IMP Reference Guide
2.21.0
The Integrative Modeling Platform
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Select hierarchy particles identified by the biological name. More...
#include <IMP/atom/Selection.h>
Select hierarchy particles identified by the biological name.
Given an atom.Hierarchy (or atom.Hierarchies) this will select a subset of the child particles by the biological name.
For example (in Python)
each select the C-terminus of the protein "myprotein" (assuming the last residue index is 133, and the residues are leaves, containing no atoms). (In C++, use one of the other constructors, then call one or more of the set_*
methods.)
Selection objects can be combined using basic set operations (union, intersection, difference, symmetric difference). In Python the equivalent operators (|, &, -, ^ respectively) can be used (the similar in-place |=, &=, -= and ^= operators also work). This requires that all of the objects being combined use the same hierarchy or hierarchies. For example (in Python)
selects all atoms in ASP residues except for CG or at the C-terminus. The resulting Selection makes a copy of the Selections it was combined from, so changing the original Selections does not change that Selection.
To actually get the selected particles, call get_selected_particle_indexes() or get_selected_particles().
This class assumes the hierarchies are valid (and if they are not, may not select the correct particles). If in doubt, call IMP::atom::Hierarchy::get_is_valid() on each one first to verify this.
Definition at line 70 of file Selection.h.
Public Types | |
enum | Terminus { NONE, C, N } |
Public Member Functions | |
Selection (Hierarchy hierarchy=None, Hierarchies hierarchies=[], Strings molecules=[], Ints residue_indexes=[], Strings chain_ids=[], AtomTypes atom_types=[], ResidueTypes residue_types=[], Strings domains=[], double resolution=0, RepresentationType representation_type=IMP.atom.BALLS, std::string molecule=None, int residue_index=None, std::string chain_id=None, AtomType atom_type=None, ResidueType residue_type=None, Ints hierarchy_types=None, Element element=None, Terminus terminus=None, std::string domain=None, core::ParticleType particle_type=None, core::ParticleTypes particle_types=[], int copy_index=-1, Ints copy_indexes=[], int state_index=-1, Ints state_indexes=[]) | |
Selection (Hierarchy h) | |
Selection (Particle *h) | |
Selection (Model *m, const ParticleIndexes &pis) | |
Selection (const Hierarchies &h) | |
Selection (const ParticlesTemp &h) | |
Selection | create_clone () |
Make a clone of this Selection. More... | |
Hierarchies | get_hierarchies () const |
Return the hierarchies that the Selection was constructed with. More... | |
ParticleIndexes | get_selected_particle_indexes (bool with_representation=true) const |
Get the indexes of the selected particles. More... | |
ParticlesTemp | get_selected_particles (bool with_representation=true) const |
Get the selected particles. More... | |
operator ParticleIndexes () const | |
operator ParticlesTemp () const | |
void | set_atom_type (AtomType types) |
Select atoms with only the passed type. More... | |
void | set_atom_types (AtomTypes types) |
Select atoms whose types are in the list, eg AT_CA. More... | |
void | set_chain_id (std::string c) |
Select with the passed chain id. More... | |
void | set_chain_ids (Strings chains) |
Select particles in chains with the given ids. More... | |
void | set_copy_index (unsigned int copy) |
Select elements with Copy::get_copy_index() that match. More... | |
void | set_copy_indexes (Ints copies) |
Select elements with Copy::get_copy_index() that are in the list. More... | |
void | set_difference (const Selection &s) |
Select elements that are in this Selection but not the passed one. More... | |
void | set_domain (std::string name) |
Select only the single domain with that name. More... | |
void | set_domains (Strings names) |
Select domains with the specified names. More... | |
void | set_element (Element e) |
Select atoms of the given Element. More... | |
void | set_hierarchy_types (Ints types) |
void | set_intersection (const Selection &s) |
Select elements that are in both this Selection and the passed one. More... | |
void | set_molecule (std::string mol) |
Select a molecule with the passed name. More... | |
void | set_molecules (Strings mols) |
Select based on the molecule name. More... | |
void | set_particle_type (core::ParticleType t) |
Select elements that match the core::ParticleType. More... | |
void | set_particle_types (core::ParticleTypes t) |
Select elements that match the core::ParticleType. More... | |
void | set_representation_type (RepresentationType t) |
Try to find this representation type. More... | |
void | set_residue_index (int i) |
Select only residues with the passed index. More... | |
void | set_residue_indexes (Ints indexes) |
Select residues whose indexes are in the passed list. More... | |
void | set_residue_type (ResidueType type) |
Select only residues with the passed type. More... | |
void | set_residue_types (ResidueTypes types) |
Select residues whose types are in the list. More... | |
void | set_resolution (double r) |
Select at a Representation node with a resolution close to r. More... | |
void | set_state_index (int state) |
Select State with the passed index. More... | |
void | set_state_indexes (Ints states) |
Select State with the passed indexes. More... | |
void | set_symmetric_difference (const Selection &s) |
Select elements that are in this Selection or the passed one but not both. More... | |
void | set_terminus (Terminus t) |
Select the leaf particles at the N or C terminus. More... | |
void | set_union (const Selection &s) |
Select elements that are in either this Selection or the passed one. More... | |
void | show (std::ostream &out=std::cout) const |
IMP::atom::Selection::Selection | ( | Hierarchy | hierarchy = None , |
Hierarchies | hierarchies = [] , |
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Strings | molecules = [] , |
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Ints | residue_indexes = [] , |
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Strings | chain_ids = [] , |
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AtomTypes | atom_types = [] , |
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ResidueTypes | residue_types = [] , |
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Strings | domains = [] , |
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double | resolution = 0 , |
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RepresentationType | representation_type = IMP.atom.BALLS , |
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std::string | molecule = None , |
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int | residue_index = None , |
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std::string | chain_id = None , |
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AtomType | atom_type = None , |
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ResidueType | residue_type = None , |
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Ints | hierarchy_types = None , |
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Element | element = None , |
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Terminus | terminus = None , |
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std::string | domain = None , |
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core::ParticleType | particle_type = None , |
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core::ParticleTypes | particle_types = [] , |
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int | copy_index = -1 , |
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Ints | copy_indexes = [] , |
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int | state_index = -1 , |
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Ints | state_indexes = [] |
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When using Python, you have much more control over construction due to the use of keyword arguments. You can provide any subset of the arguments (although one of hierarchy or hierarchies must be provided).
Selection IMP::atom::Selection::create_clone | ( | ) |
Hierarchies IMP::atom::Selection::get_hierarchies | ( | ) | const |
Return the hierarchies that the Selection was constructed with.
ParticleIndexes IMP::atom::Selection::get_selected_particle_indexes | ( | bool | with_representation = true | ) | const |
Get the indexes of the selected particles.
with_representation | If true (the default) then extend the search down the hierarchy to find all representational particles that match - that is, those with x,y,z coordinates. For example, selecting a residue name will typically return all of the Atom particles in that residue (not the Residue particle itself). If false, stop the search at the highest level of the hierarchy that matches (so, in the case above, return the Residue particle). |
ParticlesTemp IMP::atom::Selection::get_selected_particles | ( | bool | with_representation = true | ) | const |
Get the selected particles.
void IMP::atom::Selection::set_atom_type | ( | AtomType | types | ) |
Select atoms with only the passed type.
void IMP::atom::Selection::set_atom_types | ( | AtomTypes | types | ) |
Select atoms whose types are in the list, eg AT_CA.
void IMP::atom::Selection::set_chain_id | ( | std::string | c | ) |
Select with the passed chain id.
void IMP::atom::Selection::set_chain_ids | ( | Strings | chains | ) |
Select particles in chains with the given ids.
void IMP::atom::Selection::set_copy_index | ( | unsigned int | copy | ) |
Select elements with Copy::get_copy_index() that match.
void IMP::atom::Selection::set_copy_indexes | ( | Ints | copies | ) |
Select elements with Copy::get_copy_index() that are in the list.
void IMP::atom::Selection::set_difference | ( | const Selection & | s | ) |
void IMP::atom::Selection::set_domain | ( | std::string | name | ) |
Select only the single domain with that name.
void IMP::atom::Selection::set_domains | ( | Strings | names | ) |
Select domains with the specified names.
void IMP::atom::Selection::set_element | ( | Element | e | ) |
Select atoms of the given Element.
void IMP::atom::Selection::set_hierarchy_types | ( | Ints | types | ) |
void IMP::atom::Selection::set_intersection | ( | const Selection & | s | ) |
void IMP::atom::Selection::set_molecule | ( | std::string | mol | ) |
Select a molecule with the passed name.
void IMP::atom::Selection::set_molecules | ( | Strings | mols | ) |
Select based on the molecule name.
void IMP::atom::Selection::set_particle_type | ( | core::ParticleType | t | ) |
Select elements that match the core::ParticleType.
void IMP::atom::Selection::set_particle_types | ( | core::ParticleTypes | t | ) |
Select elements that match the core::ParticleType.
void IMP::atom::Selection::set_representation_type | ( | RepresentationType | t | ) |
Try to find this representation type.
Definition at line 152 of file Selection.h.
void IMP::atom::Selection::set_residue_index | ( | int | i | ) |
Select only residues with the passed index.
void IMP::atom::Selection::set_residue_indexes | ( | Ints | indexes | ) |
Select residues whose indexes are in the passed list.
void IMP::atom::Selection::set_residue_type | ( | ResidueType | type | ) |
Select only residues with the passed type.
void IMP::atom::Selection::set_residue_types | ( | ResidueTypes | types | ) |
Select residues whose types are in the list.
void IMP::atom::Selection::set_resolution | ( | double | r | ) |
Select at a Representation node with a resolution close to r.
Definition at line 150 of file Selection.h.
void IMP::atom::Selection::set_state_index | ( | int | state | ) |
Select State with the passed index.
Definition at line 155 of file Selection.h.
void IMP::atom::Selection::set_symmetric_difference | ( | const Selection & | s | ) |
void IMP::atom::Selection::set_terminus | ( | Terminus | t | ) |
Select the leaf particles at the N or C terminus.
If the leaf particles are atoms, a terminus is simply an N or C atom where its parent is also a terminus particle. Otherwise, a terminus particle is the first (for N) or last (for C) child of its parent.
void IMP::atom::Selection::set_union | ( | const Selection & | s | ) |