* Package: sci-chemistry/modeller-9.25 * Repository: gentoo * Maintainer: alexxy@gentoo.org sci-chemistry@gentoo.org * USE: abi_x86_64 amd64 elibc_musl kernel_linux python_targets_python3_8 python_targets_python3_9 userland_GNU * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox @@@@@ PLEASE PAY ATTENTION HERE!!! @@@@@ This information may help you to understand if this is a duplicate or if this bug exists after you pushed a fix; This ebuild was merged at the following commit: https://github.com/gentoo-mirror/gentoo/commit/d43e44fd025825ec24fe5791ac96f5692143b27b (Fri Feb 4 09:37:03 UTC 2022) @@@@@ END @@@@@ ################## # emerge --info: # ################## !!! It seems /run is not mounted. Process management may malfunction. Portage 3.0.30 (python 3.10.2-final-0, default/linux/amd64/17.0/musl/hardened, gcc-11.2.1, musl-1.2.2-r7, 4.19.174-gentoo x86_64) ================================================================= System uname: Linux-4.19.174-gentoo-x86_64-Intel-R-_Xeon-R-_CPU_E5-2650_v4_@_2.20GHz-with-libc KiB Mem: 264046488 total, 61637124 free KiB Swap: 0 total, 0 free Timestamp of repository gentoo: Fri, 04 Feb 2022 09:37:00 +0000 sh bash 5.1_p16 ld GNU ld (Gentoo 2.37_p1 p2) 2.37 app-misc/pax-utils: 1.3.3::gentoo app-shells/bash: 5.1_p16::gentoo dev-lang/perl: 5.34.0-r6::gentoo dev-lang/python: 3.8.12_p1-r2::gentoo, 3.9.10-r1::gentoo, 3.10.2-r1::gentoo dev-util/cmake: 3.22.2::gentoo dev-util/meson: 0.60.3::gentoo sys-apps/baselayout: 2.8::gentoo sys-apps/openrc: 0.44.10::gentoo sys-apps/sandbox: 2.29::gentoo sys-devel/autoconf: 2.71-r1::gentoo sys-devel/automake: 1.16.5::gentoo sys-devel/binutils: 2.37_p1-r2::gentoo sys-devel/binutils-config: 5.4::gentoo sys-devel/gcc: 11.2.1_p20220115::gentoo sys-devel/gcc-config: 2.5-r1::gentoo sys-devel/libtool: 2.4.6-r6::gentoo sys-devel/make: 4.3::gentoo sys-kernel/linux-headers: 5.16::gentoo (virtual/os-headers) sys-libs/musl: 1.2.2-r7::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 sync-rsync-verify-metamanifest: yes sync-rsync-verify-max-age: 24 sync-rsync-verify-jobs: 1 sync-rsync-extra-opts: ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* modeller" CBUILD="x86_64-gentoo-linux-musl" CFLAGS="-O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0" CHOST="x86_64-gentoo-linux-musl" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" CXXFLAGS="-O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0" DISTDIR="/var/tmp/portage/sci-chemistry/modeller-9.25/distdir" EMERGE_DEFAULT_OPTS="--with-bdeps=y -1 -k -b" ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN GOPATH PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR" FCFLAGS="-O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0" FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs binpkg-multi-instance buildpkg buildpkg-live config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms sign split-log strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0" GENTOO_MIRRORS="http://mirror.leaseweb.com/gentoo/ http://ftp.snt.utwente.nl/pub/os/linux/gentoo/ http://ftp.belnet.be/pub/rsync.gentoo.org/gentoo/ http://distfiles.gentoo.org" INSTALL_MASK="charset.alias /usr/share/locale/locale.alias" LANG="C.UTF8" LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0" MAKEOPTS="-j16" PKGDIR="/root/tbci/binpkg" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git" PORTAGE_TMPDIR="/var/tmp" SHELL="/bin/bash" USE="acl amd64 bzip2 crypt elogind hardened iconv ipv6 jumbo-build libglvnd libtirpc native-symlinks ncurses nls nptl openmp pam pcre pie readline seccomp split-usr ssl ssp unicode xattr xtpax zlib" ABI_X86="64" ELIBC="musl" KERNEL="linux" PYTHON_TARGETS="python3_8 python3_9" USERLAND="GNU" Unset: ADDR2LINE, AR, ARFLAGS, AS, ASFLAGS, CC, CCLD, CONFIG_SHELL, CPP, CPPFLAGS, CTARGET, CXX, CXXFILT, ELFEDIT, EXTRA_ECONF, F77FLAGS, FC, GCOV, GPROF, LC_ALL, LD, LEX, LFLAGS, LIBTOOL, LINGUAS, MAKE, MAKEFLAGS, NM, OBJCOPY, OBJDUMP, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, RANLIB, READELF, RUSTFLAGS, SIZE, STRINGS, STRIP, YACC, YFLAGS ############################## # emerge history (qlop -mv): # ############################## 2022-02-04T10:50:32 >>> dev-lang/swig-4.0.2 ####################################### # installed packages (qlist -ICvUSS): # ####################################### acct-group/audio-0-r1:0 acct-group/cdrom-0-r1:0 acct-group/dialout-0-r1:0 acct-group/disk-0-r1:0 acct-group/input-0-r1:0 acct-group/kmem-0-r1:0 acct-group/kvm-0-r1:0 acct-group/lp-0-r1:0 acct-group/man-0-r1:0 acct-group/messagebus-0-r1:0 acct-group/portage-0:0 acct-group/render-0-r1:0 acct-group/sgx-0:0 acct-group/sshd-0-r1:0 acct-group/tape-0-r1:0 acct-group/tty-0-r1:0 acct-group/video-0-r1:0 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virtual/libudev-232-r5:0/1 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -systemd virtual/man-0-r4:0 virtual/os-headers-0-r2:0 virtual/package-manager-1:0 virtual/pager-0:0 virtual/perl-Carp-1.520.0-r1:0 virtual/perl-Compress-Raw-Bzip2-2.101.0:0 virtual/perl-Compress-Raw-Zlib-2.101.0:0 virtual/perl-CPAN-2.290.0:0 virtual/perl-CPAN-Meta-2.150.10-r5:0 virtual/perl-CPAN-Meta-Requirements-2.140.0-r7:0 virtual/perl-CPAN-Meta-YAML-0.18.0-r7:0 virtual/perl-Data-Dumper-2.179.0:0 virtual/perl-Digest-MD5-2.580.0:0 virtual/perl-Encode-3.120.0:0 virtual/perl-Exporter-5.760.0:0 virtual/perl-ExtUtils-CBuilder-0.280.236:0 virtual/perl-ExtUtils-Install-2.200.0:0 virtual/perl-ExtUtils-MakeMaker-7.620.0:0 virtual/perl-ExtUtils-Manifest-1.730.0:0 virtual/perl-ExtUtils-ParseXS-3.430.0:0 virtual/perl-File-Spec-3.800.0:0 virtual/perl-File-Temp-0.231.100:0 virtual/perl-Getopt-Long-2.520.0:0 virtual/perl-IO-1.460.0:0 virtual/perl-IO-Compress-2.102.0:0 virtual/perl-IO-Socket-IP-0.410.0:0 virtual/perl-JSON-PP-4.60.0:0 virtual/perl-libnet-3.130.0:0 ssl virtual/perl-MIME-Base64-3.160.0:0 virtual/perl-Module-Metadata-1.0.37-r1:0 virtual/perl-parent-0.238.0-r1:0 virtual/perl-Parse-CPAN-Meta-2.150.10-r5:0 virtual/perl-Perl-OSType-1.10.0-r5:0 virtual/perl-podlators-4.140.0-r2:0 virtual/perl-Scalar-List-Utils-1.560.0:0 virtual/perl-Test-Harness-3.430.0:0 virtual/perl-Text-ParseWords-3.300.0-r8:0 virtual/perl-Time-Local-1.300.0:0 virtual/perl-version-0.992.800:0 virtual/perl-XSLoader-0.300.0-r4:0 virtual/pkgconfig-2-r1:0 virtual/service-manager-1:0 virtual/ssh-0:0 -minimal virtual/tmpfiles-0-r1:0 virtual/ttf-fonts-1-r1:0 virtual/udev-217-r3:0 virtual/yacc-0:0 www-client/pybugz-0.13-r1:0 python_targets_python3_8 python_targets_python3_9 x11-libs/cairo-1.16.0-r5:0 -X -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -aqua -debug -gles2-only glib -opengl -static-libs svg -utils -valgrind x11-libs/pixman-0.40.0:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -cpu_flags_arm_iwmmxt -cpu_flags_arm_iwmmxt2 -cpu_flags_arm_neon -cpu_flags_ppc_altivec cpu_flags_x86_mmxext cpu_flags_x86_sse2 cpu_flags_x86_ssse3 -loongson2f -static-libs x11-misc/shared-mime-info-2.1:0 ####################### # build.log # ####################### >>> Unpacking source... >>> Unpacking modeller-9.25.tar.gz to /var/tmp/portage/sci-chemistry/modeller-9.25/work >>> Source unpacked in /var/tmp/portage/sci-chemistry/modeller-9.25/work >>> Preparing source in /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25 ... RefactoringTool: Skipping optional fixer: buffer RefactoringTool: Skipping optional fixer: idioms RefactoringTool: Skipping optional fixer: set_literal RefactoringTool: Skipping optional fixer: ws_comma RefactoringTool: Refactored modlib/modeller/__init__.py --- modlib/modeller/__init__.py (original) +++ modlib/modeller/__init__.py (refactored) @@ -48,7 +48,7 @@ return sys.maxsize > 2**32 # This works on older Pythons, but not in Python 3 else: - return type(sys.dllhandle) == long + return type(sys.dllhandle) == int # Special processing on Windows to find _modeller.pyd and Modeller DLLs: if hasattr(config, 'install_dir') and hasattr(sys, 'dllhandle'): RefactoringTool: No changes to modlib/modeller/alignment.py RefactoringTool: No changes to modlib/modeller/alnsequence.py RefactoringTool: No changes to modlib/modeller/alnstructure.py RefactoringTool: No changes to modlib/modeller/atom_type.py RefactoringTool: Refactored modlib/modeller/coordinates.py --- modlib/modeller/coordinates.py (original) +++ modlib/modeller/coordinates.py (refactored) @@ -147,7 +147,7 @@ (startres, endres) = self._get_resind() (startatm, endatm) = get_residue_atom_indices(self.seq, startres, endres) - return (range(startatm+1, endatm+1), self.seq) + return (list(range(startatm+1, endatm+1)), self.seq) atoms = property(__get_atoms, doc="List of all atoms in this chain") @@ -158,7 +158,7 @@ def get_atom_indices(self): (startind, endind) = get_residue_atom_indices(self.mdl, self._num, self._num + 1) - return range(startind + 1, endind + 1), self.mdl + return list(range(startind + 1, endind + 1)), self.mdl def __repr__(self): # Get residue number before we do anything else. For alignment @@ -252,7 +252,7 @@ def get_atom_indices(self): (startind, endind) = get_residue_atom_indices(self.mdl, self.offset, self.offset + len(self)) - return range(startind + 1, endind + 1), self.mdl + return list(range(startind + 1, endind + 1)), self.mdl def __getitem__(self, indx): ret = modutil.handle_seq_indx(self, indx, self.mdl._indxres, @@ -398,7 +398,7 @@ return self.mdl.natm def get_atom_indices(self): - return range(self.offset + 1, self.offset + len(self) + 1), self.mdl + return list(range(self.offset + 1, self.offset + len(self) + 1)), self.mdl def __getitem__(self, indx): ret = modutil.handle_seq_indx(self, indx, self.mdl._indxatm, RefactoringTool: No changes to modlib/modeller/density.py RefactoringTool: No changes to modlib/modeller/energy_data.py RefactoringTool: No changes to modlib/modeller/energy_profile.py RefactoringTool: No changes to modlib/modeller/environ.py RefactoringTool: No changes to modlib/modeller/excluded_pair.py RefactoringTool: No changes to modlib/modeller/excluded_pair_list.py RefactoringTool: No changes to modlib/modeller/features.py RefactoringTool: No changes to modlib/modeller/forms.py RefactoringTool: No changes to modlib/modeller/gbsa.py RefactoringTool: No changes to modlib/modeller/group_restraints.py RefactoringTool: Refactored modlib/modeller/id_table.py --- modlib/modeller/id_table.py (original) +++ modlib/modeller/id_table.py (refactored) @@ -40,7 +40,7 @@ def write_seqid_matrix(fh, coder, mat): """Write a sequence identity matrix to a file""" nseq = len(mat) - print(" " * 9 + "".join([ s[:8] for s in coder ])) + print((" " * 9 + "".join([ s[:8] for s in coder ]))) for n1 in range(nseq): fh.write(coder[n1][:8] + " " + \ "".join(["%8d" % (mat[n1][n2]+0.5) for n2 in range(nseq)])) RefactoringTool: No changes to modlib/modeller/information.py RefactoringTool: No changes to modlib/modeller/io_data.py RefactoringTool: Refactored modlib/modeller/libraries.py --- modlib/modeller/libraries.py (original) +++ modlib/modeller/libraries.py (refactored) @@ -32,7 +32,7 @@ return BytesIO(*args) else: def _make_bytes_io(self, *args): - from cStringIO import StringIO + from io import StringIO return StringIO(*args) def __getstate__(self): RefactoringTool: Refactored modlib/modeller/model.py --- modlib/modeller/model.py (original) +++ modlib/modeller/model.py (refactored) @@ -121,7 +121,7 @@ def get_atom_indices(self): """Get the indices of all atoms in this model""" - return (range(1, self.natm+1), self) + return (list(range(1, self.natm+1)), self) def read(self, file, model_format='PDB', model_segment=('FIRST:@', 'LAST:'), io=None, @@ -340,7 +340,7 @@ dope_score = sel.assess_dope() scorer = normalized_dope.DOPEScorer(self) z_score = scorer.get_z_score(dope_score) - print(">> Normalized DOPE z score: %.3f" % z_score) + print((">> Normalized DOPE z score: %.3f" % z_score)) return z_score def assess_normalized_dopehr(self): @@ -351,7 +351,7 @@ dope_score = sel.assess_dopehr() scorer = normalized_dope.DOPEHRScorer(self) z_score = scorer.get_z_score(dope_score) - print(">> Normalized DOPE-HR z score: %.3f" % z_score) + print((">> Normalized DOPE-HR z score: %.3f" % z_score)) return z_score def get_normalized_dope_profile(self): RefactoringTool: Refactored modlib/modeller/model_topology.py --- modlib/modeller/model_topology.py (original) +++ modlib/modeller/model_topology.py (refactored) @@ -50,7 +50,7 @@ self.check_args = args def __iter__(self): return self - def next(self): + def __next__(self): while True: atoms = self.__int_next() if self.check_func is None \ @@ -82,7 +82,7 @@ self.check_args = args def __iter__(self): return self - def next(self): + def __next__(self): while True: atoms = self.__int_next() if self.check_func is None \ RefactoringTool: No changes to modlib/modeller/modfile.py RefactoringTool: No changes to modlib/modeller/normalized_dope.py RefactoringTool: No changes to modlib/modeller/orient.py RefactoringTool: No changes to modlib/modeller/parameters.py RefactoringTool: Refactored modlib/modeller/physical.py --- modlib/modeller/physical.py (original) +++ modlib/modeller/physical.py (refactored) @@ -31,7 +31,7 @@ def __init__(self, default=1.0, **keys): self._default = default self._dict = {} - for (term,val) in keys.items(): + for (term,val) in list(keys.items()): term = eval("%s" % term) self[term] = val RefactoringTool: No changes to modlib/modeller/profile.py RefactoringTool: No changes to modlib/modeller/pseudo_atom.py RefactoringTool: No changes to modlib/modeller/pseudo_atom_list.py RefactoringTool: No changes to modlib/modeller/pssmdb.py RefactoringTool: No changes to modlib/modeller/residue.py RefactoringTool: No changes to modlib/modeller/restraints.py RefactoringTool: No changes to modlib/modeller/rigid_body.py RefactoringTool: No changes to modlib/modeller/rigid_body_list.py RefactoringTool: Refactored modlib/modeller/salign.py --- modlib/modeller/salign.py (original) +++ modlib/modeller/salign.py (refactored) @@ -38,8 +38,8 @@ return aln.salign(auto_overhang=True, overhang_auto_limit=5, overhang_factor=1, **keys) except modeller.ModellerError: - print("SALIGN with auto_overhang failed: %s" \ - % str(sys.exc_info()[1])) + print(("SALIGN with auto_overhang failed: %s" \ + % str(sys.exc_info()[1]))) print("Retrying without auto_overhang") return aln.salign(**keys) @@ -118,13 +118,13 @@ self.qscore = res.qscorepct self.aln.write(file=output_aln_file, alignment_format='PIR') better = True - print("Qlty scrs %g\t%g\t%g" % (open_penalty, extend_penalty, - res.qscorepct)) + print(("Qlty scrs %g\t%g\t%g" % (open_penalty, extend_penalty, + res.qscorepct))) except modeller.ModellerError: - print("Set of parameters %s %g %g resulted in the " + print(("Set of parameters %s %g %g resulted in the " "following error\t%s" % (str(weights), open_penalty, extend_penalty, - str(sys.exc_info()[1]))) + str(sys.exc_info()[1])))) return better @@ -181,7 +181,7 @@ best.try_struc_align(opfile, opfile2, fw2, ogp3d, egp3d, align_block) - print("final max quality = %g" % best.qscore) + print(("final max quality = %g" % best.qscore)) if best.found_struc_align: aln.clear() RefactoringTool: Refactored modlib/modeller/saxsdata.py --- modlib/modeller/saxsdata.py (original) +++ modlib/modeller/saxsdata.py (refactored) @@ -206,7 +206,7 @@ try: fh = open(saxsfilename,'r') except: - print("file "+saxsfilename+" not found :(") + print(("file "+saxsfilename+" not found :(")) return fh.close() ns = 0 @@ -225,8 +225,8 @@ s_low = s_min - .001 if (not s_hi): s_hi = s_max + .001 - print("s_min=%s, s_max=%s" % (str(s_min), str(s_max))) - print("s_low=%s, s_hi=%s" % (str(s_low), str(s_hi))) + print(("s_min=%s, s_max=%s" % (str(s_min), str(s_max)))) + print(("s_low=%s, s_hi=%s" % (str(s_low), str(s_hi)))) self.ini_saxs(atmsel, filename=formfacfilename, s_min=s_min, s_max=s_max, maxs=ns, nmesh=ns, natomtyp=natomtyp, RefactoringTool: No changes to modlib/modeller/schedule.py RefactoringTool: No changes to modlib/modeller/secondary_structure.py RefactoringTool: Refactored modlib/modeller/selection.py --- modlib/modeller/selection.py (original) +++ modlib/modeller/selection.py (refactored) @@ -23,7 +23,7 @@ return self.mdl.atoms[obj - 1] else: def next(self): - obj = self.seliter.next() + obj = next(self.seliter) return self.mdl.atoms[obj - 1] class selection(object): @@ -52,7 +52,7 @@ :rtype: list of ints """ if sys.version_info[:2] == (2,3): - keys = self.__selection.keys() + keys = list(self.__selection.keys()) keys.sort() else: keys = sorted(self.__selection.keys()) @@ -722,9 +722,9 @@ def assess(self, assessor, output='SHORT NO_REPORT', **vars): """Assess with the given assessor object (e.g. :class:`soap_loop.Scorer`).""" - print(">> Model assessment by %s" % assessor.name) + print((">> Model assessment by %s" % assessor.name)) molpdf, terms = assessor._assess(self, output=output, **vars) - print("%s : %12.6f" % (assessor.name, molpdf)) + print(("%s : %12.6f" % (assessor.name, molpdf))) return molpdf def _dope_energy(self, gprsr, name, output='SHORT NO_REPORT', @@ -733,7 +733,7 @@ nonbond_spline=1.), **vars): """Internal function to do DOPE or DOPE-HR assessment""" mdl = self.__mdl - print(">> Model assessment by %s potential" % name) + print((">> Model assessment by %s potential" % name)) edat = self.get_dope_energy_data() old_gprsr = mdl.group_restraints mdl.group_restraints = gprsr @@ -744,7 +744,7 @@ **vars) finally: mdl.group_restraints = old_gprsr - print("%s score : %12.6f" % (name, molpdf)) + print(("%s score : %12.6f" % (name, molpdf))) return molpdf def debug_function(self, residue_span_range=(0, 99999), RefactoringTool: No changes to modlib/modeller/sequence.py RefactoringTool: No changes to modlib/modeller/sequence_db.py RefactoringTool: No changes to modlib/modeller/soap_loop.py RefactoringTool: No changes to modlib/modeller/soap_peptide.py RefactoringTool: No changes to modlib/modeller/soap_pp.py RefactoringTool: No changes to modlib/modeller/soap_protein_od.py RefactoringTool: No changes to modlib/modeller/superpose.py RefactoringTool: No changes to modlib/modeller/symmetry.py RefactoringTool: No changes to modlib/modeller/symmetry_list.py RefactoringTool: No changes to modlib/modeller/terms.py RefactoringTool: Refactored modlib/modeller/test.py --- modlib/modeller/test.py (original) +++ modlib/modeller/test.py (refactored) @@ -2,7 +2,7 @@ import modeller import math try: - from cStringIO import StringIO + from io import StringIO except ImportError: from io import StringIO import sys @@ -150,7 +150,7 @@ diff = abs(num1 - num2) if msg is None: msg = "%f != %f within %g" % (num1, num2, tolerance) - self.assert_(diff < tolerance, msg) + self.assertTrue(diff < tolerance, msg) def run_capture_stdout(self, method, *args, **keys): """Run a method and capture its standard output. Returns both the RefactoringTool: No changes to modlib/modeller/topology.py RefactoringTool: No changes to modlib/modeller/virtual_atom.py RefactoringTool: No changes to modlib/modeller/automodel/__init__.py RefactoringTool: No changes to modlib/modeller/automodel/allhmodel.py RefactoringTool: No changes to modlib/modeller/automodel/assess.py RefactoringTool: Refactored modlib/modeller/automodel/automodel.py --- modlib/modeller/automodel/automodel.py (original) +++ modlib/modeller/automodel/automodel.py (refactored) @@ -203,13 +203,13 @@ def write_ok_summary(self, all, modeltyp): """Print out a summary of all successfully generated models""" - print("\n>> Summary of successfully produced %s:" % modeltyp) - fields = [x for x in all[0].keys() if x.endswith(' score')] + print(("\n>> Summary of successfully produced %s:" % modeltyp)) + fields = [x for x in list(all[0].keys()) if x.endswith(' score')] fields.sort() fields = ['molpdf'] + fields header = '%-25s ' % 'Filename' + " ".join(['%14s' % x for x in fields]) print(header) - print('-' * len(header)) + print(('-' * len(header))) for mdl in all: text = '%-25s' % mdl['name'] for field in fields: @@ -222,9 +222,9 @@ def write_failure_summary(self, all, modeltyp): """Print out a summary of all failed models""" - print("\n>> Summary of failed %s:" % modeltyp) + print(("\n>> Summary of failed %s:" % modeltyp)) for mdl in all: - print("%-25s %s" % (mdl['name'], mdl['failure'])) + print(("%-25s %s" % (mdl['name'], mdl['failure']))) print('') def rd_restraints(self): @@ -692,8 +692,8 @@ elif atmsel.get_model() is not self: raise ModellerError("selection is defined on the wrong model") elif len(atmsel) < len(self.atoms): - print("%d (of %d total) atoms selected for optimization" \ - % (len(atmsel), len(self.atoms))) + print(("%d (of %d total) atoms selected for optimization" \ + % (len(atmsel), len(self.atoms)))) return atmsel def mkhomcsr(self, atmsel, aln): @@ -774,9 +774,9 @@ selstd = selection(self).only_std_residues() selca = selstd.only_atom_types('CA') - print("%d atoms in HETATM/BLK residues constrained\n" % len(selhet) \ + print(("%d atoms in HETATM/BLK residues constrained\n" % len(selhet) \ + "to protein atoms within %.2f angstroms\n" % bond_distance \ - + "and protein CA atoms within %.2f angstroms" % ca_distance) + + "and protein CA atoms within %.2f angstroms" % ca_distance)) # Build the bonds first; this avoids duplicated CA-ligand bonds since # make_distance() will not build restraints that are already on the # nonbond exclusion list @@ -823,8 +823,8 @@ selhet = selhet.only_no_topology() # Intra-residue: - print("%d atoms in residues without defined topology\n" % len(selhet) \ - + "constrained to be rigid bodies") + print(("%d atoms in residues without defined topology\n" % len(selhet) \ + + "constrained to be rigid bodies")) rsr = self.restraints rsr.make_distance(selhet, selhet, aln=aln, distance_rsr_model=7, maximal_distance=10.0, @@ -898,8 +898,8 @@ print("\nThe following CHARMM atom type assignments were made:") print(" Atom Old type New type") for atom, old_type, new_type in zip(sel, old_types, new_types): - print(" %-20s %-15s %-15s" - % (str(atom), fmt_typ(old_type), fmt_typ(new_type))) + print((" %-20s %-15s %-15s" + % (str(atom), fmt_typ(old_type), fmt_typ(new_type)))) def select_atoms(self): """Select atoms to be optimized in the model building procedure. By RefactoringTool: No changes to modlib/modeller/automodel/autosched.py RefactoringTool: No changes to modlib/modeller/automodel/dope_loopmodel.py RefactoringTool: No changes to modlib/modeller/automodel/dopehr_loopmodel.py RefactoringTool: Refactored modlib/modeller/automodel/generate.py --- modlib/modeller/automodel/generate.py (original) +++ modlib/modeller/automodel/generate.py (refactored) @@ -88,11 +88,11 @@ to_rebuild.append(r) _unbuild_ring(r, ring_atoms + extra_atoms) if len(to_rebuild) > 0: - print("The following %d residues contain 6-membered rings with " + print(("The following %d residues contain 6-membered rings with " "poor geometries\nafter transfer from templates. Rebuilding " "rings from internal coordinates:\n %s" \ % (len(to_rebuild), - "\n ".join([str(r) for r in to_rebuild]))) + "\n ".join([str(r) for r in to_rebuild])))) mdl.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES') def read_xyz(mdl, aln): RefactoringTool: Refactored modlib/modeller/automodel/loopmodel.py --- modlib/modeller/automodel/loopmodel.py (original) +++ modlib/modeller/automodel/loopmodel.py (refactored) @@ -105,7 +105,7 @@ lendef = len(self._defined_indices) if lenall > lendef: s = selection(self) - s - print(""" + print((""" The following %d atoms were not found in the input model's non-loop region, and were added automatically by Modeller in order to determine correct interactions between the loop and the rest of the protein: @@ -115,7 +115,7 @@ rest of the protein may exist (note, however, that the score of the loop does not include protein-protein internal interactions, so will not be adversely affected by any clashes).""" \ -% (lenall - lendef, ", ".join([repr(a) for a in s]))) +% (lenall - lendef, ", ".join([repr(a) for a in s])))) if self.loop.write_defined_only: print(""" @@ -406,7 +406,7 @@ elif len(atmsel.only_no_topology()) > 0: raise ModellerError("some selected residues have no topology") else: - print("%d atoms selected for loop refinement" % len(atmsel)) + print(("%d atoms selected for loop refinement" % len(atmsel))) return atmsel def optimize_loop(self, atmsel, sched, actions): RefactoringTool: No changes to modlib/modeller/automodel/parallel.py RefactoringTool: No changes to modlib/modeller/automodel/randomize.py RefactoringTool: No changes to modlib/modeller/automodel/refine.py RefactoringTool: No changes to modlib/modeller/library_restraints/angles.py RefactoringTool: No changes to modlib/modeller/library_restraints/bonds.py RefactoringTool: No changes to modlib/modeller/library_restraints/chi1.py RefactoringTool: No changes to modlib/modeller/library_restraints/chi2.py RefactoringTool: No changes to modlib/modeller/library_restraints/chi3.py RefactoringTool: No changes to modlib/modeller/library_restraints/chi4.py RefactoringTool: No changes to modlib/modeller/library_restraints/impropers.py RefactoringTool: No changes to modlib/modeller/library_restraints/omega_dihedrals.py RefactoringTool: No changes to modlib/modeller/library_restraints/phi_psi.py RefactoringTool: No changes to modlib/modeller/mmcif/data.py RefactoringTool: Refactored modlib/modeller/mmcif/writer.py --- modlib/modeller/mmcif/writer.py (original) +++ modlib/modeller/mmcif/writer.py (refactored) @@ -4,7 +4,7 @@ # which works as far back as 2.3, so imports need to be protected by a # version check -from __future__ import print_function + import sys import textwrap @@ -12,7 +12,7 @@ if sys.version_info[0] >= 3: _long_type = int else: - _long_type = long + _long_type = int class _LineWriter(object): def __init__(self, writer, line_len=80): RefactoringTool: No changes to modlib/modeller/optimizers/actions.py RefactoringTool: Refactored modlib/modeller/optimizers/builtin_optimizer.py --- modlib/modeller/optimizers/builtin_optimizer.py (original) +++ modlib/modeller/optimizers/builtin_optimizer.py (refactored) @@ -9,7 +9,7 @@ # delete the key entirely, as __getstate__ must return a non-empty # dict in order for our __setstate__ method to be called). d = self.__dict__.copy() - for key in self.__dict__.keys(): + for key in list(self.__dict__.keys()): if key.endswith("_modpt") or key.endswith("__optpt"): d[key] = None return d @@ -21,7 +21,7 @@ vars = params.copy() self._update_params(vars, ok_keys, extravars) for key in ok_keys: - if key not in vars.keys() \ + if key not in list(vars.keys()) \ and key not in ("edat", "libs", "actions", "schedule_scale"): raise ValueError("a value must be given for %s" % key) RefactoringTool: No changes to modlib/modeller/optimizers/conjugate_gradients.py RefactoringTool: No changes to modlib/modeller/optimizers/molecular_dynamics.py RefactoringTool: Refactored modlib/modeller/optimizers/optimizer.py --- modlib/modeller/optimizers/optimizer.py (original) +++ modlib/modeller/optimizers/optimizer.py (refactored) @@ -10,7 +10,7 @@ return self.atmsel def _update_params(self, params, ok_keys, vars): - for key in vars.keys(): + for key in list(vars.keys()): if key in ok_keys: params[key] = vars[key] else: RefactoringTool: No changes to modlib/modeller/optimizers/quasi_newton.py RefactoringTool: No changes to modlib/modeller/optimizers/state_optimizer.py RefactoringTool: No changes to modlib/modeller/parallel/communicator.py RefactoringTool: Refactored modlib/modeller/parallel/data_types.py --- modlib/modeller/parallel/data_types.py (original) +++ modlib/modeller/parallel/data_types.py (refactored) @@ -3,7 +3,7 @@ import sys try: - import cPickle as pickle + import pickle as pickle except ImportError: import pickle RefactoringTool: Refactored modlib/modeller/parallel/job.py --- modlib/modeller/parallel/job.py (original) +++ modlib/modeller/parallel/job.py (refactored) @@ -106,7 +106,7 @@ if id and id in pending_slaves: slave = pending_slaves.pop(id) connected_slaves[id] = slave - print("Identified slave %s " % str(slave)) + print(("Identified slave %s " % str(slave))) slave.accept_connection(sock) slave.set_directory(self.cwd) if sys.path[0] != '': @@ -117,7 +117,7 @@ return slave elif id and id in connected_slaves: slave = connected_slaves[id] - print("Reconnect from slave %s " % str(slave)) + print(("Reconnect from slave %s " % str(slave))) slave.accept_connection(sock) else: print("Ignoring request from unknown slave") @@ -159,7 +159,7 @@ """Run all tasks and return all the results, in the same order that they were submitted, when all the jobs have completed.""" tasks = self.tasks[:] - print("Running %d tasks on %d slaves" % (len(tasks), len(self))) + print(("Running %d tasks on %d slaves" % (len(tasks), len(self)))) self.push_tasks_to_slaves() while True: try: @@ -174,7 +174,7 @@ def yield_tasks_unordered(self): """Run all tasks and return their results (as a generator), in whatever order they complete.""" - print("Running %d tasks on %d slaves" % (len(self.tasks), len(self))) + print(("Running %d tasks on %d slaves" % (len(self.tasks), len(self)))) self.push_tasks_to_slaves() while True: try: @@ -215,7 +215,7 @@ task = obj.task_results() if task: # The slave completed its task - print("%s on %s completed" % (str(task), str(obj))) + print(("%s on %s completed" % (str(task), str(obj)))) if len(self.tasks) > 0: obj.run_task(self.tasks.pop(0)) return task @@ -225,14 +225,14 @@ except (NetworkError, TaskSetupError): self.kill_slaves((obj,), sys.exc_info()[1]) else: - print("Warning: slave %s reports data, but is not running a task" \ - % str(obj)) + print(("Warning: slave %s reports data, but is not running a task" \ + % str(obj))) def kill_slaves(self, slaves, err=""): if err != "": err = "(%s) " % err for s in slaves: - print("%s failed %s- removing from %s" % (s, err, self)) + print(("%s failed %s- removing from %s" % (s, err, self))) task = s.kill() if task: self.tasks.append(task) @@ -248,8 +248,8 @@ timedout = [a for a in self if a.running_task() and \ a.contact_timeout(self.heartbeat_timeout)] if len(timedout) > 0: - print("Did not hear from slaves %s in %d seconds" % \ - (str(timedout), self.heartbeat_timeout)) + print(("Did not hear from slaves %s in %d seconds" % \ + (str(timedout), self.heartbeat_timeout))) self.kill_slaves(timedout) def push_tasks_to_slaves(self): @@ -264,8 +264,8 @@ slave.run_task(t) # If a network error occurred, kill the slave and requeue the task except socket.error: - print("slave %s failed on run task with %s; removing from job" \ - % (slave, sys.exc_info()[1])) + print(("slave %s failed on run task with %s; removing from job" \ + % (slave, sys.exc_info()[1]))) slave.kill() self.tasks.insert(0, t) self.expand_for_tasks() RefactoringTool: No changes to modlib/modeller/parallel/local_slave.py RefactoringTool: No changes to modlib/modeller/parallel/mypopen4.py RefactoringTool: Refactored modlib/modeller/parallel/myspawn.py --- modlib/modeller/parallel/myspawn.py (original) +++ modlib/modeller/parallel/myspawn.py (refactored) @@ -10,7 +10,7 @@ ``output``.""" fp = open(output, "w") - print("%s >& %s" % (cmd, output)) + print(("%s >& %s" % (cmd, output))) if sys.platform == 'win32': _myspawn_win32(cmd, fp) else: @@ -27,4 +27,4 @@ # Ignore Windows "file not found" errors, so that behavior is consistent # between Unix and Windows except WindowsError: - print("WindowsError: %s (ignored)" % sys.exc_info()[1]) + print(("WindowsError: %s (ignored)" % sys.exc_info()[1])) RefactoringTool: No changes to modlib/modeller/parallel/sge_pe_job.py RefactoringTool: No changes to modlib/modeller/parallel/sge_pe_slave.py RefactoringTool: Refactored modlib/modeller/parallel/sge_qsub_array.py --- modlib/modeller/parallel/sge_qsub_array.py (original) +++ modlib/modeller/parallel/sge_qsub_array.py (refactored) @@ -36,7 +36,7 @@ outlines = output.readlines() output.close() for line in outlines: - print(line.rstrip('\r\n')) + print((line.rstrip('\r\n'))) a.require_clean_exit() self._set_jobid(outlines) RefactoringTool: No changes to modlib/modeller/parallel/sge_qsub_job.py RefactoringTool: Refactored modlib/modeller/parallel/sge_qsub_slave.py --- modlib/modeller/parallel/sge_qsub_slave.py (original) +++ modlib/modeller/parallel/sge_qsub_slave.py (refactored) @@ -38,7 +38,7 @@ qsub = "qsub -S /bin/sh -o '%s' -N '%s' %s %s" % \ (output, name, self.standard_options, self._options) cmd = "%s -slave %s" % (path, id) - print("%s | %s" % (cmd, qsub)) + print(("%s | %s" % (cmd, qsub))) a = MyPopen4(qsub) (input, output) = (a.stdin, a.stdout) input.write(cmd + '\n') @@ -46,7 +46,7 @@ outlines = output.readlines() output.close() for line in outlines: - print(line.rstrip('\r\n')) + print((line.rstrip('\r\n'))) a.require_clean_exit() self._set_jobid(outlines) RefactoringTool: No changes to modlib/modeller/parallel/slave.py RefactoringTool: No changes to modlib/modeller/parallel/slave_communicator.py RefactoringTool: Refactored modlib/modeller/parallel/slaveloop.py --- modlib/modeller/parallel/slaveloop.py (original) +++ modlib/modeller/parallel/slaveloop.py (refactored) @@ -51,14 +51,14 @@ master.send_data(communicator.ErrorWrapper(detail)) except socket.error: detail2 = sys.exc_info()[1] - print("Warning: ignored exception " + str(detail2) \ + print(("Warning: ignored exception " + str(detail2) \ + " when trying to send error state " \ - + str(detail) + " back to master") + + str(detail) + " back to master")) raise detail raise def run(self): - print("Slave startup: connect to master at %s" % self.addr) + print(("Slave startup: connect to master at %s" % self.addr)) (host, port, identifier) = self.addr.split(":", 2) port = int(port) lock = threading.Lock() RefactoringTool: No changes to modlib/modeller/parallel/slavestate.py RefactoringTool: No changes to modlib/modeller/parallel/ssh_slave.py RefactoringTool: No changes to modlib/modeller/parallel/task.py RefactoringTool: No changes to modlib/modeller/scripts/align_strs_seq.py RefactoringTool: No changes to modlib/modeller/scripts/asgl_principal_components.py RefactoringTool: No changes to modlib/modeller/scripts/cispeptide.py RefactoringTool: No changes to modlib/modeller/scripts/complete_pdb.py RefactoringTool: No changes to modlib/modeller/scripts/fit.py RefactoringTool: No changes to modlib/modeller/scripts/principal_components.py RefactoringTool: No changes to modlib/modeller/scripts/sequence_srch.py RefactoringTool: Refactored modlib/modeller/top_interpreter/__init__.py --- modlib/modeller/top_interpreter/__init__.py (original) +++ modlib/modeller/top_interpreter/__init__.py (refactored) @@ -65,7 +65,7 @@ if len(line) > 0: try: self._parse_top_ini_line(line.split(None, 4), vars) - except TypeError, detail: + except TypeError as detail: mod_log_write("read_top__E> " + str(detail)) mod_log_write(" top.ini line: " + line) raise @@ -113,7 +113,7 @@ self._set_top_vars(vars) try: fh = self._open_include_file(self.variables['include_file']) - except IOError, detail: + except IOError as detail: mod_log_write("runlines__E> " + str(detail)) mod_log_write(" TOP Command line: " + line) raise @@ -160,7 +160,7 @@ indxca = self._run_top_cmd(cmd, indxca, lines, callstack, subrout) _modeller.mod_top_post() - except (IndexError, SyntaxError, TypeError), detail: + except (IndexError, SyntaxError, TypeError) as detail: mod_log_write("runlines__E> " + str(detail)) mod_log_write(" TOP Command line: " + line) raise RefactoringTool: No changes to modlib/modeller/top_interpreter/commands.py RefactoringTool: Refactored modlib/modeller/top_interpreter/topcmds.py --- modlib/modeller/top_interpreter/topcmds.py (original) +++ modlib/modeller/top_interpreter/topcmds.py (refactored) @@ -19,7 +19,7 @@ if not isinstance(vars, (list, tuple)): vars = (vars,) for var in vars: - if keys.has_key(var): + if var in keys: args.append(keys[var]) else: args.append(self.vars[var]) RefactoringTool: Refactored modlib/modeller/top_interpreter/util.py --- modlib/modeller/top_interpreter/util.py (original) +++ modlib/modeller/top_interpreter/util.py (refactored) @@ -1,7 +1,7 @@ import _modeller def set_topvars(topvardict, vars, topini): - for name in topvardict.keys(): + for name in list(topvardict.keys()): value = topvardict[name] if value is None: continue RefactoringTool: Refactored modlib/modeller/top_interpreter/variables.py --- modlib/modeller/top_interpreter/variables.py (original) +++ modlib/modeller/top_interpreter/variables.py (refactored) @@ -32,11 +32,11 @@ def __init__(self, topcmds): self._topcmds = topcmds self._topvars = {} - for var in self._deftops.keys(): + for var in list(self._deftops.keys()): self._ourvars[var] = self._deftops[var] - for var in self._edat_members.keys(): + for var in list(self._edat_members.keys()): self._ourvars[var] = self._edat_members[var] - for var in self._io_members.keys(): + for var in list(self._io_members.keys()): self._ourvars[var] = self._io_members[var] def __setitem__(self, key, value): RefactoringTool: No changes to modlib/modeller/util/array.py RefactoringTool: No changes to modlib/modeller/util/logger.py RefactoringTool: No changes to modlib/modeller/util/matrix.py RefactoringTool: No changes to modlib/modeller/util/modlist.py RefactoringTool: Refactored modlib/modeller/util/modobject.py --- modlib/modeller/util/modobject.py (original) +++ modlib/modeller/util/modobject.py (refactored) @@ -1,8 +1,8 @@ class modobject(object): def __setattr__(self, name, val): if name not in dir(self): - print("runcmd_____W>: creation of new member '%s' in %s: " - "possible typo!" % (name, str(self))) + print(("runcmd_____W>: creation of new member '%s' in %s: " + "possible typo!" % (name, str(self)))) object.__setattr__(self, name, val) def __getstate__(self): @@ -11,7 +11,7 @@ # delete the key entirely, as __getstate__ must return a non-empty # dict in order for our __setstate__ method to be called). d = self.__dict__.copy() - for key in self.__dict__.keys(): + for key in list(self.__dict__.keys()): if key.endswith("_modpt"): d[key] = None return d RefactoringTool: Refactored modlib/modeller/util/modutil.py --- modlib/modeller/util/modutil.py (original) +++ modlib/modeller/util/modutil.py (refactored) @@ -17,7 +17,7 @@ else: return indx elif isinstance(indx, slice): - return range(*indx.indices(len(seqtype))) + return list(range(*indx.indices(len(seqtype)))) elif lookup_func is not None: args = lookup_args + (indx,) int_indx = lookup_func(*args) RefactoringTool: Files that were modified: RefactoringTool: modlib/modeller/__init__.py RefactoringTool: modlib/modeller/alignment.py RefactoringTool: modlib/modeller/alnsequence.py RefactoringTool: modlib/modeller/alnstructure.py RefactoringTool: modlib/modeller/atom_type.py RefactoringTool: modlib/modeller/coordinates.py RefactoringTool: modlib/modeller/density.py RefactoringTool: modlib/modeller/energy_data.py RefactoringTool: modlib/modeller/energy_profile.py RefactoringTool: modlib/modeller/environ.py RefactoringTool: modlib/modeller/excluded_pair.py RefactoringTool: modlib/modeller/excluded_pair_list.py RefactoringTool: modlib/modeller/features.py RefactoringTool: modlib/modeller/forms.py RefactoringTool: modlib/modeller/gbsa.py RefactoringTool: modlib/modeller/group_restraints.py RefactoringTool: modlib/modeller/id_table.py RefactoringTool: modlib/modeller/information.py RefactoringTool: modlib/modeller/io_data.py RefactoringTool: modlib/modeller/libraries.py RefactoringTool: modlib/modeller/model.py RefactoringTool: modlib/modeller/model_topology.py RefactoringTool: modlib/modeller/modfile.py RefactoringTool: modlib/modeller/normalized_dope.py RefactoringTool: modlib/modeller/orient.py RefactoringTool: modlib/modeller/parameters.py RefactoringTool: modlib/modeller/physical.py RefactoringTool: modlib/modeller/profile.py RefactoringTool: modlib/modeller/pseudo_atom.py RefactoringTool: modlib/modeller/pseudo_atom_list.py RefactoringTool: modlib/modeller/pssmdb.py RefactoringTool: modlib/modeller/residue.py RefactoringTool: modlib/modeller/restraints.py RefactoringTool: modlib/modeller/rigid_body.py RefactoringTool: modlib/modeller/rigid_body_list.py RefactoringTool: modlib/modeller/salign.py RefactoringTool: modlib/modeller/saxsdata.py RefactoringTool: modlib/modeller/schedule.py RefactoringTool: modlib/modeller/secondary_structure.py RefactoringTool: modlib/modeller/selection.py RefactoringTool: modlib/modeller/sequence.py RefactoringTool: modlib/modeller/sequence_db.py RefactoringTool: modlib/modeller/soap_loop.py RefactoringTool: modlib/modeller/soap_peptide.py RefactoringTool: modlib/modeller/soap_pp.py RefactoringTool: modlib/modeller/soap_protein_od.py RefactoringTool: modlib/modeller/superpose.py RefactoringTool: modlib/modeller/symmetry.py RefactoringTool: modlib/modeller/symmetry_list.py RefactoringTool: modlib/modeller/terms.py RefactoringTool: modlib/modeller/test.py RefactoringTool: modlib/modeller/topology.py RefactoringTool: modlib/modeller/virtual_atom.py RefactoringTool: modlib/modeller/automodel/__init__.py RefactoringTool: modlib/modeller/automodel/allhmodel.py RefactoringTool: modlib/modeller/automodel/assess.py RefactoringTool: modlib/modeller/automodel/automodel.py RefactoringTool: modlib/modeller/automodel/autosched.py RefactoringTool: modlib/modeller/automodel/dope_loopmodel.py RefactoringTool: modlib/modeller/automodel/dopehr_loopmodel.py RefactoringTool: modlib/modeller/automodel/generate.py RefactoringTool: modlib/modeller/automodel/loopmodel.py RefactoringTool: modlib/modeller/automodel/parallel.py RefactoringTool: modlib/modeller/automodel/randomize.py RefactoringTool: modlib/modeller/automodel/refine.py RefactoringTool: modlib/modeller/library_restraints/angles.py RefactoringTool: modlib/modeller/library_restraints/bonds.py RefactoringTool: modlib/modeller/library_restraints/chi1.py RefactoringTool: modlib/modeller/library_restraints/chi2.py RefactoringTool: modlib/modeller/library_restraints/chi3.py RefactoringTool: modlib/modeller/library_restraints/chi4.py RefactoringTool: modlib/modeller/library_restraints/impropers.py RefactoringTool: modlib/modeller/library_restraints/omega_dihedrals.py RefactoringTool: modlib/modeller/library_restraints/phi_psi.py RefactoringTool: modlib/modeller/mmcif/data.py RefactoringTool: modlib/modeller/mmcif/writer.py RefactoringTool: modlib/modeller/optimizers/actions.py RefactoringTool: modlib/modeller/optimizers/builtin_optimizer.py RefactoringTool: modlib/modeller/optimizers/conjugate_gradients.py RefactoringTool: modlib/modeller/optimizers/molecular_dynamics.py RefactoringTool: modlib/modeller/optimizers/optimizer.py RefactoringTool: modlib/modeller/optimizers/quasi_newton.py RefactoringTool: modlib/modeller/optimizers/state_optimizer.py RefactoringTool: modlib/modeller/parallel/communicator.py RefactoringTool: modlib/modeller/parallel/data_types.py RefactoringTool: modlib/modeller/parallel/job.py RefactoringTool: modlib/modeller/parallel/local_slave.py RefactoringTool: modlib/modeller/parallel/mypopen4.py RefactoringTool: modlib/modeller/parallel/myspawn.py RefactoringTool: modlib/modeller/parallel/sge_pe_job.py RefactoringTool: modlib/modeller/parallel/sge_pe_slave.py RefactoringTool: modlib/modeller/parallel/sge_qsub_array.py RefactoringTool: modlib/modeller/parallel/sge_qsub_job.py RefactoringTool: modlib/modeller/parallel/sge_qsub_slave.py RefactoringTool: modlib/modeller/parallel/slave.py RefactoringTool: modlib/modeller/parallel/slave_communicator.py RefactoringTool: modlib/modeller/parallel/slaveloop.py RefactoringTool: modlib/modeller/parallel/slavestate.py RefactoringTool: modlib/modeller/parallel/ssh_slave.py RefactoringTool: modlib/modeller/parallel/task.py RefactoringTool: modlib/modeller/scripts/align_strs_seq.py RefactoringTool: modlib/modeller/scripts/asgl_principal_components.py RefactoringTool: modlib/modeller/scripts/cispeptide.py RefactoringTool: modlib/modeller/scripts/complete_pdb.py RefactoringTool: modlib/modeller/scripts/fit.py RefactoringTool: modlib/modeller/scripts/principal_components.py RefactoringTool: modlib/modeller/scripts/sequence_srch.py RefactoringTool: modlib/modeller/top_interpreter/__init__.py RefactoringTool: modlib/modeller/top_interpreter/commands.py RefactoringTool: modlib/modeller/top_interpreter/topcmds.py RefactoringTool: modlib/modeller/top_interpreter/util.py RefactoringTool: modlib/modeller/top_interpreter/variables.py RefactoringTool: modlib/modeller/util/array.py RefactoringTool: modlib/modeller/util/logger.py RefactoringTool: modlib/modeller/util/matrix.py RefactoringTool: modlib/modeller/util/modlist.py RefactoringTool: modlib/modeller/util/modobject.py RefactoringTool: modlib/modeller/util/modutil.py >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25 ... /var/tmp/portage/sci-chemistry/modeller-9.25/temp/environment: line 2726: type: locale: not found >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25 ... * python3_8: running distutils-r1_run_phase python_compile python3.8 setup.py build -j 16 running build running build_ext building '_modeller' extension creating /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25-python3_8/temp.linux-x86_64-3.8 x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I../include -I../include/x86_64-intel8 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/python3.8 -c modeller_wrap.c -o /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25-python3_8/temp.linux-x86_64-3.8/modeller_wrap.o modeller_wrap.c: In function 'pyfile_strreadlinefunc': modeller_wrap.c:4319:18: warning: initialization discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 4319 | char *utf8 = PyUnicode_AsUTF8(result); | ^~~~~~~~~~~~~~~~ x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25-python3_8/temp.linux-x86_64-3.8/modeller_wrap.o -L../../lib/x86_64-intel8 -L/usr/lib -lmodeller -lglib-2.0 -o /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25-python3_8/lib/_modeller.cpython-38-x86_64-linux-gnu.so * python3_9: running distutils-r1_run_phase python_compile python3.9 setup.py build -j 16 running build running build_ext building '_modeller' extension creating /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25-python3_9/temp.linux-x86_64-3.9 x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I../include -I../include/x86_64-intel8 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/python3.9 -c modeller_wrap.c -o /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25-python3_9/temp.linux-x86_64-3.9/modeller_wrap.o modeller_wrap.c: In function 'python_cb_fangle': modeller_wrap.c:3206:3: warning: 'PyEval_CallObjectWithKeywords' is deprecated [-Wdeprecated-declarations] 3206 | result = PyEval_CallObject(func, arglist); | ^~~~~~ In file included from /usr/include/python3.9/Python.h:140, from modeller_wrap.c:154: /usr/include/python3.9/ceval.h:17:43: note: declared here 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ modeller_wrap.c: In function 'python_cb_feval': modeller_wrap.c:3235:3: warning: 'PyEval_CallObjectWithKeywords' is deprecated [-Wdeprecated-declarations] 3235 | result = PyEval_CallObject(func, arglist); | ^~~~~~ In file included from /usr/include/python3.9/Python.h:140, from modeller_wrap.c:154: /usr/include/python3.9/ceval.h:17:43: note: declared here 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ modeller_wrap.c: In function 'python_cb_fderiv': modeller_wrap.c:3265:3: warning: 'PyEval_CallObjectWithKeywords' is deprecated [-Wdeprecated-declarations] 3265 | result = PyEval_CallObject(func, arglist); | ^~~~~~ In file included from /usr/include/python3.9/Python.h:140, from modeller_wrap.c:154: /usr/include/python3.9/ceval.h:17:43: note: declared here 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ modeller_wrap.c: In function 'python_cb_teval': modeller_wrap.c:3309:3: warning: 'PyEval_CallObjectWithKeywords' is deprecated [-Wdeprecated-declarations] 3309 | result = PyEval_CallObject(func, arglist); | ^~~~~~ In file included from /usr/include/python3.9/Python.h:140, from modeller_wrap.c:154: /usr/include/python3.9/ceval.h:17:43: note: declared here 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ modeller_wrap.c: In function 'python_cb_simloc': modeller_wrap.c:3367:3: warning: 'PyEval_CallObjectWithKeywords' is deprecated [-Wdeprecated-declarations] 3367 | result = PyEval_CallObject(func, arglist); | ^~~~~~ In file included from /usr/include/python3.9/Python.h:140, from modeller_wrap.c:154: /usr/include/python3.9/ceval.h:17:43: note: declared here 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ modeller_wrap.c: In function 'python_cb_reval': modeller_wrap.c:3405:3: warning: 'PyEval_CallObjectWithKeywords' is deprecated [-Wdeprecated-declarations] 3405 | result = PyEval_CallObject(func, arglist); | ^~~~~~ In file included from /usr/include/python3.9/Python.h:140, from modeller_wrap.c:154: /usr/include/python3.9/ceval.h:17:43: note: declared here 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ modeller_wrap.c: In function 'python_cb_range': modeller_wrap.c:3454:3: warning: 'PyEval_CallObjectWithKeywords' is deprecated [-Wdeprecated-declarations] 3454 | result = PyEval_CallObject(func, arglist); | ^~~~~~ In file included from /usr/include/python3.9/Python.h:140, from modeller_wrap.c:154: /usr/include/python3.9/ceval.h:17:43: note: declared here 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ modeller_wrap.c: In function 'python_cb_violation': modeller_wrap.c:3503:3: warning: 'PyEval_CallObjectWithKeywords' is deprecated [-Wdeprecated-declarations] 3503 | result = PyEval_CallObject(func, arglist); | ^~~~~~ In file included from /usr/include/python3.9/Python.h:140, from modeller_wrap.c:154: /usr/include/python3.9/ceval.h:17:43: note: declared here 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ modeller_wrap.c: In function 'python_cb_mean': modeller_wrap.c:3539:3: warning: 'PyEval_CallObjectWithKeywords' is deprecated [-Wdeprecated-declarations] 3539 | result = PyEval_CallObject(func, arglist); | ^~~~~~ In file included from /usr/include/python3.9/Python.h:140, from modeller_wrap.c:154: /usr/include/python3.9/ceval.h:17:43: note: declared here 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ modeller_wrap.c: In function 'python_cb_action': modeller_wrap.c:3559:3: warning: 'PyEval_CallObjectWithKeywords' is deprecated [-Wdeprecated-declarations] 3559 | result = PyEval_CallObject(func, arglist); | ^~~~~~ In file included from /usr/include/python3.9/Python.h:140, from modeller_wrap.c:154: /usr/include/python3.9/ceval.h:17:43: note: declared here 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ modeller_wrap.c: In function 'python_cb_log': modeller_wrap.c:3583:3: warning: 'PyEval_CallObjectWithKeywords' is deprecated [-Wdeprecated-declarations] 3583 | result = PyEval_CallObject(func, arglist); | ^~~~~~ In file included from /usr/include/python3.9/Python.h:140, from modeller_wrap.c:154: /usr/include/python3.9/ceval.h:17:43: note: declared here 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ modeller_wrap.c: In function 'pyfile_strreadlinefunc': modeller_wrap.c:4319:18: warning: initialization discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 4319 | char *utf8 = PyUnicode_AsUTF8(result); | ^~~~~~~~~~~~~~~~ x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25-python3_9/temp.linux-x86_64-3.9/modeller_wrap.o -L../../lib/x86_64-intel8 -L/usr/lib -lmodeller -lglib-2.0 -o /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25-python3_9/lib/_modeller.cpython-39-x86_64-linux-gnu.so >>> Source compiled. >>> Test phase [not enabled]: sci-chemistry/modeller-9.25 >>> Install sci-chemistry/modeller-9.25 into /var/tmp/portage/sci-chemistry/modeller-9.25/image * python3_8: running distutils-r1_run_phase python_install python3.8 setup.py install --skip-build --root=/var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.8 running install running install_lib creating /var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.8 creating /var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.8/usr creating /var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.8/usr/lib creating /var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.8/usr/lib/python3.8 creating /var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.8/usr/lib/python3.8/site-packages copying /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25-python3_8/lib/_modeller.cpython-38-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.8/usr/lib/python3.8/site-packages running install_egg_info Writing /var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.8/usr/lib/python3.8/site-packages/Modeller-0.0.0-py3.8.egg-info * python3_9: running distutils-r1_run_phase python_install python3.9 setup.py install --skip-build --root=/var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.9 running install running install_lib creating /var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.9 creating /var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.9/usr creating /var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.9/usr/lib creating /var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.9/usr/lib/python3.9 creating /var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.9/usr/lib/python3.9/site-packages copying /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25-python3_9/lib/_modeller.cpython-39-x86_64-linux-gnu.so -> /var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.9/usr/lib/python3.9/site-packages running install_egg_info Writing /var/tmp/portage/sci-chemistry/modeller-9.25/image/_python3.9/usr/lib/python3.9/site-packages/Modeller-0.0.0-py3.9.egg-info * Using python3.9 in global scope * python3_9: running distutils-r1_run_phase python_install_all * python3_8: running python_domodule modlib/modeller * python3_9: running python_domodule modlib/modeller * python3_8: running python_doscript bin/modslave.py * python3_9: running python_doscript bin/modslave.py >>> Completed installing sci-chemistry/modeller-9.25 into /var/tmp/portage/sci-chemistry/modeller-9.25/image * Final size of build directory: 150004 KiB (146.4 MiB) * Final size of installed tree: 64204 KiB ( 62.6 MiB) * QA Notice: Unresolved soname dependencies: * * /opt/modeller/bin/mod9.25_x86_64-intel8: libc.so.6 * /opt/modeller/lib/x86_64-intel8/libhdf5.so.103: libc.so.6 libdl.so.2 libm.so.6 librt.so.1 * /opt/modeller/lib/x86_64-intel8/libhdf5_hl.so.100: libc.so.6 libdl.so.2 libm.so.6 librt.so.1 * /opt/modeller/lib/x86_64-intel8/libifcore.so.5: libc.so.6 libm.so.6 * /opt/modeller/lib/x86_64-intel8/libimf.so: libc.so.6 * /opt/modeller/lib/x86_64-intel8/libintlc.so.5: libc.so.6 * /opt/modeller/lib/x86_64-intel8/libmodeller.so.12: libc.so.6 libdl.so.2 * /opt/modeller/lib/x86_64-intel8/libpython2.3.so.1.0: libc.so.6 libdl.so.2 libm.so.6 libpthread.so.0 libutil.so.1 * /opt/modeller/lib/x86_64-intel8/libsaxs.so: libc.so.6 * /opt/modeller/lib/x86_64-intel8/libsvml.so: libc.so.6 * * Verifying compiled files in /usr/lib/python3.8/site-packages * Verifying compiled files in /usr/lib/python3.9/site-packages strip: x86_64-gentoo-linux-musl-strip --strip-unneeded -N __gentoo_check_ldflags__ -R .comment -R .GCC.command.line -R .note.gnu.gold-version /usr/lib/python3.8/site-packages/_modeller.cpython-38-x86_64-linux-gnu.so /opt/modeller/lib/x86_64-intel8/libintlc.so.5 /opt/modeller/lib/x86_64-intel8/libsaxs.so /opt/modeller/lib/x86_64-intel8/libsvml.so /usr/lib/python3.9/site-packages/_modeller.cpython-39-x86_64-linux-gnu.so /opt/modeller/lib/x86_64-intel8/libifcore.so.5 /opt/modeller/lib/x86_64-intel8/libimf.so >>> Done. * Obtain a license Key from * http://salilab.org/modeller/registration.html * And run this before using modeller: * emerge --config =sci-chemistry/modeller-9.25 * That way you can [re]enter your license key.