#include <IMP/atom/Selection.h>

Inheritance diagram for IMP::atom::Selection:

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)

Detailed Description

Select a part of an atom.Hiearchy or atom.Hierarchies that is identified by the biological name.

For example (in python)

Selection(hierarchy=h, molecule="myprotein", terminus=Selection.C)
Selection(hierarchy=h, molecule="myprotein", residue_index=133)
Selection(hierarchy=h, molecule="myprotein", residue_indexes=[(133,134)])

each get the C-terminus of the protein "myprotein" (assuming the last residue index is 133).

Note: Only representational particles are selected. That is, ones with x,y,z coordinates. And the highest resolution representation that fits is returned. If you want lower resolution, use the target_radius parameter to select the desired radius (pass a very large number to get the coarsest representation).

Definition at line 44 of file Selection.h.

Constructor & Destructor Documentation

IMP::atom::Selection::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 = `[]`
	)

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).

Member Function Documentation

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.