IMP  2.2.1
The Integrative Modeling Platform
hierarchy_tools.h File Reference

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>
#include <boost/unordered_map.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

 IMP
 All IMP::kernel code is brought into the IMP namespace.
 
 IMP::atom
 See IMP.atom 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

kernel::Restraint * IMP::atom::create_excluded_volume_restraint (const Hierarchies &hs, double resolution=-1)
 
Hierarchy IMP::atom::create_protein (kernel::Model *m, std::string name, double target_radius, int number_of_residues, int first_residue_index=0, double volume=-1)
 Create a coarse grained molecule. More...
 
Hierarchy IMP::atom::create_protein (kernel::Model *m, std::string name, double target_radius, const Ints domain_boundaries)
 
Hierarchy IMP::atom::create_simplified_assembly_from_volume (Hierarchy h, double resolution)
 
Hierarchy IMP::atom::create_simplified_from_volume (Hierarchy h, double resolution)
 
HierarchyTree IMP::atom::get_hierarchy_tree (Hierarchy h)
 
HierarchyTreeVertexIndex IMP::atom::get_vertex_index (const HierarchyTree &g)
 
void IMP::atom::setup_as_approximation (kernel::Particle *h, const kernel::ParticlesTemp &other)
 
void IMP::atom::setup_as_approximation (Hierarchy h)
 
void IMP::atom::show_as_graphviz (const HierarchyTree &name, base::TextOutput out)
 
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.

Ints IMP::atom::get_residue_indexes (Hierarchy h)
 
ResidueType IMP::atom::get_residue_type (Hierarchy h)
 
char IMP::atom::get_chain_id_char (Hierarchy h)
 
AtomType IMP::atom::get_atom_type (Hierarchy h)
 
std::string IMP::atom::get_domain_name (Hierarchy h)
 

Detailed Description

Copyright 2007-2014 IMP Inventors. All rights reserved.

Definition in file hierarchy_tools.h.