IMP  2.0.0
The Integrative Modeling Platform
IMP::atom::Molecule Member List

This is the complete list of members for IMP::atom::Molecule, including all inherited members.

add_child(Hierarchy o)IMP::atom::Hierarchy
add_child(Hierarchy h) const (defined in IMP::core::Hierarchy)IMP::core::Hierarchy
add_child_at(Hierarchy h, unsigned int pos) (defined in IMP::core::Hierarchy)IMP::core::Hierarchy
clear_children() (defined in IMP::core::Hierarchy)IMP::core::Hierarchy
create_clone(Hierarchy d)IMP::atom::Hierarchyrelated
create_clone_one(Hierarchy d)IMP::atom::Hierarchyrelated
create_excluded_volume_restraint(const Hierarchies &hs, double resolution=-1)IMP::atom::Hierarchyrelated
create_fragment(const Hierarchies &ps)IMP::atom::Hierarchyrelated
create_protein(Model *m, std::string name, double resolution, int number_of_residues, int first_residue_index=0, double volume=-1)IMP::atom::Hierarchyrelated
decorate_particle(::IMP::kernel::Particle *p) (defined in IMP::atom::Molecule)IMP::atom::Moleculestatic
IMP::atom::Hierarchy::decorate_particle(Particle *p)IMP::atom::Hierarchystatic
decorate_particle(::IMP::kernel::Particle *p, const HierarchyTraits &tr=get_default_traits()) (defined in IMP::core::Hierarchy)IMP::core::Hierarchystatic
Decorator(Model *m, ParticleIndex pi) (defined in IMP::kernel::Decorator)IMP::kernel::Decoratorprotected
Decorator(Particle *p) (defined in IMP::kernel::Decorator)IMP::kernel::Decoratorprotected
Decorator() (defined in IMP::kernel::Decorator)IMP::kernel::Decoratorprotected
Decorator(Particle *p)IMP::kernel::Decorator
Decorator()IMP::kernel::Decorator
DecoratorTraits typedef (defined in IMP::core::Hierarchy)IMP::core::Hierarchy
DecoratorTraitsBase typedef (defined in IMP::core::Hierarchy)IMP::core::Hierarchy
destroy(Hierarchy d)IMP::atom::Hierarchyrelated
find_breadth_first(HD h, F f)IMP::core::Hierarchyrelated
gather(H h, F f, Out out)IMP::core::Hierarchyrelated
gather_by_attribute(H h, K k, V v, Out out)IMP::core::Hierarchyrelated
gather_by_attributes(H h, K0 k0, V0 v0, K1 k1, V1 v1, Out out)IMP::core::Hierarchyrelated
gather_slice(H h, F f, Out out)IMP::core::Hierarchyrelated
get_all_descendants(Hierarchy mhd)IMP::core::Hierarchyrelated
get_as_atom() const (defined in IMP::atom::Hierarchy)IMP::atom::Hierarchy
get_as_chain() const (defined in IMP::atom::Hierarchy)IMP::atom::Hierarchy
get_as_domain() const (defined in IMP::atom::Hierarchy)IMP::atom::Hierarchy
get_as_fragment() const (defined in IMP::atom::Hierarchy)IMP::atom::Hierarchy
get_as_mass() const (defined in IMP::atom::Hierarchy)IMP::atom::Hierarchy
get_as_molecule() const (defined in IMP::atom::Hierarchy)IMP::atom::Hierarchy
get_as_residue() const (defined in IMP::atom::Hierarchy)IMP::atom::Hierarchy
get_as_xyz() const (defined in IMP::atom::Hierarchy)IMP::atom::Hierarchy
get_as_xyzr() const (defined in IMP::atom::Hierarchy)IMP::atom::Hierarchy
get_atom(Residue rd, AtomType at)IMP::atom::Hierarchyrelated
get_bounding_sphere(const Hierarchy &h)IMP::atom::Hierarchyrelated
get_by_type(Hierarchy mhd, GetByType t)IMP::atom::Hierarchyrelated
get_child(unsigned int i) const IMP::atom::Hierarchy
get_child_index() const (defined in IMP::core::Hierarchy)IMP::core::Hierarchy
get_children() const IMP::atom::Hierarchy
get_children() const IMP::atom::Hierarchy
get_decorator_traits() const (defined in IMP::core::Hierarchy)IMP::core::Hierarchy
get_default_decorator_traits() (defined in IMP::core::Hierarchy)IMP::core::Hierarchystatic
get_default_traits()IMP::core::Hierarchystatic
get_hierarchy_tree(Hierarchy h)IMP::atom::Hierarchyrelated
get_internal(Hierarchy mhd)IMP::core::Hierarchyrelated
get_is_valid(bool print_info) const IMP::atom::Hierarchy
get_leaves(Hierarchy h)IMP::atom::Hierarchyrelated
get_leaves(const Hierarchies &h)IMP::atom::Hierarchyrelated
get_leaves(const Selection &h)IMP::atom::Hierarchyrelated
IMP::core::Hierarchy::get_leaves(Hierarchy mhd)IMP::core::Hierarchyrelated
get_model() const IMP::kernel::Decorator
get_number_of_children() const (defined in IMP::core::Hierarchy)IMP::core::Hierarchy
get_parent() const IMP::atom::Hierarchy
get_particle() const IMP::kernel::Decorator
get_particle_index() const (defined in IMP::kernel::Decorator)IMP::kernel::Decorator
get_residue(Atom d, bool nothrow=false)IMP::atom::Hierarchyrelated
get_residue(Hierarchy mhd, unsigned int index)IMP::atom::Hierarchyrelated
get_root(Hierarchy h)IMP::atom::Hierarchyrelated
IMP::core::Hierarchy::get_root(Hierarchy h)IMP::core::Hierarchyrelated
get_traits()IMP::atom::Hierarchystatic
get_traits() const (defined in IMP::core::Hierarchy)IMP::core::Hierarchy
Hierarchy(Particle *p) (defined in IMP::atom::Hierarchy)IMP::atom::Hierarchyexplicit
Hierarchy(Model *m, ParticleIndex pi) (defined in IMP::atom::Hierarchy)IMP::atom::Hierarchy
Hierarchy()IMP::atom::Hierarchy
Hierarchy(IMP::core::Hierarchy h)IMP::atom::Hierarchyexplicit
Hierarchy(Model *m, ParticleIndex id, const HierarchyTraits &tr) (defined in IMP::core::Hierarchy)IMP::core::Hierarchy
Hierarchy(const HierarchyTraits &tr) (defined in IMP::core::Hierarchy)IMP::core::Hierarchy
Hierarchy(::IMP::kernel::Particle *p, const HierarchyTraits &tr=get_default_traits()) (defined in IMP::core::Hierarchy)IMP::core::Hierarchyexplicit
Molecule() (defined in IMP::atom::Molecule)IMP::atom::Molecule
Molecule(Model *m, ParticleIndex id) (defined in IMP::atom::Molecule)IMP::atom::Molecule
Molecule(::IMP::kernel::Particle *p) (defined in IMP::atom::Molecule)IMP::atom::Moleculeexplicit
particle_is_instance(Particle *p) (defined in IMP::atom::Molecule)IMP::atom::Moleculestatic
particle_is_instance(Model *m, ParticleIndex p) (defined in IMP::atom::Hierarchy)IMP::atom::Hierarchystatic
IMP::core::Hierarchy::particle_is_instance(Particle *, HierarchyTraits=Hierarchy::get_default_traits())IMP::core::Hierarchystatic
read_pdb(base::TextInput input, Model *model, PDBSelector *selector, bool select_first_model=true) (defined in IMP::atom::Hierarchy)IMP::atom::Hierarchyrelated
remove_child(unsigned int i) (defined in IMP::core::Hierarchy)IMP::core::Hierarchy
remove_child(Hierarchy h) (defined in IMP::core::Hierarchy)IMP::core::Hierarchy
setup_as_approximation(Hierarchy h)IMP::atom::Hierarchyrelated
setup_particle(Particle *p)IMP::atom::Moleculestatic
setup_particle(Particle *p, Molecule)IMP::atom::Moleculestatic
setup_particle(Particle *p, const ParticlesTemp &children) (defined in IMP::atom::Hierarchy)IMP::atom::Hierarchystatic
IMP::atom::Hierarchy::setup_particle(Model *m, ParticleIndex pi, const ParticlesTemp &children=ParticlesTemp())IMP::atom::Hierarchystatic
IMP::core::Hierarchy::setup_particle(Particle *p, HierarchyTraits traits=Hierarchy::get_default_traits())IMP::core::Hierarchystatic
IMP::core::Hierarchy::setup_particle(Particle *p, const Particles &children, HierarchyTraits traits=Hierarchy::get_default_traits())IMP::core::Hierarchystatic
show(std::ostream &out=std::cout) const (defined in IMP::atom::Molecule)IMP::atom::Molecule
IMP::atom::Hierarchy::show(Hierarchy h, std::ostream &out=std::cout)IMP::atom::Hierarchyrelated
IMP::core::Hierarchy::show(Hierarchy h, std::ostream &out=std::cout)IMP::core::Hierarchyrelated
Value() (defined in IMP::base::Value)IMP::base::Valueprotected
visit_breadth_first(HD d, F f)IMP::core::Hierarchyrelated
visit_breadth_first_with_data(HD d, F f, typename F::result_type i)IMP::core::Hierarchyrelated
visit_depth_first(HD d, F f)IMP::core::Hierarchyrelated
visit_depth_first_with_data(HD d, F f, typename F::result_type i)IMP::core::Hierarchyrelated