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IMP Reference Guide  2.11.1
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
 Base functionality and abstract base classes for representation, scoring and sampling.
 
 IMP::atom
 Functionality for loading, creating, manipulating and scoring atomic structures.
 

Typedefs

typedef boost::graph IMP::atom::HierarchyTree
 A graph for representing a Hierarchy so you can view it nicely. More...
 
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 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 (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)
 Get a graph for the passed Hierarchy. More...
 
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::show_as_graphviz (const HierarchyTree &name, TextOutput out)
 
void IMP::atom::transform (Hierarchy h, const algebra::Transformation3D &tr)
 Transform a hierarchy. This is aware of rigid bodies. More...
 

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

Detailed Description

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

Copyright 2007-2019 IMP Inventors. All rights reserved.

Definition in file hierarchy_tools.h.