Molecular_conformation

A package providing classes to store biomolecule conformations. Reference Manual – User Manual . Authors: F. Cazals and T. Dreyfus and C. Le Breton

Main classes:

• T_Conformation_builder_cartesian_default<Conformation>: default builder for conformations with cartesian coordinates.

• T_Conformation_traits<Conformation>: traits class to be specialized.

• T_Conformation_traits<CGAL::Point_d<Kernel>>: class specializing SBL::CSB::T_Conformation_traits by storing the conformation as Point_d.

• T_Conformation_traits<std::vector<NT>>: class specializing SBL::CSB::T_Conformation_traits by storing the conformation as a vector of coordinates of a user-specified type.

• T_Conformation_traits<T_Conformation_as_vector<NT>> : deprecated.

• T_Conformation_with_covalent_structure : provides the struct SBL::CSB::T_Conformation_with_covalent_structure which enhances a conformation with a covalent structure e.g. from the package Molecular_covalent_structure. NB: the covalent structure is used to compute the potential energy of a molecular conformation.

• T_Conformation_traits<T_Conformation_with_covalent_structure<ConformationBase, CovalentStructure>>: Class specializing SBL::CSB::T_Conformation_traits by storing the conformation enhanced by a molecular covalent structure (SBL::CSB::T_Conformation_with_covalent_structure).

• T_Conformation_with_height : provides the struct SBL::CSB::T_Conformation_with_implicit_height which enhances a conformation with coordinates by adding a height.

• T_Conformation_traits<T_Conformation_with_height<ConformationBase, HeightType>> : provides the struct SBL::CSB::T_Conformation_with_height which enhances a conformation with coordinates by adding a height; this class then used to specialize SBL::CSB::T_Conformation_traits.

• T_Conformation_with_implicit_height : provides the struct SBL::CSB::T_Conformation_with_implicit_height which enhances a conformation with coordinates by adding a height and also takes a functor to apply a function to the height.

• T_Conformation_traits<T_Conformation_with_implicit_height<ConformationBase, HeightFunctor>>: Class specializing SBL::CSB::T_Conformation_traits by storing the conformation enhanced by a height and a function applying onto the height. (SBL::CSB::T_Conformation_with_implicit_height).

• T_Conformation_loader : Class for loading conformations from a list of PDB / cif files, or from a plain txt file listing the conformations as Point_d.