Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
SBL Namespace Reference

[includes] More...

Namespaces

 Batch_manager
 
 Binding_affinity_utils
 
 CADS
 
 Colored_MISA
 
 Combinations_of_variables_model_evaluation
 
 Connectivity_inference_analysis
 
 Connectivity_inference_data_structures
 
 Connectivity_inference_engine
 
 CSB
 
 DB_hit_manager
 
 DB_manipulators
 
 Density_difference_based_clustering_commons
 
 EL_comparators
 
 EMD_comparators
 
 FunChat_hit_filters
 
 GT
 
 HMMER_Wrapper
 
 IO
 
 iRMSD
 
 lrmsd
 
 mci_serialize_pickle_xml
 
 mci_table
 
 mcibootstrap_iterative
 
 MinimumConnectivityInference
 
 MISA_ColorEngines
 
 Models
 
 Modules
 
 Molecular_cradle_step1
 
 Molecular_cradle_step2
 
 Molecular_cradle_step2_1
 
 Molecular_cradle_step2_selected
 
 Molecular_cradle_step3
 
 Molecular_cradle_utils_dendogram
 
 Molecular_cradle_utils_distance
 
 Molecular_cradle_utils_label_selection
 
 Molecular_distances_flexible-python
 
 Multiple_interface_string_alignment
 
 PALSE
 
 PDB_complex_to_unbound_partners_matchings
 
 Protein_complex_analysis_molecular_data_structures
 
 Rigid_blocks_sequence_analyzer
 
 Samples_2_generator
 
 SBL_Genetrank_application
 
 SBL_Genetrank_gene_radar_scatter_plot
 
 SBL_Genetrank_gene_to_protein
 
 SBL_Genetrank_network_statistical_analysis
 
 SBL_Genetrank_ppi_loader
 
 SBL_Genetrank_simulation
 
 SBL_Genetrank_simulation_statistics
 
 SBL_pytools
 
 Sequence_annotators
 
 Sequence_filters
 
 Space_filling_model_interface
 
 Spheres_d_generator
 
 Structural_motifs
 
 TG_builders
 
 TG_weights_from_normalized_boltzmann
 
 WL_ATM_plot
 

Typedefs

typedef double FT
 
typedef SBL::Models::T_Unit_system_traits_none_AKMA< FTUST_base
 
typedef SBL::Models::T_Unit_system_traits_for_potential_energy< UST_baseUnit_system_traits
 
typedef std::vector< FTConformation
 
typedef SBL::Models::T_Conformation_traits< ConformationConformation_traits
 
typedef SBL::Models::T_Conformations_file_loader< ConformationConformations_loader
 
typedef SBL::Models::T_Atom_with_hierarchical_info_traits Particle_traits
 
typedef SBL::CSB::T_Particle_info_for_proteins< Particle_traitsParticle_info
 
typedef SBL::CSB::T_Molecular_covalent_structure< Particle_infoCovalent_structure_base
 
typedef SBL::CSB::T_Molecular_covalent_structure_builder_for_proteins< Covalent_structure_baseCovalent_structure_builder
 
typedef SBL::IO::T_Molecular_covalent_structure_loader_from_PDB< Particle_traits, Covalent_structure_base, Covalent_structure_builderCovalent_structure_loader
 
typedef SBL::IO::T_Potential_energy_parameters< Covalent_structure_base, Unit_system_traits, FTPotential_energy_parameters_loader
 
typedef SBL::CSB::T_Molecular_potential_energy_structure_parameters_traits_optimal< Covalent_structure_base, Potential_energy_parameters_loaderStructure_parameters_traits
 
typedef Structure_parameters_traits::Covalent_structure Covalent_structure
 
typedef Structure_parameters_traits::Potential_energy_parameters Potential_energy_parameters
 
typedef Structure_parameters_traits::Build_structure_parameters Build_structure_parameters
 
typedef SBL::CSB::T_Bonded_particles_visitor< Covalent_structureBonds_visitor
 
typedef SBL::CSB::T_Bond_angles_visitor< Covalent_structureBond_angles_visitor
 
typedef SBL::CSB::T_Dihedral_angles_visitor< Covalent_structureProper_angles_visitor
 
typedef SBL::CSB::T_Unbonded_particles_with_threshold_visitor< Covalent_structure, ConformationNon_bonded_visitor
 
typedef SBL::CSB::T_Molecular_potential_energy_bonded_contribution< Conformation, Covalent_structure, Potential_energy_parametersBonded_contributions
 
typedef SBL::CSB::T_Molecular_potential_energy_Lennard_Jones_term< Conformation, Covalent_structure, Potential_energy_parametersLennard_Jones_term
 
typedef SBL::CSB::T_Molecular_potential_energy_electrostatic_term< Conformation, Covalent_structure, Potential_energy_parametersElectrostatic_term
 
typedef SBL::CSB::T_Molecular_potential_energy_bond_length_gradient_harmonic< Conformation, Covalent_structure, Potential_energy_parametersBond_length_gradient_term
 
typedef SBL::CSB::T_Molecular_potential_energy_bond_angle_gradient_harmonic< Conformation, Covalent_structure, Potential_energy_parametersBond_angle_gradient_term
 
typedef SBL::CSB::T_Molecular_potential_energy_torsion_angle_gradient_periodic< Conformation, Covalent_structure, Potential_energy_parametersTorsion_angle_gradient_term
 
typedef SBL::CSB::T_Molecular_potential_energy_Lennard_Jones_gradient< Conformation, Covalent_structure, Potential_energy_parametersLennard_Jones_gradient_term
 
typedef SBL::CSB::T_Molecular_potential_energy_electrostatic_gradient< Conformation, Covalent_structure, Potential_energy_parametersElectrostatic_gradient_term
 
typedef SBL::CSB::T_Molecular_potential_energy_contribution< Non_bonded_visitor, Lennard_Jones_term, Electrostatic_termNon_bonded_contributions
 
typedef SBL::CSB::T_Molecular_potential_energy_gradient_contribution< Bonds_visitor, Bond_length_gradient_termBond_length_gradient_contribution
 
typedef SBL::CSB::T_Molecular_potential_energy_gradient_contribution< Bond_angles_visitor, Bond_angle_gradient_termBond_angle_gradient_contribution
 
typedef SBL::CSB::T_Molecular_potential_energy_gradient_contribution< Proper_angles_visitor, Torsion_angle_gradient_termTorsion_angle_gradient_contribution
 
typedef SBL::CSB::T_Molecular_potential_energy_gradient_contribution< Non_bonded_visitor, Lennard_Jones_gradient_termLennard_Jones_gradient_contribution
 
typedef SBL::CSB::T_Molecular_potential_energy_gradient_contribution< Non_bonded_visitor, Electrostatic_gradient_termElectrostatic_gradient_contribution
 
typedef Electrostatic_gradient_contribution::Molar_energy_gradient_quantity Molar_energy_gradient_quantity
 
typedef SBL::CSB::T_Molecular_potential_energy< Bonded_contributions, Non_bonded_contributionsMolecular_potential_energy
 
typedef SBL::CSB::T_Molecular_potential_energy_numerical_gradient< Molecular_potential_energy, Potential_energy_parametersMolecular_potential_energy_numerical_gradient
 

Functions

def get_env (name)
 accessing env variable More...
 
def get_env_or_die (name)
 
def make_modules_path (directory)
 Loading all modules of SBL, if they were not installed. More...
 

Variables

def SBL_DIR = get_env("SBL_DIR")
 
string SBL_APPLICATIONS_DIR = "%s/Applications" % SBL_DIR
 
string SBL_CORE_DIR = "%s/Core" % SBL_DIR
 

Packages

[includes]

Typedef Documentation

◆ Bond_angle_gradient_contribution

◆ Bond_angle_gradient_term

◆ Bond_angles_visitor

◆ Bond_length_gradient_contribution

◆ Bond_length_gradient_term

◆ Bonded_contributions

◆ Bonds_visitor

◆ Build_structure_parameters

◆ Conformation

typedef std::vector<FT> Conformation

◆ Conformation_traits

◆ Conformations_loader

◆ Covalent_structure

◆ Covalent_structure_base

◆ Covalent_structure_builder

◆ Covalent_structure_loader

◆ Electrostatic_gradient_contribution

◆ Electrostatic_gradient_term

◆ Electrostatic_term

◆ FT

typedef double FT

◆ Lennard_Jones_gradient_contribution

◆ Lennard_Jones_gradient_term

◆ Lennard_Jones_term

◆ Molar_energy_gradient_quantity

typedef Electrostatic_gradient_contribution::Molar_energy_gradient_quantity Molar_energy_gradient_quantity

◆ Molecular_potential_energy

◆ Molecular_potential_energy_numerical_gradient

◆ Non_bonded_contributions

◆ Non_bonded_visitor

◆ Particle_info

◆ Particle_traits

◆ Potential_energy_parameters

◆ Potential_energy_parameters_loader

◆ Proper_angles_visitor

◆ Structure_parameters_traits

◆ Torsion_angle_gradient_contribution

◆ Torsion_angle_gradient_term

◆ Unit_system_traits

◆ UST_base

Function Documentation

◆ get_env()

def SBL.get_env (   name)

accessing env variable

◆ get_env_or_die()

def SBL.get_env_or_die (   name)

◆ make_modules_path()

def SBL.make_modules_path (   directory)

Loading all modules of SBL, if they were not installed.

Variable Documentation

◆ SBL_APPLICATIONS_DIR

string SBL_APPLICATIONS_DIR = "%s/Applications" % SBL_DIR

◆ SBL_CORE_DIR

string SBL_CORE_DIR = "%s/Core" % SBL_DIR

◆ SBL_DIR

def SBL_DIR = get_env("SBL_DIR")