▼Reference Manuals  
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  
ConformationTraits  
Connectivity_inference  
D_family_matching  
Density_difference_based_clustering  
Dijkstra_shortest_paths_with_landmarks  
Directed_acyclic_graph  
Earth_mover_distance  
Energy_landscape_analysis  
Energy_landscape_comparison  
Greedy_selection  
Landscape_explorer  
Maximum_clique  
Minimal_oriented_spanning_forest  
Module_base  
Molecular_coordinates  
Molecular_covalent_structure  
Molecular_distances  
Molecular_geometric_model_classifier  
Molecular_interfaces  
Molecular_potential_energy  
Molecular_structure_classifier  
Molecular_viewers  Viewer writing in VMD file format 
MolecularGeometryLoader  
MolecularSystemLabelsTraits  
Morse_Smale_Witten_chain_complex  
Morse_theory_based_analyzer  
Multiple_archives_serialization  
Nearest_neighbors_graph_builder  
Ordered_forest_edit_distance  
PALSE  
ParticleAnnotator  
ParticleTraits  
Point_cloud_rigid_registration_3  
Pointwise_interactions  
Product_graph  
Random_generation  
Real_value_function_minimizer  
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  
Spherical_kernel_extension_3  
Tertiary_quaternary_structure_annotator  
Transition_graph_of_energy_landscape_builders  
Transition_graph_traits  
Triangulations_extensions_3  
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  
▼Models  
ConformationMoveset  This package provides different methods for extending a conformation to a new one
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus and C. Roth

ConformationTraits  Concept defining geometric (and possibly biophysical) properties of a conformation.
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus and C. Roth

MolecularGeometryLoader  Concept defining how to load a molecular geometric model from a file.
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus

MolecularSystemLabelsTraits  Concept defining labels to identify particles in a molecular system associated to a molecular structure
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus

ParticleAnnotator  Concept defining how to decorate particles with supplemental information.
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus

ParticleTraits  Concept defining geometric (and possibly biophysical) properties of a particle.
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus

UnitSystemTraits  Concept defining types and constants for physical unit systems
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus

▼Modules  Modules framework for defining a workflow for the applications 
Module_base  Framework for building generic blocks of algorithms and generic workflows for applications.
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus

▼Core  Generic algorithms of the SBL library 
►CADS  Combinatorial Algorithms and Data Structures 
Cell_complex_shelling_diagram  Under Construction.
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus

D_family_matching  Computing matchings between clusters of clusters with diameter constraints.
Reference Manual – User Manual . Authors: R. Tetley and F. Cazals and D. Mazauric

Dijkstra_shortest_paths_with_landmarks  Under Construction.
Reference Manual – User Manual . Authors: F. Cazals and T.Dreyfus and A. Lheritier

Directed_acyclic_graph  Data structure representing a Directed Acyclic Graph (DAG)
Reference Manual – User Manual . Authors: F. Cazals and T.Dreyfus

Earth_mover_distance  Earth mover distance solver
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus and D. Mazauric

Greedy_selection  Algorithms for a greedy selection of arrangements of cells minimizing their overlaps.
Reference Manual – User Manual . Authors: F. Cazals and T.Dreyfus

Maximum_clique  Algorithm computing a maximum clique of an input graph.
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus and N. MalodDognin

Minimal_oriented_spanning_forest  Algorithm for computing the Minimal Spanning Forest of a graph.
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus and D. Mazauric

Ordered_forest_edit_distance  Algorithm computing the distance between two graphs by morphing the source graph to the target graph.
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus and N. MalodDognin

Product_graph  Data structures for building the product graph of two input graphs
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus

Specialized_iterators  Iterators over different kind of containers
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus

Union_find  Enriched UnionFind data structure for maintaining the number of connected components of a set of data
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus

►GT  Geometry and Topology 
Alpha_complexes_extensions  Data structures and algorithms enriching the complex data structure of CGAL
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus

Betti_numbers  Algorithms for computing Betti numbers from graphs and complex
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus

Cluster_engines  A package providing classical clustering algorithms within a unified framework
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus

Morse_Smale_Witten_chain_complex  Data structure and algorithms for building the Morse Smale Witten Chain Complex from an elevated graph
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus and C. Roth

Morse_theory_based_analyzer  Algorithms for analyzing an elevated graph using Morse theory tools
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus and C. Roth

Nearest_neighbors_graph_builder  Algorithms building Nearest Neighbor Graphs (NNG) using spatial search engines.
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus and C. Roth

Point_cloud_rigid_registration_3  Algorithm superimposing two 3D points' clouds by rotating and translating them.
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus

Spatial_search  Data structures and algorithms to search the nearest neighbors of an input point in a data base of points.
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus

Spherical_kernel_extension_3  Supplemental predicates and constructions for the CGAL Spherical_kernel_3
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus

Triangulations_extensions_3  Data structures and algorithms enriching the 3D Triangulations of CGAL
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus

Union_of_balls_boundary_3  Data structure and algorithms to compute the boundary of the union of 3D balls.
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus

Union_of_balls_boundary_patch_shelling_3  Data structure and algorithm to compute the depth of 3D balls in a patch at the surface of the union of 3D balls.
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus

Union_of_balls_medial_axis_3  Data structure and algorithm to compute the medialaxis of the union of a family of 3D balls.
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus

Union_of_balls_mesh_3  Algorithm for meshing and sampling the boundary of the union of a family of 3D balls
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus

Union_of_balls_surface_volume_3  Data structure and algorithm to compute the surface area and the volume of the union of a family of 3D balls.
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus and S. Loriot

►CSB  Computational Structural Biology 
Alignment_engines  Engines performing alignments of sequences or structures
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus and S. Marillet and R. Tetley

Alpha_complex_of_molecular_model  3D weighted complex from the CGAL library where vertices have an attached particle
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus

Apurva  Structural alignment ...
Reference Manual – User Manual . Authors: N. MalodDognin and R. Andonov

Buried_surface_area  Algorithm for computing the surface area of a molecule buried in another molecule
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus

Molecular_coordinates  Conversion between coordinate systems for a molecule
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus

Molecular_covalent_structure  Representation of the topology of a molecule
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus

Molecular_distances  Algorithms computing different kind of distances between molecular conformations.
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus

Molecular_geometric_model_classifier  Data structure classifying the contacts between atoms of a molecular geometric model.
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus

Molecular_interfaces  Data structures and algorithms for computing the interface patches between different partners in a molecule
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus

Molecular_potential_energy  Computation of the potential energy of a molecule
Reference Manual – User Manual . Authors: F. Cazals and A. Chevallier and T. Dreyfus

Molecular_structure_classifier  Data structure classifying contacts between atoms of different partners in a molecule
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus

Pointwise_interactions  A package to report pointwise interactions from atomic data
Reference Manual – User Manual . Authors: F. Cazals and R. Tetley

Real_value_function_minimizer  Under Construction
Reference Manual – User Manual . Authors: A. Roth and F. Cazals and T. Dreyfus

Tertiary_quaternary_structure_annotator  A package to annotate contacts within tertiary and quaternary structures
Reference Manual – User Manual . Authors: F. Cazals and and T. Dreyfus and R. Tetley

Transition_graph_traits  Under Construction
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus

STATS  Statistics 
►IO  Input / Output 
Molecular_viewers  Data structures and framework for writing visualization files for molecular softwares
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus

Multiple_archives_serialization  Boost based framework for serializing a data structure over multiple files.
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus

▼Applications  This page lists all program programs of the SBL library. These programs are either applications, or short programs associated with packages from the Core 
►Space Filling Model  Applications dealing with molecular geometric models defined by union of balls 
Space_filling_model_coarse_graining  Space_filling_model_coarse_graining is a package of applications proposing various volume based geometric approximation schemes to coarse grain molecular models defined by unions of balls.
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus

Space_filling_model_interface  Space_filling_model_interface is a package of applications to model interfaces within a macromolecular assembly, at atomic or coarse grain resolution. The interface particles are reported, together with a number of geometric, topological and biophysical statistics describing the interfaces.
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus

Space_filling_model_interface_finder  Space_filling_model_interface is a package proposing algorithms to automatically identify all the interfaces present in a molecular structure. Interfaces may be sought between different chains or between regions of different chains. The interface identified by Space_filling_model_interface_finder may be further analyzed with applications of the package Space_filling_model_interface.
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus

Space_filling_model_shelling_diagram_comparison  Space_filling_model_shelling_diagram_comparison is a package of applications focusing on the comparison of binding patches as computed in Space_filling_model_shelling_diagram_surface_encoding. In particular, the binding patches may be compared from a geometric of topological standpoint, the latter being more lenient than the former.
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus and N. MalodDognin

Space_filling_model_shelling_diagram_surface_encoding  Consider a binding patch i.e.. the atoms of a complex directly in contact with a partner. Space_filling_model_shelling_diagram_surface_encoding is a package providing several encodings of a binding patch, and notably the atom shelling tree, which generalizes corerim models. Binding patches can be compared using the applications of Space_filling_model_shelling_diagram_comparison.
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus

Space_filling_model_surface_volume  Space_filling_model_surface_volume is a package of applications providing numerically certified estimates of the surface area and of the volume of a model defined by a collection of balls, e.g. a van der Waals or solvent accessible model.
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus and S. Loriot

►Conformational Analysis  Applications dealing with molecular flexibility 
Conformational_ensemble_analysis  This package provides methods to assess the conformational diversity of an ensemble of conformations.
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus and C. Roth

Conformational_ensemble_comparison  This package provides methods to compare, from a geometric/structural standpoint, two ensembles of conformations.
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus and C. Roth

Energy_landscape_analysis  This package provides various methods to analyze sampled energy landscapes, with in particular various statistics on its transition and connectivity graphs.
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus and C. Roth

Energy_landscape_comparison  This package package provides method to perform various comparisons of two samples energy landscapes, taking into account the location of local minima, their occupancy probabilities, and possible their connections as encoded in a transition graph.
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus and D. Mazauric

Landscape_explorer  This package provides sampling algorithms for energy landscapes, in the Monte Carlo realm, namely, basin hopping, rapidly expanding random trees, and hybrid algorithms mixing the previous two algorithms.
Reference Manual – User Manual . Authors: F.Cazals and T. Dreyfus and C. Robert and A. Roth

Transition_graph_of_energy_landscape_builders  This package provides methods to build transition graphs, i.e. graphs connecting local minima of an energy landscape, across index one saddles.
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus and C. Roth

►Data Management  Applications used to handle input data and results 
Batch_manager  This package provides tools to automate the execution of a given program on a collection of datasets, while varying parameters.
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus

PALSE  PALSE is a python package providing tools for parsing XML files sharing the same structure. PALSE relies on the XPath query language. Using PALSE, plots and statistics are a few lines of python code away once the results have been generated.
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus and A. Lheritier and N. MalodDognin

Random_generation  Here you should put an abstract of your package
Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus

►Data Analysis  Applications used to perform analysis on various data 
Density_difference_based_clustering  Beyond Twosampletests: Localizing Data Discrepancies in Highdimensional Spaces
Reference Manual – User Manual . Authors: A. Lheritier and F. Cazals

►Assemblies  Applications dealing with macromolecular assemblies 
Connectivity_inference  Connectivity_inference is a package providing programs enumerating the possible pairwise subunits interactions within an assembly from oligomers of this assembly
Reference Manual – User Manual . Authors: D. Agarwal and C. Caillouet and F. Cazals and D. Coudert

►Integrated Analysis  Applications combining several ingredients from the previous groups 
Binding_affinity_prediction  Binding_affinity_prediction is package implementing a complete workflow to predict affinities from geometrical and biophysical parameters using bound and unbound crystallographic structures. It generates and evaluates linear models using various combinations of these parameters and selects the most accurate ones.
Reference Manual – User Manual . Authors: S. Marillet and P. Boudinot and F. Cazals
