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
