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Select a part of an atom.Hiearchy or atom.Hierarchies that is identified by the biological name.
For example (in python)
each get the C-terminus of the protein "myprotein" (assuming the last residue index is 133).
Examples: dependency graph, displaying ensembles, markers, dock with crosslinks, rigid brownian dynamics, setup, nup84 cg, nup84 rb
Public Types | |
| enum | Terminus { NONE, C, N } |
Public Member Functions | |
| Selection (Hierarchy hierarchy=None, Hierarchies hierarchies=[], Strings molecules=[], Ints residue_indexes=[], Strings chains=[], AtomTypes atom_types=[], ResidueTypes residue_types=[], Strings domains=[], double target_radius=0, std::string molecule=None, int residue_index=None, char chain=None, AtomType atom_type=None, ResidueType residue_type=None, Terminus terminus=None, std::string domain=None, core::ParticleType particle_type=None, core::ParticleTypes particle_types=[], int copy_index=-1, Ints copy_indexs=[]) | |
| Selection (Hierarchy h) | |
| Selection (Hierarchies h) | |
| Selection (Hierarchy h, std::string molname, int residue_index) | |
| Hierarchies | get_hierarchies () const |
| Return the hierarchies that the Selection was constructed with. | |
| ParticlesTemp | get_selected_particles () const |
| Get the selected particles. | |
| void | set_atom_type (AtomType types) |
| void | set_atom_types (AtomTypes types) |
| void | set_chain (char c) |
| void | set_chains (std::string chains) |
| void | set_copy_index (unsigned int copy) |
| void | set_copy_indexes (const Ints &copies) |
| void | set_domain (std::string name) |
| void | set_domains (Strings types) |
| void | set_molecule (std::string mol) |
| void | set_molecules (Strings mols) |
| void | set_particle_type (core::ParticleType t) |
| void | set_particle_types (core::ParticleTypes t) |
| void | set_residue_index (int i) |
| void | set_residue_indexes (Ints indexes) |
| void | set_residue_type (ResidueType type) |
| void | set_residue_types (ResidueTypes types) |
| void | set_target_radius (double r) |
| void | set_terminus (Terminus t) |
| void | show (std::ostream &out=std::cout) const |
Related Functions | |
(Note that these are not member functions.) | |
| Restraint * | create_connectivity_restraint (const Selections &s, double k) |
| Restraint * | create_connectivity_restraint (const Selections &s, double x0, double k) |
| core::XYZR | create_cover (Selection s, std::string name=std::string()) |
| Restraint * | create_distance_restraint (const Selection &n0, const Selection &n1, double x0, double k) |
| Restraint * | create_internal_connectivity_restraint (const Selection &s, double k) |
| Restraint * | create_internal_connectivity_restraint (const Selection &s, double x0, double k) |
| double | get_mass (Selection h) |
| double | get_radius_of_gyration (Selection h) |
| 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 | chains = [], |
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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 | target_radius = 0, |
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| std::string | molecule = None, |
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| int | residue_index = None, |
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| char | chain = None, |
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| AtomType | atom_type = None, |
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| ResidueType | residue_type = 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_indexs = [] |
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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).
| Hierarchies IMP::atom::Selection::get_hierarchies | ( | ) | const |
Return the hierarchies that the Selection was constructed with.
| ParticlesTemp IMP::atom::Selection::get_selected_particles | ( | ) | const |
Get the selected particles.
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related |
Create a restraint connecting the selections.
If one or more of the selections is a rigid body, this will be used to accelerate the computation.
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related |
Create a restraint connecting the selections. The particles are allowed to be appart by x0 and still count as connected.
If one or more of the selections is a rigid body, this will be used to accelerate the computation.
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related |
Create an XYZR particle which always includes the particles in the selection in its bounding volume. If all the particles in the selection are part of the same rigid body, then the created particle is added as part of that rigid body. Otherwise it uses an IMP::core::Cover to maintain the cover property.
Doing this can be a useful way to accelerate computations when it is OK to replace a potential complicated set of geometry represented by the selection with a much simpler one.
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related |
Create a distance restraint between the selections.
If one or more of the selections is a rigid body, this will be used to accelerate the computation.
Create a restraint connecting the selection.
If one or more of the selections is a rigid body, this will be used to accelerate the computation.
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related |
Create a restraint connecting the selection. The particles are allowed to be appart by x0 and still count as connected.
If one or more of the selections is a rigid body, this will be used to accelerate the computation.
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related |
Get the total mass of a hierarchy. In daltons.