IMP
2.0.0
The Integrative Modeling Platform
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#include <IMP/atom/Selection.h>
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, HierarchyType hierarchy_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 (Particle *h) | |
Selection (Model *m, const ParticleIndexes &pis) | |
Selection (const Hierarchies &h) | |
Selection (const ParticlesTemp &h) | |
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 names) |
void | set_hierarchy_types (const Ints &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, std::string name="Connectivity%1%") |
Restraint * | create_connectivity_restraint (const Selections &s, double x0, double k, std::string name="Connectivity%1%") |
core::XYZR | create_cover (const Selection &s, std::string name=std::string()) |
Restraint * | create_distance_restraint (const Selection &n0, const Selection &n1, double x0, double k, std::string name="Distance%1%") |
Restraint * | create_internal_connectivity_restraint (const Selection &s, double k, std::string name="Connectivity%1%") |
Restraint * | create_internal_connectivity_restraint (const Selection &s, double x0, double k, std::string name="Connectivity%1%") |
double | get_mass (const Selection &s) |
double | get_radius_of_gyration (const Selection &s) |
double | get_surface_area (const Selection &s) |
double | get_volume (const Selection &s) |
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).
Definition at line 44 of file 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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HierarchyType | hierarchy_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).
void IMP::atom::Selection::set_atom_type | ( | AtomType | types | ) |
Select atoms with only the passed type.
Definition at line 162 of file Selection.h.
void IMP::atom::Selection::set_atom_types | ( | AtomTypes | types | ) |
Select atoms whose types are in the list, eg AT_CA.
Definition at line 134 of file Selection.h.
void IMP::atom::Selection::set_chain | ( | char | c | ) |
Select a chain with the passed id
Definition at line 154 of file Selection.h.
void IMP::atom::Selection::set_chains | ( | std::string | chains | ) |
Select particles in chains whose id is in the passed string.
Definition at line 124 of file Selection.h.
void IMP::atom::Selection::set_copy_index | ( | unsigned int | copy | ) |
Select elements with Copy::get_copy_index() that match.
Definition at line 174 of file Selection.h.
void IMP::atom::Selection::set_copy_indexes | ( | const Ints & | copies | ) |
Select elements with Copy::get_copy_index() that are in the list.
Definition at line 178 of file Selection.h.
void IMP::atom::Selection::set_domain | ( | std::string | name | ) |
Select only the single domain with that name
Definition at line 170 of file Selection.h.
void IMP::atom::Selection::set_domains | ( | Strings | names | ) |
Select domains with the specificed names.
Definition at line 145 of file Selection.h.
void IMP::atom::Selection::set_hierarchy_types | ( | const Ints & | types | ) |
Select only particles whose type matches the passed type, eg Molecule, Fragment, Residue etc. See GetByType for how to specify the types. Ints are used to make swig happy.
Definition at line 194 of file Selection.h.
void IMP::atom::Selection::set_molecule | ( | std::string | mol | ) |
Select a molecule with the passed name.
Definition at line 150 of file Selection.h.
void IMP::atom::Selection::set_molecules | ( | Strings | mols | ) |
Select based on the molecule name.
Definition at line 110 of file Selection.h.
void IMP::atom::Selection::set_particle_type | ( | core::ParticleType | t | ) |
Select elements that match the core::ParticleType.
Definition at line 183 of file Selection.h.
void IMP::atom::Selection::set_particle_types | ( | core::ParticleTypes | t | ) |
Select elements that match the core::ParticleType.
Definition at line 187 of file Selection.h.
void IMP::atom::Selection::set_residue_index | ( | int | i | ) |
Select only residues with the passed index.
Definition at line 158 of file Selection.h.
void IMP::atom::Selection::set_residue_indexes | ( | Ints | indexes | ) |
Select residues whose indexes are in the passed list.
Definition at line 129 of file Selection.h.
void IMP::atom::Selection::set_residue_type | ( | ResidueType | type | ) |
Select only residues with the passed type.
Definition at line 166 of file Selection.h.
void IMP::atom::Selection::set_residue_types | ( | ResidueTypes | types | ) |
Select residues whose types are in the list. Not sure why you would do this.
Definition at line 140 of file Selection.h.
void IMP::atom::Selection::set_target_radius | ( | double | r | ) |
Select particles whose radii are close to r.
Definition at line 115 of file Selection.h.
void IMP::atom::Selection::set_terminus | ( | Terminus | t | ) |
Select the n or c terminus.
Definition at line 119 of file Selection.h.
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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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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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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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Create a distance restraint between the selections.
This restraint applies a harmonic to the minimum distance between a particle in selection n0 and a particle in selection n1.
If one or more of the selections is a rigid body, this will be used to accelerate the computation.
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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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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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Get the total mass of a hierarchy. In daltons.
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Get the total surface area of a hierarchy. In square angstroms. The get_surface_area requires CGAL in order to function.
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Get the total volume of a hierarchy. In cubic angstroms. The get_volume requires CGAL in order to function.