Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W | Y A add_angle_range() (cgexplore.forcefields.ForceFieldLibrary method) (cgexplore.forcefields.MartiniForceFieldLibrary method) add_bond_range() (cgexplore.forcefields.ForceFieldLibrary method) (cgexplore.forcefields.MartiniForceFieldLibrary method) add_conformer() (cgexplore.molecular.Ensemble method) add_entries() (cgexplore.utilities.AtomliteDatabase method) add_forcefield_dict() (cgexplore.systems_optimisation.ChromosomeGenerator method) add_gene() (cgexplore.systems_optimisation.ChromosomeGenerator method) add_molecule() (cgexplore.utilities.AtomliteDatabase method) add_nonbonded_range() (cgexplore.forcefields.ForceFieldLibrary method) (cgexplore.forcefields.MartiniForceFieldLibrary method) add_properties() (cgexplore.utilities.AtomliteDatabase method) add_structure_to_ax() (in module cgexplore.utilities) add_text_to_ax() (in module cgexplore.utilities) add_torsion_range() (cgexplore.forcefields.ForceFieldLibrary method) (cgexplore.forcefields.MartiniForceFieldLibrary method) allowed_num_components (cgexplore.scram.TopologyIterator attribute) angle (cgexplore.terms.Angle attribute) (cgexplore.terms.TargetAngle attribute) (cgexplore.terms.TargetMartiniAngle attribute) (cgexplore.terms.TargetPyramidAngle attribute) Angle (class in cgexplore.terms) angle_k (cgexplore.terms.Angle attribute) (cgexplore.terms.CosineAngle attribute) (cgexplore.terms.TargetAngle attribute) (cgexplore.terms.TargetCosineAngle attribute) (cgexplore.terms.TargetMartiniAngle attribute) (cgexplore.terms.TargetPyramidAngle attribute) angle_ks (cgexplore.terms.MartiniAngleRange attribute) (cgexplore.terms.PyramidAngleRange attribute) (cgexplore.terms.TargetAngleRange attribute) (cgexplore.terms.TargetCosineAngleRange attribute) angles (cgexplore.terms.MartiniAngleRange attribute) (cgexplore.terms.PyramidAngleRange attribute) (cgexplore.terms.TargetAngleRange attribute) assign_terms() (cgexplore.forcefields.ForceField method) (cgexplore.forcefields.MartiniForceField method) AssignedSystem (class in cgexplore.forcefields) atom_id (cgexplore.terms.Nonbonded attribute) atom_ids (cgexplore.terms.Angle attribute) (cgexplore.terms.Bond attribute) (cgexplore.terms.CosineAngle attribute) (cgexplore.terms.FoundAngle attribute) (cgexplore.terms.FoundTorsion attribute) (cgexplore.terms.Torsion attribute) atom_names (cgexplore.terms.Angle attribute) (cgexplore.terms.Bond attribute) (cgexplore.terms.CosineAngle attribute) (cgexplore.terms.Torsion attribute) AtomliteDatabase (class in cgexplore.utilities) atoms (cgexplore.terms.Angle attribute) (cgexplore.terms.Bond attribute) (cgexplore.terms.CosineAngle attribute) (cgexplore.terms.FoundAngle attribute) (cgexplore.terms.FoundTorsion attribute) B b (cgexplore.terms.CosineAngle attribute) (cgexplore.terms.TargetCosineAngle attribute) bead_class (cgexplore.molecular.CgBead attribute) (cgexplore.terms.Nonbonded attribute) (cgexplore.terms.TargetNonbonded attribute) (cgexplore.terms.TargetNonbondedRange attribute) bead_distance (cgexplore.molecular.PrecursorGenerator attribute) bead_element (cgexplore.terms.Nonbonded attribute) (cgexplore.terms.TargetNonbonded attribute) (cgexplore.terms.TargetNonbondedRange attribute) bead_set (cgexplore.forcefields.AssignedSystem attribute) (cgexplore.forcefields.MartiniSystem attribute) bead_type (cgexplore.molecular.CgBead attribute) BeadLibrary (class in cgexplore.molecular) binder_beads (cgexplore.molecular.GeneratedPrecursor attribute) (cgexplore.molecular.LinearPrecursor attribute) (cgexplore.molecular.PrecursorGenerator attribute) (cgexplore.molecular.SquarePrecursor attribute) (cgexplore.molecular.TrianglePrecursor attribute) (cgexplore.molecular.VaBeneGenerator attribute) Bond (class in cgexplore.terms) bond_k (cgexplore.terms.Bond attribute) (cgexplore.terms.TargetBond attribute) (cgexplore.terms.TargetMartiniBond attribute) bond_ks (cgexplore.terms.MartiniBondRange attribute) (cgexplore.terms.TargetBondRange attribute) bond_r (cgexplore.terms.Bond attribute) (cgexplore.terms.TargetBond attribute) (cgexplore.terms.TargetMartiniBond attribute) bond_rs (cgexplore.terms.MartiniBondRange attribute) (cgexplore.terms.TargetBondRange attribute) bs (cgexplore.terms.TargetCosineAngleRange attribute) building_block (cgexplore.molecular.VaBene attribute) building_block_counts (cgexplore.scram.TopologyIterator attribute) building_blocks (cgexplore.scram.TopologyIterator attribute) C calculate() (cgexplore.analysis.ShapeMeasure method) (cgexplore.systems_optimisation.FitnessCalculator method) (cgexplore.systems_optimisation.StructureCalculator method) calculate_angles() (cgexplore.analysis.GeomMeasure method) calculate_bonds() (cgexplore.analysis.GeomMeasure method) calculate_elite_fitness() (cgexplore.systems_optimisation.Generation method) calculate_energy() (cgexplore.optimisation.CGOMMDynamics method) (cgexplore.optimisation.CGOMMOptimizer method) (cgexplore.optimisation.CGOMMSinglePoint method) calculate_energy_decomposition() (cgexplore.optimisation.CGOMMDynamics method) (cgexplore.optimisation.CGOMMOptimizer method) (cgexplore.optimisation.CGOMMSinglePoint method) calculate_fitness_values() (cgexplore.systems_optimisation.Generation method) calculate_from_centroids() (cgexplore.analysis.ShapeMeasure method) calculate_max_diameter() (cgexplore.analysis.GeomMeasure method) calculate_min_distance() (cgexplore.analysis.GeomMeasure method) calculate_minb2b() (cgexplore.analysis.GeomMeasure method) calculate_molecule_energy_decomposition() (cgexplore.optimisation.CGOMMSinglePoint method) calculate_radius_gyration() (cgexplore.analysis.GeomMeasure method) calculate_torsions() (cgexplore.analysis.GeomMeasure method) calculation_output (cgexplore.systems_optimisation.FitnessCalculator attribute) (cgexplore.systems_optimisation.StructureCalculator attribute) CgBead (class in cgexplore.molecular) cgexplore module cgexplore.analysis module cgexplore.atomistic module cgexplore.forcefields module cgexplore.molecular module cgexplore.optimisation module cgexplore.scram module cgexplore.systems_optimisation module cgexplore.terms module cgexplore.topologies module cgexplore.utilities module CGM12L24 (class in cgexplore.topologies) CGM4L8 (class in cgexplore.topologies) CGOMMDynamics (class in cgexplore.optimisation) CGOMMOptimizer (class in cgexplore.optimisation) CGOMMSinglePoint (class in cgexplore.optimisation) cgx_optimisation_sequence() (in module cgexplore.atomistic) check_directory() (in module cgexplore.utilities) check_fit() (in module cgexplore.molecular) Chromosome (class in cgexplore.systems_optimisation) chromosome_generator (cgexplore.systems_optimisation.FitnessCalculator attribute) chromosome_map (cgexplore.systems_optimisation.ChromosomeGenerator attribute) chromosome_types (cgexplore.systems_optimisation.ChromosomeGenerator attribute) chromosomed_terms (cgexplore.systems_optimisation.Chromosome attribute) (cgexplore.systems_optimisation.ChromosomeGenerator attribute) ChromosomeGenerator (class in cgexplore.systems_optimisation) chromosomes (cgexplore.systems_optimisation.Generation attribute) clone() (cgexplore.topologies.CGM12L24 method) (cgexplore.topologies.CGM4L8 method) (cgexplore.topologies.M4L82 method) (cgexplore.topologies.M6L122 method) (cgexplore.topologies.M8L162 method) (cgexplore.topologies.UnalignedM1L2 method) composition (cgexplore.molecular.GeneratedPrecursor attribute) (cgexplore.molecular.LinearPrecursor attribute) (cgexplore.molecular.PrecursorGenerator attribute) configuration (cgexplore.scram.ConfiguredCode attribute) Configuration (class in cgexplore.scram) ConfiguredCode (class in cgexplore.scram) Conformer (class in cgexplore.molecular) conformer_id (cgexplore.molecular.Conformer attribute) (cgexplore.molecular.SpindryConformer attribute) construct() (cgexplore.topologies.CGM12L24 method) (cgexplore.topologies.CGM4L8 method) (cgexplore.topologies.CustomTopology method) (cgexplore.topologies.M4L82 method) (cgexplore.topologies.M6L122 method) (cgexplore.topologies.M8L162 method) (cgexplore.topologies.UnalignedM1L2 method) contains_doubles() (cgexplore.scram.TopologyCode method) contains_parallels() (cgexplore.scram.TopologyCode method) contains_xs() (cgexplore.scram.TopologyCode method) convert_pyramid_angle() (in module cgexplore.utilities) coordination (cgexplore.molecular.CgBead attribute) cosine_periodic_angle_force() (in module cgexplore.forcefields) CosineAngle (class in cgexplore.terms) count_graphs() (cgexplore.scram.TopologyIterator method) Crest (class in cgexplore.atomistic) crossover_population() (cgexplore.systems_optimisation.ChromosomeGenerator method) custom_excluded_volume_force() (in module cgexplore.forcefields) custom_lennard_jones_force() (in module cgexplore.forcefields) CustomTopology (class in cgexplore.topologies) D database_path (cgexplore.systems_optimisation.FitnessCalculator attribute) (cgexplore.systems_optimisation.StructureCalculator attribute) db_key (cgexplore.molecular.GeneratedPrecursor attribute) dedupe_population() (cgexplore.systems_optimisation.ChromosomeGenerator method) define_angle() (in module cgexplore.systems_optimisation) define_bond() (in module cgexplore.systems_optimisation) define_chromosomes() (cgexplore.systems_optimisation.ChromosomeGenerator method) define_cosine_angle() (in module cgexplore.systems_optimisation) define_lennardjones() (in module cgexplore.systems_optimisation) define_nonbonded() (in module cgexplore.systems_optimisation) define_pyramid_angle() (in module cgexplore.systems_optimisation) define_torsion() (in module cgexplore.systems_optimisation) definer_dict (cgexplore.systems_optimisation.Chromosome attribute) (cgexplore.systems_optimisation.ChromosomeGenerator attribute) draw_pie() (in module cgexplore.utilities) E element1 (cgexplore.terms.MartiniAngleRange attribute) (cgexplore.terms.MartiniBondRange attribute) (cgexplore.terms.PyramidAngleRange attribute) (cgexplore.terms.TargetAngle attribute) (cgexplore.terms.TargetAngleRange attribute) (cgexplore.terms.TargetBond attribute) (cgexplore.terms.TargetBondRange attribute) (cgexplore.terms.TargetCosineAngle attribute) (cgexplore.terms.TargetCosineAngleRange attribute) (cgexplore.terms.TargetMartiniAngle attribute) (cgexplore.terms.TargetMartiniBond attribute) (cgexplore.terms.TargetPyramidAngle attribute) element2 (cgexplore.terms.MartiniAngleRange attribute) (cgexplore.terms.MartiniBondRange attribute) (cgexplore.terms.PyramidAngleRange attribute) (cgexplore.terms.TargetAngle attribute) (cgexplore.terms.TargetAngleRange attribute) (cgexplore.terms.TargetBond attribute) (cgexplore.terms.TargetBondRange attribute) (cgexplore.terms.TargetCosineAngle attribute) (cgexplore.terms.TargetCosineAngleRange attribute) (cgexplore.terms.TargetMartiniAngle attribute) (cgexplore.terms.TargetMartiniBond attribute) (cgexplore.terms.TargetPyramidAngle attribute) element3 (cgexplore.terms.MartiniAngleRange attribute) (cgexplore.terms.PyramidAngleRange attribute) (cgexplore.terms.TargetAngle attribute) (cgexplore.terms.TargetAngleRange attribute) (cgexplore.terms.TargetCosineAngle attribute) (cgexplore.terms.TargetCosineAngleRange attribute) (cgexplore.terms.TargetMartiniAngle attribute) (cgexplore.terms.TargetPyramidAngle attribute) element_from_type() (in module cgexplore.systems_optimisation) element_string (cgexplore.molecular.CgBead attribute) energy_decomposition (cgexplore.molecular.Conformer attribute) (cgexplore.molecular.SpindryConformer attribute) Ensemble (class in cgexplore.molecular) epsilon (cgexplore.terms.Nonbonded attribute) (cgexplore.terms.TargetNonbonded attribute) epsilons (cgexplore.terms.TargetNonbondedRange attribute) extract_ditopic_ensemble() (in module cgexplore.atomistic) extract_property() (in module cgexplore.utilities) F fill_position_matrix_molecule() (cgexplore.analysis.ShapeMeasure method) find_angles() (in module cgexplore.terms) find_torsions() (in module cgexplore.terms) fitness_calculator (cgexplore.systems_optimisation.Generation attribute) fitness_function (cgexplore.systems_optimisation.FitnessCalculator attribute) FitnessCalculator (class in cgexplore.systems_optimisation) force (cgexplore.terms.Angle attribute) (cgexplore.terms.Bond attribute) (cgexplore.terms.CosineAngle attribute) (cgexplore.terms.Nonbonded attribute) (cgexplore.terms.TargetNonbonded attribute) (cgexplore.terms.TargetNonbondedRange attribute) (cgexplore.terms.Torsion attribute) ForceField (class in cgexplore.forcefields) forcefield_terms (cgexplore.forcefields.AssignedSystem attribute) (cgexplore.forcefields.MartiniSystem attribute) ForceFieldLibrary (class in cgexplore.forcefields) ForceFieldUnavailableError ForceFieldUnitError FoundAngle (class in cgexplore.terms) FoundTorsion (class in cgexplore.terms) FourC0Arm (class in cgexplore.molecular) FourC1Arm (class in cgexplore.molecular) from_bead_types() (cgexplore.molecular.BeadLibrary class method) from_forcefield() (cgexplore.analysis.GeomMeasure class method) funct (cgexplore.terms.Angle attribute) (cgexplore.terms.Bond attribute) (cgexplore.terms.MartiniAngleRange attribute) (cgexplore.terms.MartiniBondRange attribute) (cgexplore.terms.MartiniTorsionRange attribute) (cgexplore.terms.TargetBond attribute) (cgexplore.terms.TargetMartiniAngle attribute) (cgexplore.terms.TargetMartiniBond attribute) (cgexplore.terms.TargetMartiniTorsion attribute) (cgexplore.terms.TargetTorsion attribute) (cgexplore.terms.Torsion attribute) G gene_dict (cgexplore.systems_optimisation.Chromosome attribute) GeneratedPrecursor (class in cgexplore.molecular) Generation (class in cgexplore.systems_optimisation) GeomMeasure (class in cgexplore.analysis) get_all_possible_terms() (cgexplore.forcefields.ForceField method) (cgexplore.forcefields.MartiniForceField method) get_as_string() (cgexplore.scram.TopologyCode method) get_base_molecule() (cgexplore.molecular.Ensemble method) (cgexplore.optimisation.OMMTrajectory method) get_bb_va_topology_code_graph() (in module cgexplore.scram) get_bc_ids() (cgexplore.systems_optimisation.ChromosomeGenerator method) get_bead_library() (cgexplore.forcefields.ForceField method) (cgexplore.forcefields.MartiniForceField method) get_bead_set() (cgexplore.molecular.FourC0Arm method) (cgexplore.molecular.FourC1Arm method) (cgexplore.molecular.Precursor method) (cgexplore.molecular.Single method) (cgexplore.molecular.SixBead method) (cgexplore.molecular.StericSevenBead method) (cgexplore.molecular.StericSixBead method) (cgexplore.molecular.StericTwoC1Arm method) (cgexplore.molecular.ThreeC0Arm method) (cgexplore.molecular.ThreeC1Arm method) (cgexplore.molecular.ThreeC2Arm method) (cgexplore.molecular.TwoC0Arm method) (cgexplore.molecular.TwoC1Arm method) (cgexplore.molecular.TwoC2Arm method) (cgexplore.molecular.TwoC3Arm method) get_building_block() (cgexplore.molecular.FourC0Arm method) (cgexplore.molecular.FourC1Arm method) (cgexplore.molecular.GeneratedPrecursor method) (cgexplore.molecular.LinearPrecursor method) (cgexplore.molecular.Precursor method) (cgexplore.molecular.PrecursorGenerator method) (cgexplore.molecular.Single method) (cgexplore.molecular.SixBead method) (cgexplore.molecular.SquarePrecursor method) (cgexplore.molecular.StericSevenBead method) (cgexplore.molecular.StericSixBead method) (cgexplore.molecular.StericTwoC1Arm method) (cgexplore.molecular.ThreeC0Arm method) (cgexplore.molecular.ThreeC1Arm method) (cgexplore.molecular.ThreeC2Arm method) (cgexplore.molecular.TrianglePrecursor method) (cgexplore.molecular.TwoC0Arm method) (cgexplore.molecular.TwoC1Arm method) (cgexplore.molecular.TwoC2Arm method) (cgexplore.molecular.TwoC3Arm method) (cgexplore.molecular.VaBene method) get_building_block_configurations() (cgexplore.systems_optimisation.Chromosome method) get_building_blocks() (cgexplore.systems_optimisation.Chromosome method) (cgexplore.topologies.CGM12L24 method) (cgexplore.topologies.CGM4L8 method) (cgexplore.topologies.M4L82 method) (cgexplore.topologies.M6L122 method) (cgexplore.topologies.M8L162 method) (cgexplore.topologies.UnalignedM1L2 method) get_configurations() (cgexplore.scram.TopologyIterator method) get_conformer() (cgexplore.molecular.Ensemble method) get_data() (cgexplore.optimisation.OMMTrajectory method) get_database() (cgexplore.utilities.AtomliteDatabase method) get_ditopic_aligned_bb() (in module cgexplore.atomistic) get_edges_from_topology_code() (cgexplore.scram.TopologyIterator method) get_energy_per_bb() (in module cgexplore.utilities) get_entries() (cgexplore.utilities.AtomliteDatabase method) get_entry() (cgexplore.utilities.AtomliteDatabase method) get_entry_list() (cgexplore.utilities.AtomliteDatabase method) get_forcefield() (cgexplore.systems_optimisation.Chromosome method) get_forcefield_dictionary() (cgexplore.forcefields.ForceField method) (cgexplore.forcefields.MartiniForceField method) get_forcefield_from_dict() (in module cgexplore.systems_optimisation) get_from_class() (cgexplore.molecular.BeadLibrary method) get_from_element() (cgexplore.molecular.BeadLibrary method) get_from_type() (cgexplore.molecular.BeadLibrary method) get_generation_size() (cgexplore.systems_optimisation.Generation method) get_graph() (cgexplore.scram.ConfiguredCode method) (cgexplore.scram.TopologyCode method) get_hashable_idx_dict() (cgexplore.scram.Configuration method) get_hr_file_name() (cgexplore.forcefields.ForceField method) (cgexplore.forcefields.MartiniForceField method) get_identifier() (cgexplore.forcefields.ForceField method) (cgexplore.forcefields.MartiniForceField method) get_layout() (cgexplore.scram.TopologyCode method) get_lowest_e_conformer() (cgexplore.molecular.Ensemble method) get_martini_mass_by_type() (in module cgexplore.forcefields) get_molecule() (cgexplore.utilities.AtomliteDatabase method) get_molecule_num_atoms() (cgexplore.molecular.Ensemble method) get_name() (cgexplore.molecular.FourC0Arm method) (cgexplore.molecular.FourC1Arm method) (cgexplore.molecular.Precursor method) (cgexplore.molecular.Single method) (cgexplore.molecular.SixBead method) (cgexplore.molecular.StericSevenBead method) (cgexplore.molecular.StericSixBead method) (cgexplore.molecular.StericTwoC1Arm method) (cgexplore.molecular.ThreeC0Arm method) (cgexplore.molecular.ThreeC1Arm method) (cgexplore.molecular.ThreeC2Arm method) (cgexplore.molecular.TwoC0Arm method) (cgexplore.molecular.TwoC1Arm method) (cgexplore.molecular.TwoC2Arm method) (cgexplore.molecular.TwoC3Arm method) get_neighbour_library() (in module cgexplore.systems_optimisation) get_node_dictionary() (cgexplore.scram.Configuration method) get_num_building_block() (cgexplore.topologies.CGM12L24 method) (cgexplore.topologies.CGM4L8 method) (cgexplore.topologies.M4L82 method) (cgexplore.topologies.M6L122 method) (cgexplore.topologies.M8L162 method) (cgexplore.topologies.UnalignedM1L2 method) get_num_building_blocks() (cgexplore.scram.TopologyIterator method) get_num_chromosomes() (cgexplore.systems_optimisation.ChromosomeGenerator method) get_num_conformers() (cgexplore.molecular.Ensemble method) get_num_entries() (cgexplore.utilities.AtomliteDatabase method) get_num_property_entries() (cgexplore.utilities.AtomliteDatabase method) get_number_connected_components() (cgexplore.scram.TopologyCode method) get_nx_graph() (cgexplore.scram.TopologyCode method) get_openmm_system() (cgexplore.forcefields.AssignedSystem method) (cgexplore.forcefields.MartiniSystem method) (cgexplore.forcefields.MartiniTopology method) get_openmm_topology() (cgexplore.forcefields.AssignedSystem method) (cgexplore.forcefields.MartiniSystem method) (cgexplore.forcefields.MartiniTopology method) get_population_neighbours() (cgexplore.systems_optimisation.ChromosomeGenerator method) get_prec_ids() (cgexplore.systems_optimisation.ChromosomeGenerator method) get_precursors() (cgexplore.molecular.VaBeneGenerator method) (cgexplore.systems_optimisation.Chromosome method) get_prefix() (cgexplore.forcefields.ForceField method) (cgexplore.forcefields.MartiniForceField method) get_present_beads() (cgexplore.forcefields.ForceField method) (cgexplore.forcefields.MartiniForceField method) (cgexplore.molecular.BeadLibrary method) get_property() (cgexplore.utilities.AtomliteDatabase method) get_property_df() (cgexplore.utilities.AtomliteDatabase method) get_property_entries() (cgexplore.utilities.AtomliteDatabase method) get_property_entry() (cgexplore.utilities.AtomliteDatabase method) get_regraphed_molecule() (in module cgexplore.scram) get_separated_string() (cgexplore.systems_optimisation.Chromosome method) get_shape_molecule_byelements() (cgexplore.analysis.ShapeMeasure method) get_smiles() (cgexplore.molecular.GeneratedPrecursor method) (cgexplore.molecular.PrecursorGenerator method) (cgexplore.molecular.VaBene method) get_stk_topology_code() (in module cgexplore.scram) get_string() (cgexplore.systems_optimisation.Chromosome method) get_supramolecule() (in module cgexplore.utilities) get_targets() (cgexplore.forcefields.ForceField method) (cgexplore.forcefields.MartiniForceField method) get_term_ids() (cgexplore.systems_optimisation.ChromosomeGenerator method) get_topo_ids() (cgexplore.systems_optimisation.ChromosomeGenerator method) get_topology_information() (cgexplore.systems_optimisation.Chromosome method) get_unforced_supramolecule() (in module cgexplore.utilities) get_va_ids() (cgexplore.systems_optimisation.ChromosomeGenerator method) get_vdw_bond_cutoff() (cgexplore.forcefields.ForceField method) (cgexplore.forcefields.MartiniForceField method) get_vertex_alignments() (cgexplore.systems_optimisation.Chromosome method) (cgexplore.topologies.CGM12L24 method) (cgexplore.topologies.CGM4L8 method) (cgexplore.topologies.M4L82 method) (cgexplore.topologies.M6L122 method) (cgexplore.topologies.M8L162 method) (cgexplore.topologies.UnalignedM1L2 method) (in module cgexplore.scram) get_vertex_prototypes() (cgexplore.scram.TopologyIterator method) get_vertexset_molecule() (in module cgexplore.scram) get_weighted_graph() (cgexplore.scram.TopologyCode method) graph_directory (cgexplore.scram.TopologyIterator attribute) graph_exists() (cgexplore.scram.TopologyIterator method) graph_optimise_cage() (in module cgexplore.scram) graph_set (cgexplore.scram.TopologyIterator attribute) graph_type (cgexplore.scram.TopologyIterator attribute) H has_molecule() (cgexplore.utilities.AtomliteDatabase method) human_readable() (cgexplore.terms.TargetAngle method) (cgexplore.terms.TargetBond method) (cgexplore.terms.TargetCosineAngle method) (cgexplore.terms.TargetMartiniAngle method) (cgexplore.terms.TargetMartiniBond method) (cgexplore.terms.TargetMartiniTorsion method) (cgexplore.terms.TargetNonbonded method) (cgexplore.terms.TargetPyramidAngle method) (cgexplore.terms.TargetTorsion method) I idx (cgexplore.scram.Configuration attribute) (cgexplore.scram.TopologyCode attribute) (cgexplore.scram.VertexAlignment attribute) is_isomorphic() (cgexplore.scram.ConfiguredCode method) is_type_possible() (cgexplore.scram.TopologyIterator method) iterator (cgexplore.scram.TopologyIterator attribute) K keep_if() (cgexplore.utilities.AtomliteDatabase method) known_shape_vectors() (in module cgexplore.analysis) L LinearPrecursor (class in cgexplore.molecular) load_data() (cgexplore.molecular.Ensemble method) load_trajectory() (cgexplore.molecular.Ensemble method) M M4L82 (class in cgexplore.topologies) M6L122 (class in cgexplore.topologies) M8L162 (class in cgexplore.topologies) MartiniAngleRange (class in cgexplore.terms) MartiniBondRange (class in cgexplore.terms) MartiniForceField (class in cgexplore.forcefields) MartiniForceFieldLibrary (class in cgexplore.forcefields) MartiniSystem (class in cgexplore.forcefields) MartiniTopology (class in cgexplore.forcefields) MartiniTorsionRange (class in cgexplore.terms) mass (cgexplore.forcefields.AssignedSystem attribute) max_samples (cgexplore.scram.TopologyIterator attribute) measured_atom_ids (cgexplore.terms.MartiniTorsionRange attribute) (cgexplore.terms.TargetMartiniTorsion attribute) (cgexplore.terms.TargetTorsion attribute) (cgexplore.terms.TargetTorsionRange attribute) merge_definer_dicts() (in module cgexplore.systems_optimisation) module cgexplore cgexplore.analysis cgexplore.atomistic cgexplore.forcefields cgexplore.molecular cgexplore.optimisation cgexplore.scram cgexplore.systems_optimisation cgexplore.terms cgexplore.topologies cgexplore.utilities molecule (cgexplore.forcefields.AssignedSystem attribute) (cgexplore.forcefields.MartiniSystem attribute) (cgexplore.molecular.Conformer attribute) (cgexplore.molecular.GeneratedPrecursor attribute) (cgexplore.molecular.Timestep attribute) mutate_population() (cgexplore.systems_optimisation.ChromosomeGenerator method) N n (cgexplore.terms.CosineAngle attribute) (cgexplore.terms.TargetCosineAngle attribute) name (cgexplore.systems_optimisation.Chromosome attribute) node_counts (cgexplore.scram.TopologyIterator attribute) node_idx_dict (cgexplore.scram.Configuration attribute) node_to_bb_map (cgexplore.scram.TopologyIterator attribute) node_types (cgexplore.scram.Configuration attribute) Nonbonded (class in cgexplore.terms) ns (cgexplore.terms.TargetCosineAngleRange attribute) num_beads (cgexplore.molecular.VaBeneGenerator attribute) num_processes (cgexplore.systems_optimisation.Generation attribute) O OMMTrajectory (class in cgexplore.optimisation) opposite_angle (cgexplore.terms.TargetPyramidAngle attribute) optimise_cage() (in module cgexplore.scram) optimise_from_files() (in module cgexplore.scram) optimise_ligand() (in module cgexplore.utilities) optimize() (cgexplore.atomistic.Crest method) (cgexplore.optimisation.CGOMMDynamics method) (cgexplore.optimisation.CGOMMOptimizer method) (cgexplore.optimisation.CGOMMSinglePoint method) options (cgexplore.systems_optimisation.FitnessCalculator attribute) (cgexplore.systems_optimisation.StructureCalculator attribute) P paired_wall_1_coord (cgexplore.topologies.M4L82 attribute) (cgexplore.topologies.M6L122 attribute) (cgexplore.topologies.M8L162 attribute) paired_wall_2_coord (cgexplore.topologies.M4L82 attribute) (cgexplore.topologies.M6L122 attribute) (cgexplore.topologies.M8L162 attribute) paired_wall_3_coord (cgexplore.topologies.M6L122 attribute) (cgexplore.topologies.M8L162 attribute) paired_wall_4_coord (cgexplore.topologies.M8L162 attribute) passes_graph_bb_va_iso() (in module cgexplore.scram) periodic_table() (in module cgexplore.molecular) phi0 (cgexplore.terms.TargetMartiniTorsion attribute) (cgexplore.terms.TargetTorsion attribute) (cgexplore.terms.Torsion attribute) phi0s (cgexplore.terms.MartiniTorsionRange attribute) (cgexplore.terms.TargetTorsionRange attribute) placer_beads (cgexplore.molecular.GeneratedPrecursor attribute) (cgexplore.molecular.LinearPrecursor attribute) (cgexplore.molecular.PrecursorGenerator attribute) (cgexplore.molecular.SquarePrecursor attribute) (cgexplore.molecular.TrianglePrecursor attribute) (cgexplore.molecular.VaBeneGenerator attribute) points_on_sphere() (in module cgexplore.scram) Precursor (class in cgexplore.molecular) PrecursorGenerator (class in cgexplore.molecular) prefix (cgexplore.systems_optimisation.Chromosome attribute) (cgexplore.systems_optimisation.ChromosomeGenerator attribute) present_beads (cgexplore.molecular.LinearPrecursor attribute) (cgexplore.molecular.PrecursorGenerator attribute) (cgexplore.molecular.SquarePrecursor attribute) (cgexplore.molecular.TrianglePrecursor attribute) (cgexplore.molecular.VaBene attribute) (cgexplore.molecular.VaBeneGenerator attribute) (cgexplore.systems_optimisation.Chromosome attribute) (cgexplore.systems_optimisation.ChromosomeGenerator attribute) Pymol (class in cgexplore.utilities) PyramidAngleRange (class in cgexplore.terms) R rattle() (in module cgexplore.utilities) read_final_energy_decomposition() (cgexplore.optimisation.CGOMMDynamics method) (cgexplore.optimisation.CGOMMOptimizer method) (cgexplore.optimisation.CGOMMSinglePoint method) reference_shape_dict() (cgexplore.analysis.ShapeMeasure method) remove_entry() (cgexplore.utilities.AtomliteDatabase method) remove_property() (cgexplore.utilities.AtomliteDatabase method) rmsd_checker() (in module cgexplore.utilities) run_conformer_analysis() (in module cgexplore.atomistic) run_constrained_optimisation() (in module cgexplore.utilities) run_dynamics() (cgexplore.optimisation.CGOMMDynamics method) run_optimisation() (in module cgexplore.utilities) run_soft_md_cycle() (in module cgexplore.utilities) run_structures() (cgexplore.systems_optimisation.Generation method) S scale (cgexplore.molecular.VaBeneGenerator attribute) scale_multiplier (cgexplore.scram.TopologyIterator attribute) search_estring (cgexplore.terms.MartiniTorsionRange attribute) (cgexplore.terms.TargetMartiniTorsion attribute) (cgexplore.terms.TargetTorsion attribute) (cgexplore.terms.TargetTorsionRange attribute) search_string (cgexplore.terms.MartiniTorsionRange attribute) (cgexplore.terms.TargetMartiniTorsion attribute) (cgexplore.terms.TargetTorsion attribute) (cgexplore.terms.TargetTorsionRange attribute) seed (cgexplore.molecular.VaBeneGenerator attribute) select_all() (cgexplore.systems_optimisation.Generation method) select_best() (cgexplore.systems_optimisation.Generation method) select_chromosome() (cgexplore.systems_optimisation.ChromosomeGenerator method) select_elite() (cgexplore.systems_optimisation.Generation method) select_random_population() (cgexplore.systems_optimisation.ChromosomeGenerator method) select_similar_chromosome() (cgexplore.systems_optimisation.ChromosomeGenerator method) select_worst() (cgexplore.systems_optimisation.Generation method) set_property() (cgexplore.utilities.AtomliteDatabase method) ShapeMeasure (class in cgexplore.analysis) shift_beads() (in module cgexplore.utilities) sigma (cgexplore.terms.Nonbonded attribute) (cgexplore.terms.TargetNonbonded attribute) sigmas (cgexplore.terms.TargetNonbondedRange attribute) Single (class in cgexplore.molecular) SixBead (class in cgexplore.molecular) soften_forcefield() (in module cgexplore.utilities) source (cgexplore.molecular.Conformer attribute) (cgexplore.molecular.SpindryConformer attribute) spd_to_stk() (in module cgexplore.molecular) SpindryConformer (class in cgexplore.molecular) SquarePrecursor (class in cgexplore.molecular) StericSevenBead (class in cgexplore.molecular) StericSixBead (class in cgexplore.molecular) StericTwoC1Arm (class in cgexplore.molecular) stoich_map() (in module cgexplore.topologies) string_to_atom_number() (in module cgexplore.molecular) structure_calculator (cgexplore.systems_optimisation.Generation attribute) structure_function (cgexplore.systems_optimisation.StructureCalculator attribute) structure_output (cgexplore.systems_optimisation.FitnessCalculator attribute) (cgexplore.systems_optimisation.StructureCalculator attribute) StructureCalculator (class in cgexplore.systems_optimisation) supramolecule (cgexplore.molecular.SpindryConformer attribute) system_xml (cgexplore.forcefields.AssignedSystem attribute) (cgexplore.forcefields.MartiniSystem attribute) T target_optimisation() (in module cgexplore.scram) TargetAngle (class in cgexplore.terms) TargetAngleRange (class in cgexplore.terms) TargetBond (class in cgexplore.terms) TargetBondRange (class in cgexplore.terms) TargetCosineAngle (class in cgexplore.terms) TargetCosineAngleRange (class in cgexplore.terms) TargetMartiniAngle (class in cgexplore.terms) TargetMartiniBond (class in cgexplore.terms) TargetMartiniTorsion (class in cgexplore.terms) TargetNonbonded (class in cgexplore.terms) TargetNonbondedRange (class in cgexplore.terms) TargetPyramidAngle (class in cgexplore.terms) TargetTorsion (class in cgexplore.terms) TargetTorsionRange (class in cgexplore.terms) ThreeC0Arm (class in cgexplore.molecular) ThreeC1Arm (class in cgexplore.molecular) ThreeC2Arm (class in cgexplore.molecular) timestep (cgexplore.molecular.Timestep attribute) Timestep (class in cgexplore.molecular) to_stk_molecule() (cgexplore.molecular.SpindryConformer method) topology_code (cgexplore.scram.ConfiguredCode attribute) topology_itp (cgexplore.forcefields.MartiniSystem attribute) topology_xml (cgexplore.forcefields.AssignedSystem attribute) TopologyCode (class in cgexplore.scram) TopologyIterator (class in cgexplore.scram) Torsion (class in cgexplore.terms) torsion_k (cgexplore.terms.TargetMartiniTorsion attribute) (cgexplore.terms.TargetTorsion attribute) (cgexplore.terms.Torsion attribute) torsion_ks (cgexplore.terms.MartiniTorsionRange attribute) (cgexplore.terms.TargetTorsionRange attribute) torsion_n (cgexplore.terms.TargetMartiniTorsion attribute) (cgexplore.terms.TargetTorsion attribute) (cgexplore.terms.Torsion attribute) torsion_ns (cgexplore.terms.MartiniTorsionRange attribute) (cgexplore.terms.TargetTorsionRange attribute) TrianglePrecursor (class in cgexplore.molecular) try_except_construction() (in module cgexplore.scram) TwoC0Arm (class in cgexplore.molecular) TwoC1Arm (class in cgexplore.molecular) TwoC2Arm (class in cgexplore.molecular) TwoC3Arm (class in cgexplore.molecular) type1 (cgexplore.terms.MartiniAngleRange attribute) (cgexplore.terms.MartiniBondRange attribute) (cgexplore.terms.PyramidAngleRange attribute) (cgexplore.terms.TargetAngle attribute) (cgexplore.terms.TargetAngleRange attribute) (cgexplore.terms.TargetBond attribute) (cgexplore.terms.TargetBondRange attribute) (cgexplore.terms.TargetCosineAngle attribute) (cgexplore.terms.TargetCosineAngleRange attribute) (cgexplore.terms.TargetMartiniAngle attribute) (cgexplore.terms.TargetMartiniBond attribute) (cgexplore.terms.TargetPyramidAngle attribute) type2 (cgexplore.terms.MartiniAngleRange attribute) (cgexplore.terms.MartiniBondRange attribute) (cgexplore.terms.PyramidAngleRange attribute) (cgexplore.terms.TargetAngle attribute) (cgexplore.terms.TargetAngleRange attribute) (cgexplore.terms.TargetBond attribute) (cgexplore.terms.TargetBondRange attribute) (cgexplore.terms.TargetCosineAngle attribute) (cgexplore.terms.TargetCosineAngleRange attribute) (cgexplore.terms.TargetMartiniAngle attribute) (cgexplore.terms.TargetMartiniBond attribute) (cgexplore.terms.TargetPyramidAngle attribute) type3 (cgexplore.terms.MartiniAngleRange attribute) (cgexplore.terms.PyramidAngleRange attribute) (cgexplore.terms.TargetAngle attribute) (cgexplore.terms.TargetAngleRange attribute) (cgexplore.terms.TargetCosineAngle attribute) (cgexplore.terms.TargetCosineAngleRange attribute) (cgexplore.terms.TargetMartiniAngle attribute) (cgexplore.terms.TargetPyramidAngle attribute) U unaligned_vertex_prototypes (cgexplore.scram.TopologyIterator attribute) UnalignedM1L2 (class in cgexplore.topologies) V VaBene (class in cgexplore.molecular) VaBeneGenerator (class in cgexplore.molecular) vdw_bond_cutoff (cgexplore.forcefields.AssignedSystem attribute) (cgexplore.forcefields.MartiniSystem attribute) (cgexplore.systems_optimisation.Chromosome attribute) (cgexplore.systems_optimisation.ChromosomeGenerator attribute) vector() (cgexplore.terms.TargetAngle method) (cgexplore.terms.TargetBond method) (cgexplore.terms.TargetCosineAngle method) (cgexplore.terms.TargetNonbonded method) (cgexplore.terms.TargetPyramidAngle method) (cgexplore.terms.TargetTorsion method) vector_key() (cgexplore.terms.TargetAngle method) (cgexplore.terms.TargetBond method) (cgexplore.terms.TargetCosineAngle method) (cgexplore.terms.TargetNonbonded method) (cgexplore.terms.TargetPyramidAngle method) (cgexplore.terms.TargetTorsion method) verbose (cgexplore.scram.TopologyIterator attribute) vertex_dict (cgexplore.scram.VertexAlignment attribute) vertex_map (cgexplore.scram.TopologyCode attribute) vertex_prototypes (cgexplore.scram.TopologyIterator attribute) vertex_types_by_fg (cgexplore.scram.TopologyIterator attribute) VertexAlignment (class in cgexplore.scram) visualise() (cgexplore.utilities.Pymol method) visualise_host_guest() (cgexplore.utilities.Pymol method) W wall_1_shift (cgexplore.topologies.M4L82 attribute) (cgexplore.topologies.M6L122 attribute) (cgexplore.topologies.M8L162 attribute) wall_2_shift (cgexplore.topologies.M4L82 attribute) (cgexplore.topologies.M6L122 attribute) (cgexplore.topologies.M8L162 attribute) wall_3_shift (cgexplore.topologies.M6L122 attribute) (cgexplore.topologies.M8L162 attribute) wall_4_shift (cgexplore.topologies.M8L162 attribute) with_building_blocks() (cgexplore.topologies.CGM12L24 method) (cgexplore.topologies.CGM4L8 method) (cgexplore.topologies.M4L82 method) (cgexplore.topologies.M6L122 method) (cgexplore.topologies.M8L162 method) (cgexplore.topologies.UnalignedM1L2 method) write_chemiscope_json() (in module cgexplore.utilities) write_conformers_to_file() (cgexplore.molecular.Ensemble method) write_human_readable() (cgexplore.forcefields.ForceField method) (cgexplore.forcefields.MartiniForceField method) Y yield_angles() (cgexplore.terms.MartiniAngleRange method) (cgexplore.terms.PyramidAngleRange method) (cgexplore.terms.TargetAngleRange method) (cgexplore.terms.TargetCosineAngleRange method) yield_bonds() (cgexplore.terms.MartiniBondRange method) (cgexplore.terms.TargetBondRange method) yield_chromosomes() (cgexplore.systems_optimisation.ChromosomeGenerator method) yield_configured_codes() (cgexplore.scram.TopologyIterator method) yield_conformers() (cgexplore.molecular.Ensemble method) (cgexplore.optimisation.OMMTrajectory method) yield_forcefields() (cgexplore.forcefields.ForceFieldLibrary method) (cgexplore.forcefields.MartiniForceFieldLibrary method) yield_graphs() (cgexplore.scram.TopologyIterator method) yield_near_models() (in module cgexplore.systems_optimisation) (in module cgexplore.utilities) yield_nonbondeds() (cgexplore.terms.TargetNonbondedRange method) yield_shifted_models() (in module cgexplore.utilities) yield_torsions() (cgexplore.terms.MartiniTorsionRange method) (cgexplore.terms.TargetTorsionRange method)