Applications

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.

Description

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-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.