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/ortep.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/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 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/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/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+ 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-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+ 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+ 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-mini-rsr.man man/coot.man man/findligand.man man/findwaters.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+ 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+ 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/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+ 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/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+ 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+ 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 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+ 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 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