├── .appveyor.yml ├── .clang-tidy ├── .editorconfig ├── .github ├── codeql.yml └── workflows │ ├── ci.yml │ ├── codeql.yml │ ├── testwheel.yml │ └── wheels2.yml ├── .gitignore ├── .readthedocs.yaml ├── CMakeLists.txt ├── LICENSE.txt ├── README.md ├── benchmarks ├── elem.cpp ├── mod.cpp ├── niggli.cpp ├── pdb.cpp ├── resinfo.cpp ├── round.cpp ├── smat33.cpp ├── stoi.cpp ├── sym.cpp └── writecif.cpp ├── docs ├── .ignore ├── Makefile ├── P0C805.fasta ├── _static │ ├── cpp.png │ ├── custom.css │ └── py.png ├── _templates │ └── page.html ├── align-help.txt ├── analysis.rst ├── blobs-help.txt ├── cell.rst ├── chemistry.rst ├── cif.rst ├── cif2json-help.txt ├── cif2mtz-help.txt ├── cif2mtz-spec.txt ├── cifdiff-help.txt ├── code │ ├── cell.cpp │ ├── cif_cc.cpp │ ├── elem.cpp │ ├── mutate.cpp │ ├── newmtz.cpp │ ├── resinfo.cpp │ ├── smcif.cpp │ └── sym.cpp ├── components.cif ├── conf.py ├── contact-help.txt ├── contents-help.txt ├── convert-help.txt ├── crd-help.txt ├── ecalc-help.txt ├── fprime-help.txt ├── gemmi-help.txt ├── grep-help.txt ├── grid.rst ├── h-help.txt ├── headers.rst ├── hkl.rst ├── img │ ├── 3nwh.png │ ├── 5dei-Ioversigma.png │ ├── 5xg2.png │ ├── FP_Fmeas_1d_5wkd.png │ ├── FP_vs_Fmeas_5wkd.png │ ├── M10-isomorphism.png │ ├── aud_lsa.png │ ├── patterson_slice.png │ ├── periodic-table-thumb.png │ ├── ramachandran-per-aa.png │ ├── rmerge-1997.png │ ├── rmerge-2006.png │ ├── solvent-content-old.png │ ├── solvent-content-recent.png │ └── trilinear-tricubic.png ├── index.rst ├── install.rst ├── json2cif-help.txt ├── map-help.txt ├── map2sf-help.txt ├── mask-help.txt ├── merge-help.txt ├── misc.rst ├── mol.rst ├── mondiff-help.txt ├── mtz-help.txt ├── mtz2cif-help.txt ├── program.rst ├── reindex-help.txt ├── requirements.txt ├── residues-help.txt ├── rmsz-help.txt ├── scattering.rst ├── set-help.txt ├── sf2map-help.txt ├── sfcalc-help.txt ├── sg-help.txt ├── ss-help.txt ├── symmetry.rst ├── tags-help.txt ├── validate-help.txt ├── wcn-help.txt └── xds2mtz-help.txt ├── examples ├── aafreq.py ├── auth_label.cpp ├── ccd_gi.py ├── ccd_subgraph.py ├── check_conn.cpp ├── check_symmetry.cpp ├── cif_i_sigi.py ├── col_order.py ├── from_json.py ├── long_geom.py ├── map2mtz.py ├── maskcheck.py ├── maskdiff.py ├── matthews.py ├── merge_mtz_mmcif.py ├── monomers.py ├── mtrix_iso.py ├── mtz_i_sigi.py ├── multiproc.py ├── patterson_slice.py ├── qq-plot.py ├── rama_gather.py ├── rama_plot.py ├── read_cif.py ├── refln-stats.py ├── simple_search.py ├── sub_ccd.py ├── to_rdkit.py ├── torsion_in_ring.cpp ├── weight.py └── with_bgl.cpp ├── fortran ├── Makefile ├── fsym.f90 ├── ftest.f90 ├── gemmi.yaml └── write.cpp ├── include └── gemmi │ ├── addends.hpp │ ├── align.hpp │ ├── assembly.hpp │ ├── asudata.hpp │ ├── asumask.hpp │ ├── atof.hpp │ ├── atox.hpp │ ├── bessel.hpp │ ├── binner.hpp │ ├── blob.hpp │ ├── bond_idx.hpp │ ├── c4322.hpp │ ├── calculate.hpp │ ├── ccp4.hpp │ ├── cellred.hpp │ ├── chemcomp.hpp │ ├── cif.hpp │ ├── cif2mtz.hpp │ ├── cifdoc.hpp │ ├── contact.hpp │ ├── crd.hpp │ ├── ddl.hpp │ ├── dencalc.hpp │ ├── dirwalk.hpp │ ├── dssp.hpp │ ├── ecalc.hpp │ ├── eig3.hpp │ ├── elem.hpp │ ├── enumstr.hpp │ ├── fail.hpp │ ├── fileutil.hpp │ ├── flat.hpp │ ├── floodfill.hpp │ ├── formfact.hpp │ ├── fourier.hpp │ ├── fprime.hpp │ ├── fstream.hpp │ ├── glob.hpp │ ├── grid.hpp │ ├── gz.hpp │ ├── input.hpp │ ├── intensit.hpp │ ├── interop.hpp │ ├── it92.hpp │ ├── iterator.hpp │ ├── json.hpp │ ├── levmar.hpp │ ├── linkhunt.hpp │ ├── logger.hpp │ ├── math.hpp │ ├── metadata.hpp │ ├── mmcif.hpp │ ├── mmcif_impl.hpp │ ├── mmdb.hpp │ ├── mmread.hpp │ ├── mmread_gz.hpp │ ├── model.hpp │ ├── modify.hpp │ ├── monlib.hpp │ ├── mtz.hpp │ ├── mtz2cif.hpp │ ├── neighbor.hpp │ ├── neutron92.hpp │ ├── numb.hpp │ ├── pdb.hpp │ ├── pdb_id.hpp │ ├── pirfasta.hpp │ ├── polyheur.hpp │ ├── pymol_select.hpp │ ├── qcp.hpp │ ├── read_cif.hpp │ ├── recgrid.hpp │ ├── reciproc.hpp │ ├── refln.hpp │ ├── resinfo.hpp │ ├── riding_h.hpp │ ├── scaling.hpp │ ├── select.hpp │ ├── seqalign.hpp │ ├── seqid.hpp │ ├── seqtools.hpp │ ├── serialize.hpp │ ├── sfcalc.hpp │ ├── small.hpp │ ├── smcif.hpp │ ├── solmask.hpp │ ├── span.hpp │ ├── sprintf.hpp │ ├── stats.hpp │ ├── symmetry.hpp │ ├── third_party │ ├── fast_float.h │ ├── half.hpp │ ├── pocketfft_hdronly.h │ ├── tao │ │ ├── LICENSE │ │ ├── NOTES │ │ ├── pegtl.hpp │ │ └── pegtl │ │ │ ├── analysis │ │ │ ├── analyze_cycles.hpp │ │ │ ├── counted.hpp │ │ │ ├── generic.hpp │ │ │ ├── grammar_info.hpp │ │ │ ├── insert_guard.hpp │ │ │ ├── rule_info.hpp │ │ │ └── rule_type.hpp │ │ │ ├── analyze.hpp │ │ │ ├── apply_mode.hpp │ │ │ ├── argv_input.hpp │ │ │ ├── ascii.hpp │ │ │ ├── buffer_input.hpp │ │ │ ├── change_action.hpp │ │ │ ├── change_action_and_state.hpp │ │ │ ├── change_action_and_states.hpp │ │ │ ├── change_control.hpp │ │ │ ├── change_state.hpp │ │ │ ├── change_states.hpp │ │ │ ├── config.hpp │ │ │ ├── cstream_input.hpp │ │ │ ├── disable_action.hpp │ │ │ ├── discard_input.hpp │ │ │ ├── discard_input_on_failure.hpp │ │ │ ├── discard_input_on_success.hpp │ │ │ ├── enable_action.hpp │ │ │ ├── eol.hpp │ │ │ ├── eol_pair.hpp │ │ │ ├── file_input.hpp │ │ │ ├── input_error.hpp │ │ │ ├── internal │ │ │ ├── action.hpp │ │ │ ├── action_input.hpp │ │ │ ├── alnum.hpp │ │ │ ├── alpha.hpp │ │ │ ├── always_false.hpp │ │ │ ├── any.hpp │ │ │ ├── apply.hpp │ │ │ ├── apply0.hpp │ │ │ ├── apply0_single.hpp │ │ │ ├── apply_single.hpp │ │ │ ├── at.hpp │ │ │ ├── bof.hpp │ │ │ ├── bol.hpp │ │ │ ├── bump.hpp │ │ │ ├── bump_help.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_posix.hpp │ │ │ ├── file_opener.hpp │ │ │ ├── file_reader.hpp │ │ │ ├── has_apply.hpp │ │ │ ├── has_apply0.hpp │ │ │ ├── has_match.hpp │ │ │ ├── identifier.hpp │ │ │ ├── if_apply.hpp │ │ │ ├── if_missing.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 │ │ │ ├── must.hpp │ │ │ ├── not_at.hpp │ │ │ ├── one.hpp │ │ │ ├── opt.hpp │ │ │ ├── pad.hpp │ │ │ ├── pad_opt.hpp │ │ │ ├── peek_char.hpp │ │ │ ├── peek_mask_uint.hpp │ │ │ ├── peek_mask_uint8.hpp │ │ │ ├── peek_uint.hpp │ │ │ ├── peek_uint8.hpp │ │ │ ├── peek_utf16.hpp │ │ │ ├── peek_utf32.hpp │ │ │ ├── peek_utf8.hpp │ │ │ ├── pegtl_string.hpp │ │ │ ├── plus.hpp │ │ │ ├── raise.hpp │ │ │ ├── range.hpp │ │ │ ├── ranges.hpp │ │ │ ├── read_uint.hpp │ │ │ ├── rematch.hpp │ │ │ ├── rep.hpp │ │ │ ├── rep_min.hpp │ │ │ ├── rep_min_max.hpp │ │ │ ├── rep_opt.hpp │ │ │ ├── require.hpp │ │ │ ├── result_on_found.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 │ │ │ ├── match.hpp │ │ │ ├── memory_input.hpp │ │ │ ├── mmap_input.hpp │ │ │ ├── normal.hpp │ │ │ ├── nothing.hpp │ │ │ ├── parse.hpp │ │ │ ├── parse_error.hpp │ │ │ ├── position.hpp │ │ │ ├── read_input.hpp │ │ │ ├── require_apply.hpp │ │ │ ├── require_apply0.hpp │ │ │ ├── rewind_mode.hpp │ │ │ ├── rules.hpp │ │ │ ├── string_input.hpp │ │ │ ├── tracking_mode.hpp │ │ │ ├── uint16.hpp │ │ │ ├── uint32.hpp │ │ │ ├── uint64.hpp │ │ │ ├── uint8.hpp │ │ │ ├── utf16.hpp │ │ │ ├── utf32.hpp │ │ │ ├── utf8.hpp │ │ │ └── version.hpp │ └── tinydir.h │ ├── to_chemcomp.hpp │ ├── to_cif.hpp │ ├── to_json.hpp │ ├── to_mmcif.hpp │ ├── to_pdb.hpp │ ├── topo.hpp │ ├── twin.hpp │ ├── unitcell.hpp │ ├── utf.hpp │ ├── util.hpp │ ├── version.hpp │ ├── xds2mtz.hpp │ └── xds_ascii.hpp ├── prog ├── align.cpp ├── blobs.cpp ├── cif2json.cpp ├── cif2mtz.cpp ├── cifdiff.cpp ├── cifmod.h ├── contact.cpp ├── contents.cpp ├── convert.cpp ├── crd.cpp ├── ecalc.cpp ├── fprime.cpp ├── grep.cpp ├── h.cpp ├── histogram.h ├── json2cif.cpp ├── main.cpp ├── map.cpp ├── map2sf.cpp ├── mapcoef.cpp ├── mapcoef.h ├── mask.cpp ├── merge.cpp ├── mixmtz.cpp ├── mondiff.cpp ├── monlib_opt.cpp ├── monlib_opt.h ├── mtz.cpp ├── mtz2cif.cpp ├── options.cpp ├── options.h ├── reindex.cpp ├── residues.cpp ├── rmsz.cpp ├── set.cpp ├── sf2map.cpp ├── sfcalc.cpp ├── sg.cpp ├── ss.cpp ├── tags.cpp ├── timer.h ├── validate.cpp ├── validate_mon.cpp ├── validate_mon.h ├── wcn.cpp └── xds2mtz.cpp ├── pyproject.toml ├── python ├── align.cpp ├── array.h ├── ccp4.cpp ├── chemcomp.cpp ├── cif.cpp ├── common.h ├── elem.cpp ├── gemmi.cpp ├── gemmi │ ├── __init__.py │ └── fetch.py ├── grid.cpp ├── hkl.cpp ├── make_iterator.h ├── meta.cpp ├── meta.h ├── mol.cpp ├── monlib.cpp ├── mtz.cpp ├── read.cpp ├── recgrid.cpp ├── scaling.cpp ├── search.cpp ├── serial.h ├── sf.cpp ├── small.cpp ├── stubs.pat ├── sym.cpp ├── topo.cpp ├── unitcell.cpp └── write.cpp ├── run-tests.sh ├── setup.cfg ├── src ├── align.cpp ├── assembly.cpp ├── calculate.cpp ├── ccp4.cpp ├── crd.cpp ├── ddl.cpp ├── dssp.cpp ├── eig3.cpp ├── flat.cpp ├── fprime.cpp ├── gz.cpp ├── intensit.cpp ├── json.cpp ├── mmcif.cpp ├── mmread_gz.cpp ├── monlib.cpp ├── mtz.cpp ├── mtz2cif.cpp ├── pdb.cpp ├── polyheur.cpp ├── read_cif.cpp ├── resinfo.cpp ├── riding_h.cpp ├── select.cpp ├── sprintf.cpp ├── symmetry.cpp ├── to_json.cpp ├── to_mmcif.cpp ├── to_pdb.cpp ├── topo.cpp └── xds_ascii.cpp ├── tests ├── 1011031.cif ├── 1lzh.pdb.gz ├── 1orc.pdb ├── 1pfe.cif.gz ├── 1pfe.json ├── 1pfe_asu.msk.gz ├── 2013551.cif ├── 2242624.cif ├── 2242624.hkl ├── 3dg1_final.cif ├── 3wup.json.gz ├── 4003024.cif ├── 4aap-sf-subset.cif ├── 4hhh_frag.pdb ├── 4oz7.pdb ├── 5cvz_final.pdb ├── 5e5z.mtz ├── 5e5z.pdb ├── 5i55.cif ├── 5i55_tiny.ccp4 ├── 5moo_header.pdb ├── 5wkd.pdb ├── 5wkd_phases.mtz.gz ├── HEM.cif ├── HEM.pdb ├── HEN.cif ├── INTEGRATE-tiny.HKL ├── SO3.cif ├── cc12-hkl.cif ├── cif.cpp ├── common.py ├── disulf.cpp ├── ener_lib.cif ├── eol-test.cif ├── iota_yzx.ccp4.gz ├── list │ └── mon_lib_list.cif ├── main.cpp ├── misc.cif ├── misc.json ├── mmcif_pdbx_v50_frag.dic ├── pdb1gdr.ent ├── r5wkdsf.ent ├── rnase_frag.pdb ├── test_align.py ├── test_cif.py ├── test_cif_json.py ├── test_elem.py ├── test_examples.py ├── test_fetch.py ├── test_grid.py ├── test_hkl.py ├── test_misc.py ├── test_mol.py ├── test_monlib.py ├── test_neighbor.py ├── test_prog.py ├── test_seq.py ├── test_sf.py ├── test_smallmol.py ├── test_symmetry.py ├── test_twin.py ├── test_unitcell.py └── windowsh.cpp ├── third_party ├── README ├── doctest.h ├── linalg.h ├── optionparser.h ├── sajson.h ├── serializer.h ├── stb_sprintf.h └── zlib │ ├── LICENSE │ ├── NOTE │ ├── adler32.c │ ├── crc32.c │ ├── gzguts.h │ ├── gzlib.c │ ├── gzread.c │ ├── inffast.c │ ├── inffast.h │ ├── inffixed.h │ ├── inflate.c │ ├── inflate.h │ ├── inftrees.c │ ├── inftrees.h │ ├── zconf.h │ ├── zlib.h │ ├── zutil.c │ └── zutil.h ├── tools ├── FindZLIB_NG.cmake ├── check_serialize.py ├── cmp-size.py ├── compare_mask.sh ├── compare_pdb.sh ├── compare_record.sh ├── compare_wheels.py ├── crd-diff.py ├── docs-help.sh ├── gemmi-config.cmake.in ├── gen_reciprocal_asu.py ├── gen_sg_table.py ├── header-list.py ├── linux-wheels.sh ├── ob_spacegroups.py ├── pdb_ids.txt ├── refmac-crd.sh ├── release.txt ├── resinfo.py ├── syminfo.py └── upstream-check.py └── wasm ├── .ignore ├── Makefile ├── README.md ├── cell.cpp ├── common.h ├── gemmi.cpp ├── gemmi.d.ts ├── 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