[gentoo-commits] proj/sci:master commit in: sci-chemistry/modeller/files/, sci-chemistry/modeller/

[gentoo-commits] proj/sci:master commit in: sci-chemistry/modeller/files/, sci-chemistry/modeller/

[Alexey Shvetsov]

commit:     87d9cf08f438478856d352c15b7096998928c4de
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Thu Oct  8 10:54:03 2020 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Thu Oct  8 10:54:03 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=87d9cf08

sci-chemistry/modeller: Version bump

Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Alexey Shvetsov <alexxy <AT> gentoo.org>

 sci-chemistry/modeller/files/9v5-setup.patch       |  12 -
 .../modeller/files/modeller-9.25-convert2to3.patch | 702 +++++++++++++++++++++
 sci-chemistry/modeller/modeller-9.19.ebuild        | 145 -----
 ...odeller-9.12-r3.ebuild => modeller-9.25.ebuild} |  16 +-
 4 files changed, 712 insertions(+), 163 deletions(-)

diff --git a/sci-chemistry/modeller/files/9v5-setup.patch b/sci-chemistry/modeller/files/9v5-setup.patch
deleted file mode 100644
index 5fe460580..000000000
--- a/sci-chemistry/modeller/files/9v5-setup.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -Nu -Nu -uarN modeller-9v3.orig/src/swig/setup.py modeller-9v3/src/swig/setup.py
---- modeller-9v4.orig/src/swig/setup.py	2008-04-15 12:57:50.000000000 +0200
-+++ modeller-9v4/src/swig/setup.py	2008-04-15 12:57:59.000000000 +0200
-@@ -19,7 +19,7 @@
-                 include_dirs=['../include', '../include/%s' % exetype] + \
-                              glib['include_dirs'],
-                 libraries=['modeller'] + glib['libraries'],
--                library_dirs=['../../lib/%s' % exetype] + glib['library_dirs'])
-+                library_dirs=['../../lib/%s' % exetype])
- 
- setup(name='Modeller',
-       description='Protein structure modeling by satisfaction of ' \

diff --git a/sci-chemistry/modeller/files/modeller-9.25-convert2to3.patch b/sci-chemistry/modeller/files/modeller-9.25-convert2to3.patch
new file mode 100644
index 000000000..d7df05ce6
--- /dev/null
+++ b/sci-chemistry/modeller/files/modeller-9.25-convert2to3.patch
@@ -0,0 +1,702 @@
+--- modeller-9.25/modlib/modeller/__init__.py	(original)
++++ modeller-9.25/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'):
+--- modeller-9.25/modlib/modeller/coordinates.py	(original)
++++ modeller-9.25/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,
+--- modeller-9.25/modlib/modeller/id_table.py	(original)
++++ modeller-9.25/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)]))
+--- modeller-9.25/modlib/modeller/libraries.py	(original)
++++ modeller-9.25/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):
+--- modeller-9.25/modlib/modeller/model.py	(original)
++++ modeller-9.25/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):
+--- modeller-9.25/modlib/modeller/model_topology.py	(original)
++++ modeller-9.25/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 \
+--- modeller-9.25/modlib/modeller/physical.py	(original)
++++ modeller-9.25/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
+ 
+--- modeller-9.25/modlib/modeller/salign.py	(original)
++++ modeller-9.25/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()
+--- modeller-9.25/modlib/modeller/saxsdata.py	(original)
++++ modeller-9.25/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,
+--- modeller-9.25/modlib/modeller/selection.py	(original)
++++ modeller-9.25/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),
+--- modeller-9.25/modlib/modeller/test.py	(original)
++++ modeller-9.25/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
+--- modeller-9.25/modlib/modeller/automodel/automodel.py	(original)
++++ modeller-9.25/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
+--- modeller-9.25/modlib/modeller/automodel/generate.py	(original)
++++ modeller-9.25/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):
+--- modeller-9.25/modlib/modeller/automodel/loopmodel.py	(original)
++++ modeller-9.25/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):
+--- modeller-9.25/modlib/modeller/mmcif/writer.py	(original)
++++ modeller-9.25/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):
+--- modeller-9.25/modlib/modeller/optimizers/builtin_optimizer.py	(original)
++++ modeller-9.25/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)
+ 
+--- modeller-9.25/modlib/modeller/optimizers/optimizer.py	(original)
++++ modeller-9.25/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:
+--- modeller-9.25/modlib/modeller/parallel/data_types.py	(original)
++++ modeller-9.25/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
+ 
+--- modeller-9.25/modlib/modeller/parallel/job.py	(original)
++++ modeller-9.25/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()
+--- modeller-9.25/modlib/modeller/parallel/myspawn.py	(original)
++++ modeller-9.25/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]))
+--- modeller-9.25/modlib/modeller/parallel/sge_qsub_array.py	(original)
++++ modeller-9.25/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)
+ 
+--- modeller-9.25/modlib/modeller/parallel/sge_qsub_slave.py	(original)
++++ modeller-9.25/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)
+ 
+--- modeller-9.25/modlib/modeller/parallel/slaveloop.py	(original)
++++ modeller-9.25/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()
+--- modeller-9.25/modlib/modeller/top_interpreter/__init__.py	(original)
++++ modeller-9.25/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
+--- modeller-9.25/modlib/modeller/top_interpreter/topcmds.py	(original)
++++ modeller-9.25/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])
+--- modeller-9.25/modlib/modeller/top_interpreter/util.py	(original)
++++ modeller-9.25/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
+--- modeller-9.25/modlib/modeller/top_interpreter/variables.py	(original)
++++ modeller-9.25/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):
+--- modeller-9.25/modlib/modeller/util/modobject.py	(original)
++++ modeller-9.25/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
+--- modeller-9.25/modlib/modeller/util/modutil.py	(original)
++++ modeller-9.25/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)

diff --git a/sci-chemistry/modeller/modeller-9.19.ebuild b/sci-chemistry/modeller/modeller-9.19.ebuild
deleted file mode 100644
index 0d29c3843..000000000
--- a/sci-chemistry/modeller/modeller-9.19.ebuild
+++ /dev/null
@@ -1,145 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 eutils multilib versionator
-
-DESCRIPTION="Homology or comparative modeling of protein three-dimensional structures"
-HOMEPAGE="http://salilab.org/modeller/"
-SRC_URI="http://salilab.org/${PN}/${PV}/${P}.tar.gz"
-
-LICENSE="modeller"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc examples"
-SLOT="0"
-
-RESTRICT="mirror"
-
-DEPEND=">=dev-lang/swig-1.3"
-RDEPEND=""
-
-INPATH="${EPREFIX}"/opt/modeller${ver}
-
-QA_PREBUILT="/opt/*"
-
-pkg_setup() {
-	case ${ARCH} in
-		x86)
-			EXECTYPE="i386-intel8";;
-		amd64)
-			EXECTYPE="x86_64-intel8";;
-		*)
-			die "Your arch "${ARCH}" does not appear supported at this time.";;
-	esac
-}
-
-python_prepare_all(){
-	sed "s:i386-intel8:${EXECTYPE}:g" -i src/swig/setup.py || die
-	distutils-r1_python_prepare_all
-}
-
-python_compile(){
-	cd src/swig || die
-	swig -python -keyword -nodefaultctor -nodefaultdtor -noproxy modeller.i || die
-	distutils-r1_python_compile
-}
-
-python_install() {
-	cd src/swig || die
-	distutils-r1_python_install
-}
-
-python_install_all(){
-	cd "${S}" || die
-	sed \
-		-e "/^EXECUTABLE_TYPE/s:xxx:${EXECTYPE}:g" \
-		-e "/MODINSTALL/s:xxx:\"${INPATH}\":g" \
-		-i bin/modscript || die
-
-	sed -e "s;@TOPDIR\@;\"${INPATH}\";" \
-		-e "s;@EXETYPE\@;${EXECTYPE};" \
-		bin/modpy.sh.in > "${T}/modpy.sh"
-
-	insinto ${INPATH}
-	doins -r modlib
-	python_foreach_impl python_domodule modlib/modeller
-
-	insinto ${INPATH}/bin
-	doins -r bin/{lib,*top}
-
-	exeinto ${INPATH}/bin
-	doexe bin/{modscript,mod${PV}_${EXECTYPE}} "${T}"/modpy.sh
-
-	python_foreach_impl python_doscript bin/modslave.py
-	dosym ${INPATH}/bin/modscript /opt/bin/mod${PV}
-	dosym ${INPATH}/bin/modpy.sh /opt/bin/modpy.sh
-
-	exeinto ${INPATH}/lib/${EXECTYPE}/
-	doexe lib/${EXECTYPE}/lib*
-	dosym libmodeller.so.8 ${INPATH}/lib/${EXECTYPE}/libmodeller.so
-	dosym ../../${INPATH}/lib/${EXECTYPE}/libmodeller.so.8 /usr/$(get_libdir)/libmodeller.so.8
-
-	use doc && HTML_DOCS=( doc/. )
-	distutils-r1_python_install_all
-
-	if use examples; then
-		insinto /usr/share/${PN}/
-		doins -r examples
-	fi
-
-	insinto /etc/revdep-rebuild
-	cat >> "${T}"/40-${PN} <<- EOF
-	SEARCH_DIRS_MASK="${EPREFIX}/opt/modeller/lib/"
-	EOF
-	doins "${T}"/40-${PN}
-}
-
-pkg_postinst() {
-	if [[ ! -e "${INPATH}/modlib/modeller/config.py" ]]; then
-		echo install_dir = \"${INPATH}/\"> ${INPATH}/modlib/modeller/config.py
-	fi
-
-	if grep -q license ${INPATH}/modlib/modeller/config.py; then
-		einfo "A license key file is already present in ${IN_PATH}/modlib/modeller/config.py"
-	else
-		ewarn "Obtain a license Key from"
-		ewarn "http://salilab.org/modeller/registration.html"
-		ewarn "And run this before using modeller:"
-		ewarn "emerge --config =${CATEGORY}/${PF}"
-		ewarn "That way you can [re]enter your license key."
-	fi
-}
-
-pkg_postrm() {
-	ewarn "This package leaves a license Key file in ${INPATH}/modlib/modeller/config.py"
-	ewarn "that you need to remove to completely get rid of modeller."
-}
-
-pkg_config() {
-	ewarn "Your license key is NOT checked for validity here."
-	ewarn "  Make sure you type it in correctly."
-	eerror "If you CTRL+C out of this, modeller will not run!"
-	while true
-	do
-		einfo "Please enter your license key:"
-		read license_key1
-		einfo "Please re-enter your license key:"
-		read license_key2
-		if [[ "$license_key1" == "" ]]
-		then
-			echo "You entered a blank license key.  Try again."
-		else
-			if [[ "$license_key1" == "$license_key2" ]]
-			then
-				echo license = '"'$license_key1'"' >> "${INPATH}/modlib/modeller/config.py"
-				einfo "Thank you!"
-				break
-			else
-				eerror "Your license key entries do not match.  Try again."
-			fi
-		fi
-	done
-}

diff --git a/sci-chemistry/modeller/modeller-9.12-r3.ebuild b/sci-chemistry/modeller/modeller-9.25.ebuild
similarity index 90%
rename from sci-chemistry/modeller/modeller-9.12-r3.ebuild
rename to sci-chemistry/modeller/modeller-9.25.ebuild
index de64378e1..cf3af567e 100644
--- a/sci-chemistry/modeller/modeller-9.12-r3.ebuild
+++ b/sci-chemistry/modeller/modeller-9.25.ebuild
@@ -1,15 +1,15 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-PYTHON_COMPAT=( python2_7 )
+PYTHON_COMPAT=( python3_{6,7,8,9} )
 
-inherit distutils-r1 eutils multilib versionator
+inherit distutils-r1 eutils multilib
 
 DESCRIPTION="Homology or comparative modeling of protein three-dimensional structures"
-HOMEPAGE="http://salilab.org/modeller/"
-SRC_URI="http://salilab.org/${PN}/${PV}/${P}.tar.gz"
+HOMEPAGE="https://salilab.org/modeller/"
+SRC_URI="https://salilab.org/${PN}/${PV}/${P}.tar.gz"
 
 LICENSE="modeller"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
@@ -25,6 +25,8 @@ INPATH="${EPREFIX}"/opt/modeller${ver}
 
 QA_PREBUILT="/opt/*"
 
+PATCHES=( "${FILESDIR}/${P}-convert2to3.patch" )
+
 pkg_setup() {
 	case ${ARCH} in
 		x86)
@@ -38,6 +40,8 @@ pkg_setup() {
 
 python_prepare_all(){
 	sed "s:i386-intel8:${EXECTYPE}:g" -i src/swig/setup.py || die
+	rm -rf modlib/modeller/python_library || die
+	sed -i '1 i\#!/usr/bin/python' bin/modslave.py
 	distutils-r1_python_prepare_all
 }
 

[gentoo-commits] proj/sci:master commit in: sci-chemistry/modeller/files/, sci-chemistry/modeller/

[Aisha Tammy]

commit:     53f4815ede1a74949c87692ebf4c6b8f94ac3c42
Author:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
AuthorDate: Thu Dec 31 15:01:03 2020 +0000
Commit:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
CommitDate: Thu Dec 31 15:01:03 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=53f4815e

sci-chemistry/modeller: break patch into 2

Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Aisha Tammy <gentoo <AT> aisha.cc>

 .../files/modeller-9.25-convert2to3-p1.patch       | 339 +++++++++++++++++++++
 ...o3.patch => modeller-9.25-convert2to3-p2.patch} | 339 ---------------------
 sci-chemistry/modeller/modeller-9.25.ebuild        |   7 +-
 3 files changed, 344 insertions(+), 341 deletions(-)

diff --git a/sci-chemistry/modeller/files/modeller-9.25-convert2to3-p1.patch b/sci-chemistry/modeller/files/modeller-9.25-convert2to3-p1.patch
new file mode 100644
index 000000000..deab6d68f
--- /dev/null
+++ b/sci-chemistry/modeller/files/modeller-9.25-convert2to3-p1.patch
@@ -0,0 +1,339 @@
+--- modeller-9.25/modlib/modeller/__init__.py	(original)
++++ modeller-9.25/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'):
+--- modeller-9.25/modlib/modeller/coordinates.py	(original)
++++ modeller-9.25/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,
+--- modeller-9.25/modlib/modeller/id_table.py	(original)
++++ modeller-9.25/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)]))
+--- modeller-9.25/modlib/modeller/libraries.py	(original)
++++ modeller-9.25/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):
+--- modeller-9.25/modlib/modeller/model.py	(original)
++++ modeller-9.25/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):
+--- modeller-9.25/modlib/modeller/model_topology.py	(original)
++++ modeller-9.25/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 \
+--- modeller-9.25/modlib/modeller/physical.py	(original)
++++ modeller-9.25/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
+ 
+--- modeller-9.25/modlib/modeller/salign.py	(original)
++++ modeller-9.25/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()
+--- modeller-9.25/modlib/modeller/saxsdata.py	(original)
++++ modeller-9.25/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,
+--- modeller-9.25/modlib/modeller/selection.py	(original)
++++ modeller-9.25/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),
+--- modeller-9.25/modlib/modeller/test.py	(original)
++++ modeller-9.25/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
+--- modeller-9.25/modlib/modeller/automodel/automodel.py	(original)
++++ modeller-9.25/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

diff --git a/sci-chemistry/modeller/files/modeller-9.25-convert2to3.patch b/sci-chemistry/modeller/files/modeller-9.25-convert2to3-p2.patch
similarity index 51%
rename from sci-chemistry/modeller/files/modeller-9.25-convert2to3.patch
rename to sci-chemistry/modeller/files/modeller-9.25-convert2to3-p2.patch
index d7df05ce6..bd86d9cef 100644
--- a/sci-chemistry/modeller/files/modeller-9.25-convert2to3.patch
+++ b/sci-chemistry/modeller/files/modeller-9.25-convert2to3-p2.patch
@@ -1,342 +1,3 @@
---- modeller-9.25/modlib/modeller/__init__.py	(original)
-+++ modeller-9.25/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'):
---- modeller-9.25/modlib/modeller/coordinates.py	(original)
-+++ modeller-9.25/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,
---- modeller-9.25/modlib/modeller/id_table.py	(original)
-+++ modeller-9.25/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)]))
---- modeller-9.25/modlib/modeller/libraries.py	(original)
-+++ modeller-9.25/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):
---- modeller-9.25/modlib/modeller/model.py	(original)
-+++ modeller-9.25/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):
---- modeller-9.25/modlib/modeller/model_topology.py	(original)
-+++ modeller-9.25/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 \
---- modeller-9.25/modlib/modeller/physical.py	(original)
-+++ modeller-9.25/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
- 
---- modeller-9.25/modlib/modeller/salign.py	(original)
-+++ modeller-9.25/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()
---- modeller-9.25/modlib/modeller/saxsdata.py	(original)
-+++ modeller-9.25/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,
---- modeller-9.25/modlib/modeller/selection.py	(original)
-+++ modeller-9.25/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),
---- modeller-9.25/modlib/modeller/test.py	(original)
-+++ modeller-9.25/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
---- modeller-9.25/modlib/modeller/automodel/automodel.py	(original)
-+++ modeller-9.25/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
 --- modeller-9.25/modlib/modeller/automodel/generate.py	(original)
 +++ modeller-9.25/modlib/modeller/automodel/generate.py	(refactored)
 @@ -88,11 +88,11 @@

diff --git a/sci-chemistry/modeller/modeller-9.25.ebuild b/sci-chemistry/modeller/modeller-9.25.ebuild
index 8db00ea11..cac137131 100644
--- a/sci-chemistry/modeller/modeller-9.25.ebuild
+++ b/sci-chemistry/modeller/modeller-9.25.ebuild
@@ -4,7 +4,7 @@
 EAPI=7
 
 PYTHON_COMPAT=( python3_{7,8,9} )
-
+DISTUTILS_USE_SETUPTOOLS=no
 inherit distutils-r1 eutils multilib
 
 DESCRIPTION="Homology or comparative modeling of protein three-dimensional structures"
@@ -24,7 +24,10 @@ INPATH="${EPREFIX}"/opt/modeller${ver}
 
 QA_PREBUILT="/opt/*"
 
-PATCHES=( "${FILESDIR}/${P}-convert2to3.patch" )
+PATCHES=(
+	"${FILESDIR}/${P}-convert2to3-p1.patch"
+	"${FILESDIR}/${P}-convert2to3-p2.patch"
+)
 
 pkg_setup() {
 	case ${ARCH} in

[gentoo-commits] proj/sci:master commit in: sci-chemistry/modeller/files/, sci-chemistry/modeller/

[Andrew Ammerlaan]

commit:     b169f6ef9508cb12bd94d826e2a2906da8cfccb5
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Wed Feb 17 20:03:15 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Wed Feb 17 20:03:15 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b169f6ef

sci-chemistry/modeller: remove duplicate, exact same version is in ::gentoo

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 .../files/modeller-9.25-convert2to3-p1.patch       | 339 -------------------
 .../files/modeller-9.25-convert2to3-p2.patch       | 363 ---------------------
 sci-chemistry/modeller/metadata.xml                |   8 -
 sci-chemistry/modeller/modeller-9.25.ebuild        | 151 ---------
 4 files changed, 861 deletions(-)

diff --git a/sci-chemistry/modeller/files/modeller-9.25-convert2to3-p1.patch b/sci-chemistry/modeller/files/modeller-9.25-convert2to3-p1.patch
deleted file mode 100644
index deab6d68f..000000000
--- a/sci-chemistry/modeller/files/modeller-9.25-convert2to3-p1.patch
+++ /dev/null
@@ -1,339 +0,0 @@
---- modeller-9.25/modlib/modeller/__init__.py	(original)
-+++ modeller-9.25/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'):
---- modeller-9.25/modlib/modeller/coordinates.py	(original)
-+++ modeller-9.25/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,
---- modeller-9.25/modlib/modeller/id_table.py	(original)
-+++ modeller-9.25/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)]))
---- modeller-9.25/modlib/modeller/libraries.py	(original)
-+++ modeller-9.25/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):
---- modeller-9.25/modlib/modeller/model.py	(original)
-+++ modeller-9.25/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):
---- modeller-9.25/modlib/modeller/model_topology.py	(original)
-+++ modeller-9.25/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 \
---- modeller-9.25/modlib/modeller/physical.py	(original)
-+++ modeller-9.25/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
- 
---- modeller-9.25/modlib/modeller/salign.py	(original)
-+++ modeller-9.25/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()
---- modeller-9.25/modlib/modeller/saxsdata.py	(original)
-+++ modeller-9.25/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,
---- modeller-9.25/modlib/modeller/selection.py	(original)
-+++ modeller-9.25/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),
---- modeller-9.25/modlib/modeller/test.py	(original)
-+++ modeller-9.25/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
---- modeller-9.25/modlib/modeller/automodel/automodel.py	(original)
-+++ modeller-9.25/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

diff --git a/sci-chemistry/modeller/files/modeller-9.25-convert2to3-p2.patch b/sci-chemistry/modeller/files/modeller-9.25-convert2to3-p2.patch
deleted file mode 100644
index bd86d9cef..000000000
--- a/sci-chemistry/modeller/files/modeller-9.25-convert2to3-p2.patch
+++ /dev/null
@@ -1,363 +0,0 @@
---- modeller-9.25/modlib/modeller/automodel/generate.py	(original)
-+++ modeller-9.25/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):
---- modeller-9.25/modlib/modeller/automodel/loopmodel.py	(original)
-+++ modeller-9.25/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):
---- modeller-9.25/modlib/modeller/mmcif/writer.py	(original)
-+++ modeller-9.25/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):
---- modeller-9.25/modlib/modeller/optimizers/builtin_optimizer.py	(original)
-+++ modeller-9.25/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)
- 
---- modeller-9.25/modlib/modeller/optimizers/optimizer.py	(original)
-+++ modeller-9.25/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:
---- modeller-9.25/modlib/modeller/parallel/data_types.py	(original)
-+++ modeller-9.25/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
- 
---- modeller-9.25/modlib/modeller/parallel/job.py	(original)
-+++ modeller-9.25/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()
---- modeller-9.25/modlib/modeller/parallel/myspawn.py	(original)
-+++ modeller-9.25/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]))
---- modeller-9.25/modlib/modeller/parallel/sge_qsub_array.py	(original)
-+++ modeller-9.25/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)
- 
---- modeller-9.25/modlib/modeller/parallel/sge_qsub_slave.py	(original)
-+++ modeller-9.25/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)
- 
---- modeller-9.25/modlib/modeller/parallel/slaveloop.py	(original)
-+++ modeller-9.25/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()
---- modeller-9.25/modlib/modeller/top_interpreter/__init__.py	(original)
-+++ modeller-9.25/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
---- modeller-9.25/modlib/modeller/top_interpreter/topcmds.py	(original)
-+++ modeller-9.25/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])
---- modeller-9.25/modlib/modeller/top_interpreter/util.py	(original)
-+++ modeller-9.25/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
---- modeller-9.25/modlib/modeller/top_interpreter/variables.py	(original)
-+++ modeller-9.25/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):
---- modeller-9.25/modlib/modeller/util/modobject.py	(original)
-+++ modeller-9.25/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
---- modeller-9.25/modlib/modeller/util/modutil.py	(original)
-+++ modeller-9.25/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)

diff --git a/sci-chemistry/modeller/metadata.xml b/sci-chemistry/modeller/metadata.xml
deleted file mode 100644
index da36ecbfc..000000000
--- a/sci-chemistry/modeller/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>

diff --git a/sci-chemistry/modeller/modeller-9.25.ebuild b/sci-chemistry/modeller/modeller-9.25.ebuild
deleted file mode 100644
index cac137131..000000000
--- a/sci-chemistry/modeller/modeller-9.25.ebuild
+++ /dev/null
@@ -1,151 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8,9} )
-DISTUTILS_USE_SETUPTOOLS=no
-inherit distutils-r1 eutils multilib
-
-DESCRIPTION="Homology or comparative modeling of protein three-dimensional structures"
-HOMEPAGE="https://salilab.org/modeller/"
-SRC_URI="https://salilab.org/${PN}/${PV}/${P}.tar.gz"
-
-LICENSE="modeller"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc examples"
-SLOT="0"
-
-RESTRICT="mirror"
-
-DEPEND=">=dev-lang/swig-1.3"
-
-INPATH="${EPREFIX}"/opt/modeller${ver}
-
-QA_PREBUILT="/opt/*"
-
-PATCHES=(
-	"${FILESDIR}/${P}-convert2to3-p1.patch"
-	"${FILESDIR}/${P}-convert2to3-p2.patch"
-)
-
-pkg_setup() {
-	case ${ARCH} in
-		x86)
-			EXECTYPE="i386-intel8";;
-		amd64)
-			EXECTYPE="x86_64-intel8";;
-		*)
-			die "Your arch "${ARCH}" does not appear supported at this time.";;
-	esac
-}
-
-python_prepare_all(){
-	sed "s:i386-intel8:${EXECTYPE}:g" -i src/swig/setup.py || die
-	rm -rf modlib/modeller/python_library || die
-	sed -i '1 i\#!/usr/bin/python' bin/modslave.py
-	distutils-r1_python_prepare_all
-}
-
-python_compile(){
-	cd src/swig || die
-	swig -python -keyword -nodefaultctor -nodefaultdtor -noproxy modeller.i || die
-	distutils-r1_python_compile
-}
-
-python_install() {
-	cd src/swig || die
-	distutils-r1_python_install
-}
-
-python_install_all(){
-	cd "${S}" || die
-	sed \
-		-e "/^EXECUTABLE_TYPE/s:xxx:${EXECTYPE}:g" \
-		-e "/MODINSTALL/s:xxx:\"${INPATH}\":g" \
-		-i bin/modscript || die
-
-	sed -e "s;@TOPDIR\@;\"${INPATH}\";" \
-		-e "s;@EXETYPE\@;${EXECTYPE};" \
-		bin/modpy.sh.in > "${T}/modpy.sh"
-
-	insinto ${INPATH}
-	doins -r modlib
-	python_foreach_impl python_domodule modlib/modeller
-
-	insinto ${INPATH}/bin
-	doins -r bin/{lib,*top}
-
-	exeinto ${INPATH}/bin
-	doexe bin/{modscript,mod${PV}_${EXECTYPE}} "${T}"/modpy.sh
-
-	python_foreach_impl python_doscript bin/modslave.py
-	dosym ${INPATH}/bin/modscript /opt/bin/mod${PV}
-	dosym ${INPATH}/bin/modpy.sh /opt/bin/modpy.sh
-
-	exeinto ${INPATH}/lib/${EXECTYPE}/
-	doexe lib/${EXECTYPE}/lib*
-	dosym libmodeller.so.8 ${INPATH}/lib/${EXECTYPE}/libmodeller.so
-	dosym ../../${INPATH}/lib/${EXECTYPE}/libmodeller.so.8 /usr/$(get_libdir)/libmodeller.so.8
-
-	use doc && HTML_DOCS=( doc/. )
-	distutils-r1_python_install_all
-
-	if use examples; then
-		insinto /usr/share/${PN}/
-		doins -r examples
-	fi
-
-	insinto /etc/revdep-rebuild
-	cat >> "${T}"/40-${PN} <<- EOF
-	SEARCH_DIRS_MASK="${EPREFIX}/opt/modeller/lib/"
-	EOF
-	doins "${T}"/40-${PN}
-}
-
-pkg_postinst() {
-	if [[ ! -e "${INPATH}/modlib/modeller/config.py" ]]; then
-		echo install_dir = \"${INPATH}/\"> ${INPATH}/modlib/modeller/config.py
-	fi
-
-	if grep -q license ${INPATH}/modlib/modeller/config.py; then
-		einfo "A license key file is already present in ${IN_PATH}/modlib/modeller/config.py"
-	else
-		ewarn "Obtain a license Key from"
-		ewarn "http://salilab.org/modeller/registration.html"
-		ewarn "And run this before using modeller:"
-		ewarn "emerge --config =${CATEGORY}/${PF}"
-		ewarn "That way you can [re]enter your license key."
-	fi
-}
-
-pkg_postrm() {
-	ewarn "This package leaves a license Key file in ${INPATH}/modlib/modeller/config.py"
-	ewarn "that you need to remove to completely get rid of modeller."
-}
-
-pkg_config() {
-	ewarn "Your license key is NOT checked for validity here."
-	ewarn "  Make sure you type it in correctly."
-	eerror "If you CTRL+C out of this, modeller will not run!"
-	while true
-	do
-		einfo "Please enter your license key:"
-		read license_key1
-		einfo "Please re-enter your license key:"
-		read license_key2
-		if [[ "$license_key1" == "" ]]
-		then
-			echo "You entered a blank license key.  Try again."
-		else
-			if [[ "$license_key1" == "$license_key2" ]]
-			then
-				echo license = '"'$license_key1'"' >> "${INPATH}/modlib/modeller/config.py"
-				einfo "Thank you!"
-				break
-			else
-				eerror "Your license key entries do not match.  Try again."
-			fi
-		fi
-	done
-}