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Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
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Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
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| ►Reference Manuals | |
| Alignment_engines | |
| Alpha_complex_of_molecular_model | |
| Alpha_complexes_extensions | |
| Apurva | |
| ►Batch_manager | |
| 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 |
| Betti_numbers | |
| Binding_affinity_prediction | |
| Buried_surface_area | |
| Cell_complex_shelling_diagram | |
| Cluster_engines | |
| Conformational_ensemble_analysis | |
| Conformational_ensemble_comparison | |
| ConformationMoveset | |
| ConformationTraits | |
| 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 | |
| Landscape_explorer | |
| Maximum_clique | |
| Minimal_oriented_spanning_forest | |
| Module_base | |
| 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_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 | |
| 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 | |
| ►Models | Models are instantiations of concepts |
| 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. Malod-Dognin |
| 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. Malod-Dognin |
| 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 Union-Find 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 |
| Frechet_mean_S1 | Computing Frechet mean and p means for points on the unit circle Reference Manual – User Manual . Authors: F. Cazals and T. O'Donnell |
| Hamiltonian_Monte_Carlo | Here you should put an abstract of your package Reference Manual – User Manual . Authors: F. Cazals and A. Chevallier and S. Pion |
| 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 |
| Rotation_3 | Here you should put an abstract of your package Reference Manual – User Manual . Authors: F. Cazals and T.O'Donnell |
| 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 medial-axis 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 |
| Wang_Landau | A generic implementation of the Wang-Landau algorithm Reference Manual – User Manual . Authors: A. Chevallier and F. Cazals |
| ►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. Malod-Dognin 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 |
| DB_manipulator | A package providing methods to ease the access to various protein related databases Reference Manual – User Manual . Authors: R. Tetley and F. Cazals |
| HMMER_Wrapper | A python wrapper for HMMER Reference Manual – User Manual . Authors: R. Tetley and F. Cazals |
| Iterative_alignment | A generic algorithm performing rounds of dynamic programming alignment and rigid superposition until a final structural alignment is reached. Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus and R. Tetley |
| Molecular_coordinates | Conversion between coordinate systems for a molecule Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus and T. O'Donnell |
| Molecular_covalent_structure | Representation of the topology of a molecule Reference Manual – User Manual . Authors: F. Cazals and A. Chevallier 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 |
| Protein_representation | A package providing classes to easily access all pieces of information attached to proteins. Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus and R. Tetley |
| Protein_sequence_annotator | A package providing methods to annotate protein sequences Reference Manual – User Manual . Authors: R. Tetley and F. Cazals |
| 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 |
| Tripeptide_loop_closure | Here you should put an abstract of your package Reference Manual – User Manual . Authors: F. Cazals and T.O'Donnell |
| 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 macro-molecular assembly, at atomic or coarse grain resolution. The interface particles are reported, together with a number of geometric, topological and bio-physical 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. Malod-Dognin |
| 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 core-rim 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 |
| Correlated_motions_by_domain | Correlation analsysis between rigid motions undergone by protein domains Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus |
| 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 |
| Molecular_distances_flexible | This package provides methods to compute combined RMSD on user defined protein sub-domains introducing a notion of flexibility. Reference Manual – User Manual . Authors: F. Cazals and R. Tetley |
| Structural_motifs | A package providing methods to locate structural motifs shard by two structures Reference Manual – User Manual . Authors: F. Cazals and R. Tetley |
| 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. Malod-Dognin |
| 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 Two-sample-tests: Localizing Data Discrepancies in High-dimensional Spaces Reference Manual – User Manual . Authors: A. Lheritier and F. Cazals |
| ►Assemblies | Applications dealing with macro-molecular 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 |
| FunChaT | A package to build biased HMMs by exploiting the results of Structural motifs. Reference Manual – User Manual . Authors: R. Tetley and F. Cazals |
| Genetrank | Gene ranking based on random walk with restarts in Protein Protein Interaction Networks Reference Manual – User Manual . Authors: F. Cazals and A. Jean-Marie and D. Mazauric and J. Roux and G. Sales Santa Cruz |
| Molecular_cradle | A package to identify almost rigid regions in complex biomolecules Reference Manual – User Manual . Authors: M. Simsir and F. Cazals |
| Multiple_interface_string_alignment | MISA provide a coloring of interface strings ie amino acids found at interfaces with various biological and biophysical quantities. Reference Manual – User Manual . Authors: S. Bereux and F. Cazals |
1.9.1