_pe_slave.py
RefactoringTool: Refactored modlib/modeller/parallel/sge_qsub_array.py
--- modlib/modeller/parallel/sge_qsub_array.py	(original)
+++ modlib/modeller/parallel/sge_qsub_array.py	(refactored)
@@ -36,7 +36,7 @@
         outlines = output.readlines()
         output.close()
         for line in outlines:
-            print(line.rstrip('\r\n'))
+            print((line.rstrip('\r\n')))
         a.require_clean_exit()
         self._set_jobid(outlines)
 
RefactoringTool: No changes to modlib/modeller/parallel/sge_qsub_job.py
RefactoringTool: Refactored modlib/modeller/parallel/sge_qsub_slave.py
--- modlib/modeller/parallel/sge_qsub_slave.py	(original)
+++ modlib/modeller/parallel/sge_qsub_slave.py	(refactored)
@@ -38,7 +38,7 @@
         qsub = "qsub -S /bin/sh -o '%s' -N '%s' %s %s" % \
               (output, name, self.standard_options, self._options)
         cmd = "%s -slave %s" % (path, id)
-        print("%s | %s" % (cmd, qsub))
+        print(("%s | %s" % (cmd, qsub)))
         a = MyPopen4(qsub)
         (input, output) = (a.stdin, a.stdout)
         input.write(cmd + '\n')
@@ -46,7 +46,7 @@
         outlines = output.readlines()
         output.close()
         for line in outlines:
-            print(line.rstrip('\r\n'))
+            print((line.rstrip('\r\n')))
         a.require_clean_exit()
         self._set_jobid(outlines)
 
RefactoringTool: No changes to modlib/modeller/parallel/slave.py
RefactoringTool: No changes to modlib/modeller/parallel/slave_communicator.py
RefactoringTool: Refactored modlib/modeller/parallel/slaveloop.py
--- modlib/modeller/parallel/slaveloop.py	(original)
+++ modlib/modeller/parallel/slaveloop.py	(refactored)
@@ -51,14 +51,14 @@
                         master.send_data(communicator.ErrorWrapper(detail))
                     except socket.error:
                         detail2 = sys.exc_info()[1]
-                        print("Warning: ignored exception " + str(detail2) \
+                        print(("Warning: ignored exception " + str(detail2) \
                               + " when trying to send error state " \
-                              + str(detail) + " back to master")
+                              + str(detail) + " back to master"))
                         raise detail
                 raise
 
     def run(self):
-        print("Slave startup: connect to master at %s" % self.addr)
+        print(("Slave startup: connect to master at %s" % self.addr))
         (host, port, identifier) = self.addr.split(":", 2)
         port = int(port)
         lock = threading.Lock()
RefactoringTool: No changes to modlib/modeller/parallel/slavestate.py
RefactoringTool: No changes to modlib/modeller/parallel/ssh_slave.py
RefactoringTool: No changes to modlib/modeller/parallel/task.py
RefactoringTool: No changes to modlib/modeller/scripts/align_strs_seq.py
RefactoringTool: No changes to modlib/modeller/scripts/asgl_principal_components.py
RefactoringTool: No changes to modlib/modeller/scripts/cispeptide.py
RefactoringTool: No changes to modlib/modeller/scripts/complete_pdb.py
RefactoringTool: No changes to modlib/modeller/scripts/fit.py
RefactoringTool: No changes to modlib/modeller/scripts/principal_components.py
RefactoringTool: No changes to modlib/modeller/scripts/sequence_srch.py
RefactoringTool: Refactored modlib/modeller/top_interpreter/__init__.py
--- modlib/modeller/top_interpreter/__init__.py	(original)
+++ modlib/modeller/top_interpreter/__init__.py	(refactored)
@@ -65,7 +65,7 @@
             if len(line) > 0:
                 try:
                     self._parse_top_ini_line(line.split(None, 4), vars)
-                except TypeError, detail:
+                except TypeError as detail:
                     mod_log_write("read_top__E> " + str(detail))
                     mod_log_write("             top.ini line: " + line)
                     raise
@@ -113,7 +113,7 @@
                 self._set_top_vars(vars)
                 try:
                     fh = self._open_include_file(self.variables['include_file'])
-                except IOError, detail:
+                except IOError as detail:
                     mod_log_write("runlines__E> " + str(detail))
                     mod_log_write("             TOP Command line: " + line)
                     raise
@@ -160,7 +160,7 @@
                     indxca = self._run_top_cmd(cmd, indxca, lines, callstack,
                                                subrout)
                     _modeller.mod_top_post()
-            except (IndexError, SyntaxError, TypeError), detail:
+            except (IndexError, SyntaxError, TypeError) as detail:
                 mod_log_write("runlines__E> " + str(detail))
                 mod_log_write("             TOP Command line: " + line)
                 raise
RefactoringTool: No changes to modlib/modeller/top_interpreter/commands.py
RefactoringTool: Refactored modlib/modeller/top_interpreter/topcmds.py
--- modlib/modeller/top_interpreter/topcmds.py	(original)
+++ modlib/modeller/top_interpreter/topcmds.py	(refactored)
@@ -19,7 +19,7 @@
         if not isinstance(vars, (list, tuple)):
             vars = (vars,)
         for var in vars:
-            if keys.has_key(var):
+            if var in keys:
                 args.append(keys[var])
             else:
                 args.append(self.vars[var])
RefactoringTool: Refactored modlib/modeller/top_interpreter/util.py
--- modlib/modeller/top_interpreter/util.py	(original)
+++ modlib/modeller/top_interpreter/util.py	(refactored)
@@ -1,7 +1,7 @@
 import _modeller
 
 def set_topvars(topvardict, vars, topini):
-    for name in topvardict.keys():
+    for name in list(topvardict.keys()):
         value = topvardict[name]
         if value is None:
             continue
RefactoringTool: Refactored modlib/modeller/top_interpreter/variables.py
--- modlib/modeller/top_interpreter/variables.py	(original)
+++ modlib/modeller/top_interpreter/variables.py	(refactored)
@@ -32,11 +32,11 @@
     def __init__(self, topcmds):
         self._topcmds = topcmds
         self._topvars = {}
-        for var in self._deftops.keys():
+        for var in list(self._deftops.keys()):
             self._ourvars[var] = self._deftops[var]
-        for var in self._edat_members.keys():
+        for var in list(self._edat_members.keys()):
             self._ourvars[var] = self._edat_members[var]
-        for var in self._io_members.keys():
+        for var in list(self._io_members.keys()):
             self._ourvars[var] = self._io_members[var]
 
     def __setitem__(self, key, value):
RefactoringTool: No changes to modlib/modeller/util/array.py
RefactoringTool: No changes to modlib/modeller/util/logger.py
RefactoringTool: No changes to modlib/modeller/util/matrix.py
RefactoringTool: No changes to modlib/modeller/util/modlist.py
RefactoringTool: Refactored modlib/modeller/util/modobject.py
--- modlib/modeller/util/modobject.py	(original)
+++ modlib/modeller/util/modobject.py	(refactored)
@@ -1,8 +1,8 @@
 class modobject(object):
     def __setattr__(self, name, val):
         if name not in dir(self):
-            print("runcmd_____W>: creation of new member '%s' in %s: "
-                  "possible typo!" % (name, str(self)))
+            print(("runcmd_____W>: creation of new member '%s' in %s: "
+                  "possible typo!" % (name, str(self))))
         object.__setattr__(self, name, val)
 
     def __getstate__(self):
@@ -11,7 +11,7 @@
         # delete the key entirely, as __getstate__ must return a non-empty
         # dict in order for our __setstate__ method to be called).
         d = self.__dict__.copy()
-        for key in self.__dict__.keys():
+        for key in list(self.__dict__.keys()):
             if key.endswith("_modpt"):
                 d[key] = None
         return d
RefactoringTool: Refactored modlib/modeller/util/modutil.py
--- modlib/modeller/util/modutil.py	(original)
+++ modlib/modeller/util/modutil.py	(refactored)
@@ -17,7 +17,7 @@
         else:
             return indx
     elif isinstance(indx, slice):
-        return range(*indx.indices(len(seqtype)))
+        return list(range(*indx.indices(len(seqtype))))
     elif lookup_func is not None:
         args = lookup_args + (indx,)
         int_indx = lookup_func(*args)
RefactoringTool: Files that were modified:
RefactoringTool: modlib/modeller/__init__.py
RefactoringTool: modlib/modeller/alignment.py
RefactoringTool: modlib/modeller/alnsequence.py
RefactoringTool: modlib/modeller/alnstructure.py
RefactoringTool: modlib/modeller/atom_type.py
RefactoringTool: modlib/modeller/coordinates.py
RefactoringTool: modlib/modeller/density.py
RefactoringTool: modlib/modeller/energy_data.py
RefactoringTool: modlib/modeller/energy_profile.py
RefactoringTool: modlib/modeller/environ.py
RefactoringTool: modlib/modeller/excluded_pair.py
RefactoringTool: modlib/modeller/excluded_pair_list.py
RefactoringTool: modlib/modeller/features.py
RefactoringTool: modlib/modeller/forms.py
RefactoringTool: modlib/modeller/gbsa.py
RefactoringTool: modlib/modeller/group_restraints.py
RefactoringTool: modlib/modeller/id_table.py
RefactoringTool: modlib/modeller/information.py
RefactoringTool: modlib/modeller/io_data.py
RefactoringTool: modlib/modeller/libraries.py
RefactoringTool: modlib/modeller/model.py
RefactoringTool: modlib/modeller/model_topology.py
RefactoringTool: modlib/modeller/modfile.py
RefactoringTool: modlib/modeller/normalized_dope.py
RefactoringTool: modlib/modeller/orient.py
RefactoringTool: modlib/modeller/parameters.py
RefactoringTool: modlib/modeller/physical.py
RefactoringTool: modlib/modeller/profile.py
RefactoringTool: modlib/modeller/pseudo_atom.py
RefactoringTool: modlib/modeller/pseudo_atom_list.py
RefactoringTool: modlib/modeller/pssmdb.py
RefactoringTool: modlib/modeller/residue.py
RefactoringTool: modlib/modeller/restraints.py
RefactoringTool: modlib/modeller/rigid_body.py
RefactoringTool: modlib/modeller/rigid_body_list.py
RefactoringTool: modlib/modeller/salign.py
RefactoringTool: modlib/modeller/saxsdata.py
RefactoringTool: modlib/modeller/schedule.py
RefactoringTool: modlib/modeller/secondary_structure.py
RefactoringTool: modlib/modeller/selection.py
RefactoringTool: modlib/modeller/sequence.py
RefactoringTool: modlib/modeller/sequence_db.py
RefactoringTool: modlib/modeller/soap_loop.py
RefactoringTool: modlib/modeller/soap_peptide.py
RefactoringTool: modlib/modeller/soap_pp.py
RefactoringTool: modlib/modeller/soap_protein_od.py
RefactoringTool: modlib/modeller/superpose.py
RefactoringTool: modlib/modeller/symmetry.py
RefactoringTool: modlib/modeller/symmetry_list.py
RefactoringTool: modlib/modeller/terms.py
RefactoringTool: modlib/modeller/test.py
RefactoringTool: modlib/modeller/topology.py
RefactoringTool: modlib/modeller/virtual_atom.py
RefactoringTool: modlib/modeller/automodel/__init__.py
RefactoringTool: modlib/modeller/automodel/allhmodel.py
RefactoringTool: modlib/modeller/automodel/assess.py
RefactoringTool: modlib/modeller/automodel/automodel.py
RefactoringTool: modlib/modeller/automodel/autosched.py
RefactoringTool: modlib/modeller/automodel/dope_loopmodel.py
RefactoringTool: modlib/modeller/automodel/dopehr_loopmodel.py
RefactoringTool: modlib/modeller/automodel/generate.py
RefactoringTool: modlib/modeller/automodel/loopmodel.py
RefactoringTool: modlib/modeller/automodel/parallel.py
RefactoringTool: modlib/modeller/automodel/randomize.py
RefactoringTool: modlib/modeller/automodel/refine.py
RefactoringTool: modlib/modeller/library_restraints/angles.py
RefactoringTool: modlib/modeller/library_restraints/bonds.py
RefactoringTool: modlib/modeller/library_restraints/chi1.py
RefactoringTool: modlib/modeller/library_restraints/chi2.py
RefactoringTool: modlib/modeller/library_restraints/chi3.py
RefactoringTool: modlib/modeller/library_restraints/chi4.py
RefactoringTool: modlib/modeller/library_restraints/impropers.py
RefactoringTool: modlib/modeller/library_restraints/omega_dihedrals.py
RefactoringTool: modlib/modeller/library_restraints/phi_psi.py
RefactoringTool: modlib/modeller/mmcif/data.py
RefactoringTool: modlib/modeller/mmcif/writer.py
RefactoringTool: modlib/modeller/optimizers/actions.py
RefactoringTool: modlib/modeller/optimizers/builtin_optimizer.py
RefactoringTool: modlib/modeller/optimizers/conjugate_gradients.py
RefactoringTool: modlib/modeller/optimizers/molecular_dynamics.py
RefactoringTool: modlib/modeller/optimizers/optimizer.py
RefactoringTool: modlib/modeller/optimizers/quasi_newton.py
RefactoringTool: modlib/modeller/optimizers/state_optimizer.py
RefactoringTool: modlib/modeller/parallel/communicator.py
RefactoringTool: modlib/modeller/parallel/data_types.py
RefactoringTool: modlib/modeller/parallel/job.py
RefactoringTool: modlib/modeller/parallel/local_slave.py
RefactoringTool: modlib/modeller/parallel/mypopen4.py
RefactoringTool: modlib/modeller/parallel/myspawn.py
RefactoringTool: modlib/modeller/parallel/sge_pe_job.py
RefactoringTool: modlib/modeller/parallel/sge_pe_slave.py
RefactoringTool: modlib/modeller/parallel/sge_qsub_array.py
RefactoringTool: modlib/modeller/parallel/sge_qsub_job.py
RefactoringTool: modlib/modeller/parallel/sge_qsub_slave.py
RefactoringTool: modlib/modeller/parallel/slave.py
RefactoringTool: modlib/modeller/parallel/slave_communicator.py
RefactoringTool: modlib/modeller/parallel/slaveloop.py
RefactoringTool: modlib/modeller/parallel/slavestate.py
RefactoringTool: modlib/modeller/parallel/ssh_slave.py
RefactoringTool: modlib/modeller/parallel/task.py
RefactoringTool: modlib/modeller/scripts/align_strs_seq.py
RefactoringTool: modlib/modeller/scripts/asgl_principal_components.py
RefactoringTool: modlib/modeller/scripts/cispeptide.py
RefactoringTool: modlib/modeller/scripts/complete_pdb.py
RefactoringTool: modlib/modeller/scripts/fit.py
RefactoringTool: modlib/modeller/scripts/principal_components.py
RefactoringTool: modlib/modeller/scripts/sequence_srch.py
RefactoringTool: modlib/modeller/top_interpreter/__init__.py
RefactoringTool: modlib/modeller/top_interpreter/commands.py
RefactoringTool: modlib/modeller/top_interpreter/topcmds.py
RefactoringTool: modlib/modeller/top_interpreter/util.py
RefactoringTool: modlib/modeller/top_interpreter/variables.py
RefactoringTool: modlib/modeller/util/array.py
RefactoringTool: modlib/modeller/util/logger.py
RefactoringTool: modlib/modeller/util/matrix.py
RefactoringTool: modlib/modeller/util/modlist.py
RefactoringTool: modlib/modeller/util/modobject.py
RefactoringTool: modlib/modeller/util/modutil.py
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25 ...
 * python3_8: running distutils-r1_run_phase python_compile
python3.8 setup.py build -j 1
Package glib-2.0 was not found in the pkg-config search path.
Perhaps you should add the directory containing `glib-2.0.pc'
to the PKG_CONFIG_PATH environment variable
No package 'glib-2.0' found
Traceback (most recent call last):
  File "setup.py", line 25, in <module>
    glib = pkgconfig("glib-2.0")
  File "setup.py", line 19, in pkgconfig
    for token in getoutput(["pkg-config", "--libs",
  File "setup.py", line 11, in getoutput
    return subprocess.check_output(args, universal_newlines=True)
  File "/usr/lib/python3.8/subprocess.py", line 415, in check_output
    return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
  File "/usr/lib/python3.8/subprocess.py", line 516, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['pkg-config', '--libs', '--cflags', 'glib-2.0']' returned non-zero exit status 1.
 * ERROR: sci-chemistry/modeller-9.25::gentoo failed (compile phase):
 *   (no error message)
 * 
 * Call stack:
 *     ebuild.sh, line  125:  Called src_compile
 *   environment, line 3036:  Called distutils-r1_src_compile
 *   environment, line 1175:  Called _distutils-r1_run_foreach_impl 'python_compile'
 *   environment, line  472:  Called python_foreach_impl 'distutils-r1_run_phase' 'python_compile'
 *   environment, line 2680:  Called multibuild_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile'
 *   environment, line 2140:  Called _multibuild_run '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile'
 *   environment, line 2138:  Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'python_compile'
 *   environment, line  765:  Called distutils-r1_run_phase 'python_compile'
 *   environment, line 1168:  Called python_compile
 *   environment, line 2453:  Called distutils-r1_python_compile
 *   environment, line 1008:  Called esetup.py 'build' '-j' '1'
 *   environment, line 1590:  Called die
 * The specific snippet of code:
 *       "${@}" || die "${die_args[@]}";
 * 
 * If you need support, post the output of `emerge --info '=sci-chemistry/modeller-9.25::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-chemistry/modeller-9.25::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-chemistry:modeller-9.25:20210320-084012.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-chemistry/modeller-9.25/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/modeller-9.25/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25/src/swig'
 * S: '/var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25'