Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: Coot
Upstream-Contact: https://github.com/pemsley/coot/issues
Source: https://github.com/pemsley/coot
Files-Excluded:
 fonts

Files: *
Copyright: 2001-2007, The University of York
 2007-2012, The University of Oxford
 2012-2016, Medical Research Council
 1999-2024, Paul Emsley
License: GPL-3+

Files: analysis/b-factor-histogram.cc
 analysis/coot-daca.cc
 analysis/daca.cc
 analysis/daca.hh
 analysis/improper-dihedrals.cc
 analysis/mogul-interface.hh
 analysis/rna-backbone.cc
 analysis/rna-backbone.hh
 analysis/test-align.cc
 analysis/test-cablam.cc
 analysis/test-mogul.cc
 analysis/test-rna-backbone.cc
 analysis/test-stats.cc
 analysis/typed-distances.cc
 analysis/typed-distances.hh
 api/add-terminal-residue.cc
 api/add-terminal-residue.hh
 api/api-cell.hh
 api/atom-pull.hh
 api/blender-mesh.cc
 api/blender-mesh.hh
 api/bond-colour.hh
 api/cell.hh
 api/clipper-ccp4-map-file-wrapper.hh
 api/colour-functions.cc
 api/colour-functions.hh
 api/coot-colour.hh
 api/coot-molecule-backup.cc
 api/coot-molecule-blender.cc
 api/coot-molecule-bonds-instanced.cc
 api/coot-molecule-bonds.hh
 api/coot-molecule-change-chain-id.cc
 api/coot-molecule-maps.cc
 api/coot-molecule-merge-molecules.cc
 api/coot-molecule-moltris.cc
 api/coot-molecule-refine.cc
 api/coot-molecule-replace-fragment.cc
 api/coot-molecule-validation.cc
 api/coot-molecule.cc
 api/coot-molecule.hh
 coords/graphical-bonds-container.hh
 coords/graphics-line.hh
 coords/loop-path.cc
 coords/loop-path.hh
 coords/phenix-geo-bonds.cc
 coords/phenix-geo.cc
 coords/phenix-geo.hh
 coords/phi-psi-prob.cc
 coords/phi-psi-prob.hh
 coords/rama-plot-phi-psi.cc
 coords/rama-plot-phi-psi.hh
 coords/ramachandran-container.hh
 coords/ramachandran-validation.cc
 coords/ramachandran-validation.hh
 coords/rotamer-container.hh
 coords/rotamer-markup.cc
 coords/test-phenix-geo.cc
 coords/test-transform.cc
 coords/torus-description.hh
 coot-utils/3d-texture.cc
 coot-utils/3d-texture.hh
 coot-utils/amp-reso.hh
 coot-utils/arc-info.hh
 coot-utils/atom-tools.cc
 coot-utils/atom-tools.hh
 coot-utils/atom-tree.hh
 coot-utils/atom-vertex.hh
 coot-utils/blob-line.cc
 coot-utils/blob-line.hh
 coot-utils/bonded-atoms.cc
 coot-utils/bonded-atoms.hh
 coot-utils/bricks.cc
 coot-utils/c-beta-deviations.cc
 coot-utils/c-beta-deviations.hh
 coot-utils/cablam-markup.cc
 coot-utils/cablam-markup.hh
 coot-utils/cis-peptide-info.hh
 coot-utils/cmtz-interface.cc
 coot-utils/cmtz-interface.hh
 coot-utils/cod-db-access.cc
 coot-utils/contact-info.cc
 coot-utils/contact-info.hh
 coot-utils/contacts-by-bricks.cc
 coot-utils/contacts-by-bricks.hh
 coot-utils/coot-least-squares.hh
 coot-utils/cylinder-with-rotation-translation.cc
 coot-utils/cylinder-with-rotation-translation.hh
 coot-utils/cylinder.cc
 coot-utils/cylinder.hh
 coot-utils/diff-diff-map-peaks.cc
 coot-utils/diff-diff-map-peaks.hh
 coot-utils/emma.hh
 coot-utils/exp-fit.cc
 coot-utils/exp-fit.hh
 coot-utils/fast-eigens.cc
 coot-utils/fast-eigens.hh
 coot-utils/fib-sphere.cc
 coot-utils/fib-sphere.hh
 coot-utils/find-pepflip-using-difference-map.cc
 coot-utils/find-pepflip-using-difference-map.hh
 coot-utils/find-water-baddies.cc
 coot-utils/find-water-baddies.hh
 coot-utils/fragment-container.cc
 coot-utils/fragment-container.hh
 coot-utils/g_triangle.hh
 coot-utils/gltf-export.cc
 coot-utils/glyco-tree.hh
 coot-utils/helix-like.cc
 coot-utils/helix-like.hh
 coot-utils/jed-flip.cc
 coot-utils/jed-flip.hh
 coot-utils/lidia-core-functions.cc
 coot-utils/lidia-core-functions.hh
 coot-utils/make-cablam-like-stats.cc
 coot-utils/map-index.hh
 coot-utils/merge-C-and-N-terminii.cc
 coot-utils/merge-C-and-N-terminii.hh
 coot-utils/merge-atom-selections.cc
 coot-utils/merge-atom-selections.hh
 coot-utils/merge-molecules.cc
 coot-utils/merge-molecules.hh
 coot-utils/mmrrcc.cc
 coot-utils/mtz-column-auto-read.hh
 coot-utils/mutate.cc
 coot-utils/oct.cc
 coot-utils/oct.hh
 coot-utils/parse-pisa.cc
 coot-utils/parse-pisa.hh
 coot-utils/pepflip-using-difference-map.cc
 coot-utils/pepflip-using-difference-map.hh
 coot-utils/plane-utils.cc
 coot-utils/plane-utils.hh
 coot-utils/polar-atoms.cc
 coot-utils/polar-atoms.hh
 coot-utils/positron.cc
 coot-utils/positron.hh
 coot-utils/prideout-octasphere.hh
 coot-utils/reduce.cc
 coot-utils/reduce.hh
 coot-utils/secondary-structure-headers.cc
 coot-utils/secondary-structure-headers.hh
 coot-utils/segmap.cc
 coot-utils/segmap.hh
 coot-utils/sfcalc-genmap.hh
 coot-utils/shape-types.hh
 coot-utils/shapes.cc
 coot-utils/shapes.hh
 coot-utils/simple-mesh.cc
 coot-utils/simple-mesh.hh
 coot-utils/spherical-harmonics.cc
 coot-utils/spherical-harmonics.hh
 coot-utils/stack-and-pair.cc
 coot-utils/stack-and-pair.hh
 coot-utils/strand-fragments.cc
 coot-utils/strand-fragments.hh
 coot-utils/strand-like.hh
 coot-utils/test-5-residue-fragments.cc
 coot-utils/test-cod-atom-types-from-sm-cif.cc
 coot-utils/test-convolute.cc
 coot-utils/test-coot-probe.cc
 coot-utils/test-diff-diff-map-peaks.cc
 coot-utils/test-emma.cc
 coot-utils/test-parse-pisa.cc
 coot-utils/test-segmap.cc
 coot-utils/vertex.hh
 density-contour/gaussian-surface.cc
 density-contour/gaussian-surface.hh
 density-contour/occlusion.cc
 density-contour/occlusion.hh
 density-contour/test-gaussian-surface.cc
 density-contour/test-occlusion.cc
 density-contour/transfer-occlusions.hh
 geometry/bonded-quad.hh
 geometry/chem_mods.hh
 geometry/cif-parse-mon-lib.cc
 geometry/compare-dictionaries.cc
 geometry/dict-mismatches.hh
 geometry/dict-utils.cc
 geometry/dict-utils.hh
 geometry/dictionary-bond-distributions.cc
 geometry/dreiding.cc
 geometry/gphl-chem-comp-info.hh
 geometry/hb-types.hh
 geometry/hydrophobic.cc
 geometry/hydrophobic.hh
 geometry/intercept-3GP.cc
 geometry/main-chain.cc
 geometry/main-chain.hh
 geometry/make-shelx-restraints.cc
 geometry/match-results.hh
 geometry/mol-utils-2.cc
 geometry/mol-utils-2.hh
 geometry/mol-utils.cc
 geometry/mol-utils.hh
 geometry/pdbe-chem-comp-atom-depiction.hh
 geometry/pdbx-chem-comp-description-generator.hh
 geometry/protein-donor-acceptors.cc
 geometry/protein-donor-acceptors.hh
 geometry/read-metals-json.cc
 geometry/residue-and-atom-specs.cc
 geometry/srs-interface.cc
 geometry/srs-interface.hh
 high-res/high-res.hh
 ideal/coot-compare-residues.cc
 ideal/crankshaft-test.cc
 ideal/crankshaft.cc
 ideal/crankshaft.hh
 ideal/extra-restraints.hh
 ideal/lv.cc
 ideal/model-bond-deltas.cc
 ideal/model-bond-deltas.hh
 ideal/neutron.cc
 ideal/new-linked-residue-t.hh
 ideal/ng.cc
 ideal/parallel-planes.cc
 ideal/parallel-planes.hh
 ideal/phi-psi.cc
 ideal/phi-psi.hh
 ideal/process-dfs-in-range.cc
 ideal/process-dfs-in-range.hh
 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
 ideal/zo-rama.hh
 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
 ligand/ligand-score-card.hh
 ligand/map-point-cluster.hh
 ligand/multi-peptide.hh
 ligand/new-residue-by-3-phi-psi.cc
 ligand/new-residue-by-3-phi-psi.hh
 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
 ligand/scored-node.hh
 ligand/side-chain-densities.cc
 ligand/side-chain-densities.hh
 ligand/side-chain.cc
 ligand/side-chain.hh
 ligand/smith-waterman.hh
 ligand/test-tube-finder.cc
 ligand/tube-finder.cc
 ligand/tube-finder.hh
 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
 src/9.ssao_geometry.shader
 src/Basic.shader
 src/HUDMesh.cc
 src/HUDMesh.hh
 src/HUDTextureMesh.cc
 src/HUDTextureMesh.hh
 src/Instanced-Markup-Mesh.cc
 src/Instanced-Markup-Mesh.hh
 src/LigandViewMesh.cc
 src/LigandViewMesh.hh
 src/LinesMesh.cc
 src/LinesMesh.hh
 src/Material.hh
 src/Mesh-from-glTF.cc
 src/Mesh-from-graphical-bonds-instanced.cc
 src/Mesh-from-graphical-bonds.cc
 src/Mesh.cc
 src/Mesh.hh
 src/Model.cc
 src/Model.hh
 src/Particle.cc
 src/Particle.hh
 src/Shader.cc
 src/Shader.hh
 src/TemplateMesh.hh
 src/Texture.cc
 src/Texture.hh
 src/TextureMesh.cc
 src/TextureMesh.hh
 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
 src/blur-y.shader
 src/blur.shader
 src/boids.cc
 src/boids.hh
 src/bond-colour-mode.hh
 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
 src/cc-interface-graphics.hh
 src/cc-interface-image.hh
 src/cc-interface-map-utils.cc
 src/cc-interface-merge.cc
 src/cc-interface-molecular-representation.cc
 src/cc-interface-molecular-representation.hh
 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/central-cube.shader
 src/cfc-widgets.hh
 src/cfc.cc
 src/cfc.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
 src/colour-holder-to-glm.hh
 src/coot-application.cc
 src/coot-application.hh
 src/coot-colour.cc
 src/coot-phi-psi.cc
 src/coot-phi-psi.hh
 src/coot-setup-python.hh
 src/coot-version.hh
 src/create-menu-item-actions.cc
 src/create-menu-item-actions.hh
 src/crunch-model.hh
 src/curl-utils.hh
 src/curlew-gtk4.cc
 src/curlew-gtk4.hh
 src/curlew.h
 src/data-pair-remover.hh
 src/density-results-container-t.hh
 src/depth-of-field.shader
 src/draw-2.hh
 src/draw-generic-display-objects.cc
 src/draw-map-cap.shader
 src/draw.cc
 src/draw.hh
 src/dynamic-validation.cc
 src/dynamic-validation.hh
 src/effects.shader
 src/event-controller-callbacks.cc
 src/event-controller-callbacks.hh
 src/extra-distance-restraint-markup.hh
 src/extra-distance-restraints.shader
 src/extra-restraints-representation.hh
 src/eyes.cc
 src/eyes.hh
 src/fit-loop-gui.cc
 src/fit-loop-gui.hh
 src/fit-loop.cc
 src/fit-loop.hh
 src/fixup-interface.h.sh
 src/framebuffer.cc
 src/framebuffer.hh
 src/fresnel-settings.hh
 src/ft-character.hh
 src/gaussian-surface.cc
 src/generic-vertex.hh
 src/gensurf.hh
 src/gl-rama-plot.cc
 src/gl-rama-plot.hh
 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
 src/model-molecule-meshes.hh
 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/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/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
License: LGPL-3+

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.cpp
 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+

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

Files: api/filo-tests.cc
 api/filo-tests.hh
 coot-utils/coot-h-bonds.hh
 coot-utils/coot-hole.hh
 coot-utils/coot-lsq-types.h
 coot-utils/elastic.cc
 coot-utils/elastic.hh
 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-align.cc
 src/coot-align.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/gl-matrix.cc
 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/seq-view-interface.c
 src/seq-view-interface.h
 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+

Files: build/CalphaBuild.cc
 build/CalphaBuild.hh
 build/testcabuild.cc
 coords/Bond_lines_ext.cc
 coords/Cartesian.cc
 coords/Cartesian.h
 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.h
 coords/mmdb-extras.cc
 coords/mmdb-extras.h
 coords/mmdb.hh
 coords/utils.cc
 coords/utils.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/gl-matrix.h
 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
 src/sequence-view.cc
 src/sequence-view.hh
 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+

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-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-mini-rsr.man
 man/coot.man
 man/findligand.man
 man/findwaters.man
 pli/Makefile.am
 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+

Files: Makefile.am
 analysis/Makefile.am
 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+

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

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+

Files: 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.
License: GPL-3+

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+

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/protein-ligand-interactions.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
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License: GPL-3+

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
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License: LGPL-3+

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+

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
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License: GPL-3+

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
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License: GPL-3+

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
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License: LGPL-3+

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
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License: GPL-3+

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
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License: GPL-3+

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
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License: GPL-3+

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.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
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License: LGPL-3+

Files: coords/Bond_lines.h
 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
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  2007, The University of York
  2013, 2016, Medical Research Council
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License: LGPL-3+

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+

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
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  2013-2016, Medical Research Council
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License: GPL-3+

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
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License: LGPL-3+

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+

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
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  2013-2016, Medical Research Council
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License: LGPL-3+

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
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Files: MoleculesToTriangles/CXXClasses/ar-lib
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Copyright: 2004-2006, Paul Emsley, The University of York
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Files: MoleculesToTriangles/CXXClasses/m4/ltoptions.m4
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 ligand/Makefile.simple
Copyright: 2001-2007, The University of York
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Files: python/gap.py
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 python/povray.py
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 python/refmac.py
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Files: ligand/coot-identify-protein
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