Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
Molecular_potential_energy

Classes

class  T_AD_buffer< Dummy >
 Todo. More...
 
class  T_AD_stack< Dummy >
 Todo. More...
 
class  T_Phi_psi_dihedral_angles_visitor< CovalentStructure >
 Defines iterator over all successive pairs of dihedrals. More...
 
class  T_Unbonded_particles_visitor< CovalentStructure >
 Defines iterator over all distinct pairs of particles. More...
 
class  T_Unbonded_particles_with_threshold_visitor< CovalentStructure, ConformationType >
 Defines iterator over all distinct pairs of particles. More...
 
class  T_Bonded_particles_visitor< CovalentStructure >
 Defines iterator over the bonds of a covalent structure. More...
 
class  T_Bond_angles_visitor< CovalentStructure >
 Defines iterator over the bond angles of a covalent structure. More...
 
class  T_Dihedral_angles_visitor< CovalentStructure >
 Defines iterator over the dihedral angles of a covalent structure. More...
 
class  T_Improper_angles_visitor< CovalentStructure >
 Defines iterator over the improper angles of a covalent structure. More...
 
class  T_Molecular_potential_energy_bond_length_term_harmonic< ConformationType, CovalentStructure, PotentialEnergyParameters >
 Defines the standard term associated to the bond length contribution. More...
 
class  T_Molecular_potential_energy_bond_angle_term_harmonic< ConformationType, CovalentStructure, PotentialEnergyParameters >
 Defines the standard term associated to the bond angle contribution. More...
 
class  T_Molecular_potential_energy_bond_angle_term_Urey_Bradley< ConformationType, CovalentStructure, PotentialEnergyParameters >
 Defines the Urey-Bradley term associated to a bond angle. More...
 
class  T_Molecular_potential_energy_torsion_angle_term_harmonic< ConformationType, CovalentStructure, PotentialEnergyParameters >
 Defines the harmonic term associated to the proper dihedral angle contribution. More...
 
class  T_Molecular_potential_energy_torsion_angle_term_periodic< ConformationType, CovalentStructure, PotentialEnergyParameters >
 Defines the periodic term associated to the proper dihedral angle contribution. More...
 
class  T_Molecular_potential_energy_torsion_angle_term_Fourier< ConformationType, CovalentStructure, PotentialEnergyParameters >
 Defines the Fourier term associated to the proper dihedral angle contribution. More...
 
class  T_Molecular_potential_energy_torsion_angle_term_Ryckaert_Bellemans< ConformationType, CovalentStructure, PotentialEnergyParameters >
 Defines the Ryckaert_Bellemans term associated to the proper dihedral angle contribution. More...
 
class  T_Molecular_potential_energy_cmap_term< ConformationType, CovalentStructure, PotentialEnergyParameters >
 Defines the CMap term associated to a pair of proper dihedral angles. More...
 
class  T_Molecular_potential_energy_Lennard_Jones_term< ConformationType, CovalentStructure, PotentialEnergyParameters >
 Defines the standard term associated to the Lennard Jones contribution. More...
 
class  T_Molecular_potential_energy_electrostatic_term< ConformationType, CovalentStructure, PotentialEnergyParameters >
 Defines a standard term associated to the electrostatic contribution. More...
 
class  T_Molecular_potential_energy_contribution< Visitor, Term, Terms >
 Contribution of an energy term to the potential energy function. More...
 
class  T_Molecular_potential_energy_bonded_contribution< ConformationType, CovalentStructure, PotentialEnergyParameters, EnergyBondedLengthsTerm, EnergyBondAnglesTerm, EnergyDihedralAnglesTerm >
 Contribution of all bonded energy terms to the potential energy function. More...
 
class  T_Molecular_potential_energy< Contribution, Contributions >
 Potential energy function adding up all the input contributions (C++11 only). More...
 
class  T_Molecular_covalent_structure_bond_length_gradient< ConformationType, CovalentStructure >
 Defines the gradient associated to the bond length. More...
 
class  T_Molecular_covalent_structure_bond_angle_gradient< ConformationType, CovalentStructure >
 Defines the gradient associated to the bond angle. More...
 
class  T_Molecular_covalent_structure_torsion_angle_gradient< ConformationType, CovalentStructure >
 Defines the gradient associated to the torsion angle. More...
 
class  T_Molecular_potential_energy_bond_length_gradient_harmonic< ConformationType, CovalentStructure, PotentialEnergyParameters >
 Defines the standard gradient associated to the bond length contribution. More...
 
class  T_Molecular_potential_energy_bond_angle_gradient_harmonic< ConformationType, CovalentStructure, PotentialEnergyParameters >
 Defines the standard gradient associated to the bond angle contribution. More...
 
class  T_Molecular_potential_energy_bond_angle_gradient_Urey_Bradley< ConformationType, CovalentStructure, PotentialEnergyParameters >
 Defines the Urey-Bradley gradient associated to a bond angle. More...
 
class  T_Molecular_potential_energy_torsion_angle_gradient_harmonic< ConformationType, CovalentStructure, PotentialEnergyParameters >
 Defines the harmonic gradient associated to the proper dihedral angle contribution. More...
 
class  T_Molecular_potential_energy_torsion_angle_gradient_periodic< ConformationType, CovalentStructure, PotentialEnergyParameters >
 Defines the periodic gradient associated to the proper dihedral angle contribution. More...
 
class  T_Molecular_potential_energy_torsion_angle_gradient_Fourier< ConformationType, CovalentStructure, PotentialEnergyParameters >
 Defines the Fourier gradient associated to the proper dihedral angle contribution. More...
 
class  T_Molecular_potential_energy_torsion_angle_gradient_Ryckaert_Bellemans< ConformationType, CovalentStructure, PotentialEnergyParameters >
 Defines the Ryckaert_Bellemans gradient associated to the proper dihedral angle contribution. More...
 
class  T_Molecular_potential_energy_torsion_angle_gradient_in_linear_structure< ConformationType, CovalentStructure, PotentialEnergyParameters >
 Defines the gradient associated to the torsion angle contribution in a linear structure. More...
 
class  T_Molecular_potential_energy_Lennard_Jones_gradient< ConformationType, CovalentStructure, PotentialEnergyParameters >
 Defines the standard gradient associated to the Lennard Jones contribution. More...
 
class  T_Molecular_potential_energy_electrostatic_gradient< ConformationType, CovalentStructure, PotentialEnergyParameters >
 Defines a standard gradient associated to the electrostatic contribution. More...
 
class  T_Molecular_potential_energy_gradient_contribution< Visitor, Term, Terms >
 Contribution of an energy gradient term to the potential energy gradient function. More...
 
class  T_Molecular_potential_energy_gradient< Contribution, Contributions >
 Sum of the contributions of an energy gradient term to the potential energy gradient function. More...
 
class  T_Molecular_potential_energy_numerical_gradient< MolecularPotentialEnergy, PotentialEnergyParameters >
 Computes numerically the gradient of a potential energy function. More...
 
class  T_Molecular_potential_energy_torsion_angle_in_linear_structure_term< ConformationType, CovalentStructure, PotentialEnergyParameters >
 Defines the term associated to the torsion angle contribution in a linear structure. More...
 

Description