.flake8
.gitignore
.readthedocs.yaml
LICENSE
README.md
justfile
pyproject.toml
python311_env.yml
python39_env.yml
rtd311.yml
.github/pull_request_template.md
.github/workflows/publish_release.yml
.github/workflows/tests.yml
docs/Makefile
docs/source/analysis.rst
docs/source/conf.py
docs/source/databasing.rst
docs/source/executables.rst
docs/source/first_paper_example.rst
docs/source/forcefields.rst
docs/source/index.rst
docs/source/modules.rst
docs/source/molecular.rst
docs/source/optimisation.rst
docs/source/systems_optimisation.rst
docs/source/terms.rst
docs/source/topologies.rst
docs/source/utilities.rst
docs/source/_autosummary/cgexplore.analysis.GeomMeasure.rst
docs/source/_autosummary/cgexplore.analysis.ShapeMeasure.rst
docs/source/_autosummary/cgexplore.analysis.known_shape_vectors.rst
docs/source/_autosummary/cgexplore.analysis.rst
docs/source/_autosummary/cgexplore.forcefields.AssignedSystem.rst
docs/source/_autosummary/cgexplore.forcefields.ForceField.rst
docs/source/_autosummary/cgexplore.forcefields.ForceFieldLibrary.rst
docs/source/_autosummary/cgexplore.forcefields.ForcedSystem.rst
docs/source/_autosummary/cgexplore.forcefields.MartiniForceField.rst
docs/source/_autosummary/cgexplore.forcefields.MartiniForceFieldLibrary.rst
docs/source/_autosummary/cgexplore.forcefields.MartiniSystem.rst
docs/source/_autosummary/cgexplore.forcefields.MartiniTopology.rst
docs/source/_autosummary/cgexplore.forcefields.cosine_periodic_angle_force.rst
docs/source/_autosummary/cgexplore.forcefields.custom_excluded_volume_force.rst
docs/source/_autosummary/cgexplore.forcefields.get_martini_mass_by_type.rst
docs/source/_autosummary/cgexplore.forcefields.rst
docs/source/_autosummary/cgexplore.molecular.BeadLibrary.rst
docs/source/_autosummary/cgexplore.molecular.CgBead.rst
docs/source/_autosummary/cgexplore.molecular.Conformer.rst
docs/source/_autosummary/cgexplore.molecular.Ensemble.rst
docs/source/_autosummary/cgexplore.molecular.FourC0Arm.rst
docs/source/_autosummary/cgexplore.molecular.FourC1Arm.rst
docs/source/_autosummary/cgexplore.molecular.GeneratedPrecursor.rst
docs/source/_autosummary/cgexplore.molecular.LinearPrecursor.rst
docs/source/_autosummary/cgexplore.molecular.Precursor.rst
docs/source/_autosummary/cgexplore.molecular.PrecursorGenerator.rst
docs/source/_autosummary/cgexplore.molecular.SpindryConformer.rst
docs/source/_autosummary/cgexplore.molecular.SquarePrecursor.rst
docs/source/_autosummary/cgexplore.molecular.ThreeC0Arm.rst
docs/source/_autosummary/cgexplore.molecular.ThreeC1Arm.rst
docs/source/_autosummary/cgexplore.molecular.ThreeC2Arm.rst
docs/source/_autosummary/cgexplore.molecular.Timestep.rst
docs/source/_autosummary/cgexplore.molecular.TrianglePrecursor.rst
docs/source/_autosummary/cgexplore.molecular.TwoC0Arm.rst
docs/source/_autosummary/cgexplore.molecular.TwoC1Arm.rst
docs/source/_autosummary/cgexplore.molecular.TwoC2Arm.rst
docs/source/_autosummary/cgexplore.molecular.TwoC3Arm.rst
docs/source/_autosummary/cgexplore.molecular.VaBene.rst
docs/source/_autosummary/cgexplore.molecular.VaBeneGenerator.rst
docs/source/_autosummary/cgexplore.molecular.check_fit.rst
docs/source/_autosummary/cgexplore.molecular.periodic_table.rst
docs/source/_autosummary/cgexplore.molecular.rst
docs/source/_autosummary/cgexplore.molecular.spd_to_stk.rst
docs/source/_autosummary/cgexplore.molecular.string_to_atom_number.rst
docs/source/_autosummary/cgexplore.optimisation.CGOMMDynamics.rst
docs/source/_autosummary/cgexplore.optimisation.CGOMMOptimizer.rst
docs/source/_autosummary/cgexplore.optimisation.CGOMMSinglePoint.rst
docs/source/_autosummary/cgexplore.optimisation.OMMTrajectory.rst
docs/source/_autosummary/cgexplore.optimisation.rst
docs/source/_autosummary/cgexplore.rst
docs/source/_autosummary/cgexplore.systems_optimisation.Chromosome.rst
docs/source/_autosummary/cgexplore.systems_optimisation.ChromosomeGenerator.rst
docs/source/_autosummary/cgexplore.systems_optimisation.FitnessCalculator.rst
docs/source/_autosummary/cgexplore.systems_optimisation.Generation.rst
docs/source/_autosummary/cgexplore.systems_optimisation.StructureCalculator.rst
docs/source/_autosummary/cgexplore.systems_optimisation.define_angle.rst
docs/source/_autosummary/cgexplore.systems_optimisation.define_bond.rst
docs/source/_autosummary/cgexplore.systems_optimisation.define_cosine_angle.rst
docs/source/_autosummary/cgexplore.systems_optimisation.define_lennardjones.rst
docs/source/_autosummary/cgexplore.systems_optimisation.define_nonbonded.rst
docs/source/_autosummary/cgexplore.systems_optimisation.define_pyramid_angle.rst
docs/source/_autosummary/cgexplore.systems_optimisation.define_torsion.rst
docs/source/_autosummary/cgexplore.systems_optimisation.element_from_type.rst
docs/source/_autosummary/cgexplore.systems_optimisation.get_forcefield_from_dict.rst
docs/source/_autosummary/cgexplore.systems_optimisation.get_neighbour_library.rst
docs/source/_autosummary/cgexplore.systems_optimisation.rst
docs/source/_autosummary/cgexplore.systems_optimisation.yield_near_models.rst
docs/source/_autosummary/cgexplore.terms.Angle.rst
docs/source/_autosummary/cgexplore.terms.Bond.rst
docs/source/_autosummary/cgexplore.terms.CosineAngle.rst
docs/source/_autosummary/cgexplore.terms.FoundAngle.rst
docs/source/_autosummary/cgexplore.terms.FoundTorsion.rst
docs/source/_autosummary/cgexplore.terms.MartiniAngleRange.rst
docs/source/_autosummary/cgexplore.terms.MartiniBondRange.rst
docs/source/_autosummary/cgexplore.terms.Nonbonded.rst
docs/source/_autosummary/cgexplore.terms.PyramidAngleRange.rst
docs/source/_autosummary/cgexplore.terms.TargetAngle.rst
docs/source/_autosummary/cgexplore.terms.TargetAngleRange.rst
docs/source/_autosummary/cgexplore.terms.TargetBond.rst
docs/source/_autosummary/cgexplore.terms.TargetBondRange.rst
docs/source/_autosummary/cgexplore.terms.TargetCosineAngle.rst
docs/source/_autosummary/cgexplore.terms.TargetCosineAngleRange.rst
docs/source/_autosummary/cgexplore.terms.TargetMartiniAngle.rst
docs/source/_autosummary/cgexplore.terms.TargetMartiniBond.rst
docs/source/_autosummary/cgexplore.terms.TargetMartiniTorsion.rst
docs/source/_autosummary/cgexplore.terms.TargetNonbonded.rst
docs/source/_autosummary/cgexplore.terms.TargetNonbondedRange.rst
docs/source/_autosummary/cgexplore.terms.TargetPairedBondRange.rst
docs/source/_autosummary/cgexplore.terms.TargetPyramidAngle.rst
docs/source/_autosummary/cgexplore.terms.TargetTorsion.rst
docs/source/_autosummary/cgexplore.terms.TargetTorsionRange.rst
docs/source/_autosummary/cgexplore.terms.Torsion.rst
docs/source/_autosummary/cgexplore.terms.find_angles.rst
docs/source/_autosummary/cgexplore.terms.find_torsions.rst
docs/source/_autosummary/cgexplore.terms.rst
docs/source/_autosummary/cgexplore.topologies.CGM12L24.rst
docs/source/_autosummary/cgexplore.topologies.CGM4L8.rst
docs/source/_autosummary/cgexplore.topologies.M4L82.rst
docs/source/_autosummary/cgexplore.topologies.rst
docs/source/_autosummary/cgexplore.utilities.AtomliteDatabase.rst
docs/source/_autosummary/cgexplore.utilities.ForceFieldUnavailableError.rst
docs/source/_autosummary/cgexplore.utilities.ForceFieldUnitError.rst
docs/source/_autosummary/cgexplore.utilities.Pymol.rst
docs/source/_autosummary/cgexplore.utilities.add_structure_to_ax.rst
docs/source/_autosummary/cgexplore.utilities.add_text_to_ax.rst
docs/source/_autosummary/cgexplore.utilities.check_directory.rst
docs/source/_autosummary/cgexplore.utilities.convert_pyramid_angle.rst
docs/source/_autosummary/cgexplore.utilities.draw_pie.rst
docs/source/_autosummary/cgexplore.utilities.extract_property.rst
docs/source/_autosummary/cgexplore.utilities.get_supramolecule.rst
docs/source/_autosummary/cgexplore.utilities.get_unforced_supramolecule.rst
docs/source/_autosummary/cgexplore.utilities.optimise_ligand.rst
docs/source/_autosummary/cgexplore.utilities.rst
docs/source/_autosummary/cgexplore.utilities.run_constrained_optimisation.rst
docs/source/_autosummary/cgexplore.utilities.run_optimisation.rst
docs/source/_autosummary/cgexplore.utilities.run_soft_md_cycle.rst
docs/source/_autosummary/cgexplore.utilities.shift_beads.rst
docs/source/_autosummary/cgexplore.utilities.soften_forcefield.rst
docs/source/_autosummary/cgexplore.utilities.write_chemiscope_json.rst
docs/source/_autosummary/cgexplore.utilities.yield_near_models.rst
docs/source/_autosummary/cgexplore.utilities.yield_shifted_models.rst
docs/source/_templates/class.rst
docs/source/_templates/module.rst
first_paper_example/analysis.py
first_paper_example/bead_libraries.py
first_paper_example/define_forcefields.py
first_paper_example/env_set.py
first_paper_example/generate_2p3.py
first_paper_example/generate_2p3_duplicate.py
first_paper_example/generate_2p4.py
first_paper_example/generate_3p4.py
first_paper_example/generation.py
first_paper_example/plot_cages.py
first_paper_example/plot_distributions.py
first_paper_example/plot_energy_parity.py
first_paper_example/plot_maps.py
first_paper_example/plot_parities.py
first_paper_example/plot_phase_spaces.py
first_paper_example/plot_shape_analysis.py
first_paper_example/save_to_chemiscope.py
first_paper_example/topologies.py
optimisation_example/optimsation_test.py
src/cgexplore/__init__.py
src/cgexplore/_version.py
src/cgexplore/analysis.py
src/cgexplore/forcefields.py
src/cgexplore/molecular.py
src/cgexplore/optimisation.py
src/cgexplore/systems_optimisation.py
src/cgexplore/terms.py
src/cgexplore/topologies.py
src/cgexplore/utilities.py
src/cgexplore.egg-info/PKG-INFO
src/cgexplore.egg-info/SOURCES.txt
src/cgexplore.egg-info/dependency_links.txt
src/cgexplore.egg-info/entry_points.txt
src/cgexplore.egg-info/requires.txt
src/cgexplore.egg-info/top_level.txt
src/cgexplore/_internal/__init__.py
src/cgexplore/_internal/analysis/__init__.py
src/cgexplore/_internal/analysis/geom.py
src/cgexplore/_internal/analysis/shape.py
src/cgexplore/_internal/forcefields/__init__.py
src/cgexplore/_internal/forcefields/assigned_system.py
src/cgexplore/_internal/forcefields/forcefield.py
src/cgexplore/_internal/forcefields/martini.py
src/cgexplore/_internal/forcefields/utilities.py
src/cgexplore/_internal/molecular/__init__.py
src/cgexplore/_internal/molecular/beads.py
src/cgexplore/_internal/molecular/conformer.py
src/cgexplore/_internal/molecular/ensembles.py
src/cgexplore/_internal/molecular/molecule_construction.py
src/cgexplore/_internal/molecular/precursor_generator.py
src/cgexplore/_internal/molecular/utilities.py
src/cgexplore/_internal/optimisation/__init__.py
src/cgexplore/_internal/optimisation/openmm_optimizer.py
src/cgexplore/_internal/scripts/__init__.py
src/cgexplore/_internal/scripts/delete_property.py
src/cgexplore/_internal/scripts/get_energies.py
src/cgexplore/_internal/scripts/get_values.py
src/cgexplore/_internal/systems_optimisation/__init__.py
src/cgexplore/_internal/systems_optimisation/calculators.py
src/cgexplore/_internal/systems_optimisation/generation.py
src/cgexplore/_internal/systems_optimisation/inputs.py
src/cgexplore/_internal/systems_optimisation/utilities.py
src/cgexplore/_internal/terms/__init__.py
src/cgexplore/_internal/terms/angles.py
src/cgexplore/_internal/terms/bonds.py
src/cgexplore/_internal/terms/nonbonded.py
src/cgexplore/_internal/terms/torsions.py
src/cgexplore/_internal/terms/utilities.py
src/cgexplore/_internal/topologies/__init__.py
src/cgexplore/_internal/topologies/graphs.py
src/cgexplore/_internal/utilities/__init__.py
src/cgexplore/_internal/utilities/chemiscope_interface.py
src/cgexplore/_internal/utilities/databases.py
src/cgexplore/_internal/utilities/errors.py
src/cgexplore/_internal/utilities/generation_utilities.py
src/cgexplore/_internal/utilities/spindry_utilities.py
src/cgexplore/_internal/utilities/utilities.py
src/cgexplore/_internal/utilities/visualisation.py
src/cgexplore/data/martini_v3.0.0.itp
tests/__init__.py
tests/assigned/__init__.py
tests/assigned/case_data.py
tests/assigned/conftest.py
tests/assigned/molecule0_assigned_tests_molecule0_syst_saved.xml
tests/assigned/molecule1_assigned_tests_molecule1_syst_saved.xml
tests/assigned/test_system_xml_writer.py
tests/assigned/test_topology_xml_writer.py
tests/databases/__init__.py
tests/databases/case_data.py
tests/databases/conftest.py
tests/databases/test_chemiscope.py
tests/databases/test_databasing.py
tests/ensemble/__init__.py
tests/ensemble/case_data.py
tests/ensemble/conftest.py
tests/ensemble/test_ensemble.py
tests/ensemble/utilities.py
tests/ensemble/output/known_ensemble0_base.mol
tests/ensemble/output/known_ensemble0_ensemble.json
tests/ensemble/output/known_ensemble0_ensemble.xyz
tests/forcefield/__init__.py
tests/forcefield/case_data.py
tests/forcefield/conftest.py
tests/forcefield/test_fflibrary.py
tests/forcefield/test_present_angles.py
tests/forcefield/test_present_bonds.py
tests/forcefield/test_present_nonbondeds.py
tests/forcefield/test_present_torsions.py
tests/forcefield/utilities.py
tests/geom/__init__.py
tests/geom/case_data.py
tests/geom/conftest.py
tests/geom/test_angles.py
tests/geom/test_bonds.py
tests/geom/test_max_diameter.py
tests/geom/test_minb2b.py
tests/geom/test_radius_gyration.py
tests/geom/test_torsions.py
tests/optimisers/__init__.py
tests/optimisers/case_data.py
tests/optimisers/conftest.py
tests/optimisers/test_optimizer.py
tests/optimisers/output/molecule0.mol
tests/optimisers/output/molecule1.mol
tests/precursors/__init__.py
tests/precursors/case_data.py
tests/precursors/conftest.py
tests/precursors/test_bead_set.py
tests/precursors/test_buildingblock.py
tests/precursors/test_functional_groups.py
tests/precursors/test_name.py
tests/shape/__init__.py
tests/shape/case_data.py
tests/shape/conftest.py
tests/shape/test_shape.py
tests/shape/test_shape_molecule.py
tests/systems_optimisation/__init__.py
tests/systems_optimisation/case_data.py
tests/systems_optimisation/conftest.py
tests/systems_optimisation/test_chromosome_generator.py
tests/systems_optimisation/test_generation.py
tests/systems_optimisation/output/t.db