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Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
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Packages | |
Space Filling Model | |
Applications dealing with molecular geometric models defined by union of balls. | |
Conformational Analysis | |
Applications dealing with molecular flexibility. | |
Data Management | |
Applications used to handle input data and results. | |
Data Analysis | |
Applications used to perform analysis on various data. | |
Assemblies | |
Applications dealing with macro-molecular assemblies. | |
Integrated Analysis | |
Applications combining several ingredients from the previous groups. | |
This page lists all program programs of the SBL library. These programs are either applications, or short programs associated with packages from the Core.
– sbl-tg-builder-lrmsd.exe : Build a transition graph from conformational ensembles or from database of conformations (Transition_graph_of_energy_landscape_builders)
– sbl-tg-builder-euclid.exe : Build a transition graph from conformational ensembles or from database of conformations (Transition_graph_of_energy_landscape_builders)
– sbl-vorlume-txt.exe : Computes the volume of a molecular complex from a txt file listing 3D spheres (Space_filling_model_surface_volume)
– sbl-vorlume-pdb.exe : Computes the volume of a molecular complex from a PDB file (Space_filling_model_surface_volume)
– sbl-vorshell-bp-IGAgW-atomic.exe : Compute the Atom Shelling Trees of atoms at a IG-Ag molecular interface (Space_filling_model_shelling_diagram_surface_encoding)
– sbl-vorshell-bp-ABW-atomic.exe : Compute the Atom Shelling Trees of atoms at a binary molecular interface (Space_filling_model_shelling_diagram_surface_encoding)
– sbl-compatch.exe : Compare two Atom Shelling Trees of atoms at a binary molecular interface (Space_filling_model_shelling_diagram_comparison)
– sbl-bif-domainsW-atomic.exe : List all binary interfaces in an input molecular complex induced by loaded labels from an input file (Space_filling_model_interface_finder)
– sbl-bif-chainsW-atomic.exe : List all water mediated binary interfaces between chains of an input molecular complex (Space_filling_model_interface_finder)
– sbl-intervor-IGAgW-coarse-grain-one-per-residue.exe : Provide statistics on a coarse grained water mediated IG-Ag molecular interface (2 particles per residue) (Space_filling_model_interface)
– sbl-intervor-IGAgW-coarse-grain-one-per-residue.exe : Provide statistics on a coarse grained water mediated IG-Ag molecular interface (1 particle per residue) (Space_filling_model_interface)
– sbl-intervor-IGAgW-atomic.exe : Provide statistics on a water mediated IG-Ag molecular interface (Space_filling_model_interface)
– sbl-intervor-domainsW-atomic.exe : Provide statistics on molecular interfaces with loaded labels from a file (Space_filling_model_interface)
– sbl-intervor-ABW-coarse-grain-two-per-residue.exe : Provide statistics on a coarse grained water mediated binary molecular interface (2 particles per residue) (Space_filling_model_interface)
– sbl-intervor-ABW-coarse-grain-one-per-residue.exe : Provide statistics on a coarse grained water mediated binary molecular interface (1 particle per residue) (Space_filling_model_interface)
– sbl-intervor-ABW-atomic.exe : Provide statistics on an atomic water mediated binary molecular interface (Space_filling_model_interface)
– sbl-ballcovor-txt.exe : Coarse grain model of a list of input spheres in a plain txt file (Space_filling_model_coarse_graining)
– sbl-ballcovor-pdb-U.exe : Coarse grain model of a molecule from an input PDB file (Uniform version) (Space_filling_model_coarse_graining)
– sbl-ballcovor-pdb-C.exe : Coarse grain model of a molecule from an input PDB file (Constrained version) (Space_filling_model_coarse_graining)
– sbl-ballcovor-pdb-A.exe : Coarse grain model of a molecule from an input PDB file (Amino Acids version) (Space_filling_model_coarse_graining)
– sbl-protein-ramachandran.exe : Loads one or more PDB file(s) and prints the Ramachandran plot following the target strategy (Protein_representation)
– sbl-protein-info.exe : Loads a PDB file and prints a number of statistics about the loaded polypetidic chains (Protein_representation)
– sbl-lrmsd-all-against-one.exe : Compute the rigid registration of all conformations in the second set against the first conformation in the first set (Point_cloud_rigid_registration_3)
– sbl-Morse-theory-based-analyzer-wg.exe : Computes the watershed transform of an ensemble of d-dimensional points embedded in an edge weighted graph (Morse_Smale_Witten_chain_complex)
– sbl-Morse-theory-based-analyzer-vwg.exe : Computes the watershed transform of an ensemble of d-dimensional points embedded in a vertex weighted graph (Morse_Smale_Witten_chain_complex)
– sbl-Morse-theory-based-analyzer-nng-euclid.exe : Computes the watershed transform of an ensemble elevated of d-dimensional points embedded in a NNG, with an euclidean distance between the points (Morse_Smale_Witten_chain_complex)
– sbl-Morse-theory-based-analyzer-nng-euclid-density-gauss.exe : Computes the watershed transform of an ensemble of d-dimensional points embedded in a NNG, with an euclidean distance between the points, and a height corresponding to a local density (Morse_Smale_Witten_chain_complex)
– sbl-Morse-theory-based-analyzer-nng-angular-density-neighbors.exe : Computes the watershed transform of an ensemble of d-dimensional points embedded in a NNG, with an angular distance between the points, and a height corresponding to a local density (Morse_Smale_Witten_chain_complex)
– sbl-energy-charmm.exe : Computes the potential energy of a list of conformations using the CHARMM force field (Molecular_potential_energy)
– sbl-energy-BLN.exe : Computes the potential energy of a list of conformations using the BLN force field (Molecular_potential_energy)
– sbl-energy-amber.exe : Computes the potential energy of a list of conformations using the Amber force field (Molecular_potential_energy)
– sbl-rmsd-flexible-proteins-kpax.exe : Given a set of homologous proteins and a sub-domain specification computes the combined RMSD between structures aligned with Kpax (Molecular_distances_flexible)
– sbl-rmsd-flexible-proteins-apurva.exe : Given a set of homologous proteins and a sub-domain specification computes the combined RMSD between structures aligned with Apurva (Molecular_distances_flexible)
– sbl-rmsd-flexible-motifs.exe : Given two polypeptide chains as well as a set of motifs computes the combined RMSD (Molecular_distances_flexible)
– sbl-rmsd-flexible-conformations.exe : Given a set of conformations of the same protein and a sub-domain specification computes the combined RMSD (Molecular_distances_flexible)
– sbl-lrmsd-conformational-ensembles-intersection.exe : Compute the symmetric difference of two sets of conformations using the l-RMSD distance between the conformations (Molecular_distances)
– sbl-lrmsd-conformational-ensembles-centroid-per-atom.exe : Compute the centroid of the input list of conformations (input is one plain txt file) (Molecular_distances)
– sbl-lrmsd-all-pairs.exe : Compute the l-RMSD distance between all pairs of conformations (input is one plain txt file) (Molecular_distances)
– sbl-lrmsd-all-against-one.exe : Compute the l-RMSD distance between the first conformation and all other ones (input is one plain txt file) (Molecular_distances)
– sbl-coordinates-file-converter.exe : Convert molecular geometry files such as PDB or XTC files into point-D file format (Molecular_coordinates)
– sbl-cartesian-internal-converter.exe : Create (Molecular_coordinates)
– sbl-landexp-TRRT-trigo-terrain.exe : Landscape exploration of an arbitrary complex function using TRRT algorithm (Landscape_explorer)
– sbl-landexp-TRRT-Rastrigin.exe : Landscape exploration of Rastrigin function using TRRT algorithm (Landscape_explorer)
– sbl-landexp-TRRT-BLN.exe : Landscape exploration of BLN69 using TRRT algorithm with the lRMSD (Landscape_explorer)
– sbl-landexp-TRRT-atomic.exe : Landscape exploration of small peptides over atomic force fields using TRRT algorithm, with the lRMSD (Landscape_explorer)
– sbl-landexp-stratified-TRRT-BLN.exe : Landscape exploration of BLN69 using stratified TRRT algorithm with the lRMSD (Landscape_explorer)
– sbl-landexp-hybrid-BH-TRRT-trigo-terrain.exe : Landscape exploration of an arbitrary complex function using hybrid algorithm with basins hopping and TTRT with quench, with the Euclidean distance (Landscape_explorer)
– sbl-landexp-hybrid-BH-TRRT-Rastrigin.exe : Landscape exploration of Rastrigin function using hybrid algorithm with basins hopping and TTRT with quench, with the Euclidean distance (Landscape_explorer)
– sbl-landexp-hybrid-BH-TRRT-BLN.exe : Landscape exploration of BLN69 using hybrid algorithm with basins hopping and TTRT with quench, with the lRMSD (Landscape_explorer)
– sbl-landexp-hybrid-BH-TRRT-atomic.exe : Landscape exploration of small peptides over atomic force fields using basins hopping / TRRT hybrid algorithm, with the lRMSD (Landscape_explorer)
– sbl-landexp-hybrid-BH-TRRT-BLN-filter.exe : Landscape exploration of BLN69 using hybrid algorithm with basins hopping and TTRT with quench, with the lRMSD, and additional filters on energy (Landscape_explorer)
– sbl-landexp-BH-trigo-terrain.exe : Landscape exploration of an arbitrary complex function using basins hopping algorithm, with the Euclidean distance (Landscape_explorer)
– sbl-landexp-BH-Rastrigin.exe : Landscape exploration of Rastrigin function using basins hopping algorithm, with the Euclidean distance (Landscape_explorer)
– sbl-landexp-BH-BLN.exe : Landscape exploration of BLN69 using basins hopping algorithm, with the lRMSD (Landscape_explorer)
– sbl-landexp-BH-atomic.exe : Landscape exploration of small peptides over atomic force fields using BH algorithm, with the lRMSD (Landscape_explorer)
– sbl-iterative-alignment-kpax.exe : An instantiation of the generic iterative structural alignment into the Kpax algorithm exploiting the K-score for seeding and the G-score for the iterations (Iterative_alignment)
– sbl-Frechet-mean-using-real-value-NT.exe : Compute p mean of set of 1D angular values (Frechet_mean_S1)
– sbl-Frechet-mean-using-interval-NT.exe : Compute p mean of set of 1D angular values (Frechet_mean_S1)
– sbl-cenergy-landscape-comparison-lrmsd.exe : Compare two transition graphs using eath mover distance algorithms with lRMSD metric (Energy_landscape_comparison)
– sbl-cenergy-landscape-comparison-euclid.exe : Compare two transition graphs using eath mover distance algorithms with Euclidean distance metric (Energy_landscape_comparison)
– sbl-cenergy-landscape-analysis-lrmsd.exe : Analyse the transition graph of an elevated sampled energy landscape using lRMSD metric (Energy_landscape_analysis)
– sbl-landexp-graph-star.exe : This executable allows one to select/extract/perform statistics on the star of a vertex in a weighted graph. (Landscape_explorer)
– sbl-cenergy-landscape-analysis-euclid.exe : Analyse the transition graph of an elevated sampled energy landscape using Euclidean distance metric (Energy_landscape_analysis)
– sbl-emd-wp-lrmsd.exe : Earth Mover Distance solver for weighted points using LRMSD metric (Earth_mover_distance)
– sbl-emd-wp-euclid.exe : Earth Mover Distance solver for weighted points using Euclidean metric (Earth_mover_distance)
– sbl-emd-tg-lrmsd.exe : Earth Mover Distance solver for transition graphs using lRMSD metric (Earth_mover_distance)
– sbl-emd-tg-euclid.exe : Earth Mover Distance solver for transition graphs using Euclidean metric (Earth_mover_distance)
– sbl-emd-sequences.exe : Earth Mover Distance solver for aligned sequences (Earth_mover_distance)
– sbl-emd-graph-lrmsd.exe : Earth Mover Distance solver for weighted points in a graph using LRMSD metric (Earth_mover_distance)
– sbl-emd-graph-euclid.exe : Earth Mover Distance solver for weighted points in a graph using Euclidean metric (Earth_mover_distance)
– sbl-cmp-clust-VI.exe : An executable which computes the variation of information to compare two clusterings of the same set (D_family_matching)
– sbl-cmp-clust-dfam.exe : An executable to compute the so called D-family matching to compare two clusterings of the same set (D_family_matching)
– sbl-comodo-domainsW-atomic.exe : Analyze the correlation between identical domains of two conformations of the same protein, or homologous domains of two different proteins (Correlated_motions_by_domain)
– sbl-conf-ensemble-comparison-lrmsd.exe : Compare two conformational ensemble with different methods (Conformational_ensemble_comparison)
– sbl-conf-ensemble-comparison-euclid.exe : Compare two conformational ensemble with different methods (Conformational_ensemble_comparison)
– sbl-conf-ensemble-analysis-lrmsd.exe : Make analysis over a conformation ensemble embedded in a metric space, and elevated by adensity function (Conformational_ensemble_analysis)
– sbl-conf-ensemble-analysis-euclid.exe : Make analysis over a conformation ensemble embedded in a metric space, and elevated by adensity function (Conformational_ensemble_analysis)
– sbl-cluster-MTB-euclid.exe : Computes a clustering of an input set of points in Euclidean space using Morse theory based algorithm (Cluster_engines)
– sbl-cluster-k-means-euclid.exe : Computes a clustering of an input set of points in Euclidean space using k-means algorithm (Cluster_engines)
– sbl-match-PDB-residues-and-atoms.exe : Matches two sequences of residues, then matches the atoms of each matched residues (Alignment_engines)
– test.exe : reproduce experiments from paper (Frechet_mean_S1)
– sbl-apurva.exe : Structural alignment based on a combinatorial / geometricx approach (Apurva)
Applications are targeting specific biophysical - structural bioinformatics problems.