A set of useful functionality on IMP::atom::Hierarchy decorators. More...

#include <IMP/atom/atom_config.h>
#include <IMP/algebra/algebra_config.h>
#include "Hierarchy.h"
#include "Residue.h"
#include "Atom.h"
#include <IMP/core/Typed.h>
#include <IMP/core/XYZR.h>
#include "Selection.h"
#include <boost/graph/adjacency_list.hpp>

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Classes
class	IMP::atom::HierarchiesGeometry
	Display an IMP::SingletonContainer of IMP::atom::Hierarchy particles as balls. More...

class	IMP::atom::HierarchyGeometry
	Display an IMP::atom::Hierarchy particle as balls. More...

Namespaces
namespace	IMP
	All IMP::kernel code is brought into the IMP namespace.

namespace	IMP::atom
	See IMP.atom Overview for more information.

Typedefs
typedef boost::graph	IMP::atom::HierarchyTree

typedef HierarchyTree::EdgeNameMap	IMP::atom::HierarchyTreeConstEdgeName

typedef HierarchyTree::VertexNameMap	IMP::atom::HierarchyTreeConstVertexName

typedef HierarchyTree::edge_descriptor	IMP::atom::HierarchyTreeEdge

typedef boost::graph_traits < HierarchyTree >	IMP::atom::HierarchyTreeTraits

typedef HierarchyTree::vertex_descriptor	IMP::atom::HierarchyTreeVertex

Functions
Restraint *	IMP::atom::create_excluded_volume_restraint (const Hierarchies &hs, double resolution=-1)

Hierarchy	IMP::atom::create_protein (Model *m, std::string name, double resolution, int number_of_residues, int first_residue_index=0, double volume=-1)
	Create a coarse grained molecule. More...

Hierarchy	IMP::atom::create_protein (Model *m, std::string name, double resolution, const Ints domain_boundaries)

HierarchyTree	IMP::atom::get_hierarchy_tree (Hierarchy h)

HierarchyTreeVertexIndex	IMP::atom::get_vertex_index (const HierarchyTree &g)

void	IMP::atom::setup_as_approximation (Particle *h, const ParticlesTemp &other)

void	IMP::atom::setup_as_approximation (Hierarchy h)

void	IMP::atom::transform (Hierarchy h, const algebra::Transformation3D &tr)

Simplification along backbone
These two methods create a simplified version of a molecule by merging residues sequentially. In one case every n residues are merged, in the other, the intervals are passed manually. The resulting molecule is not optimized by default and has no restraints automatically created. At the moment, the calls only support unmodified hierarchies loaded by read_pdb() which have only protein or DNA members. They return Hierarchy() if the input chain is empty. If keep_detailed is true, then the original high resolution structure particles are added as children of the simplified structure.
Hierarchy	IMP::atom::create_simplified_along_backbone (Hierarchy input, int num_res, bool keep_detailed=false)

Hierarchy	IMP::atom::create_simplified_along_backbone (Chain input, const IntRanges &residue_segments, bool keep_detailed=false)

Finding information
Get the attribute of the given particle or throw a ValueException if it is not applicable. The particle with the given information must be above the passed node.
std::string	IMP::atom::get_molecule_name (Hierarchy h)

Ints	IMP::atom::get_residue_indexes (Hierarchy h)

ResidueType	IMP::atom::get_residue_type (Hierarchy h)

int	IMP::atom::get_chain_id (Hierarchy h)

AtomType	IMP::atom::get_atom_type (Hierarchy h)

std::string	IMP::atom::get_domain_name (Hierarchy h)

int	IMP::atom::get_copy_index (Hierarchy h)

Detailed Description

Definition in file hierarchy_tools.h.

Classes

Namespaces

Typedefs

Functions

Simplification along backbone

Finding information

Detailed Description