| 1 | <!--
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| 2 | @Author: Tristan Croll
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| 3 | @Date: 26-Feb-2018
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| 4 | @Email: tic20@cam.ac.uk
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| 5 | @Last modified by: tic20
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| 6 | @Last modified time: 30-Apr-2018
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| 7 | @License: Creative Commons BY-NC-SA 3.0, https://creativecommons.org/licenses/by-nc-sa/3.0/.
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| 8 | @Copyright: Copyright 2017-2018 Tristan Croll
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| 9 | -->
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| 10 |
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| 11 |
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| 12 |
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| 13 | <BundleInfo name="ChimeraX-Clipper" version="0.2.1" package="chimerax.clipper"
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| 14 | minSessionVersion="1" maxSessionVersion="1">
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| 15 |
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| 16 | <!-- Additional information about bundle source -->
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| 17 | <Author>Tristan Croll</Author>
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| 18 | <Email>tic20@cam.ac.uk</Email>
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| 19 | <URL>To be completed</URL>
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| 20 |
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| 21 | <!-- Synopsis is a one-line description
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| 22 | Description is a full multi-line description -->
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| 23 | <Synopsis>Clipper: Efficient handling of volumetric data and symmetry</Synopsis>
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| 24 | <Description>
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| 25 |
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| 26 | </Description>
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| 27 |
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| 28 | <!-- Categories is a list where this bundle should appear -->
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| 29 | <Categories>
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| 30 | <Category name="General"/>
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| 31 | </Categories>
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| 32 |
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| 33 | <CModule name="contour_thread" usesNumpy="true">
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| 34 | <CompileArgument>-fvisibility=hidden -fvisibility-inlines-hidden</CompileArgument>
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| 35 | <LinkArgument>-fvisibility=hidden -fvisibility-inlines-hidden -s</LinkArgument>
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| 36 | <!-- <LinkArgument>-s</LinkArgument> -->
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| 37 | <Library>stdc++</Library>
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| 38 |
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| 39 | <SourceFile>src/contour/contour_threaded.cpp</SourceFile>
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| 40 | <SourceFile>src/contour/contourdata.cpp</SourceFile>
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| 41 | </CModule>
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| 42 |
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| 43 | <!-- Compiled modules in bundle
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| 44 | CModule gives the name of the module
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| 45 | Source files are listed in one or more SourceFile elements -->
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| 46 | <CLibrary name="mmdb2">
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| 47 | <Define>MMDB_EXPORT</Define>
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| 48 | <CompileArgument>-fvisibility=hidden -fvisibility-inlines-hidden</CompileArgument>
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| 49 | <LinkArgument>-fvisibility=hidden -fvisibility-inlines-hidden -s</LinkArgument>
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| 50 | <Library>stdc++</Library>
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| 51 | <SourceFile>src/deps/mmdb2/mmdb2/hybrid_36.cpp</SourceFile>
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| 52 | <SourceFile>src/deps/mmdb2/mmdb2/mmdb_io_stream.cpp</SourceFile>
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| 53 | <SourceFile>src/deps/mmdb2/mmdb2/mmdb_math_linalg.cpp</SourceFile>
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| 54 | <SourceFile>src/deps/mmdb2/mmdb2/mmdb_symop.cpp</SourceFile>
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| 55 | <SourceFile>src/deps/mmdb2/mmdb2/mmdb_atom.cpp</SourceFile>
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| 56 | <SourceFile>src/deps/mmdb2/mmdb2/mmdb_machine_.cpp</SourceFile>
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| 57 | <SourceFile>src/deps/mmdb2/mmdb2/mmdb_math_rand.cpp</SourceFile>
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| 58 | <SourceFile>src/deps/mmdb2/mmdb2/mmdb_tables.cpp</SourceFile>
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| 59 | <SourceFile>src/deps/mmdb2/mmdb2/mmdb_bondmngr.cpp</SourceFile>
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| 60 | <SourceFile>src/deps/mmdb2/mmdb2/mmdb_manager.cpp</SourceFile>
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| 61 | <SourceFile>src/deps/mmdb2/mmdb2/mmdb_mattype.cpp</SourceFile>
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| 62 | <SourceFile>src/deps/mmdb2/mmdb2/mmdb_title.cpp</SourceFile>
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| 63 | <SourceFile>src/deps/mmdb2/mmdb2/mmdb_chain.cpp</SourceFile>
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| 64 | <SourceFile>src/deps/mmdb2/mmdb2/mmdb_mask.cpp</SourceFile>
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| 65 | <SourceFile>src/deps/mmdb2/mmdb2/mmdb_mmcif_.cpp</SourceFile>
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| 66 | <SourceFile>src/deps/mmdb2/mmdb2/mmdb_uddata.cpp</SourceFile>
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| 67 | <SourceFile>src/deps/mmdb2/mmdb2/mmdb_cifdefs.cpp</SourceFile>
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| 68 | <SourceFile>src/deps/mmdb2/mmdb2/mmdb_math_.cpp</SourceFile>
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| 69 | <SourceFile>src/deps/mmdb2/mmdb2/mmdb_model.cpp</SourceFile>
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| 70 | <SourceFile>src/deps/mmdb2/mmdb2/mmdb_utils.cpp</SourceFile>
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| 71 | <SourceFile>src/deps/mmdb2/mmdb2/mmdb_coormngr.cpp</SourceFile>
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| 72 | <SourceFile>src/deps/mmdb2/mmdb2/mmdb_math_align.cpp</SourceFile>
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| 73 | <SourceFile>src/deps/mmdb2/mmdb2/mmdb_root.cpp</SourceFile>
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| 74 | <SourceFile>src/deps/mmdb2/mmdb2/mmdb_xml_.cpp</SourceFile>
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| 75 | <SourceFile>src/deps/mmdb2/mmdb2/mmdb_cryst.cpp</SourceFile>
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| 76 | <SourceFile>src/deps/mmdb2/mmdb2/mmdb_math_bfgsmin.cpp</SourceFile>
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| 77 | <SourceFile>src/deps/mmdb2/mmdb2/mmdb_rwbrook.cpp</SourceFile>
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| 78 | <SourceFile>src/deps/mmdb2/mmdb2/mmdb_ficif.cpp</SourceFile>
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| 79 | <SourceFile>src/deps/mmdb2/mmdb2/mmdb_math_fft.cpp</SourceFile>
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| 80 | <SourceFile>src/deps/mmdb2/mmdb2/mmdb_selmngr.cpp</SourceFile>
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| 81 | <SourceFile>src/deps/mmdb2/mmdb2/mmdb_io_file.cpp</SourceFile>
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| 82 | <SourceFile>src/deps/mmdb2/mmdb2/mmdb_math_graph.cpp</SourceFile>
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| 83 | <SourceFile>src/deps/mmdb2/mmdb2/mmdb_seqsuperpose.cpp</SourceFile>
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| 84 | </CLibrary>
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| 85 | <CLibrary name="ccp4">
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| 86 | <Define>CCP4_EXPORT</Define>
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| 87 | <CompileArgument>-fvisibility=hidden -fvisibility-inlines-hidden</CompileArgument>
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| 88 | <LinkArgument>-fvisibility=hidden -fvisibility-inlines-hidden -s</LinkArgument>
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| 89 | <Library>stdc++</Library>
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| 90 | <SourceFile>src/deps/libccp4/ccp4/ccp4_array.c</SourceFile>
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| 91 | <SourceFile>src/deps/libccp4/ccp4/cmap_data.c</SourceFile>
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| 92 | <SourceFile>src/deps/libccp4/ccp4/cmtzlib.c</SourceFile>
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| 93 | <SourceFile>src/deps/libccp4/ccp4/ccp4_general.c</SourceFile>
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| 94 | <SourceFile>src/deps/libccp4/ccp4/cmap_header.c</SourceFile>
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| 95 | <SourceFile>src/deps/libccp4/ccp4/csymlib.c</SourceFile>
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| 96 | <SourceFile>src/deps/libccp4/ccp4/ccp4_parser.c</SourceFile>
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| 97 | <SourceFile>src/deps/libccp4/ccp4/cmap_labels.c</SourceFile>
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| 98 | <SourceFile>src/deps/libccp4/ccp4/cvecmat.c</SourceFile>
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| 99 | <SourceFile>src/deps/libccp4/ccp4/ccp4_program.c</SourceFile>
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| 100 | <SourceFile>src/deps/libccp4/ccp4/cmap_open.c</SourceFile>
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| 101 | <SourceFile>src/deps/libccp4/ccp4/library_err.c</SourceFile>
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| 102 | <SourceFile>src/deps/libccp4/ccp4/ccp4_unitcell.c</SourceFile>
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| 103 | <SourceFile>src/deps/libccp4/ccp4/cmap_skew.c</SourceFile>
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| 104 | <SourceFile>src/deps/libccp4/ccp4/library_file.c</SourceFile>
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| 105 | <SourceFile>src/deps/libccp4/ccp4/cmap_accessor.c</SourceFile>
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| 106 | <SourceFile>src/deps/libccp4/ccp4/cmap_stats.c</SourceFile>
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| 107 | <SourceFile>src/deps/libccp4/ccp4/library_utils.c</SourceFile>
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| 108 | <SourceFile>src/deps/libccp4/ccp4/cmap_close.c</SourceFile>
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| 109 | <SourceFile>src/deps/libccp4/ccp4/cmap_symop.c</SourceFile>
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| 110 | <SourceFile>src/deps/libccp4/ccp4/pack_c.c</SourceFile>
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| 111 | </CLibrary>
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| 112 | <CLibrary name="clipper">
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| 113 | <Define>CLIPPER_EXPORTS</Define>
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| 114 | <Define>FFTW_MKL</Define>
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| 115 | <CompileArgument>-fvisibility=hidden -fvisibility-inlines-hidden</CompileArgument>
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| 116 | <LinkArgument>-fvisibility=hidden -fvisibility-inlines-hidden -s</LinkArgument>
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| 117 | <IncludeDir>src/deps/libccp4</IncludeDir>
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| 118 | <IncludeDir>src/deps/mmdb2</IncludeDir>
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| 119 | <IncludeDir>src/deps/clipper</IncludeDir>
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| 120 | <IncludeDir>src/deps/fftw2/include</IncludeDir>
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| 121 | <LibraryDir>src</LibraryDir>
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| 122 | <Library>mmdb2</Library>
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| 123 | <Library>ccp4</Library>
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| 124 | <Library>fftw2xc</Library>
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| 125 | <Library>stdc++</Library>
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| 126 |
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| 127 | <SourceFile>src/deps/clipper/core/atomsf.cpp</SourceFile>
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| 128 | <SourceFile>src/deps/clipper/core/coords.cpp</SourceFile>
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| 129 | <SourceFile>src/deps/clipper/core/nxmap_operator.cpp</SourceFile>
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| 130 | <SourceFile>src/deps/clipper/core/cell.cpp</SourceFile>
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| 131 | <SourceFile>src/deps/clipper/core/derivs.cpp</SourceFile>
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| 132 | <SourceFile>src/deps/clipper/core/ramachandran.cpp</SourceFile>
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| 133 | <SourceFile>src/deps/clipper/core/clipper_instance.cpp</SourceFile>
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| 134 | <SourceFile>src/deps/clipper/core/fftmap.cpp</SourceFile>
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| 135 | <SourceFile>src/deps/clipper/core/resol_basisfn.cpp</SourceFile>
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| 136 | <SourceFile>src/deps/clipper/core/clipper_memory.cpp</SourceFile>
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| 137 | <SourceFile>src/deps/clipper/core/fftmap_sparse.cpp</SourceFile>
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| 138 | <SourceFile>src/deps/clipper/core/resol_fn.cpp</SourceFile>
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| 139 | <SourceFile>src/deps/clipper/core/clipper_message.cpp</SourceFile>
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| 140 | <SourceFile>src/deps/clipper/core/hkl_compute.cpp</SourceFile>
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| 141 | <SourceFile>src/deps/clipper/core/resol_targetfn.cpp</SourceFile>
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| 142 | <SourceFile>src/deps/clipper/core/clipper_stats.cpp</SourceFile>
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| 143 | <SourceFile>src/deps/clipper/core/hkl_data.cpp</SourceFile>
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| 144 | <SourceFile>src/deps/clipper/core/rotation.cpp</SourceFile>
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| 145 | <SourceFile>src/deps/clipper/core/clipper_test.cpp</SourceFile>
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| 146 | <SourceFile>src/deps/clipper/core/hkl_datatypes.cpp</SourceFile>
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| 147 | <SourceFile>src/deps/clipper/core/spacegroup.cpp</SourceFile>
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| 148 | <SourceFile>src/deps/clipper/core/clipper_types.cpp</SourceFile>
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| 149 | <SourceFile>src/deps/clipper/core/hkl_info.cpp</SourceFile>
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| 150 | <SourceFile>src/deps/clipper/core/spacegroup_data.cpp</SourceFile>
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| 151 | <SourceFile>src/deps/clipper/core/clipper_util.cpp</SourceFile>
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| 152 | <SourceFile>src/deps/clipper/core/hkl_lookup.cpp</SourceFile>
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| 153 | <SourceFile>src/deps/clipper/core/symop.cpp</SourceFile>
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| 154 | <SourceFile>src/deps/clipper/core/container.cpp</SourceFile>
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| 155 | <SourceFile>src/deps/clipper/core/hkl_operators.cpp</SourceFile>
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| 156 | <SourceFile>src/deps/clipper/core/container_hkl.cpp</SourceFile>
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| 157 | <SourceFile>src/deps/clipper/core/map_interp.cpp</SourceFile>
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| 158 | <SourceFile>src/deps/clipper/core/container_map.cpp</SourceFile>
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| 159 | <SourceFile>src/deps/clipper/core/map_utils.cpp</SourceFile>
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| 160 | <SourceFile>src/deps/clipper/core/xmap.cpp</SourceFile>
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| 161 | <SourceFile>src/deps/clipper/core/container_types.cpp</SourceFile>
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| 162 | <SourceFile>src/deps/clipper/core/nxmap.cpp</SourceFile>
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| 163 | <SourceFile>src/deps/clipper/core/clipper_thread.cpp</SourceFile>
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| 164 | <SourceFile>src/deps/clipper/core/test_core.cpp</SourceFile>
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| 165 | <SourceFile>src/deps/clipper/core/test_data.cpp</SourceFile>
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| 166 |
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| 167 | <SourceFile>src/deps/clipper/contrib/convolution_search.cpp</SourceFile>
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| 168 | <SourceFile>src/deps/clipper/contrib/sfcalc.cpp</SourceFile>
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| 169 | <SourceFile>src/deps/clipper/contrib/edcalc.cpp</SourceFile>
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| 170 | <SourceFile>src/deps/clipper/contrib/sfcalc_obs.cpp</SourceFile>
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| 171 | <SourceFile>src/deps/clipper/contrib/fffear.cpp</SourceFile>
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| 172 | <SourceFile>src/deps/clipper/contrib/sfscale.cpp</SourceFile>
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| 173 | <SourceFile>src/deps/clipper/contrib/function_object_bases.cpp</SourceFile>
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| 174 | <SourceFile>src/deps/clipper/contrib/sfweight.cpp</SourceFile>
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| 175 | <SourceFile>src/deps/clipper/contrib/mapfilter.cpp</SourceFile>
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| 176 | <SourceFile>src/deps/clipper/contrib/skeleton.cpp</SourceFile>
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| 177 | <SourceFile>src/deps/clipper/contrib/originmatch.cpp</SourceFile>
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| 178 |
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| 179 | <SourceFile>src/deps/clipper/mmdb/clipper_mmdb.cpp</SourceFile>
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| 180 |
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| 181 | <SourceFile>src/deps/clipper/minimol/minimol.cpp</SourceFile>
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| 182 | <SourceFile>src/deps/clipper/minimol/container_minimol.cpp</SourceFile>
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| 183 | <SourceFile>src/deps/clipper/minimol/minimol_data.cpp</SourceFile>
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| 184 | <SourceFile>src/deps/clipper/minimol/minimol_io.cpp</SourceFile>
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| 185 | <SourceFile>src/deps/clipper/minimol/minimol_seq.cpp</SourceFile>
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| 186 | <SourceFile>src/deps/clipper/minimol/minimol_utils.cpp</SourceFile>
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| 187 |
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| 188 | <SourceFile>src/deps/clipper/phs/phs_io.cpp</SourceFile>
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| 189 |
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| 190 | <SourceFile>src/deps/clipper/cif/cif_data_io.cpp</SourceFile>
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| 191 |
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| 192 | <SourceFile>src/deps/clipper/ccp4/ccp4_mtz_types.cpp</SourceFile>
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| 193 | <SourceFile>src/deps/clipper/ccp4/ccp4_mtz_io.cpp</SourceFile>
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| 194 | <SourceFile>src/deps/clipper/ccp4/ccp4_map_io.cpp</SourceFile>
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| 195 | <SourceFile>src/deps/clipper/ccp4/ccp4_utils.cpp</SourceFile>
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| 196 |
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| 197 | <SourceFile>src/deps/clipper/cns/cns_hkl_io.cpp</SourceFile>
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| 198 | <SourceFile>src/deps/clipper/cns/cns_map_io.cpp</SourceFile>
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| 199 |
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| 200 | </CLibrary>
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| 201 |
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| 202 | <CLibrary name="clipper_cx" usesNumpy="true">
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| 203 | <Define>CLIPPER_CX_EXPORTS</Define>
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| 204 | <CompileArgument>-fvisibility=hidden -fvisibility-inlines-hidden</CompileArgument>
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| 205 | <LinkArgument>-fvisibility=hidden -fvisibility-inlines-hidden -s</LinkArgument>
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| 206 | <IncludeDir>src/include</IncludeDir>
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| 207 | <LibraryDir>src</LibraryDir>
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| 208 | <Library>clipper</Library>
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| 209 | <Library>stdc++</Library>
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| 210 | <SourceFile>src/clipper_ext/xtal_mgr.cpp</SourceFile>
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| 211 | <SourceFile>src/clipper_ext/edcalc_ext.cpp</SourceFile>
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| 212 | <SourceFile>src/clipper_ext/sfcalc_obs_vdw.cpp</SourceFile>
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| 213 | </CLibrary>
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| 214 |
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| 215 | <!-- <CLibrary name="_clipper" usesNumpy="true">
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| 216 | <IncludeDir>src/include</IncludeDir>
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| 217 | <LibraryDir>src</LibraryDir>
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| 218 | <CompileArgument>-fvisibility=hidden</CompileArgument>
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| 219 | <Library>clipper</Library>
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| 220 |
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| 221 | <SourceFile>src/bindings/_clipper.cpp</SourceFile>
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| 222 | </CLibrary> -->
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| 223 |
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| 224 | <CModule name="clipper_python" usesNumpy="true">
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| 225 | <CompileArgument>-fvisibility=hidden -fvisibility-inlines-hidden</CompileArgument>
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| 226 | <LinkArgument>-fvisibility=hidden -fvisibility-inlines-hidden -s</LinkArgument>
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| 227 | <IncludeDir>src/include</IncludeDir>
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| 228 | <IncludeDir>src</IncludeDir>
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| 229 | <LibraryDir>src</LibraryDir>
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| 230 | <Library>clipper</Library>
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| 231 | <Library>clipper_cx</Library>
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| 232 | <Library>stdc++</Library>
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| 233 | <!-- <CompileArgument>-Os</CompileArgument> -->
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| 234 |
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| 235 | <SourceFile>src/bindings/ext/wrap_xtal_mgr.cpp</SourceFile>
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| 236 |
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| 237 | <SourceFile>src/bindings/contrib/wrap_skeleton.cpp</SourceFile>
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| 238 | <SourceFile>src/bindings/contrib/wrap_sfweight.cpp</SourceFile>
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| 239 | <SourceFile>src/bindings/contrib/wrap_sfscale.cpp</SourceFile>
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| 240 | <SourceFile>src/bindings/contrib/wrap_sfcalc.cpp</SourceFile>
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| 241 | <SourceFile>src/bindings/contrib/wrap_sfcalc_obs.cpp</SourceFile>
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| 242 | <SourceFile>src/bindings/contrib/wrap_originmatch.cpp</SourceFile>
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| 243 | <SourceFile>src/bindings/contrib/wrap_mapfilter.cpp</SourceFile>
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| 244 | <SourceFile>src/bindings/contrib/wrap_fffear.cpp</SourceFile>
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| 245 | <SourceFile>src/bindings/contrib/wrap_edcalc.cpp</SourceFile>
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| 246 | <SourceFile>src/bindings/contrib/wrap_convolution_search.cpp</SourceFile>
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| 247 |
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| 248 |
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| 249 | <SourceFile>src/bindings/wrap_clipper_util.cpp</SourceFile>
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| 250 | <SourceFile>src/bindings/wrap_map_utils.cpp</SourceFile>
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| 251 | <SourceFile>src/bindings/wrap_ccp4_mtz_io.cpp</SourceFile>
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| 252 | <SourceFile>src/bindings/wrap_unit_cell.cpp</SourceFile>
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| 253 | <SourceFile>src/bindings/wrap_symops.cpp</SourceFile>
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| 254 | <SourceFile>src/bindings/wrap_spacegroup.cpp</SourceFile>
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| 255 | <SourceFile>src/bindings/wrap_xmap.cpp</SourceFile>
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| 256 | <SourceFile>src/bindings/wrap_nxmap.cpp</SourceFile>
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| 257 | <SourceFile>src/bindings/wrap_nxmap_operator.cpp</SourceFile>
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| 258 | <SourceFile>src/bindings/wrap_hkl_datatypes.cpp</SourceFile>
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| 259 | <SourceFile>src/bindings/wrap_hkl_data.cpp</SourceFile>
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| 260 | <SourceFile>src/bindings/wrap_derivs.cpp</SourceFile>
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| 261 | <SourceFile>src/bindings/wrap_coords.cpp</SourceFile>
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| 262 | <SourceFile>src/bindings/wrap_clipper_stats.cpp</SourceFile>
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| 263 | <SourceFile>src/bindings/wrap_cell.cpp</SourceFile>
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| 264 | <SourceFile>src/bindings/wrap_atomsf.cpp</SourceFile>
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| 265 | <SourceFile>src/bindings/wrap_symop.cpp</SourceFile>
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| 266 | <SourceFile>src/bindings/wrap_clipper_types.cpp</SourceFile>
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| 267 | <SourceFile>src/bindings/wrap_hkl_info.cpp</SourceFile>
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| 268 | <SourceFile>src/bindings/wrap_containers.cpp</SourceFile>
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| 269 | <SourceFile>src/bindings/clipper_pybind11.cpp</SourceFile>
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| 270 | </CModule>
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| 271 |
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| 272 | <CLibrary name = "_symmetry" usesNumpy="true">
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| 273 | <SourceFile>src/symmetry_cpp/symmetry.cpp</SourceFile>
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| 274 | <CompileArgument>-fvisibility=hidden -fvisibility-inlines-hidden</CompileArgument>
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| 275 | <LinkArgument>-fvisibility=hidden -fvisibility-inlines-hidden -s</LinkArgument>
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| 276 | <Library>atomstruct</Library>
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| 277 | <Library>arrays</Library>
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| 278 | <Library>stdc++</Library>
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| 279 | </CLibrary>
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| 280 |
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| 281 | <!-- Dependencies on other ChimeraX/Python packages -->
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| 282 | <Dependencies>
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| 283 | <Dependency name="ChimeraX-Core" version=">=0.7"/>
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| 284 | <Dependency name="ChimeraX-Atomic" version=">=1.0"/>
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| 285 | <!-- <Dependency name="Clipper-Python" version=">=0.1.1"/> -->
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| 286 | </Dependencies>
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| 287 |
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| 288 |
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| 289 | <!-- Python and ChimeraX-specific classifiers
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| 290 | From https://pypi.python.org/pypi?%3Aaction=list_classifiers
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| 291 | Some Python classifiers are always inserted by the build process.
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| 292 | These include the Environment and Operating System classifiers
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| 293 | as well as:
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| 294 | Framework :: ChimeraX
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| 295 | Intended Audience :: Science/Research
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| 296 | Programming Language :: Python :: 3
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| 297 | Topic :: Scientific/Engineering :: Visualization
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| 298 | Topic :: Scientific/Engineering :: Chemistry
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| 299 | Topic :: Scientific/Engineering :: Bio-Informatics
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| 300 | The "ChimeraX :: Bundle" classifier is also supplied automatically. -->
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| 301 | <DataFiles>
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| 302 | <DataFile>tests/*.pdb</DataFile>
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| 303 | <DataFile>tests/*.mtz</DataFile>
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| 304 | <DataFile platform="linux">libfftw2xc.so</DataFile>
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| 305 | <DataFile platform="linux">libfftw_mkl_core.so</DataFile>
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| 306 | <DataFile platform="mac">libfftw2xc.dylib</DataFile>
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| 307 | <DataFile platform="mac">mkl_custom.dylib</DataFile>
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| 308 | </DataFiles>
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| 309 |
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| 310 | <!-- <DataFiles>
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| 311 | <DataFile>dir/file</DataFile>
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| 312 | </DataFiles> -->
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| 313 | <Classifiers>
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| 314 | <!-- Development Status should be compatible with bundle version number -->
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| 315 | <PythonClassifier>Development Status :: 2 - Pre-Alpha</PythonClassifier>
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| 316 | <PythonClassifier>License :: Free for non-commercial use.</PythonClassifier>
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| 317 | ]
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| 318 | ]
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| 319 | </Classifiers>
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| 320 |
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| 321 | </BundleInfo>
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