diff options
Diffstat (limited to 'sci-chemistry/modeller/files/modeller-9.25-convert2to3-p2.patch')
| -rw-r--r-- | sci-chemistry/modeller/files/modeller-9.25-convert2to3-p2.patch | 363 |
1 files changed, 363 insertions, 0 deletions
diff --git a/sci-chemistry/modeller/files/modeller-9.25-convert2to3-p2.patch b/sci-chemistry/modeller/files/modeller-9.25-convert2to3-p2.patch new file mode 100644 index 000000000..bd86d9cef --- /dev/null +++ b/sci-chemistry/modeller/files/modeller-9.25-convert2to3-p2.patch @@ -0,0 +1,363 @@ +--- 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) |