Reference Manuals

Packages
	Alignment_engines
	Alpha_complex_of_molecular_model
	Alpha_complexes_extensions
	Apurva
	Batch_manager
	Betti_numbers
	Binding_affinity_prediction
	Buried_surface_area
	Cell_complex_shelling_diagram
	Cluster_engines
	Conformational_ensemble_analysis
	Conformational_ensemble_comparison
	ConformationMoveset
	Connectivity_inference
	Correlated_motions_by_domain
	D_family_matching
	DB_manipulator
	Density_difference_based_clustering
	Dijkstra_shortest_paths_with_landmarks
	Directed_acyclic_graph
	Earth_mover_distance
	Energy_landscape_analysis
	Energy_landscape_comparison
	Frechet_mean_S1
	FunChaT
	Genetrank
	Greedy_selection
	Hamiltonian_Monte_Carlo
	HMMER_Wrapper
	Iterative_alignment
	Kpax
	Landscape_explorer
	Maximum_clique
	Minimal_oriented_spanning_forest
	Module_base
	Molecular_conformation
	Molecular_coordinates
	Molecular_covalent_structure
	Molecular_cradle
	Molecular_distances
	Molecular_distances_flexible
	Molecular_geometric_model_classifier
	Molecular_interfaces
	Molecular_potential_energy
	Molecular_structure_classifier
	Molecular_system
	Molecular_viewers
	Viewer writing in VMD file format.
	MolecularGeometryLoader
	MolecularSystemLabelsTraits
	Morse_Smale_Witten_chain_complex
	Morse_theory_based_analyzer
	Multiple_archives_serialization
	Multiple_interface_string_alignment
	inspired from https://biopython3.org/DIST/docs/api/Bio.PDB.Dice-pysrc.html#ChainSelector To filter the atoms from the new .pdb file
	Nearest_neighbors_graph_builder
	Ordered_forest_edit_distance
	PALSE
	ParticleAnnotator
	ParticleTraits
	Point_cloud_rigid_registration_3
	Pointwise_interactions
	Product_graph
	Protein_representation
	Protein_sequence_annotator
	Random_generation
	Real_value_function_minimizer
	Rotation_3
	Space_filling_model_coarse_graining
	Space_filling_model_interface
	Space_filling_model_interface_finder
	Space_filling_model_shelling_diagram_comparison
	Space_filling_model_shelling_diagram_surface_encoding
	Space_filling_model_surface_volume
	Spatial_search
	Specialized_iterators
	Spectral_domain_explorer
	Spherical_kernel_extension_3
	Structural_motifs
	Tertiary_quaternary_structure_annotator
	Transition_graph_of_energy_landscape_builders
	Transition_graph_traits
	Compressed means that vertices are the minima and edges are the transitions.
	Triangulations_extensions_3
	Tripeptide_loop_closure
	Union_find
	Union_of_balls_boundary_3
	Union_of_balls_boundary_patch_shelling_3
	Union_of_balls_medial_axis_3
	Union_of_balls_mesh_3
	Union_of_balls_surface_volume_3
	UnitSystemTraits
	Wang_Landau

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