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Copyright: NONE
License: UNKNOWN
 FIXME

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 ./geometry/protein-donor-acceptors.cc
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 ./geometry/read-metals-json.cc
 ./geometry/residue-and-atom-specs.cc
 ./geometry/srs-interface.cc
 ./geometry/srs-interface.hh
 ./high-res/high-res.hh
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 ./ideal/ng.cc
 ./ideal/parallel-planes.cc
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 ./ideal/phi-psi.cc
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 ./ideal/process-dfs-in-range.cc
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 ./ideal/pull-restraint.cc
 ./ideal/rama-types.hh
 ./ideal/refinement-lights.hh
 ./ideal/refinement-results-t.hh
 ./ideal/simulated-annealing.cc
 ./ideal/test-rama-plot.cc
 ./ideal/torsion-bonds.cc
 ./ideal/torsion-bonds.hh
 ./ideal/trans-peptide.cc
 ./ideal/write-png.cc
 ./ideal/write-png.hh
 ./ideal/zo-rama.cc
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 ./lidia-core/atom-types.cc
 ./lidia-core/get-residue.cc
 ./lidia-core/get-residue.hh
 ./lidia-core/neighbour-sorter.hh
 ./lidia-core/svg-molecule.cc
 ./lidia-core/svg-molecule.hh
 ./lidia-core/test-lig-build.cc
 ./lidia-core/third-neighbour-info-t.hh
 ./lidia-core/use-rdkit.hh
 ./ligand/ca-torsion-info.cc
 ./ligand/ca-torsion-info.hh
 ./ligand/dSFMT-params19937.h
 ./ligand/joining-residues.cc
 ./ligand/libres-tracer.cc
 ./ligand/libres-tracer.hh
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 ./ligand/map-point-cluster.hh
 ./ligand/multi-peptide.hh
 ./ligand/new-residue-by-3-phi-psi.cc
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 ./ligand/rama-rsr-extend-fragments.cc
 ./ligand/rama-rsr-extend-fragments.hh
 ./ligand/refine-isolated-chain.cc
 ./ligand/refine-isolated-chain.hh
 ./ligand/res-tracer.cc
 ./ligand/scored-molecule.hh
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 ./ligand/side-chain-densities.cc
 ./ligand/side-chain-densities.hh
 ./ligand/side-chain.cc
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 ./ligand/test-tube-finder.cc
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 ./mini-mol/mol-hierarchy.cc
 ./pli/flev-annotations.cc
 ./pli/protein-ligand-interactions.hh
 ./pli/sdf-interface-for-export.hh
 ./pli/sdf-internal.hh
 ./pli/specs.cc
 ./pli/specs.hh
 ./pyrogen/cairo-molecule.cc
 ./pyrogen/cairo-molecule.hh
 ./src/9.ssao.shader
 ./src/9.ssao_blur.shader
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 ./src/Basic.shader
 ./src/HUDMesh.cc
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 ./src/Instanced-Markup-Mesh.cc
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 ./src/LigandViewMesh.cc
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 ./src/LinesMesh.cc
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 ./src/Mesh.cc
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 ./src/Model.cc
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 ./src/Shader.cc
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 ./src/animated-ligand.hh
 ./src/array-2d.hh
 ./src/atom-label-info.hh
 ./src/atom-label.shader
 ./src/atom-overlaps.cc
 ./src/atom-pull.hh
 ./src/background-image.shader
 ./src/blur-x.shader
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 ./src/blur.shader
 ./src/boids.cc
 ./src/boids.hh
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 ./src/boot-python.cc
 ./src/c-interface-bonds.cc
 ./src/c-interface-bonds.hh
 ./src/c-interface-curlew.cc
 ./src/c-interface-curlew.hh
 ./src/c-interface-geometry-distortion.hh
 ./src/c-interface-gui.hh
 ./src/c-interface-image.cc
 ./src/c-interface-ligand-search.hh
 ./src/c-interface-ligands-widgets.hh
 ./src/c-interface-mogul-scripting.cc
 ./src/c-interface-refine.hh
 ./src/c-interface-sequence.cc
 ./src/c-interface-sequence.hh
 ./src/camera-facing-quad-shader-for-testing.shader
 ./src/cc-interface-alignment.cc
 ./src/cc-interface-alignment.hh
 ./src/cc-interface-graphics.cc
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 ./src/cc-interface-image.hh
 ./src/cc-interface-map-utils.cc
 ./src/cc-interface-merge.cc
 ./src/cc-interface-molecular-representation.cc
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 ./src/cc-interface-molecular-symmetry.cc
 ./src/cc-interface-png.cc
 ./src/cc-interface-scripting.cc
 ./src/cc-interface-user-defined-atom-colours.cc
 ./src/cc-interface-user-defined-atom-colours.hh
 ./src/cc-interface-validation.cc
 ./src/central-cube.shader
 ./src/cfc-widgets.hh
 ./src/change-dir.cc
 ./src/change-dir.hh
 ./src/clip-hybrid-atom.hh
 ./src/clipper-ccp4-map-file-wrapper.hh
 ./src/clipper-to-glm.hh
 ./src/cmtz-interface-gui.hh
 ./src/colour-functions.hh
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 ./src/coot-application.cc
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 ./src/coot-colour.cc
 ./src/coot-phi-psi.cc
 ./src/coot-phi-psi.hh
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 ./src/coot-version.hh
 ./src/create-menu-item-actions.cc
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 ./src/crunch-model.hh
 ./src/curl-utils.hh
 ./src/curlew-gtk4.cc
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 ./src/curlew.h
 ./src/data-pair-remover.hh
 ./src/density-results-container-t.hh
 ./src/depth-of-field.shader
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 ./src/draw-generic-display-objects.cc
 ./src/draw-map-cap.shader
 ./src/draw.cc
 ./src/draw.hh
 ./src/dynamic-validation.cc
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 ./src/effects.shader
 ./src/event-controller-callbacks.cc
 ./src/event-controller-callbacks.hh
 ./src/extra-distance-restraint-markup.hh
 ./src/extra-distance-restraints.shader
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 ./src/eyes.cc
 ./src/eyes.hh
 ./src/fit-loop-gui.cc
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 ./src/fit-loop.cc
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 ./src/fixup-interface.h.sh
 ./src/framebuffer.cc
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 ./src/gaussian-surface.cc
 ./src/generic-vertex.hh
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 ./src/gl-rama-plot.cc
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 ./src/glarea_tick_function.hh
 ./src/globularize.cc
 ./src/graphical-molecule.cc
 ./src/graphical-molecule.hh
 ./src/graphics-info-defines-gtk4.cc
 ./src/graphics-info-draw-models.cc
 ./src/graphics-info-draw.cc
 ./src/graphics-info-init.cc
 ./src/graphics-info-intermediate.cc
 ./src/graphics-info-opengl.cc
 ./src/graphics-info-refine.cc
 ./src/graphics-info-render-scene.cc
 ./src/graphics-info-statics.cc
 ./src/graphics-info-tick-function.cc
 ./src/graphics-ligand-mesh-molecule.cc
 ./src/graphics-ligand-mesh-molecule.hh
 ./src/gtkglarea-rama-plot.hh
 ./src/hud-bars.shader
 ./src/hud-geometry-tooltip-text.shader
 ./src/hud-image-texture.shader
 ./src/hud-labels.shader
 ./src/hud-lines.shader
 ./src/hud-text.shader
 ./src/idles.hh
 ./src/init-from-gtkbuilder.cc
 ./src/init-from-gtkbuilder.hh
 ./src/init_coot_as_python_module.cc
 ./src/init_coot_as_python_module.hh
 ./src/instanced-meshes-for-shadow-map.shader
 ./src/instanced-meshes-for-ssao.shader
 ./src/instanced-meshes-with-shadows.shader
 ./src/instanced-objects.shader
 ./src/key-bindings.cc
 ./src/key-bindings.hh
 ./src/labelled-button-info.hh
 ./src/ligand-check.hh
 ./src/ligand-view.shader
 ./src/lights-info.hh
 ./src/lines-pulse.shader
 ./src/lines.shader
 ./src/make-a-dodec.cc
 ./src/make-a-dodec.hh
 ./src/map.shader
 ./src/map_triangle.hh
 ./src/matrix-utils.cc
 ./src/matrix-utils.hh
 ./src/meshed-generic-display-object.cc
 ./src/meshed-generic-display-object.hh
 ./src/meshed-particle-container.hh
 ./src/meshes-for-shadow-map.shader
 ./src/meshes-for-ssao.shader
 ./src/meshes-with-shadows.shader
 ./src/meshes.shader
 ./src/model-as-mesh.shader
 ./src/model-molecule-meshes.cc
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 ./src/model.shader
 ./src/mol-hierarchy.cc
 ./src/mol-tri.hh
 ./src/molecular-mesh-generator-mol-tris.cc
 ./src/molecular-mesh-generator.cc
 ./src/molecular-mesh-generator.hh
 ./src/molecular-triangles-mesh.hh
 ./src/molecule-class-info-alignment.cc
 ./src/molecule-class-info-analysis.cc
 ./src/molecule-class-info-bonds.cc
 ./src/molecule-class-info-dots-internal.cc
 ./src/molecule-class-info-geometry.cc
 ./src/molecule-class-info-maps-2.cc
 ./src/molecule-class-info-mol-tris.cc
 ./src/molecule-class-info-molecular-symmetry.cc
 ./src/molecule-class-info-string.cc
 ./src/moleculestotriangles.shader
 ./src/mtz-column-auto-read.hh
 ./src/new-startup.cc
 ./src/obj_loader.cc
 ./src/obj_loader.h
 ./src/old-event-callbacks.cc
 ./src/old-generic-display-object.cc
 ./src/old-generic-display-object.hh
 ./src/outline-of-active-residue.shader
 ./src/particles.shader
 ./src/pick.hh
 ./src/positron-plot.cc
 ./src/pulse-data.hh
 ./src/pumpkin.cc
 ./src/pumpkin.hh
 ./src/python-classes.cc
 ./src/python-classes.hh
 ./src/python-scripting-gui.hh
 ./src/pythonic-cfc.cc
 ./src/pythonic-cfc.hh
 ./src/rail-points.hh
 ./src/rama-balls.shader
 ./src/rama-plot-axes-and-ticks.shader
 ./src/rama-plot-phi-psi-markers.shader
 ./src/rama-plot-phi-psi.cc
 ./src/rama-plot-phi-psi.hh
 ./src/rdkit-smiles.cc
 ./src/read-cif.cc
 ./src/read-molecule.hh
 ./src/residue-markers-for-ssao.shader
 ./src/residue-markers.shader
 ./src/restore-these.hh
 ./src/rotation-centre-cross-hairs-for-ssao.shader
 ./src/rsr-functions.cc
 ./src/rsr-functions.hh
 ./src/screen.shader
 ./src/screendump-tga.cc
 ./src/screendump-tga.hh
 ./src/setup-gui-components.cc
 ./src/setup-gui-components.hh
 ./src/shadow-map-image-texture.shader
 ./src/simple-distance-object.hh
 ./src/simple-refmac.cc
 ./src/single-map-properties-dialog.cc
 ./src/single-map-properties-dialog.hh
 ./src/sound-mac.cc
 ./src/sound.cc
 ./src/sound.hh
 ./src/spherical-density.cc
 ./src/startup-utils.cc
 ./src/startup-utils.hh
 ./src/symmetry-atoms-lines.shader
 ./src/template-python-function.cc
 ./src/testing-2.cc
 ./src/text-rendering-utils.cc
 ./src/text-rendering-utils.hh
 ./src/texture-meshes-for-ssao.shader
 ./src/texture-meshes-shadow-map.shader
 ./src/texture-meshes-with-shadows.shader
 ./src/texture-meshes.shader
 ./src/tomo-tools.cc
 ./src/ud-colour-rule.hh
 ./src/updating-coordinates-molecule-parameters.hh
 ./src/updating-map-params.hh
 ./src/validation.cc
 ./src/validation.hh
 ./src/vnc-vertex-to-generic-vertex.hh
 ./src/widget-from-builder.cc
 ./src/widget-from-builder.hh
 ./src/widget-headers.hh
 ./utils/dodec.cc
 ./utils/dodec.hh
 ./utils/split-indices.cc
 ./utils/split-indices.hh
 ./utils/test-logging.cc
 ./utils/test-utils.cc
 ./utils/threads.cc
 ./utils/win-compat.cc
 ./utils/win-compat.hh
 ./validation-graphs/gtk4-test-sequence-view.cc
 ./validation-graphs/gtk4-test-validation-graph.cc
 ./validation-graphs/residue-validation-information.cc
 ./validation-graphs/residue-validation-information.hh
 ./validation-graphs/validation-graphs.cc
 ./validation-graphs/validation-graphs.hh
 ./validation-graphs/validation-information.cc
 ./validation-graphs/validation-information.hh
Copyright: 2007, Medical Research Council
  2011, Medical Research Council
  2012, Medical Research Council
  2012-2014, Medical Research Council
  2013, 2015, Medical Research Council
  2013, Medical Research Council
  2014, Medical Research Council
  2014-2015, Medical Research Council
  2015, Medical Research Council
  2016, Medical Research Council
  2017, Medical Research Council
  2018, Medical Research Council
  2019, Medical Research Council
  2020, Medical Research Council
  2021, Medical Research Council
  2022, Medical Research Council
  2023, Medical Research Council
  2024, Medical Research Council
  2025, Medical Research Council
License: LGPL-3+
 FIXME

Files: ./MoleculesToTriangles/CXXClasses/AtomPropertyRampColorRule.cpp
 ./MoleculesToTriangles/CXXClasses/AtomPropertyRampColorRule.h
 ./MoleculesToTriangles/CXXClasses/BallsPrimitive.cpp
 ./MoleculesToTriangles/CXXClasses/BallsPrimitive.h
 ./MoleculesToTriangles/CXXClasses/BondsPrimitive.cpp
 ./MoleculesToTriangles/CXXClasses/BondsPrimitive.h
 ./MoleculesToTriangles/CXXClasses/BoostWrappers.cpp
 ./MoleculesToTriangles/CXXClasses/BoxSectionPrimitive.cpp
 ./MoleculesToTriangles/CXXClasses/BoxSectionPrimitive.h
 ./MoleculesToTriangles/CXXClasses/CXXMatrix.cpp
 ./MoleculesToTriangles/CXXClasses/CXXMatrix.h
 ./MoleculesToTriangles/CXXClasses/Callbacks.h
 ./MoleculesToTriangles/CXXClasses/Camera.cpp
 ./MoleculesToTriangles/CXXClasses/Camera.h
 ./MoleculesToTriangles/CXXClasses/CameraPort.cpp
 ./MoleculesToTriangles/CXXClasses/CameraPort.h
 ./MoleculesToTriangles/CXXClasses/ColorNamesMap.h
 ./MoleculesToTriangles/CXXClasses/ColorRule.cpp
 ./MoleculesToTriangles/CXXClasses/ColorRule.h
 ./MoleculesToTriangles/CXXClasses/ColorScheme.cpp
 ./MoleculesToTriangles/CXXClasses/ColorScheme.h
 ./MoleculesToTriangles/CXXClasses/CompoundSelection.cpp
 ./MoleculesToTriangles/CXXClasses/CompoundSelection.h
 ./MoleculesToTriangles/CXXClasses/CylinderPoint.cpp
 ./MoleculesToTriangles/CXXClasses/CylinderPoint.h
 ./MoleculesToTriangles/CXXClasses/CylindersPrimitive.cpp
 ./MoleculesToTriangles/CXXClasses/CylindersPrimitive.h
 ./MoleculesToTriangles/CXXClasses/DemoApp.cpp
 ./MoleculesToTriangles/CXXClasses/DirectedPositionedEntity.cpp
 ./MoleculesToTriangles/CXXClasses/DirectedPositionedEntity.h
 ./MoleculesToTriangles/CXXClasses/DiscreteSegment.cpp
 ./MoleculesToTriangles/CXXClasses/DiscreteSegment.h
 ./MoleculesToTriangles/CXXClasses/DishyBase.cpp
 ./MoleculesToTriangles/CXXClasses/DishyBase.h
 ./MoleculesToTriangles/CXXClasses/DisplayPrimitive.cpp
 ./MoleculesToTriangles/CXXClasses/DisplayPrimitive.h
 ./MoleculesToTriangles/CXXClasses/ElectrostaticColorScheme.cpp
 ./MoleculesToTriangles/CXXClasses/ElectrostaticColorScheme.hpp
 ./MoleculesToTriangles/CXXClasses/FlatFanPrimitive.cpp
 ./MoleculesToTriangles/CXXClasses/FlatFanPrimitive.h
 ./MoleculesToTriangles/CXXClasses/GLIndexType.h
 ./MoleculesToTriangles/CXXClasses/Light.cpp
 ./MoleculesToTriangles/CXXClasses/Light.h
 ./MoleculesToTriangles/CXXClasses/LinesPrimitive.cpp
 ./MoleculesToTriangles/CXXClasses/LinesPrimitive.h
 ./MoleculesToTriangles/CXXClasses/MolecularRepresentation.cpp
 ./MoleculesToTriangles/CXXClasses/MolecularRepresentation.h
 ./MoleculesToTriangles/CXXClasses/MolecularRepresentationInstance.cpp
 ./MoleculesToTriangles/CXXClasses/MolecularRepresentationInstance.h
 ./MoleculesToTriangles/CXXClasses/MyMolecule.cpp
 ./MoleculesToTriangles/CXXClasses/MyMolecule.h
 ./MoleculesToTriangles/CXXClasses/NRStuff.h
 ./MoleculesToTriangles/CXXClasses/Polyhedron.cpp
 ./MoleculesToTriangles/CXXClasses/Polyhedron.h
 ./MoleculesToTriangles/CXXClasses/PositionedEntity.cpp
 ./MoleculesToTriangles/CXXClasses/PositionedEntity.h
 ./MoleculesToTriangles/CXXClasses/Renderer.cpp
 ./MoleculesToTriangles/CXXClasses/Renderer.h
 ./MoleculesToTriangles/CXXClasses/RendererGL.cpp
 ./MoleculesToTriangles/CXXClasses/RendererGL.h
 ./MoleculesToTriangles/CXXClasses/RendererGLSL.cpp
 ./MoleculesToTriangles/CXXClasses/RendererGLSL.hpp
 ./MoleculesToTriangles/CXXClasses/Representation.cpp
 ./MoleculesToTriangles/CXXClasses/Representation.h
 ./MoleculesToTriangles/CXXClasses/RepresentationInstance.cpp
 ./MoleculesToTriangles/CXXClasses/RepresentationInstance.h
 ./MoleculesToTriangles/CXXClasses/RotatedTranslatedScaledEntity.cpp
 ./MoleculesToTriangles/CXXClasses/RotatedTranslatedScaledEntity.h
 ./MoleculesToTriangles/CXXClasses/SceneSetup.cpp
 ./MoleculesToTriangles/CXXClasses/SceneSetup.h
 ./MoleculesToTriangles/CXXClasses/SecondaryColorScheme.cpp
 ./MoleculesToTriangles/CXXClasses/SecondaryColorScheme.h
 ./MoleculesToTriangles/CXXClasses/SolidColorRule.cpp
 ./MoleculesToTriangles/CXXClasses/SolidColorRule.h
 ./MoleculesToTriangles/CXXClasses/SpherePrimitive.cpp
 ./MoleculesToTriangles/CXXClasses/SpherePrimitive.h
 ./MoleculesToTriangles/CXXClasses/SticksPrimitive.cpp
 ./MoleculesToTriangles/CXXClasses/SticksPrimitive.h
 ./MoleculesToTriangles/CXXClasses/SurfacePrimitive.cpp
 ./MoleculesToTriangles/CXXClasses/SurfacePrimitive.h
 ./MoleculesToTriangles/CXXClasses/VertexColorNormalPrimitive.cpp
 ./MoleculesToTriangles/CXXClasses/VertexColorNormalPrimitive.h
 ./MoleculesToTriangles/CXXClasses/lfit.h
 ./MoleculesToTriangles/CXXClasses/oglPolyhedron.cpp
 ./MoleculesToTriangles/CXXClasses/oglPolyhedron.h
 ./MoleculesToTriangles/CXXSurface/CXXAlloc.h
 ./MoleculesToTriangles/CXXSurface/CXXBall.cpp
 ./MoleculesToTriangles/CXXSurface/CXXBall.h
 ./MoleculesToTriangles/CXXSurface/CXXChargeTable.cpp
 ./MoleculesToTriangles/CXXSurface/CXXChargeTable.h
 ./MoleculesToTriangles/CXXSurface/CXXCircle.cpp
 ./MoleculesToTriangles/CXXSurface/CXXCircle.h
 ./MoleculesToTriangles/CXXSurface/CXXCircleNode.cpp
 ./MoleculesToTriangles/CXXSurface/CXXCircleNode.h
 ./MoleculesToTriangles/CXXSurface/CXXCoord.cpp
 ./MoleculesToTriangles/CXXSurface/CXXCoord.h
 ./MoleculesToTriangles/CXXSurface/CXXCreator.cpp
 ./MoleculesToTriangles/CXXSurface/CXXCreator.h
 ./MoleculesToTriangles/CXXSurface/CXXException.cpp
 ./MoleculesToTriangles/CXXSurface/CXXException.h
 ./MoleculesToTriangles/CXXSurface/CXXFFTSolventMap.h
 ./MoleculesToTriangles/CXXSurface/CXXFortranFile.cpp
 ./MoleculesToTriangles/CXXSurface/CXXFortranFile.h
 ./MoleculesToTriangles/CXXSurface/CXXMatrix4x4.h
 ./MoleculesToTriangles/CXXSurface/CXXNewHood.cpp
 ./MoleculesToTriangles/CXXSurface/CXXNewHood.h
 ./MoleculesToTriangles/CXXSurface/CXXPointyBit.h
 ./MoleculesToTriangles/CXXSurface/CXXQADSurface.cpp
 ./MoleculesToTriangles/CXXSurface/CXXQADSurface.h
 ./MoleculesToTriangles/CXXSurface/CXXQADSurfaceStaticData.cpp
 ./MoleculesToTriangles/CXXSurface/CXXSpace.cpp
 ./MoleculesToTriangles/CXXSurface/CXXSpace.h
 ./MoleculesToTriangles/CXXSurface/CXXSphereElement.cpp
 ./MoleculesToTriangles/CXXSurface/CXXSphereElement.h
 ./MoleculesToTriangles/CXXSurface/CXXSphereFlatTriangle.h
 ./MoleculesToTriangles/CXXSurface/CXXSphereNode.cpp
 ./MoleculesToTriangles/CXXSurface/CXXSphereNode.h
 ./MoleculesToTriangles/CXXSurface/CXXSphereTriangle.cpp
 ./MoleculesToTriangles/CXXSurface/CXXSphereTriangle.h
 ./MoleculesToTriangles/CXXSurface/CXXSphereTriangleEdge.cpp
 ./MoleculesToTriangles/CXXSurface/CXXSphereTriangleEdge.h
 ./MoleculesToTriangles/CXXSurface/CXXSurface.cpp
 ./MoleculesToTriangles/CXXSurface/CXXSurface.h
 ./MoleculesToTriangles/CXXSurface/CXXSurfaceMaker.cpp
 ./MoleculesToTriangles/CXXSurface/CXXSurfaceMaker.h
 ./MoleculesToTriangles/CXXSurface/CXXSurfaceVertex.cpp
 ./MoleculesToTriangles/CXXSurface/CXXSurfaceVertex.h
 ./MoleculesToTriangles/CXXSurface/CXXTorusElement.cpp
 ./MoleculesToTriangles/CXXSurface/CXXTorusElement.h
 ./MoleculesToTriangles/CXXSurface/CXXTorusNode.cpp
 ./MoleculesToTriangles/CXXSurface/CXXTorusNode.h
 ./MoleculesToTriangles/CXXSurface/CXXTorusTriangle.h.h
 ./MoleculesToTriangles/CXXSurface/CXXTriangle.cpp
 ./MoleculesToTriangles/CXXSurface/CXXTriangle.h
 ./MoleculesToTriangles/CXXSurface/CXXUtils.cpp
 ./MoleculesToTriangles/CXXSurface/CXXUtils.h
 ./MoleculesToTriangles/CXXSurface/CXXVCN.cpp
 ./MoleculesToTriangles/CXXSurface/CXXVCN.h
 ./MoleculesToTriangles/CXXSurface/TokenIterator.h
Copyright: 2009, Martin Noble, University of Oxford
  2010, Martin Noble, University of Oxford
  2011, Martin Noble, University of Oxford
  2012, Martin Noble, University of Oxford
  2016, Martin Noble, University of Oxford
  2017, Martin Noble, University of Oxford
License: LGPL-3+
 FIXME

Files: ./ccp4mg-utils/mgtree.cc
 ./ccp4mg-utils/mgtree.h
 ./ccp4mg-utils/mmut/mman_base.cc
 ./ccp4mg-utils/mmut/mman_base.h
 ./ccp4mg-utils/mmut/mman_manager.cc
 ./ccp4mg-utils/mmut/mman_manager.h
 ./ccp4mg-utils/mmut/mmut_basepairs.cc
 ./ccp4mg-utils/mmut/mmut_basepairs.h
 ./ccp4mg-utils/mmut/mmut_bonds.cc
 ./ccp4mg-utils/mmut/mmut_bonds.h
 ./ccp4mg-utils/mmut/mmut_colour.cc
 ./ccp4mg-utils/mmut/mmut_colour.h
 ./ccp4mg-utils/mmut/mmut_connectivity.cc
 ./ccp4mg-utils/mmut/mmut_connectivity.h
 ./ccp4mg-utils/mmut/mmut_contact.cc
 ./ccp4mg-utils/mmut/mmut_contact.h
 ./ccp4mg-utils/mmut/mmut_hbond.cc
 ./ccp4mg-utils/mmut/mmut_hbond.h
 ./ccp4mg-utils/mmut/mmut_lipids.h
 ./ccp4mg-utils/mmut/mmut_manager.cc
 ./ccp4mg-utils/mmut/mmut_manager.h
 ./ccp4mg-utils/mmut/mmut_morph.h
 ./ccp4mg-utils/mmut/mmut_nma.cc
 ./ccp4mg-utils/mmut/mmut_nma.h
 ./ccp4mg-utils/mmut/mmut_sasarea.cc
 ./ccp4mg-utils/mmut/mmut_sasarea.h
 ./ccp4mg-utils/mmut/mmut_sbase.cc
 ./ccp4mg-utils/mmut/mmut_sbase.h
 ./ccp4mg-utils/mmut/mmut_secstr.cc
 ./ccp4mg-utils/mmut/mmut_secstr.h
 ./ccp4mg-utils/mmut/mmut_spline.cc
 ./ccp4mg-utils/mmut/mmut_util.cc
 ./ccp4mg-utils/mmut/mmut_util.h
 ./ccp4mg-utils/mmut/splineinfo.h
 ./ccp4mg-utils/pygl/atom_util.cc
 ./ccp4mg-utils/pygl/atom_util.h
 ./ccp4mg-utils/pygl/bezier.cc
 ./ccp4mg-utils/pygl/billboard.cc
 ./ccp4mg-utils/pygl/build_tree_primitives.cc
 ./ccp4mg-utils/pygl/catmull.cc
 ./ccp4mg-utils/pygl/catmull.h
 ./ccp4mg-utils/pygl/cbuild.h
 ./ccp4mg-utils/pygl/cdisplayobject.cc
 ./ccp4mg-utils/pygl/cdisplayobject.h
 ./ccp4mg-utils/pygl/cprimitive.cc
 ./ccp4mg-utils/pygl/cprimitive.h
 ./ccp4mg-utils/pygl/font_info.cc
 ./ccp4mg-utils/pygl/font_info.h
 ./ccp4mg-utils/pygl/font_util.cc
 ./ccp4mg-utils/pygl/font_util.h
 ./ccp4mg-utils/pygl/freetype_font.cc
 ./ccp4mg-utils/pygl/freetype_font.h
 ./ccp4mg-utils/pygl/help.cc
 ./ccp4mg-utils/pygl/help.h
 ./ccp4mg-utils/pygl/lincrv.h
 ./ccp4mg-utils/pygl/psutil.cc
 ./ccp4mg-utils/pygl/psutil.h
 ./ccp4mg-utils/pygl/rgbreps.cc
 ./ccp4mg-utils/pygl/rgbreps.h
 ./ccp4mg-utils/pygl/sphere.cc
 ./ccp4mg-utils/pygl/sphere.h
 ./ccp4mg-utils/pygl/sphere_1.h
 ./ccp4mg-utils/pygl/sphere_2.h
 ./ccp4mg-utils/pygl/sphere_3.h
 ./ccp4mg-utils/pygl/splineset.cc
 ./ccp4mg-utils/pygl/subdivide.cc
 ./ccp4mg-utils/pygl/subdivide.h
 ./ccp4mg-utils/pygl/symmetry.cc
 ./ccp4mg-utils/pygl/symmetry.h
 ./ccp4mg-utils/pygl/text.cc
 ./ccp4mg-utils/pygl/texture.cc
 ./ccp4mg-utils/pygl/texture.h
 ./ccp4mg-utils/pygl/win_font.cc
 ./ccp4mg-utils/pygl/win_font.h
 ./ccp4mg-utils/pygl/x11_font.cc
 ./ccp4mg-utils/pygl/x11_font.h
 ./ccp4mg-utils/pygl/zsortps.cc
 ./ccp4mg-utils/util/CParamsManager.cc
 ./ccp4mg-utils/util/CParamsManager.h
 ./ccp4mg-utils/util/cartesian.cc
 ./ccp4mg-utils/util/cartesian.h
 ./ccp4mg-utils/util/connect.cc
 ./ccp4mg-utils/util/connect.h
 ./ccp4mg-utils/util/geomutil.cc
 ./ccp4mg-utils/util/geomutil.h
 ./ccp4mg-utils/util/matrix.cc
 ./ccp4mg-utils/util/matrix.h
 ./ccp4mg-utils/util/mginterrupt.cc
 ./ccp4mg-utils/util/mginterrupt.h
 ./ccp4mg-utils/util/mgtree.cc
 ./ccp4mg-utils/util/mgtree.h
 ./ccp4mg-utils/util/mgutil.cc
 ./ccp4mg-utils/util/mgutil.h
 ./ccp4mg-utils/util/plane.cc
 ./ccp4mg-utils/util/plane.h
 ./ccp4mg-utils/util/quat.cc
 ./ccp4mg-utils/util/quat.h
 ./ccp4mg-utils/util/redirect.cc
 ./ccp4mg-utils/util/volume.cc
 ./ccp4mg-utils/util/volume.h
Copyright: 2001-2008, University of York, CCLRC
License: LGPL-3
 FIXME

Files: ./api/filo-tests.cc
 ./api/filo-tests.hh
 ./coot-utils/coot-align.cc
 ./coot-utils/coot-align.hh
 ./coot-utils/coot-h-bonds.hh
 ./coot-utils/coot-hole.hh
 ./coot-utils/coot-lsq-types.hh
 ./coot-utils/elastic.cc
 ./coot-utils/elastic.hh
 ./coot-utils/gl-matrix.cc
 ./coot-utils/helix-analysis.cc
 ./coot-utils/helix-analysis.hh
 ./coot-utils/read-sm-cif.hh
 ./coot-utils/test-elastic.cc
 ./coot-utils/test-h-bonds.cc
 ./coot-utils/test-hole.cc
 ./coot-utils/test-morph.cc
 ./coot-utils/xmap-stats.hh
 ./geometry/lbg-graph.cc
 ./geometry/lbg-graph.cc-m
 ./geometry/lbg-graph.hh
 ./geometry/test-read-components.cc
 ./ligand/chi-angles-autogen.cc
 ./ligand/primitive-chi-angles.cc
 ./ligand/primitive-chi-angles.hh
 ./ligand/read-dunbrack.awk
 ./ligand/richardson-rotamer.cc
 ./ligand/richardson-rotamers.cc
 ./skeleton/BuildCas.h
 ./skeleton/dm-utils.cc
 ./skeleton/graphical_skel.cc
 ./skeleton/graphical_skel.h
 ./src/add-c-extern.sh
 ./src/blank.cc
 ./src/c-inner-main.h
 ./src/c-interface-ligands-swig.hh
 ./src/c-interface-wii.cc
 ./src/canvas-fixes.hh
 ./src/cc-interface-mogul.hh
 ./src/cmtz-interface.hh
 ./src/command-arg.hh
 ./src/command-line.hh
 ./src/coot-colour.hh
 ./src/coot-database.hh
 ./src/coot-fileselections.h
 ./src/coot-glue.hh
 ./src/coot-hydrogens.cc
 ./src/coot-hydrogens.hh
 ./src/coot-nomenclature.hh
 ./src/coot-preferences.h
 ./src/coot-references.h
 ./src/coot-render.hh
 ./src/coot.i
 ./src/fix-nomenclature.cc
 ./src/flev.hh
 ./src/get-residue.cc
 ./src/get-residue.hh
 ./src/gl-bits.hh
 ./src/graphics-info-network.cc
 ./src/graphics-info-scripting.cc
 ./src/gtk-manual.hh
 ./src/gtk-widget-conversion-utils.cc
 ./src/gtk-widget-conversion-utils.h
 ./src/guile-fixups.h
 ./src/history_list.hh
 ./src/interface.c
 ./src/interface.h
 ./src/lbg-callbacks-outer.cc
 ./src/lbg-interface.hh
 ./src/mmcif-sfs-to-mtz-main.cc
 ./src/molecule-class-info-dots.cc
 ./src/molecule-class-info.h
 ./src/named-rotamer-score.hh
 ./src/pisa-interface.hh
 ./src/post-glade
 ./src/post-gtk2-glade.sh
 ./src/protein_db-interface.cc
 ./src/protein_db-interface.hh
 ./src/restraints-editor-c.h
 ./src/rotate-translate-modes.hh
 ./src/sdf-interface.hh
 ./src/sdf-internal.hh
 ./src/select-atom-info.hh
 ./src/support-gtk2-extras.c
 ./src/support.c
 ./src/test-chol.cc
 ./src/test-lbg-graph.cc
 ./src/testing-scm.cc
 ./src/testing-scm.hh
 ./src/triangle-extras.h
 ./src/user-mods.cc
 ./src/user-mods.hh
 ./src/xmap-utils.cc
 ./src/xmap-utils.h
Copyright: 2007, University of York
  2008, University of York
  2009, University of York
  2010, University of York
  2011, University of York
  2012, University of York
  2023, University of York
License: LGPL-3+
 FIXME

Files: ./analysis/fraction_stats.py
 ./analysis/mogul.cc
 ./analysis/peptide-projection.cc
 ./analysis/stats.cc
 ./analysis/stats.hh
 ./api/Makefile.am
 ./api/coot-colour.cc
 ./canyon/canyon-points.scm
 ./canyon/canyon.cc
 ./canyon/canyon.hh
 ./canyon/quaternion.cc
 ./coot-utils/atom-overlaps.cc
 ./coot-utils/atom-overlaps.hh
 ./coot-utils/coot-density-stats.hh
 ./coot-utils/dictionary-atom-types.cc
 ./coot-utils/slurp-map.cc
 ./coot-utils/slurp-map.hh
 ./coot-utils/test-chem-feat.cc
 ./coot-utils/test-cod-atom-types.cc
 ./coot-utils/test-q-score.cc
 ./coot-utils/test-spherical.cc
 ./lidia-core/bond-record-container-t.cc
 ./lidia-core/bond-record-container-t.hh
 ./lidia-core/bond-table-record-t.cc
 ./lidia-core/bond-table-record-t.hh
 ./lidia-core/cod-atom-type-t.cc
 ./lidia-core/cod-atom-type-t.hh
 ./lidia-core/cod-atom-types.cc
 ./lidia-core/cod-atom-types.hh
 ./lidia-core/cod-types.cc
 ./lidia-core/cod-types.hh
 ./lidia-core/primes.hh
 ./lidia-core/test-fei-vs-mine.py
 ./ligand/ligand-percentiles.cc
 ./ligand/ligands-db.cc
 ./ligand/ligands-db.hh
 ./ligand/make-ligands-db.cc
 ./ligand/smith-waterman.cc
 ./ligand/test-trace.cc
 ./ligand/trace-2.cc
 ./ligand/trace.cc
 ./ligand/trace.hh
 ./man/coot-compare-dictionaries.man
 ./man/coot-identify-protein.man
 ./man/coot-mini-rsr.man
 ./man/coot.man
 ./man/findligand.man
 ./man/findwaters.man
 ./man/layla.man
 ./man/pyrogen.man
 ./pli/Makefile.am
 ./pli/atom-ring-centre-info.hh
 ./pli/bond-to-ligand.hh
 ./pli/flev-attached-hydrogens.cc
 ./pli/pi-stacking.hh
 ./pyrogen/mmff-restraints.cc
 ./pyrogen/mmff-restraints.hh
 ./python/coot_chemical_feature_clusters.py
 ./python/ligand_validation_sliders.py
 ./scheme/3d-generator-import.scm
 ./scheme/contact-score-isolated-ligand.scm
 ./scheme/dictionary-generators.scm
 ./scheme/enhanced-ligand.scm
 ./scheme/gui-add-linked-cho.scm
 ./scheme/gui-hole.scm
 ./scheme/gui-ligand-sliders.scm
 ./scheme/gui-prosmart.scm
 ./scheme/ligand-check.scm
 ./scheme/run-mogul.scm
Copyright: 2010, Medical Research Council
  2012-2014, Medical Research Council
  2013, Medical Research Council
  2014, Medical Research Council
  2014-2015, Medical Research Council
  2015, Medical Research Council
  2016, Medical Research Council
  2017, Medical Research Council
  2018, Medical Research Council
  2019, Medical Research Council
  2020, Medical Research Council
  2021, Medical Research Council
License: GPL-3+
 FIXME

Files: ./build/CalphaBuild.cc
 ./build/CalphaBuild.hh
 ./build/testcabuild.cc
 ./coords/Bond_lines_ext.cc
 ./coords/Cartesian.cc
 ./coords/Cartesian.hh
 ./coords/Makefile.am
 ./coords/coot-close.cc
 ./coords/coot-close.hh
 ./coords/cos-sin.cc
 ./coords/cos-sin.h
 ./coords/mmdb-crystal.cc
 ./coords/mmdb-crystal.hh
 ./coords/mmdb-extras.cc
 ./coords/mmdb-extras.hh
 ./coords/mmdb.hh
 ./coords/utils.cc
 ./coords/utils.h
 ./coot-utils/gl-matrix.h
 ./density-contour/density-contour-triangles.cc
 ./density-contour/density-contour-triangles.hh
 ./geometry/Makefile.am
 ./geometry/Makefile.simple
 ./ideal/Makefile.am
 ./ideal/lograma.cpp
 ./ideal/lograma.h
 ./ideal/logramatest.cpp
 ./ideal/molmantest.cc
 ./ideal/pepflip.hh
 ./ideal/regularize-minimol.cc
 ./ideal/regularize-minimol.hh
 ./ideal/test-indexing.cc
 ./ideal/test-indexing.hh
 ./ideal/with-geometry.cc
 ./pyrogen/pyrogen-swig.i
 ./skeleton/dm-utils.h
 ./src/align.cc
 ./src/c-inner-main.c
 ./src/c-interface-gtk2.cc
 ./src/c-interface-mmdb.hh
 ./src/c-interface-python.cc
 ./src/c-interface-python.hh
 ./src/coot_pythonmodule.cc
 ./src/density-score-by-residue-src.cc
 ./src/geometry-graphs.cc
 ./src/geometry-graphs.hh
 ./src/graphics-info-lsq.cc
 ./src/graphics-info-pick.cc
 ./src/graphics-info-preferences.cc
 ./src/graphics-info-superpose.cc
 ./src/molecule-class-info-kdc.cc
 ./src/molecule-class-info-ribbons.cc
 ./src/molecule-class-info-surface.cc
 ./src/molecule-class-info-widget-work.cc
 ./src/pick.cc
 ./src/positioned-widgets.h
 ./src/rama_mousey.cc
 ./src/read-phs.h
 ./utils/Makefile.am
 ./utils/atomic-numbers.cc
 ./utils/coot-fasta.hh
 ./utils/coot-utils.hh
Copyright: 2001-2003, 2006, The University of York
  2001-2006, The University of York
  2001-2007, The University of York
  2002, The University of York
  2002-2003, The University of York
  2002-2004, The University of York
  2002-2005, The University of York
  2002-2006, The University of York
  2002-2007, The University of York
  2004, 2006, The University of York
  2004, The University of York
  2004-2005, The University of York
  2004-2006, The University of York
  2005, The University of York
  2005-2006, The University of York
  2006, The University of York
  2007, The University of York
  2008, The University of York
  2011, The University of York
  2014, The University of York
  2020, The University of York
License: LGPL-3+
 FIXME

Files: ./Makefile.am
 ./analysis/Makefile.am
 ./autogen-mac.sh
 ./autogen.sh
 ./build/Makefile.am
 ./compat/coot-sysdep.h
 ./coot-utils/atom-selection-container.cc
 ./coot-utils/atom-selection-container.hh
 ./coot-utils/coot-coord-utils-glyco.cc
 ./coot-utils/coot-map-heavy.hh
 ./coot-utils/coot-shelx.hh
 ./coot-utils/coot-trim.hh
 ./coot-utils/peak-search.hh
 ./db-main/db-main.cc
 ./db-main/db-main.hh
 ./db-main/db-strands.cc
 ./db-main/db-strands.hh
 ./db-main/testdbmain.cc
 ./density-contour/Makefile.am
 ./high-res/Makefile.am
 ./high-res/coot-atom-graph.hh
 ./high-res/coot-node-info.hh
 ./high-res/globularize.cc
 ./high-res/trace-high-res.cc
 ./ligand/chi-angles.cc
 ./ligand/chi-angles.hh
 ./ligand/dunbrack.cc
 ./ligand/dunbrack.hh
 ./ligand/fast-ss-search.hh
 ./ligand/find-waters.cc
 ./ligand/helix-placement.cc
 ./ligand/helix-placement.hh
 ./ligand/monomer-utils.cc
 ./ligand/monomer-utils.hh
 ./ligand/test-fffear-in-coot.cc
 ./ligand/test-helix-placement.cc
 ./ligand/test-random.cc
 ./ligand/wligand.hh
 ./macros/Makefile.am
 ./macros/clipper.m4
 ./macros/coot-database.m4
 ./macros/coot-windows.m4
 ./macros/glut.m4
 ./macros/guile-gtk.m4
 ./macros/with-guile.m4
 ./mini-mol/Makefile.am
 ./mini-mol/atom-quads.cc
 ./mini-mol/mini-mol-utils.cc
 ./mini-mol/mini-mol-utils.hh
 ./mini-mol/mini-mol.hh
 ./mini-mol/testminimol.cc
 ./scheme/coot-lsq.scm
 ./scheme/fitting.scm
 ./scheme/group-settings.scm
 ./scheme/refmac.scm
 ./scheme/tips-gui.scm
 ./setup/coot.csh.in
 ./setup/coot.sh.in
 ./shell-utils/shell-copyright-template.sh
 ./skeleton/BuildCas.cc
 ./skeleton/Makefile.am
Copyright: 2001-2003, 2006, The University of York
  2001-2003, The University of York
  2001-2004, 2006, The University of York
  2001-2007, The University of York
  2002, The University of York
  2002-2003, 2006, The University of York
  2002-2004, The University of York
  2002-2005, The University of York
  2002-2006, The University of York
  2003, The University of York
  2003-2004, 2006-2007, The University of York
  2003-2004, The University of York
  2004, 2006, The University of York
  2004, The University of York
  2004-2005, The University of York
  2004-2006, The University of York
  2004-2007, The University of York
  2005, The University of York
  2005-2006, The University of York
  2005-2007, The University of York
  2006, The University of York
  2007, The University of York
  2008, The University of York
  2009, The University of York
  2011, The University of York
License: GPL-3+
 FIXME

Files: ./rcrane/__init__.py
 ./rcrane/about.py
 ./rcrane/bondLength.py
 ./rcrane/buildInitSugar.py
 ./rcrane/buildPhosOxy.py
 ./rcrane/calcCoords.py
 ./rcrane/chain.py
 ./rcrane/citationPopup.py
 ./rcrane/coot_gui_adapter.py
 ./rcrane/coot_utils_adapter.py
 ./rcrane/extendChain.py
 ./rcrane/guiUtils.py
 ./rcrane/installRCrane.py
 ./rcrane/launch.py
 ./rcrane/linearInterp.py
 ./rcrane/menu.py
 ./rcrane/nextPhos.py
 ./rcrane/nucleotide.py
 ./rcrane/phenixRestraints.py
 ./rcrane/preLaunchCheck.py
 ./rcrane/pseudoMolecule.py
 ./rcrane/pseudoPredictor.py
 ./rcrane/puckerList.py
 ./rcrane/reportInputErrors.py
 ./rcrane/reviewSuitesGui.py
 ./rcrane/rotData.py
 ./rcrane/rotamerSeq.py
 ./rcrane/rotamerize.py
 ./rcrane/safelog.py
 ./rcrane/selectMapDialog.py
 ./rcrane/settings.py
 ./rcrane/smoothProb.py
 ./rcrane/stats.py
 ./rcrane/strucCalc.py
 ./rcrane/suite.py
 ./rcrane/thetaEtaPredictor.py
 ./rcrane/traceGui.py
Copyright: 2010, Kevin Keating
  2010-2011, 2102, Kevin Keating
  2010-2011, Kevin Keating
  2010-2012, Kevin Keating
  2011, Kevin Keating
  2011-2012, Kevin Keating
  2012, Kevin Keating
License: ECL-2.0
 FIXME

Files: ./geometry/cif-parse-link.cc
 ./geometry/cif-parse.cc
 ./geometry/dictionary-residue.cc
 ./geometry/glyco-tools.cc
 ./geometry/link.cc
 ./geometry/protein-geometry.cc
 ./geometry/protein-geometry.hh
 ./ideal/chi-squareds.cc
 ./ideal/chirals.cc
 ./ideal/distortion.cc
 ./ideal/flanking.cc
 ./ideal/gradients.cc
 ./ideal/link-restraints.cc
 ./ideal/make-restraints.cc
 ./ideal/mini-rsr.cc
 ./ideal/mods.cc
 ./ideal/simple-restraint.cc
 ./ideal/simple-restraint.hh
 ./src/Makefile.am
 ./src/c-interface-gui.cc
 ./src/c-interface-ligands-gui.cc
 ./src/c-interface-ligands.cc
 ./src/c-interface-maps.cc
 ./src/c-interface-ncs.cc
 ./src/c-interface-preferences.cc
 ./src/c-interface-waters-gui.cc
 ./src/c-interface-waters.cc
 ./src/generic-objects.cc
 ./src/glade-callbacks-main-window.cc
 ./src/glade-callbacks-preferences.cc
 ./src/glade-callbacks-shader-settings.cc
 ./src/glade-callbacks.cc
 ./src/graphics-info-graphs.cc
 ./src/main.cc
 ./src/molecule-class-info-ncs.cc
 ./src/molecule-class-info-other.cc
Copyright: 2001-2007, The University of York
  2002-2003, The University of York
  2002-2005, The University of York
  2002-2006, The University of York
  2002-2007, The University of York
  2003-2004, 2007, The University of York
  2003-2006, The University of York
  2004-2005, The University of York
  2004-2007, The University of York
  2005-2006, The University of York
  2007, 2009, 2011-2012, The University of Oxford
  2007, 2012, The University of Oxford
  2007, The University of Oxford
  2007, The University of York
  2007-2008, The University of Oxford
  2007-2009, The University of Oxford
  2007-2012, The University of Oxford
  2008, 2010, The University of Oxford
  2008, The University of Oxford
  2008-2009, 2011-2012, The University of Oxford
  2008-2009, The University of Oxford
  2008-2010, The University of Oxford
  2008-2012, The University of Oxford
  2009, The University of Oxford
  2012-2015, Medical Research Council
  2013, 2015-2016, Medical Research Council
  2013, Medical Research Council
  2013-2014, Medical Research Council
  2013-2015, 2018, 2020-2021, Medical Research Council
  2013-2015, Medical Research Council
  2013-2016, Medical Research Council
  2014, Medical Research Council
  2014-2015, Medical Research Council
  2014-2016, Medical Research Council
  2015-2016, Medical Research Council
  2016, Medical Research Council
License: LGPL-3+
 FIXME

Files: ./coot-utils/gl-matrix-eigensystem.cc
 ./coot-utils/voidp-buffer.hh
 ./layla/generators.cpp
 ./layla/generators.hpp
 ./layla/layla_embedded.cpp
 ./layla/layla_embedded.hpp
 ./layla/ligand_editor_canvas.cpp
 ./layla/ligand_editor_canvas.hpp
 ./layla/ligand_editor_canvas/core.cpp
 ./layla/ligand_editor_canvas/core.hpp
 ./layla/ligand_editor_canvas/model.cpp
 ./layla/ligand_editor_canvas/model.hpp
 ./layla/ligand_editor_canvas/render.cpp
 ./layla/ligand_editor_canvas/render.hpp
 ./layla/ligand_editor_canvas/tools.cpp
 ./layla/ligand_editor_canvas/tools.hpp
 ./layla/main.cpp
 ./layla/notifier.cpp
 ./layla/notifier.hpp
 ./layla/python_utils.cpp
 ./layla/python_utils.hpp
 ./layla/signals.cpp
 ./layla/state.cpp
 ./layla/state.hpp
 ./layla/ui.cpp
 ./layla/ui.hpp
 ./layla/utils.cpp
 ./layla/utils.hpp
 ./lhasa/embind.cpp
 ./lhasa/embind.hpp
 ./lhasa/glog_replacement.cpp
 ./lhasa/glog_replacement.hpp
 ./lhasa/lhasa.cpp
 ./lhasa/lhasa.hpp
Copyright: 2023, Global Phasing Ltd.
  2024, Global Phasing Ltd.
License: GPL-3+
 FIXME

Files: ./cootaneer/buccaneer-lib.cpp
 ./cootaneer/buccaneer-lib.h
 ./cootaneer/buccaneer-prot.cpp
 ./cootaneer/buccaneer-prot.h
 ./cootaneer/buccaneer-sequence.cpp
 ./cootaneer/buccaneer-sequence.h
 ./cootaneer/cootaneer-demo.cpp
 ./cootaneer/cootaneer-sequence.cpp
 ./cootaneer/cootaneer-sequence.h
 ./cootilus/cootilus-build.cpp
 ./cootilus/cootilus-build.h
 ./cootilus/cootilus-demo.cpp
 ./cootilus/nautilus-join.cpp
 ./cootilus/nautilus-join.h
 ./cootilus/nautilus-ss-find.cpp
 ./cootilus/nautilus-ss-find.h
 ./cootilus/nautilus-target.cpp
 ./cootilus/nautilus-target.h
 ./cootilus/nautilus-tools.cpp
 ./cootilus/nautilus-tools.h
 ./cootilus/nucleicacid_db.cpp
 ./cootilus/nucleicacid_db.h
 ./protein_db/protein_db.cpp
 ./protein_db/protein_db.h
 ./protein_db/protein_db_utils.cpp
 ./protein_db/protein_db_utils.h
 ./protein_db/rna_db.cpp
 ./protein_db/rna_db.h
Copyright: 2002-2006, Kevin Cowtan
  2003-2006, Kevin Cowtan
  2006, Kevin Cowtan
  2008-2009, Kevin Cowtan
  2011, Kevin Cowtan
  2012, Kevin Cowtan
License: LGPL-3+
 FIXME

Files: ./coot-utils/coot-coord-utils-nucleotides.cc
 ./coot-utils/coot-h-bonds.cc
 ./coot-utils/lsq-improve.cc
 ./coot-utils/lsq-improve.hh
 ./lidia-core/lbg-molfile.cc
 ./lidia-core/lbg-molfile.hh
 ./lidia-core/lbg-shared.cc
 ./lidia-core/lbg-shared.hh
 ./lidia-core/lig-build.cc
 ./lidia-core/rdkit-interface.hh
 ./ligand/dipole.cc
 ./ligand/dipole.hh
 ./ligand/rotamer-tables.cc
 ./macros/libglade.m4
 ./mini-mol/atom-quads.hh
 ./pli/flev-annotations.hh
 ./pli/flev.cc
 ./pli/flev.hh
 ./pli/optimise-residue-circles.cc
 ./pli/protein-ligand-interactions.cc
 ./pli/residue-circles.cc
 ./pli/sdf-interface.hh
 ./protein_db/Makefile.am
 ./rama-data/Makefile.am
 ./scheme/clear-backup.scm
 ./src/c-interface-view.cc
Copyright: 2007, The University of Oxford
  2008, The University of Oxford
  2008-2009, The University of Oxford
  2009, The University of Oxford
  2010, The University of Oxford
  2010-2011, The University of Oxford
  2010-2012, The University of Oxford
  2011, The University of Oxford
  2012, The University of Oxford
License: GPL-3+
 FIXME

Files: ./geometry/energy-lib.cc
 ./pyrogen/atom_types.cc
 ./src/additional-representation.hh
 ./src/atom-attribute.hh
 ./src/atom-name-bits.hh
 ./src/atom-selection.hh
 ./src/c-interface-generic-objects.h
 ./src/c-interface-mogul.cc
 ./src/c-interface-preferences.h
 ./src/coot-setup-python.cc
 ./src/drag-and-drop.cc
 ./src/get-monomer.cc
 ./src/lsq-dialog-values.hh
 ./src/model-view.hh
 ./src/molecule-class-info-refine.cc
 ./src/ncs.hh
 ./src/probe-clash-score.cc
 ./src/probe-clash-score.hh
 ./src/rama-rota-score.hh
 ./src/testing.cc
 ./src/view.cc
Copyright: 2008, the University of Oxford
  2008-2010, the University of Oxford
  2009, the University of Oxford
  2010, the University of Oxford
  2010-2012, the University of Oxford
  2011, the University of Oxford
  2011-2012, the University of Oxford
  2012, Medical Research Council
  2012, the University of Oxford
  2012-2013, Medical Research Council
  2013, Medical Research Council
  2014, 2016, Medical Research Council
  2014, Medical Research Council
  2014-2015, Medical Research Council
  2015, Medical Research Council
  2016, Medical Research Council
License: LGPL-3+
 FIXME

Files: ./analysis/b-factor-histogram.hh
 ./analysis/bfactan.cc
 ./analysis/bfkurt.cc
 ./analysis/bfkurt.hh
 ./analysis/cablam.hh
 ./utils/align-utils.cc
 ./utils/align-utils.hh
 ./utils/colour-holder.cc
 ./utils/colour-holder.hh
 ./utils/hsv-rgb.cc
 ./utils/insertion-sort.cc
 ./utils/insertion-sort.hh
 ./utils/logging.cc
 ./utils/logging.hh
 ./utils/pir-alignment.cc
 ./utils/pir-alignment.hh
 ./utils/radix.cc
 ./utils/radix.hh
 ./utils/setup-syminfo.cc
 ./utils/setup-syminfo.hh
Copyright: 2009, University of Oxford
License: LGPL-3+
 FIXME

Files: ./coot-utils/bonded-pairs.cc
 ./coot-utils/bonded-pairs.hh
 ./coot-utils/coot-least-squares.cc
 ./coot-utils/coot-tree-extras.cc
 ./coot-utils/glyco-torsions.cc
 ./coot-utils/glyco-torsions.hh
 ./coot-utils/hole.cc
 ./coot-utils/read-sm-cif.cc
 ./coot-utils/test-glyco-torsions.cc
 ./coot-utils/water-coordination.cc
 ./lidia-core/lig-build.hh
 ./lidia-core/rdkit-interface.cc
 ./pixmaps/Makefile.am
 ./pli/sdf-interface.cc
 ./pyrogen/Makefile.am
 ./pyrogen/Makefile.simple
 ./scheme/get-recent-pdbe.scm
 ./sounds/Makefile.am
 ./textures/Makefile.am
Copyright: 2009, The University of Oxford
  2010, The University of Oxford
  2010-2012, The University of Oxford
  2011, The University of Oxford
  2011-2012, The University of Oxford
  2012, The University of Oxford
  2012-2016, Medical Research Council
  2013, Medical Research Council
  2014, Medical Research Council
  2015, Medical Research Council
  2015-2016, Medical Research Council
  2016, Medical Research Council
License: GPL-3+
 FIXME

Files: ./api/ncs.hh
 ./doc/coot-shelx.tex
 ./doc/tutorial-2.tex
 ./lidia-core/chemical-feature-clusters.cc
 ./lidia-core/chemical-feature-clusters.hh
 ./ligand/multi-peptide.cc
 ./pli/pi-stacking.cc
 ./pyrogen/atom_types.py
 ./pyrogen/py-restraints.cc
 ./pyrogen/pyrogen.py
 ./pyrogen/restraints-boost.cc
 ./pyrogen/restraints-private.hh
 ./pyrogen/restraints.cc
 ./pyrogen/restraints.hh
 ./python/pdbe_validation_data.py
 ./scheme/get-ebi.scm
 ./scheme/ncs.scm
 ./scheme/template-key-bindings.scm
 ./scheme/user-define-restraints.scm
Copyright: 2008, the University of Oxford
  2010, the University of Oxford
  2011, the University of Oxford
  2012, the University of Oxford
  2013, Medical Research Council
  2013, the University of Oxford
  2013-2015, Medical Research Council
  2014, Medical Research Council
  2014-2015, Medical Research Council
  2015, Medical Research Council
  2016, Medical Research Council
License: GPL-3+
 FIXME

Files: ./geometry/chem_mods.cc
 ./src/c-interface-analysis.cc
 ./src/c-interface-database.hh
 ./src/c-interface-ligands.hh
 ./src/c-interface-network.cc
 ./src/c-interface-nucleotides.cc
 ./src/c-interface-pisa-gui.cc
 ./src/c-interface-pisa.cc
 ./src/c-interface-scm.cc
 ./src/c-interface-scm.hh
 ./src/c-interface-sfs.cc
 ./src/cc-interface-network.hh
 ./src/dots-representation.hh
 ./src/graphics-ligand-view.hh
 ./src/lbg-interface.cc
 ./src/nsv.hh
 ./src/restraints-editor.cc
 ./src/restraints-editor.hh
Copyright: 2007, The University of Oxford
  2007-2009, The University of Oxford
  2008, The University of Oxford
  2008-2009, The University of Oxford
  2009, 2012, The University of Oxford
  2009, The University of Oxford
  2009-2010, The University of Oxford
  2010, The University of Oxford
  2011, The University of Oxford
  2011-2012, The University of Oxford
  2012, The University of Oxford
License: LGPL-3+
 FIXME

Files: ./configure.ac
 ./coot-utils/coot-coord-extras.cc
 ./coot-utils/coot-coord-lsq.cc
 ./coot-utils/coot-rama.cc
 ./coot-utils/coot-rama.hh
 ./db-main/train-pepflip.cc
 ./ligand/base-pairing.cc
 ./ligand/base-pairing.hh
 ./ligand/rotamer.cc
 ./ligand/rotamer.hh
 ./python-tests/04_cootaneer.py
 ./python-tests/TestNCSFunctions.py
 ./python-tests/TestRNAGhostsFunctions.py
 ./python-tests/TestSSMFunctions.py
 ./python-tests/TestShelxFunctions.py
 ./python-tests/TestUtilsFunctions.py
 ./scheme/libcheck.scm
Copyright: 2001-2004, 2006, The University of York
  2001-2007, The University of York
  2002-2007, The University of York
  2004, 2006, The University of York
  2004-2007, The University of York
  2005, The University of York
  2006, The University of York
  2007, The University of Oxford
  2007-2008, The University of Oxford
  2007-2008, The University of York
  2008, The University of Oxford
  2008, The University of York
  2009, The University of Oxford
License: GPL-3+
 FIXME

Files: ./MoleculesToTriangles/CXXClasses/m4/mmdb.m4
 ./coot-utils/Makefile.am
 ./coot-utils/coot-fffear.cc
 ./coot-utils/coot-map-heavy.cc
 ./coot-utils/coot-map-utils.hh
 ./coot-utils/xmap-stats.cc
 ./high-res/coot-atom-graph.cc
 ./ligand/fast-ss-search.cc
 ./ligand/ligand-extras.cc
 ./ligand/rigid-body.cc
 ./macros/ccp4srs.m4
 ./macros/goo-canvas.m4
 ./macros/mmdb-ssm.m4
 ./macros/mmdb.m4
 ./macros/sys-build-type.m4
 ./mini-mol/mini-mol.cc
Copyright: 2001-2007, The University of York
  2002, The University of York
  2002-2005, 2007, The University of York
  2002-2006, The University of York
  2003-2004, The University of York
  2004, The University of York
  2004-2006, The University of York
  2004-2007, The University of York
  2005, The University of York
  2006, The University of York
  2008, The University of York
  2013, Medical Research Council
  2014, Medical Research Council
  2014-2015, Medical Research Council
  2015, Medical Research Council
  2016, Medical Research Council
License: GPL-3+
 FIXME

Files: ./src/c-interface-gtk-widgets.h
 ./src/c-interface-refmac.h
 ./src/c-interface-widgets.hh
 ./src/c-interface.h
 ./src/cc-interface.hh
 ./src/drag-and-drop.hh
 ./src/generic-display-objects-c.h
 ./src/graphics-info-restraints-editor.cc
 ./src/graphics-info.h
 ./src/molecule-class-info-maps.cc
 ./src/molecule-class-info-patterson.cc
 ./src/molecule-class-info-residues.cc
 ./src/molecule-class-info.cc
 ./src/rama_mousey.hh
 ./src/read-cif.h
Copyright: 2001-2007, The University of York
  2002-2007, The University of York
  2007, Paul Emsley
  2007-2008, The University of Oxford
  2007-2009, The University of Oxford
  2007-2010, The University of Oxford
  2007-2012, The University of Oxford
  2008-2012, The University of Oxford
  2013-2016, Medical Research Council
  2014-2016, Medical Research Council
  2015, Medical Research Council
  2015-2016, Medical Research Council
  2016, Medical Research Council
License: LGPL-3+
 FIXME

Files: ./coot-utils/test-shelx-reader.cc
 ./coot-utils/trim.cc
 ./high-res/high-res.cc
 ./high-res/residue-distortions.cc
 ./high-res/sequence-assignment.cc
 ./high-res/sequence-assignment.hh
 ./high-res/test-atom-graph.cc
 ./high-res/testseqalign.cc
 ./high-res/testseqassignment.cc
 ./ligand/residue_by_phi_psi.hh
 ./ligand/rigid-body.hh
 ./ligand/testdunbrack.cc
 ./scheme/gap.scm
 ./scheme/mutate.scm
Copyright: 2003-2004, Paul Emsley, The University of York
  2004, Paul Emsley, The University of York
  2004-2006, Paul Emsley, The University of York
  2005, Paul Emsley, The University of York
  2005-2006, Paul Emsley, The University of York
License: GPL-3+
 FIXME

Files: ./coords/Bond_lines.hh
 ./geometry/test-ccp4srs.cc
 ./geometry/test-geometry.cc
 ./ideal/pepflip.cc
 ./src/c-interface-superpose.cc
 ./src/cmtz-interface.cc
 ./src/command-line-extern.cc
 ./src/command-line.cc
 ./src/coot-nomenclature.cc
 ./src/graphics-info-navigation-gtk2.cc
 ./src/graphics-info-navigation.cc
 ./src/read-phs.c
 ./utils/coot-fasta.cc
Copyright: 2001-2005, The University of York
  2001-2006, The University of York
  2002, 2006, The University of York
  2002-2003, The University of York
  2002-2007, The University of York
  2003-2005, 2007, The University of York
  2004, The University of York
  2004-2006, The University of York
  2005, The University of York
  2006, The University of York
  2007, The University of York
  2013, 2016, Medical Research Council
  2013, Medical Research Council
  2014, Medical Research Council
  2015, Medical Research Council
  2015-2016, Medical Research Council
  2016, Medical Research Council
License: LGPL-3+
 FIXME

Files: ./ccp4mg-utils/cartesian.cc
 ./ccp4mg-utils/cartesian.h
 ./ccp4mg-utils/geomutil.cc
 ./ccp4mg-utils/geomutil.h
 ./ccp4mg-utils/matrix.cc
 ./ccp4mg-utils/matrix.h
 ./ccp4mg-utils/ppmutil.cc
 ./ccp4mg-utils/ppmutil.h
 ./ccp4mg-utils/quat.cc
 ./ccp4mg-utils/quat.h
Copyright: 2004, The University of York
License: LGPL-2.1+
 FIXME

Files: ./coot-utils/coot-coord-utils.hh
 ./coot-utils/coot-map-utils.cc
 ./coot-utils/coot-shelx-ins.cc
 ./coot-utils/peak-search.cc
 ./ligand/find-ligand.cc
 ./ligand/ligand-score-card.cc
 ./ligand/ligand.cc
 ./src/c-interface-test.cc
 ./src/c-interface.cc
Copyright: 2002-2005, The University of York
  2002-2007, The University of York
  2004-2007, The University of York
  2005-2006, The University of York
  2005-2007, The University of York
  2006-2007, The University of York
  2007, The University of Oxford
  2008, The University of Oxford
  2008-2009, The University of Oxford
  2008-2010, The University of Oxford
  2008-2012, The University of Oxford
  2009, The University of Oxford
  2012, 2014, Medical Research Council
  2012, 2015-2016, Medical Research Council
  2013, Medical Research Council
  2013-2015, Medical Research Council
  2013-2016, Medical Research Council
  2014, Medical Research Council
  2015, Medical Research Council
License: GPL-3+
 FIXME

Files: ./geometry/read-sbase.cc
 ./geometry/residue-and-atom-specs.hh
 ./ideal/extra-restraints.cc
 ./src/c-interface-residues.cc
 ./src/flev.cc
 ./src/graphics-ligand-view.cc
 ./src/molecule-class-info-build.cc
 ./src/nsv.cc
 ./src/sdf-interface.cc
Copyright: 2009, The University of Oxford
  2010, The University of Oxford
  2010-2012, The University of Oxford
  2011, The University of Oxford
  2011-2012, The University of Oxford
  2012, The University of Oxford
  2013, 2015, Medical Research Council
  2013, Medical Research Council
  2013-2015, Medical Research Council
  2014, Medical Research Council
  2015, Medical Research Council
  2015-2016, Medical Research Council
  2016, Medical Research Council
License: LGPL-3+
 FIXME

Files: ./coot-utils/dirichlet-process.hh
 ./data/Makefile.am
 ./data/cho-acedrg/Makefile.am
 ./data/cho-models/Makefile.am
 ./data/metal/Makefile.am
 ./data/rama-coeffs/Makefile.am
 ./lidia-core/Makefile.am
 ./ligand/identify-protein.cc
Copyright: NONE
License: GPL-3+
 FIXME

Files: ./python-tests/03_ligand.py
 ./python-tests/TestLigandFunctions.py
 ./python-tests/begin.py
 ./python/a_rapper_gui.py
 ./python/bones_reader.py
 ./python/coot_testing_utils.py
 ./python/python_coot_docs.py
 ./python/what_check.py
Copyright: 2008, Bernhard Lohkamp, The University of York
License: GPL-3+
 FIXME

Files: ./src/c-interface-build-gui.cc
 ./src/c-interface-build-main-chain.cc
 ./src/c-interface-build-morph.cc
 ./src/c-interface-build-side-chain.cc
 ./src/c-interface-build-symmetry.cc
 ./src/c-interface-build.cc
 ./src/c-interface-refine.cc
 ./src/c-interface-refmac.cc
Copyright: 2002-2008, The University of York
  2007, Bernhard Lohkamp
  2007, Paul Emsley
  2007-2009, Bernhard Lohkamp
  2007-2009, The University of Oxford
  2007-2011, The University of Oxford
  2008, Kevin Cowtan
  2013-2016, Medical Research Council
  2015, Medical Research Council
  2015-2016, Medical Research Council
  2016, Medical Research Council
License: LGPL-3+
 FIXME

Files: ./MoleculesToTriangles/CXXClasses/Quaternion.cpp
 ./MoleculesToTriangles/CXXClasses/Quaternion.hpp
 ./MoleculesToTriangles/CXXClasses/Vector.hpp
 ./MoleculesToTriangles/CXXClasses/Vector2.cpp
 ./MoleculesToTriangles/CXXClasses/Vector2.hpp
 ./MoleculesToTriangles/CXXClasses/Vector3.cpp
 ./MoleculesToTriangles/CXXClasses/Vector3.hpp
Copyright: 2007-2008, Apple Inc.
  2008, Apple Inc.
License: AML
 FIXME

Files: ./MoleculesToTriangles/CXXClasses/ar-lib
 ./MoleculesToTriangles/CXXClasses/depcomp
 ./MoleculesToTriangles/CXXClasses/missing
 ./MoleculesToTriangles/CXXSurface/depcomp
 ./MoleculesToTriangles/CXXSurface/missing
 ./depcomp
 ./missing
Copyright: 1996-2020, Free Software Foundation, Inc.
  1996-2021, Free Software Foundation, Inc.
  1999-2018, Free Software Foundation, Inc.
  1999-2020, Free Software Foundation, Inc.
  2010-2020, Free Software Foundation, Inc.
License: GPL-2+ with Autoconf-data exception
 FIXME

Files: ./python/background_demo.py
 ./python/coot_lsq.py
 ./python/filter.py
 ./python/generic_objects.py
 ./python/get_ebi.py
 ./python/mutate.py
 ./python/tips_gui.py
Copyright: 2004-2006, Paul Emsley, The University of York
  2005-2006, 2009, Bernhard Lohkamp
  2005-2006, Bernhard Lohkamp
  2005-2006, Paul Emsley, The University of York
  2006, Bernhard Lohkamp
  2006, Paul Emsley, The University of York
  2006-2007, Bernhard Lohkamp
  2006-2007, Paul Emsley, The University of York
License: GPL-3+
 FIXME

Files: ./MoleculesToTriangles/CXXClasses/m4/ltoptions.m4
 ./MoleculesToTriangles/CXXClasses/m4/ltsugar.m4
 ./MoleculesToTriangles/CXXClasses/m4/lt~obsolete.m4
 ./MoleculesToTriangles/CXXSurface/m4/ltoptions.m4
 ./MoleculesToTriangles/CXXSurface/m4/ltsugar.m4
 ./MoleculesToTriangles/CXXSurface/m4/lt~obsolete.m4
Copyright: 2004-2005, 2007, 2009, 2011-2015, Free Software
  2004-2005, 2007-2008, 2011-2015, Free Software
  2004-2005, 2007-2009, 2011-2015, Free Software
License: FSFULLR
 FIXME

Files: ./MoleculesToTriangles/CXXClasses/config.guess
 ./MoleculesToTriangles/CXXClasses/config.sub
 ./MoleculesToTriangles/CXXSurface/config.guess
 ./MoleculesToTriangles/CXXSurface/config.sub
 ./config.guess
 ./config.sub
Copyright: 1992-2018, Free Software Foundation, Inc.
  1992-2020, Free Software Foundation, Inc.
License: GPL-3+ with Autoconf-data exception
 FIXME

Files: ./analysis/chi-squared.cc
 ./analysis/chi-squared.hh
 ./validation-graphs/sequence-view-widget.cc
 ./validation-graphs/sequence-view-widget.hh
 ./validation-graphs/validation-graph-widget.cc
 ./validation-graphs/validation-graph-widget.hh
Copyright: 2023, Global Phasing Ltd.
  2025, Global Phasing Ltd.
License: LGPL-3+
 FIXME

Files: ./geometry/energy-lib.hh
 ./src/c-interface-database.cc
 ./src/globjects.h
 ./src/graphics-info-defines.cc
 ./src/gtk-manual.cc
 ./src/gtk-manual.h
Copyright: 2001-2007, The University of York
  2002-2003, The University of York
  2002-2005, The University of York
  2004-2005, The University of York
  2007, The University of Oxford
  2007, The University of York
  2008-2009, 2011-2012, The University of Oxford
  2008-2009, The University of Oxford
  2009, The University of Oxford
License: LGPL-3+
 FIXME

Files: ./ccp4mg-utils/Makefile.am
 ./ccp4mg-utils/mmut/Makefile.am
 ./ccp4mg-utils/pygl/Makefile.am
 ./ccp4mg-utils/util/Makefile.am
 ./ligand/Makefile.simple
Copyright: 2001-2007, The University of York
  2003, The University of York
  2005, The University of York
License: GPL-2+
 FIXME

Files: ./python/gap.py
 ./python/libcheck.py
 ./python/povray.py
 ./python/raster3d.py
 ./python/refmac.py
Copyright: 2004-2006, Paul Emsley, The University of York
  2005-2006, Bernhard Lohkamp
  2005-2006, Paul Emsley, The University of York
  2007, Bernhard Lohkamp, The University of York
  2007-2008, Bernhard Lohkamp, The University of York
  2007-2009, Bernhard Lohkamp, The University of York
  2008, Bernhard Lohkamp, The University of York
License: GPL-3+
 FIXME

Files: ./coot-utils/coot-coord-extras.hh
 ./ligand/Makefile.am
 ./ligand/ideal-rna.cc
 ./ligand/ideal-rna.hh
 ./scheme/generic-objects.scm
Copyright: 2001-2007, The University of York
  2004-2007, The University of York
  2006, The University of York
  2008, The University of York
  2009, the University of Oxford
  2011, the University of Oxford
License: GPL-3+
 FIXME

Files: ./MoleculesToTriangles/CXXSurface/ctpl_boost.h
 ./utils/ctpl-with-debugging.h
 ./utils/ctpl.h
 ./utils/ctpl_stl.h
Copyright: 2014, Vitaliy Vitsentiy
License: Apache-2.0
 FIXME

Files: ./MoleculesToTriangles/CXXClasses/m4/ltversion.m4
 ./MoleculesToTriangles/CXXSurface/m4/ltversion.m4
 ./macros/lib-prefix.m4
 ./macros/python.m4
Copyright: 1999-2005, 2008-2009, Free Software Foundation, Inc.
  2001-2005, Free Software Foundation, Inc.
  2004, 2011-2015, Free Software Foundation, Inc.
License: FSFULLR
 FIXME

Files: ./python/Makefile.am
 ./python/coot_fitting.py
 ./python/coot_toolbuttons.py
 ./python/tips.py
Copyright: 2004-2006, 2008-2009, The University of York
  2005-2007, Bernhard Lohkamp
  2005-2007, The University of York
  2006, Bernhard Lohkamp
  2006, The University of York
  2006-2007, The University of York
  2007, Bernhard Lohkamp
  2009, Bernhard Lohkamp
License: GPL-3+
 FIXME

Files: ./api/coot-molecule-bonds.cc
 ./coot-utils/coot-coord-utils.cc
 ./scheme/coot-crash-catcher.scm
 ./scheme/coot-utils.scm
Copyright: 2000, Paul Emsley
  2002-2007, The University of York
  2004-2007, The University of York
  2006, The University of York
  2007, Paul Emsley
  2007-2009, The University of Oxford
  2008, The University of York
  2008-2009, The University of Oxford
  2008-2012, The University of Oxford
  2012-2016, Medical Research Council
  2013, Medical Research Council
  2013-2016, Medical Research Council
License: GPL-3+
 FIXME

Files: ./cootaneer/Makefile.am
 ./cootilus/Makefile.am
 ./ligand/penultimate-to-code.awk
 ./scheme/coot-gui.scm
Copyright: 2007, Paul Emsley
License: GPL-3+
 FIXME

Files: ./src/graphics-info-gui.cc
 ./src/graphics-info-refmac.cc
 ./src/graphics-info.cc
 ./src/view.hh
Copyright: 2002-2007, the University of York
  2007-2009, the University of Oxford
  2014, 2016, Medical Research Council
  2014-2016, Medical Research Council
  2015, Medical Research Council
  2016, Medical Research Council
License: LGPL-3+
 FIXME

Files: ./ligand/coot-findligand
 ./ligand/coot-findwaters
 ./ligand/coot-identify-protein
 ./src/dynarama
Copyright: 2004-2006, Paul Emsley, University of York
License: UNKNOWN
 FIXME

Files: ./coot-utils/pugiconfig.hpp
 ./coot-utils/pugixml.cpp
 ./coot-utils/pugixml.hpp
Copyright: 2006-2023, Arseny Kapoulkine (arseny.kapoulkine@gmail.com)
License: Expat
 FIXME

Files: ./build-it
 ./build-it-3-3
 ./build-it-gtk3
Copyright: 2004-2008, The University of York
  2009-2012, The University of York
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  2014-2021, Medical Research Council
  2019-2024, Medical Research Council
License: GPL-3+
 FIXME

Files: ./scheme/greg-extensions.scm
 ./scheme/shelx-extensions.scm
 ./scheme/shelx.scm
Copyright: 2004-2006, The University of York
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License: GPL-3+
 FIXME

Files: ./src/c-interface-info.cc
 ./src/c-interface-mutate.cc
 ./src/globjects.cc
Copyright: 2002-2006, The University of York
  2002-2007, The University of York
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  2007, Bernhard Lohkamp
  2007, Paul Emsley
  2007, The University of Oxford
  2007, The University of York
  2007-2008, Bernhard Lohkamp
  2007-2008, The University of York
  2007-2009, The University of Oxford
  2008, The University of Oxford
  2008-2009, The University of Oxford
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License: LGPL-3+
 FIXME

Files: ./coot-utils/sfcalc-genmap.cc
 ./coot-utils/shiftfield.cpp
 ./coot-utils/shiftfield.h
Copyright: 2003-2004, Kevin Cowtan & University of York
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License: LGPL-3+
 FIXME

Files: ./coords/Bond_lines.cc
 ./coords/mmdb.cc
 ./src/graphics-info-modelling.cc
Copyright: 2002-2006, The University of York
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License: LGPL-3+
 FIXME

Files: ./src/graphics-info-mutate.cc
 ./src/graphics-info-state.cc
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Copyright: 2002-2006, The University of York
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  2010, The University of Oxford.
License: LGPL-3+
 FIXME

Files: ./src/c-interface-mogul.hh
 ./src/get-monomer.hh
 ./src/testing.hh
Copyright: 2008-2009, the University of Oxford
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License: LGPL-3+
 FIXME

Files: ./ideal/coot-ligand-validation
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Copyright: 2004-2006, Paul Emsley, University of York
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License: UNKNOWN
 FIXME

Files: ./ligand/test-ligand.cc
 ./ligand/torsion-general.cc
 ./ligand/torsion-general.hh
Copyright: 2007, The University of Oxford
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License: UNKNOWN
 FIXME

Files: ./MoleculesToTriangles/CXXClasses/install-sh
 ./MoleculesToTriangles/CXXSurface/install-sh
 ./install-sh
Copyright: 1994, X Consortium
License: X11
 FIXME

Files: ./MoleculesToTriangles/CXXClasses/m4/libtool.m4
 ./MoleculesToTriangles/CXXSurface/m4/libtool.m4
Copyright: 1996-2001, 2003-2015, Free Software Foundation, Inc.
License: (FSFULLR and/or GPL-2) with Libtool exception
 FIXME

Files: ./utils/backward.cpp
 ./utils/backward.hpp
Copyright: 2013, Google Inc.
License: Expat
 FIXME

Files: ./coot-utils/json.hpp
 ./src/json.hpp
Copyright: 2013-2019, Niels Lohmann <http://nlohmann.me>.
License: Expat
 FIXME

Files: ./coot-utils/stb_image.h
 ./coot-utils/stb_image_write.h
Copyright: 2017, Sean Barrett
License: Expat and/or Unlicense
 FIXME

Files: ./MoleculesToTriangles/CXXClasses/INSTALL
 ./MoleculesToTriangles/CXXSurface/INSTALL
Copyright: 1994-1996, 1999-2002, 2004-2013, Free Software Foundation,
License: FSFAP
 FIXME

Files: ./MoleculesToTriangles/CXXClasses/m4/ax_boost_base.m4
 ./macros/ax_boost_base.m4
Copyright: 2008, Thomas Porschberg <thomas@randspringer.de>
  2009, Peter Adolphs
License: FSFAP
 FIXME

Files: ./cycle-page-builder.scm
 ./greg-tests/03-ligand.scm
Copyright: 2007-2008, The University of Oxford
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License: GPL
 FIXME

Files: ./greg-tests/01-pdb+mtz.scm
 ./greg-tests/02-shelx.scm
Copyright: 2007-2008, The University of Oxford
License: GPL
 FIXME

Files: ./macros/guile.m4
 ./scheme/my-readline.scm
Copyright: 1997, 1999-2002, Free Software Foundation, Inc.
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License: GPL-2+
 FIXME

Files: ./src/coot-gtk2.defs
 ./src/coot.defs
Copyright: 1998-1999, 2002, Free Software Foundation, Inc.
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 FIXME

Files: ./density-contour/Vectors.cpp
 ./density-contour/Vectors.h
Copyright: 2000, Raghavendra Chandrashekara
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License: GPL-2+
 FIXME

Files: ./MoleculesToTriangles/CXXClasses/m4/m4_ax_check_gl.m4
 ./MoleculesToTriangles/CXXClasses/m4/m4_ax_check_glu.m4
Copyright: 2009, Braden McDaniel <braden@endoframe.com>
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 FIXME

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 FIXME

Files: ./COPYING
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License: GPL-3
 FIXME

Files: ./python-tests/coot_unittest.py
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License: GPL-3+
 FIXME

Files: ./python/extensions.py
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 FIXME

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License: GPL-3+
 FIXME

Files: ./python-tests/01_pdb_mtz.py
 ./python-tests/TestPdbMtzFunctions.py
Copyright: 2007-2008, The University of Oxford
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 FIXME

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 FIXME

Files: ./coot-utils/test-coot-utils.cc
 ./ligand/residue_by_phi_psi.cc
Copyright: 2005, Paul Emsley, The University of York
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License: GPL-3+
 FIXME

Files: ./ligand/backrub-rotamer.cc
 ./ligand/backrub-rotamer.hh
Copyright: 2009, The University of Oxford.
License: GPL-3+
 FIXME

Files: ./MoleculesToTriangles/CXXClasses/m4/ax_python_devel.m4
 ./macros/ax_python_devel.m4
Copyright: 2009, Alan W. Irwin
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  2009, Matteo Settenvini <matteo@member.fsf.org>
  2009, Rafael Laboissiere <rafael@laboissiere.net>
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Files: ./COPYING.LESSERv3
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License: LGPL-3
 FIXME

Files: ./src/c-interface-validate.cc
 ./src/rama_plot_with_canvas.cc
Copyright: 2002-2007, The University of York
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  2006-2007, Bernhard Lohkamp
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License: LGPL-3+
 FIXME

Files: ./src/gtk-utils.cc
 ./src/gtk-utils.hh
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 FIXME

Files: ./coot-utils/coot_shiftfield.cpp
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Copyright: 2018, Kevin Cowtan & The University of York
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 FIXME

Files: ./ideal/extra-restraints-kk.cc
 ./src/molecule-class-info-kk.cc
Copyright: 2011-2012, Kevin Keating
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 FIXME

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 ./utils/coot-utils.cc
Copyright: 2002-2006, The University of York
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 FIXME

Files: ./src/gtkglarea-rama-plot.cc
 ./utils/xdg-base.hh
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 FIXME

Files: ./coords/Bond_lines_ext.hh
 ./src/scm-boot-guile.hh
Copyright: 2003, the University of York
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License: LGPL-3+
 FIXME

Files: ./utils/base64-encode-decode.cc
 ./utils/base64-encode-decode.hh
Copyright: 2004-2008, René Nyffenegger
License: UNKNOWN
 FIXME

Files: ./po/es.po
 ./po/es_ES.po
Copyright: 2005, The University of York
License: UNKNOWN
 FIXME

Files: ./scheme/json-reader.scm
Copyright: 2010, Corey Thomasson
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 FIXME

Files: ./cmake/FindCairo.cmake
Copyright: 2012, Raphael Kubo da Costa <rakuco@webkit.org>
  2017, Alain Vaucher
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 FIXME

Files: ./ligand/LICENSE.txt
Copyright: 2002, 2011, Mutsuo Saito, Makoto Matsumoto, Hiroshima
  2007-2009, Mutsuo Saito, Makoto Matsumoto
License: BSD-3-clause
 FIXME

Files: ./layla/qed.hpp
Copyright: 2009-2017, Novartis Institutes for BioMedical Research Inc.,
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 FIXME

Files: ./rcrane/README.txt
Copyright: 2010-2012, Kevin Keating, and is licensed under the
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 FIXME

Files: ./utils/subprocess.hpp
Copyright: 2016-2018, Arun Muralidharan.
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License: Expat
 FIXME

Files: ./coot-utils/tiny_gltf.h
Copyright: 2015, Present Syoyo Fujita, Aurélien Chatelain and many
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 FIXME

Files: ./compat/dirent.h
Copyright: 1998-2019, Toni Ronkko
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 FIXME

Files: ./coot-utils/prideout-octasphere.cc
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License: Expat and/or LGPL-3+
 FIXME

Files: ./macros/ax_python_module.m4
Copyright: 2008, Andrew Collier
License: FSFAP
 FIXME

Files: ./macros/ax_cxx_compile_stdcxx_0x.m4
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License: FSFAP
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Files: ./macros/ax_cxx_compile_stdcxx.m4
Copyright: 2008, Benjamin Kosnik <bkoz@redhat.com>
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  2014-2015, Google Inc.; contributed by Alexey Sokolov <sokolov@google.com>
  2015, Moritz Klammler <moritz@klammler.eu>
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License: FSFAP
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License: FSFAP
 FIXME

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License: FSFAP
 FIXME

Files: ./macros/ax_cxx_have_thread.m4
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Files: ./macros/ax_cxx_compile_stdcxx_17.m4
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Files: ./macros/ax_boost_thread.m4
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License: FSFAP
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Files: ./pixmaps/README
Copyright: 2001, The University of York
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 FIXME

Files: ./copyright-disclaimer.txt
Copyright: control people at your university/institution (and send it
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 FIXME

Files: ./shell-utils/change-licence-to-lesser.sh
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License: GPL and/or LGPL
 FIXME

Files: ./intltool-merge.in
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Files: ./intltool-update.in
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Files: ./compat/coot-getopt.h
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 FIXME

Files: ./scheme/gtkin.scm
Copyright: 2000, Brett Viren
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 FIXME

Files: ./scheme/brute-lsqman.scm
Copyright: 2003, Charlie Bond, The University of Dundee
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 FIXME

Files: ./density-contour/CIsoSurface.h
Copyright: 2000, Cory Gene Bloyd
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 FIXME

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Files: ./intltool-extract.in
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Files: ./ltmain.sh-unneeded
Copyright: 1996-2001, 2003-2008, Free Software Foundation, Inc.
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Files: ./python/clear_backup.py
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License: GPL-3
 FIXME

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 FIXME

Files: ./compat/sleep-fixups.h
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 FIXME

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License: GPL-3+
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License: GPL-3+
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 FIXME

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 FIXME

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 FIXME

Files: ./coot-utils/peak-search-from-list.cc
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 FIXME

Files: ./MoleculesToTriangles/CXXSurface/ElectroSurface.cpp
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 FIXME

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 FIXME

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 FIXME

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 FIXME

Files: ./scheme/cns2coot.scm
Copyright: 2006, Joel Bard
  2006, Paul Emsley
License: UNKNOWN
 FIXME

Files: ./rcrane/NOTICE.txt
Copyright: 2010-2012, Kevin Keating
License: UNKNOWN
 FIXME

Files: ./ligand/dSFMT.h
Copyright: 2007-2008, Mutsuo Saito, Makoto Matsumoto and
  2012, Mutsuo Saito, Makoto Matsumoto,
License: UNKNOWN
 FIXME

Files: ./ligand/dSFMT.c
Copyright: 2007-2008, Mutsuo Saito, Makoto Matsumoto and Hiroshima
License: UNKNOWN
 FIXME

Files: ./ligand/dSFMT-common.h
Copyright: 2006-2007, Mutsuo Saito, Makoto Matsumoto and Hiroshima
  2012, Mutsuo Saito, Makoto Matsumoto, Hiroshima
License: UNKNOWN
 FIXME

Files: ./scheme/matrices.scm
Copyright: 1999, Paul Emsley
License: UNKNOWN
 FIXME

Files: ./coot-gtk2-try2.glade
Copyright: 2000, 2007, Paul Emsley
  2002-2007, The University of York
  2007, The University of Oxford
License: UNKNOWN
 FIXME

Files: ./coot.appdata.xml
Copyright: 2014-2024, Paul Emsley <pemsley@mrc-lmb.cam.ac.uk> -->
License: UNKNOWN
 FIXME

Files: ./src/graphics-info-trackball.cc
Copyright: 1993-1994, Silicon Graphics, Inc.
License: UNKNOWN
 FIXME

Files: ./analysis/kolmogorov.cc
Copyright: 2012, The Medical Research Council
License: UNKNOWN
 FIXME

Files: ./po/Makefile.in.in
Copyright: 1995-1997, Ulrich Drepper <drepper@gnu.ai.mit.edu>
License: UNKNOWN
 FIXME

Files: ./src/coot-relocatable-binaries.in
Copyright: 2004-2007, University of York
License: UNKNOWN
 FIXME

Files: ./shell-utils/license-checker-2.sh
Copyright: done
License: UNKNOWN
 FIXME

Files: ./shell-utils/license-checker.sh
Copyright: fi
License: UNKNOWN
 FIXME

Files: ./doc/coot-reference-manual.texi
Copyright: page.
License: UNKNOWN
 FIXME

