IMP Reference Guide
2.20.2
The Integrative Modeling Platform
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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>
Go to the source code of this file.
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) |
A set of useful functionality on IMP::atom::Hierarchy decorators.
Copyright 2007-2022 IMP Inventors. All rights reserved.
Definition in file hierarchy_tools.h.