#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 resolution=0, std::string molecule=None, int residue_index=None, std::string 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=[], int state_index=-1, Ints state_indexes=[])

	Selection (Hierarchy h)

	Selection (kernel::Particle *h)

	Selection (kernel::Model *m, const kernel::ParticleIndexes &pis)

	Selection (const Hierarchies &h)

	Selection (const kernel::ParticlesTemp &h)

Hierarchies	get_hierarchies () const
	Return the hierarchies that the Selection was constructed with.

kernel::ParticleIndexes	get_selected_particle_indexes () const
	Get the indexes of the selected particles.

kernel::ParticlesTemp	get_selected_particles () const
	Get the selected particles.

	operator ParticleIndexes () const

	operator ParticlesTemp () const

void	set_atom_type (AtomType types)

void	set_atom_types (AtomTypes types)

void	set_chain (char c)

void	set_chain_id (std::string c)

void	set_chain_ids (Strings chains)

void	set_copy_index (unsigned int copy)

void	set_copy_indexes (Ints copies)

void	set_domain (std::string name)

void	set_domains (Strings names)

void	set_hierarchy_types (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_resolution (double r)

void	set_state_index (int state)

void	set_state_indexes (Ints states)

void	set_terminus (Terminus t)

void	show (std::ostream &out=std::cout) const

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=range(133,138))

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 resolution parameter to select the desired resolution (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	resolution = `0`,
		std::string	molecule = `None`,
		int	residue_index = `None`,
		std::string	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 = `[]`,
		int	state_index = `-1`,
		Ints	state_indexes = `[]`
	)

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.

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 ( char c )

Deprecated:: As of IMP release 2.2. See the IMP Deprecation Policy for more information about deprecation in IMP. Pass a string

Definition at line 141 of file Selection.h.

Here is the call graph for this function:

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 whose id is in the passed string.

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_domain ( std::string name )

Select only the single domain with that name

void IMP::atom::Selection::set_domains ( Strings names )

Select domains with the specificed names.

void IMP::atom::Selection::set_hierarchy_types ( 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.

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_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. Not sure why you would do this.

void IMP::atom::Selection::set_resolution ( double r )

Select at a Representation node with a resolution close to r.

Definition at line 108 of file Selection.h.

void IMP::atom::Selection::set_state_index ( int state )

Select State with the passed index.

Definition at line 110 of file Selection.h.

void IMP::atom::Selection::set_state_indexes ( Ints states )

Select State with the passed index.

void IMP::atom::Selection::set_terminus ( Terminus t )

Select the n or c terminus.

The documentation for this class was generated from the following file:

Selection.h

Public Types

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation