diff options
author | 2020-12-31 15:01:03 +0000 | |
---|---|---|
committer | 2020-12-31 15:01:03 +0000 | |
commit | 53f4815ede1a74949c87692ebf4c6b8f94ac3c42 (patch) | |
tree | 912aec30a7d63619403abb09cbfa1774c08e6196 /sci-chemistry/modeller/files/modeller-9.25-convert2to3-p1.patch | |
parent | sci-libs/spyking-circus: version bump, bump py targets (diff) | |
download | sci-53f4815ede1a74949c87692ebf4c6b8f94ac3c42.tar.gz sci-53f4815ede1a74949c87692ebf4c6b8f94ac3c42.tar.bz2 sci-53f4815ede1a74949c87692ebf4c6b8f94ac3c42.zip |
sci-chemistry/modeller: break patch into 2
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Aisha Tammy <gentoo@aisha.cc>
Diffstat (limited to 'sci-chemistry/modeller/files/modeller-9.25-convert2to3-p1.patch')
-rw-r--r-- | sci-chemistry/modeller/files/modeller-9.25-convert2to3-p1.patch | 339 |
1 files changed, 339 insertions, 0 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 |