├── .clang-format ├── .clangd ├── .gitattributes ├── .github └── workflows │ └── push.yml ├── .gitignore ├── CHANGELOG.md ├── CONTRIBUTING.md ├── INSTALL ├── LICENSE ├── Makefile.am ├── README.md ├── configure.ac ├── doc ├── Doxyfile.in ├── Makefile.am ├── README.md ├── doxy-main.md ├── doxygen-footer.html ├── doxygen-header.html ├── fig │ ├── lnr_circles.svg │ ├── lnr_circles.tex │ ├── lnr_slice.svg │ └── lnr_slice.tex ├── license.md └── man │ └── freesasa.1.in ├── m4 ├── ax_compare_version.m4 └── ax_cxx_compile_stdcxx.m4 ├── scripts ├── chemcomp2config.pl ├── config2c.pl └── rsa │ ├── ALA.pdb │ ├── ARG.pdb │ ├── ASN.pdb │ ├── ASP.pdb │ ├── CYS.pdb │ ├── GLN.pdb │ ├── GLU.pdb │ ├── GLY.pdb │ ├── HIS.pdb │ ├── ILE.pdb │ ├── LEU.pdb │ ├── LYS.pdb │ ├── MET.pdb │ ├── PHE.pdb │ ├── PRO.pdb │ ├── SER.pdb │ ├── THR.pdb │ ├── TRP.pdb │ ├── TYR.pdb │ └── VAL.pdb ├── share ├── Makefile.am ├── dssp.config ├── naccess.config ├── oons.config └── protor.config ├── src ├── Makefile.am ├── cif.cc ├── cif.hh ├── classifier.c ├── classifier.h ├── classifier_naccess.c ├── classifier_oons.c ├── classifier_protor.c ├── coord.c ├── coord.h ├── example.c ├── freesasa.c ├── freesasa.h ├── freesasa_internal.h ├── json.c ├── lexer.c ├── lexer.h ├── lexer.l ├── log.c ├── main.cc ├── nb.c ├── nb.h ├── node.c ├── parser.c ├── parser.h ├── parser.y ├── pdb.c ├── pdb.h ├── rsa.c ├── sasa_lr.c ├── sasa_sr.c ├── selection.c ├── selection.h ├── structure.c ├── util.c └── xml.c ├── tests ├── .gitignore ├── Makefile.am ├── compare-cif-pdb │ ├── .gitignore │ ├── AsyncResult.fs │ ├── Command.fs │ ├── Download.fs │ ├── Program.fs │ ├── README.md │ ├── compare-cif-pdb.fsproj │ └── compare-cif-pdb.sln ├── data │ ├── 1a0q.pdb │ ├── 1d3z.cif │ ├── 1d3z.pdb │ ├── 1sui.cif │ ├── 1sui.pdb │ ├── 1ubq.B.pdb │ ├── 1ubq.cif │ ├── 1ubq.occ.pdb │ ├── 1ubq.pdb │ ├── 2isk.cif │ ├── 2isk.pdb │ ├── 2jo4.cif │ ├── 2jo4.pdb │ ├── 3bkr.cif │ ├── 3bkr.pdb │ ├── 3bzd_trimmed.pdb │ ├── 3gnn.cif │ ├── 3gnn.pdb │ ├── 5dx9.cif │ ├── 5dx9.pdb │ ├── 5hdn.cif │ ├── 5hdn.pdb │ ├── 7cma-assembly1.cif │ ├── alt_model_twochain.pdb │ ├── diverse_pdbs_2000.txt │ ├── dummy.pdb │ ├── empty.pdb │ ├── empty_model.pdb │ ├── err.config │ ├── icode.pdb │ ├── model_mismatch.pdb │ ├── reference_bfactors.pdb │ ├── restype.reference │ ├── rsa │ ├── seq.reference │ └── test.config ├── test-cli.in ├── test_classifier.c ├── test_coord.c ├── test_freesasa.c ├── test_json.c ├── test_main.c ├── test_nb.c ├── test_node.c ├── test_pdb.c ├── test_selection.c ├── test_structure.c ├── test_xml.c ├── tools.c └── tools.h └── third-party └── gemmi ├── .gitignore ├── LICENSE.txt ├── README.md └── include └── gemmi ├── atox.hpp ├── cif.hpp ├── cifdoc.hpp ├── elem.hpp ├── enumstr.hpp ├── fail.hpp ├── input.hpp ├── iterator.hpp ├── math.hpp ├── metadata.hpp ├── mmcif.hpp ├── mmcif_impl.hpp ├── model.hpp ├── numb.hpp ├── seqid.hpp ├── span.hpp ├── symmetry.hpp ├── third_party ├── fast_float.h ├── pocketfft_hdronly.h ├── sajson.h ├── stb_sprintf.h ├── tao │ ├── LICENSE │ ├── NOTES │ ├── pegtl.hpp │ └── pegtl │ │ ├── analysis │ │ ├── analyze_cycles.hpp │ │ ├── counted.hpp │ │ ├── generic.hpp │ │ ├── grammar_info.hpp │ │ ├── insert_guard.hpp │ │ ├── insert_rules.hpp │ │ ├── rule_info.hpp │ │ └── rule_type.hpp │ │ ├── analyze.hpp │ │ ├── apply_mode.hpp │ │ ├── argv_input.hpp │ │ ├── ascii.hpp │ │ ├── buffer_input.hpp │ │ ├── config.hpp │ │ ├── cstream_input.hpp │ │ ├── eol.hpp │ │ ├── eol_pair.hpp │ │ ├── file_input.hpp │ │ ├── input_error.hpp │ │ ├── internal │ │ ├── action.hpp │ │ ├── action_input.hpp │ │ ├── alnum.hpp │ │ ├── alpha.hpp │ │ ├── any.hpp │ │ ├── apply.hpp │ │ ├── apply0.hpp │ │ ├── apply0_single.hpp │ │ ├── apply_single.hpp │ │ ├── at.hpp │ │ ├── bof.hpp │ │ ├── bol.hpp │ │ ├── bump_help.hpp │ │ ├── bump_impl.hpp │ │ ├── bytes.hpp │ │ ├── control.hpp │ │ ├── cr_crlf_eol.hpp │ │ ├── cr_eol.hpp │ │ ├── crlf_eol.hpp │ │ ├── cstream_reader.hpp │ │ ├── cstring_reader.hpp │ │ ├── demangle.hpp │ │ ├── demangle_cxxabi.hpp │ │ ├── demangle_nop.hpp │ │ ├── demangle_sanitise.hpp │ │ ├── disable.hpp │ │ ├── discard.hpp │ │ ├── dusel_mode.hpp │ │ ├── duseltronik.hpp │ │ ├── enable.hpp │ │ ├── endian.hpp │ │ ├── endian_gcc.hpp │ │ ├── endian_win.hpp │ │ ├── eof.hpp │ │ ├── eol.hpp │ │ ├── eolf.hpp │ │ ├── file_mapper.hpp │ │ ├── file_opener.hpp │ │ ├── file_reader.hpp │ │ ├── has_apply.hpp │ │ ├── has_apply0.hpp │ │ ├── identifier.hpp │ │ ├── if_apply.hpp │ │ ├── if_must.hpp │ │ ├── if_must_else.hpp │ │ ├── if_then_else.hpp │ │ ├── input_pair.hpp │ │ ├── integer_sequence.hpp │ │ ├── istream_reader.hpp │ │ ├── istring.hpp │ │ ├── iterator.hpp │ │ ├── lf_crlf_eol.hpp │ │ ├── lf_eol.hpp │ │ ├── list.hpp │ │ ├── list_must.hpp │ │ ├── list_tail.hpp │ │ ├── list_tail_pad.hpp │ │ ├── marker.hpp │ │ ├── minus.hpp │ │ ├── must.hpp │ │ ├── not_at.hpp │ │ ├── one.hpp │ │ ├── opt.hpp │ │ ├── pad.hpp │ │ ├── pad_opt.hpp │ │ ├── peek_char.hpp │ │ ├── peek_utf16.hpp │ │ ├── peek_utf32.hpp │ │ ├── peek_utf8.hpp │ │ ├── pegtl_string.hpp │ │ ├── plus.hpp │ │ ├── raise.hpp │ │ ├── range.hpp │ │ ├── ranges.hpp │ │ ├── rep.hpp │ │ ├── rep_min.hpp │ │ ├── rep_min_max.hpp │ │ ├── rep_opt.hpp │ │ ├── require.hpp │ │ ├── result_on_found.hpp │ │ ├── rule_conjunction.hpp │ │ ├── rules.hpp │ │ ├── seq.hpp │ │ ├── skip_control.hpp │ │ ├── sor.hpp │ │ ├── star.hpp │ │ ├── star_must.hpp │ │ ├── state.hpp │ │ ├── string.hpp │ │ ├── trivial.hpp │ │ ├── try_catch_type.hpp │ │ └── until.hpp │ │ ├── istream_input.hpp │ │ ├── memory_input.hpp │ │ ├── mmap_input.hpp │ │ ├── normal.hpp │ │ ├── nothing.hpp │ │ ├── parse.hpp │ │ ├── parse_error.hpp │ │ ├── position.hpp │ │ ├── read_input.hpp │ │ ├── rewind_mode.hpp │ │ ├── rules.hpp │ │ ├── string_input.hpp │ │ ├── tracking_mode.hpp │ │ ├── utf16.hpp │ │ ├── utf32.hpp │ │ ├── utf8.hpp │ │ └── version.hpp └── tinydir.h ├── to_cif.hpp ├── unitcell.hpp └── util.hpp /.clang-format: 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