protocols::helical_bundle Namespace Reference

Namespaces
	parameters

Classes
class	BundleGridSampler
class	BundleGridSamplerCreator
class	BundleGridSamplerHelper
	BundleGridSamplerHelper class, which stores options for the PerturbBundle mover. More...
class	FitSimpleHelix
class	FitSimpleHelixCreator
class	FitSimpleHelixMultiFunc
	Multifunction class for fitting a simple (straight) helix to the Crick parameters. More...
class	MakeBundle
class	MakeBundleCreator
class	MakeBundleHelix
class	MakeBundleHelixCreator
class	PerturbBundle
class	PerturbBundleCreator
class	PerturbBundleHelix
class	PerturbBundleHelixCreator
class	PerturbBundleOptions
	PerturbBundleOptions class, which stores options for the PerturbBundle mover. More...

Typedefs
typedef utility::pointer::shared_ptr < BundleGridSampler >	BundleGridSamplerOP
typedef utility::pointer::shared_ptr < BundleGridSampler const >	BundleGridSamplerCOP
typedef utility::vector1 < BundleGridSamplerOP >	BundleGridSamplerOPs
typedef utility::vector1 < BundleGridSamplerCOP >	BundleGridSamplerCOPs
typedef utility::pointer::weak_ptr < BundleGridSamplerHelper >	BundleGridSamplerHelperAP
typedef utility::pointer::weak_ptr < BundleGridSamplerHelper const >	BundleGridSamplerHelperCAP
typedef utility::pointer::shared_ptr < BundleGridSamplerHelper >	BundleGridSamplerHelperOP
typedef utility::pointer::shared_ptr < BundleGridSamplerHelper const >	BundleGridSamplerHelperCOP
typedef utility::vector1 < BundleGridSamplerHelperOP >	BundleGridSamplerHelperOPs
typedef utility::vector1 < BundleGridSamplerHelperCOP >	BundleGridSamplerHelperCOPs
typedef utility::vector1 < BundleGridSamplerHelperCAP >	BundleGridSamplerHelperCAPs
typedef utility::pointer::shared_ptr < FitSimpleHelix >	FitSimpleHelixOP
typedef utility::pointer::shared_ptr < FitSimpleHelix const >	FitSimpleHelixCOP
typedef utility::vector1 < FitSimpleHelixOP >	FitSimpleHelixOPs
typedef utility::vector1 < FitSimpleHelixCOP >	FitSimpleHelixCOPs
typedef utility::pointer::shared_ptr < MakeBundle >	MakeBundleOP
typedef utility::pointer::shared_ptr < MakeBundle const >	MakeBundleCOP
typedef utility::vector1 < MakeBundleOP >	MakeBundleOPs
typedef utility::vector1 < MakeBundleCOP >	MakeBundleCOPs
typedef utility::pointer::shared_ptr < MakeBundleHelix >	MakeBundleHelixOP
typedef utility::pointer::shared_ptr < MakeBundleHelix const >	MakeBundleHelixCOP
typedef utility::vector1 < MakeBundleHelixOP >	MakeBundleHelixOPs
typedef utility::vector1 < MakeBundleHelixCOP >	MakeBundleHelixCOPs
typedef utility::pointer::shared_ptr < PerturbBundle >	PerturbBundleOP
typedef utility::pointer::shared_ptr < PerturbBundle const >	PerturbBundleCOP
typedef utility::vector1 < PerturbBundleOP >	PerturbBundleOPs
typedef utility::vector1 < PerturbBundleCOP >	PerturbBundleCOPs
typedef utility::pointer::shared_ptr < PerturbBundleHelix >	PerturbBundleHelixOP
typedef utility::pointer::shared_ptr < PerturbBundleHelix const >	PerturbBundleHelixCOP
typedef utility::vector1 < PerturbBundleHelixOP >	PerturbBundleHelixOPs
typedef utility::vector1 < PerturbBundleHelixCOP >	PerturbBundleHelixCOPs
typedef utility::pointer::weak_ptr < PerturbBundleOptions >	PerturbBundleOptionsAP
typedef utility::pointer::weak_ptr < PerturbBundleOptions const >	PerturbBundleOptionsCAP
typedef utility::pointer::shared_ptr < PerturbBundleOptions >	PerturbBundleOptionsOP
typedef utility::pointer::shared_ptr < PerturbBundleOptions const >	PerturbBundleOptionsCOP
typedef utility::vector1 < PerturbBundleOptionsOP >	PerturbBundleOptionsOPs
typedef utility::vector1 < PerturbBundleOptionsCOP >	PerturbBundleOptionsCOPs
typedef utility::vector1 < PerturbBundleOptionsCAP >	PerturbBundleOptionsCAPs

Enumerations
enum	DoFType {   bgsh_r0 = 1, bgsh_omega0, bgsh_delta_omega0, bgsh_delta_omega1,   bgsh_delta_t, bgsh_undefined_dof }
	The type of bundle parameter that will be sampled by the BundleGridSampler mover. More...
enum	PertType { pt_uniform = 1, pt_gaussian, pt_undefined_perturbation }
	The type of random perturbation that will be used. More...

Functions
static thread_local basic::Tracer	TR ("protocols.helical_bundle.BundleGridSampler")
static thread_local basic::Tracer	TR ("protocols.helical_bundle.BundleGridSamplerHelper")
static thread_local basic::Tracer	TR ("protocols.helical_bundle.FitSimpleHelix")
static thread_local basic::Tracer	TR ("protocols.helical_bundle.MakeBundle")
static thread_local basic::Tracer	TR ("protocols.helical_bundle.MakeBundleHelix")
static thread_local basic::Tracer	TR ("protocols.helical_bundle.PerturbBundle")
static thread_local basic::Tracer	TR ("protocols.helical_bundle.PerturbBundleHelix")
static thread_local basic::Tracer	TR ("protocols.helical_bundle.PerturbBundleOptions")
static thread_local basic::Tracer	TR ("protocols.helical_bundle.util")
void	write_minor_helix_params (std::string const &filename, utility::vector1< core::Real > const &r1, core::Real const &omega1, core::Real const &z1, utility::vector1< core::Real > const &delta_omega1, utility::vector1< core::Real > const &delta_z1)
void	read_minor_helix_params (std::string const &filename, utility::vector1< core::Real > &r1, core::Real &omega1, core::Real &z1, utility::vector1< core::Real > &delta_omega1, utility::vector1< core::Real > &delta_z1)
void	generate_atom_positions (utility::vector1< utility::vector1< numeric::xyzVector< core::Real > > > &outvector, core::pose::Pose const &helixpose, core::Size const helix_start, core::Size const helix_end, core::Real const &r0, core::Real const &omega0, core::Real const &delta_omega0, core::Real const &delta_t, bool const invert_helix, utility::vector1< core::Real > const &r1, core::Real const &omega1, core::Real const &z1, utility::vector1< core::Real > const &delta_omega1, core::Real const &delta_omega1_all, utility::vector1< core::Real > const &delta_z1, bool &failed)
	Generate the x,y,z coordinates of the mainchain atoms using the Crick equations. More...
void	place_atom_positions (core::pose::Pose &pose, utility::vector1< utility::vector1< numeric::xyzVector< core::Real > > > const &atom_positions, core::Size const helix_start, core::Size const helix_end)
	Place the helix mainchain atoms based on the Crick equations. More...
void	copy_helix_bondlengths (core::pose::Pose &pose, core::pose::Pose const &ref_pose, core::Size const helix_start, core::Size const helix_end)
	Copy backbone bond length values from one pose, where helix mainchain atom coordinates have been set with the Crick equations, to another with ideal geometry. More...
void	copy_helix_bondangles (core::pose::Pose &pose, core::pose::Pose const &ref_pose, core::Size const helix_start, core::Size const helix_end)
	Copy backbone bond angle values from one pose, where helix mainchain atom coordinates have been set with the Crick equations, to another with ideal geometry. More...
void	copy_helix_dihedrals (core::pose::Pose &pose, core::pose::Pose const &ref_pose, core::Size const helix_start, core::Size const helix_end)
	Copy backbone dihedral values from one pose, where helix mainchain atom coordinates have been set with the Crick equations, to another with ideal geometry. More...
void	align_mainchain_atoms (core::pose::Pose &pose, core::pose::Pose const &ref_pose, core::Size const helix_start, core::Size const helix_end)
	Align mainchain atoms of pose to ref_pose mainchain atoms. More...
void	align_mainchain_atoms_of_residue_range (core::pose::Pose &pose, core::pose::Pose const &ref_pose, core::Size const helix_start, core::Size const helix_end)
	Align mainchain atoms of pose to ref_pose mainchain atoms, moving ONLY the residues involved in the alignment. More...

Typedef Documentation

typedef utility::pointer::shared_ptr< BundleGridSampler const > protocols::helical_bundle::BundleGridSamplerCOP

typedef utility::vector1<BundleGridSamplerCOP> protocols::helical_bundle::BundleGridSamplerCOPs

typedef utility::pointer::weak_ptr< BundleGridSamplerHelper > protocols::helical_bundle::BundleGridSamplerHelperAP

typedef utility::pointer::weak_ptr< BundleGridSamplerHelper const > protocols::helical_bundle::BundleGridSamplerHelperCAP

typedef utility::vector1< BundleGridSamplerHelperCAP > protocols::helical_bundle::BundleGridSamplerHelperCAPs

typedef utility::pointer::shared_ptr< BundleGridSamplerHelper const > protocols::helical_bundle::BundleGridSamplerHelperCOP

typedef utility::vector1< BundleGridSamplerHelperCOP > protocols::helical_bundle::BundleGridSamplerHelperCOPs

typedef utility::pointer::shared_ptr< BundleGridSamplerHelper > protocols::helical_bundle::BundleGridSamplerHelperOP

typedef utility::vector1< BundleGridSamplerHelperOP > protocols::helical_bundle::BundleGridSamplerHelperOPs

typedef utility::pointer::shared_ptr< BundleGridSampler > protocols::helical_bundle::BundleGridSamplerOP

typedef utility::vector1<BundleGridSamplerOP> protocols::helical_bundle::BundleGridSamplerOPs

typedef utility::pointer::shared_ptr< FitSimpleHelix const > protocols::helical_bundle::FitSimpleHelixCOP

typedef utility::vector1<FitSimpleHelixCOP> protocols::helical_bundle::FitSimpleHelixCOPs

typedef utility::pointer::shared_ptr< FitSimpleHelix > protocols::helical_bundle::FitSimpleHelixOP

typedef utility::vector1<FitSimpleHelixOP> protocols::helical_bundle::FitSimpleHelixOPs

typedef utility::pointer::shared_ptr< MakeBundle const > protocols::helical_bundle::MakeBundleCOP

typedef utility::vector1<MakeBundleCOP> protocols::helical_bundle::MakeBundleCOPs

typedef utility::pointer::shared_ptr< MakeBundleHelix const > protocols::helical_bundle::MakeBundleHelixCOP

typedef utility::vector1<MakeBundleHelixCOP> protocols::helical_bundle::MakeBundleHelixCOPs

typedef utility::pointer::shared_ptr< MakeBundleHelix > protocols::helical_bundle::MakeBundleHelixOP

typedef utility::vector1<MakeBundleHelixOP> protocols::helical_bundle::MakeBundleHelixOPs

typedef utility::pointer::shared_ptr< MakeBundle > protocols::helical_bundle::MakeBundleOP

typedef utility::vector1<MakeBundleOP> protocols::helical_bundle::MakeBundleOPs

typedef utility::pointer::shared_ptr< PerturbBundle const > protocols::helical_bundle::PerturbBundleCOP

typedef utility::vector1<PerturbBundleCOP> protocols::helical_bundle::PerturbBundleCOPs

typedef utility::pointer::shared_ptr< PerturbBundleHelix const > protocols::helical_bundle::PerturbBundleHelixCOP

typedef utility::vector1<PerturbBundleHelixCOP> protocols::helical_bundle::PerturbBundleHelixCOPs

typedef utility::pointer::shared_ptr< PerturbBundleHelix > protocols::helical_bundle::PerturbBundleHelixOP

typedef utility::vector1<PerturbBundleHelixOP> protocols::helical_bundle::PerturbBundleHelixOPs

typedef utility::pointer::shared_ptr< PerturbBundle > protocols::helical_bundle::PerturbBundleOP

typedef utility::vector1<PerturbBundleOP> protocols::helical_bundle::PerturbBundleOPs

typedef utility::pointer::weak_ptr< PerturbBundleOptions > protocols::helical_bundle::PerturbBundleOptionsAP

typedef utility::pointer::weak_ptr< PerturbBundleOptions const > protocols::helical_bundle::PerturbBundleOptionsCAP

typedef utility::vector1< PerturbBundleOptionsCAP > protocols::helical_bundle::PerturbBundleOptionsCAPs

typedef utility::pointer::shared_ptr< PerturbBundleOptions const > protocols::helical_bundle::PerturbBundleOptionsCOP

typedef utility::vector1< PerturbBundleOptionsCOP > protocols::helical_bundle::PerturbBundleOptionsCOPs

typedef utility::pointer::shared_ptr< PerturbBundleOptions > protocols::helical_bundle::PerturbBundleOptionsOP

typedef utility::vector1< PerturbBundleOptionsOP > protocols::helical_bundle::PerturbBundleOptionsOPs

Enumeration Type Documentation

enum protocols::helical_bundle::DoFType

The type of bundle parameter that will be sampled by the BundleGridSampler mover.

Enumerator
bgsh_r0
bgsh_omega0
bgsh_delta_omega0
bgsh_delta_omega1
bgsh_delta_t
bgsh_undefined_dof

enum protocols::helical_bundle::PertType

The type of random perturbation that will be used.

Enumerator
pt_uniform
pt_gaussian
pt_undefined_perturbation

Function Documentation

void protocols::helical_bundle::align_mainchain_atoms	(	core::pose::Pose &	pose,
		core::pose::Pose const &	ref_pose,
		core::Size const	helix_start,
		core::Size const	helix_end
	)

Align mainchain atoms of pose to ref_pose mainchain atoms.

References core::id::BOGUS_ATOM_ID, core::pose::initialize_atomid_map(), core::conformation::Residue::n_mainchain_atoms(), core::pose::Pose::residue(), and core::scoring::superimpose_pose().

Referenced by protocols::helical_bundle::MakeBundleHelix::apply().

void protocols::helical_bundle::align_mainchain_atoms_of_residue_range	(	core::pose::Pose &	pose,
		core::pose::Pose const &	ref_pose,
		core::Size const	helix_start,
		core::Size const	helix_end
	)

Align mainchain atoms of pose to ref_pose mainchain atoms, moving ONLY the residues involved in the alignment.

References core::id::BOGUS_ATOM_ID, core::pose::initialize_atomid_map(), core::conformation::Residue::n_mainchain_atoms(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::scoring::superimpose_pose(), and core::pose::Pose::update_residue_neighbors().

Referenced by protocols::helical_bundle::PerturbBundleHelix::apply().

void protocols::helical_bundle::copy_helix_bondangles	(	core::pose::Pose &	pose,
		core::pose::Pose const &	ref_pose,
		core::Size const	helix_start,
		core::Size const	helix_end
	)

Copy backbone bond angle values from one pose, where helix mainchain atom coordinates have been set with the Crick equations, to another with ideal geometry.

References core::pose::Pose::conformation(), core::conformation::Residue::n_mainchain_atoms(), core::pose::Pose::residue(), core::conformation::Conformation::set_bond_angle(), core::pose::Pose::update_residue_neighbors(), and core::pose::Pose::xyz().

Referenced by protocols::helical_bundle::MakeBundleHelix::apply(), and protocols::helical_bundle::PerturbBundleHelix::apply().

void protocols::helical_bundle::copy_helix_bondlengths	(	core::pose::Pose &	pose,
		core::pose::Pose const &	ref_pose,
		core::Size const	helix_start,
		core::Size const	helix_end
	)

Copy backbone bond length values from one pose, where helix mainchain atom coordinates have been set with the Crick equations, to another with ideal geometry.

References core::pose::Pose::conformation(), numeric::xyzVector< class >::distance(), core::conformation::Residue::n_mainchain_atoms(), core::pose::Pose::residue(), core::conformation::Conformation::set_bond_length(), core::pose::Pose::update_residue_neighbors(), and core::pose::Pose::xyz().

Referenced by protocols::helical_bundle::MakeBundleHelix::apply(), and protocols::helical_bundle::PerturbBundleHelix::apply().

void protocols::helical_bundle::copy_helix_dihedrals	(	core::pose::Pose &	pose,
		core::pose::Pose const &	ref_pose,
		core::Size const	helix_start,
		core::Size const	helix_end
	)

Copy backbone dihedral values from one pose, where helix mainchain atom coordinates have been set with the Crick equations, to another with ideal geometry.

References core::id::BB, core::pose::Pose::conformation(), core::conformation::Residue::mainchain_torsions(), core::pose::Pose::residue(), core::conformation::Conformation::set_torsion(), core::conformation::Conformation::torsion(), and core::pose::Pose::update_residue_neighbors().

Referenced by protocols::helical_bundle::MakeBundleHelix::apply(), and protocols::helical_bundle::PerturbBundleHelix::apply().

void protocols::helical_bundle::generate_atom_positions	(	utility::vector1< utility::vector1< numeric::xyzVector< core::Real > > > &	outvector,
		core::pose::Pose const &	helixpose,
		core::Size const	helix_start,
		core::Size const	helix_end,
		core::Real const &	r0,
		core::Real const &	omega0,
		core::Real const &	delta_omega0,
		core::Real const &	delta_t,
		bool const	invert_helix,
		utility::vector1< core::Real > const &	r1,
		core::Real const &	omega1,
		core::Real const &	z1,
		utility::vector1< core::Real > const &	delta_omega1,
		core::Real const &	delta_omega1_all,
		utility::vector1< core::Real > const &	delta_z1,
		bool &	failed
	)

Generate the x,y,z coordinates of the mainchain atoms using the Crick equations.

Coordinates will be returned as a vector of vectors of xyzVectors. The outer index will refer to residue number, and the inner index will refer to atom number. Returns failed=true if coordinates could not be generated, false otherwise.

References core::conformation::Residue::n_mainchain_atoms(), numeric::constants::d::pi, core::pose::Pose::residue(), x(), numeric::crick_equations::XYZ_BUNDLE(), and z().

Referenced by protocols::helical_bundle::MakeBundleHelix::apply(), and protocols::helical_bundle::PerturbBundleHelix::apply().

void protocols::helical_bundle::place_atom_positions	(	core::pose::Pose &	pose,
		utility::vector1< utility::vector1< numeric::xyzVector< core::Real > > > const &	atom_positions,
		core::Size const	helix_start,
		core::Size const	helix_end
	)

Place the helix mainchain atoms based on the Crick equations.

References core::pose::Pose::set_xyz(), size(), and core::pose::Pose::update_residue_neighbors().

Referenced by protocols::helical_bundle::MakeBundleHelix::apply(), and protocols::helical_bundle::PerturbBundleHelix::apply().

void protocols::helical_bundle::read_minor_helix_params	(	std::string const &	filename,
		utility::vector1< core::Real > &	r1,
		core::Real &	omega1,
		core::Real &	z1,
		utility::vector1< core::Real > &	delta_omega1,
		utility::vector1< core::Real > &	delta_z1
	)

References utility::file::file_basename(), utility::file::file_extension(), utility::io::izstream::open(), basic::database::open(), runtime_assert_string_msg, and TR().

Referenced by protocols::helical_bundle::MakeBundleHelix::set_minor_helix_params_from_file().

static thread_local basic::Tracer protocols::helical_bundle::TR ( "protocols.helical_bundle.PerturbBundleOptions"  )

static

static thread_local basic::Tracer protocols::helical_bundle::TR ( "protocols.helical_bundle.BundleGridSamplerHelper"  )

static

static thread_local basic::Tracer protocols::helical_bundle::TR ( "protocols.helical_bundle.FitSimpleHelix"  )

static

static thread_local basic::Tracer protocols::helical_bundle::TR ( "protocols.helical_bundle.MakeBundleHelix"  )

static

static thread_local basic::Tracer protocols::helical_bundle::TR ( "protocols.helical_bundle.MakeBundle"  )

static

static thread_local basic::Tracer protocols::helical_bundle::TR ( "protocols.helical_bundle.PerturbBundleHelix"  )

static

static thread_local basic::Tracer protocols::helical_bundle::TR ( "protocols.helical_bundle.PerturbBundle"  )

static

static thread_local basic::Tracer protocols::helical_bundle::TR ( "protocols.helical_bundle.util"  )

static

static thread_local basic::Tracer protocols::helical_bundle::TR ( "protocols.helical_bundle.BundleGridSampler"  )

static

Referenced by protocols::helical_bundle::FitSimpleHelix::apply(), protocols::helical_bundle::MakeBundleHelix::apply(), protocols::helical_bundle::PerturbBundleHelix::apply(), protocols::helical_bundle::MakeBundle::apply(), protocols::helical_bundle::PerturbBundle::apply(), protocols::helical_bundle::PerturbBundleOptions::delta(), protocols::helical_bundle::FitSimpleHelixMultiFunc::dfunc(), protocols::helical_bundle::BundleGridSamplerHelper::initialize_samples(), protocols::helical_bundle::FitSimpleHelixMultiFunc::operator()(), protocols::helical_bundle::MakeBundle::parse_my_tag(), protocols::helical_bundle::PerturbBundle::parse_my_tag(), protocols::helical_bundle::PerturbBundle::perturb_values(), read_minor_helix_params(), protocols::helical_bundle::MakeBundle::set_dofs_from_tag(), protocols::helical_bundle::MakeBundle::set_helix_params_from_tag(), protocols::helical_bundle::MakeBundle::set_minor_helix_params_from_tag(), protocols::helical_bundle::MakeBundle::set_minorhelix_defaults_from_tag(), protocols::helical_bundle::MakeBundle::set_other_defaults_from_tag(), protocols::helical_bundle::MakeBundle::set_other_helix_params_from_tag(), protocols::helical_bundle::MakeBundle::set_symmetry_options_from_tag(), and protocols::helical_bundle::PerturbBundle::write_report().

void protocols::helical_bundle::write_minor_helix_params	(	std::string const &	filename,
		utility::vector1< core::Real > const &	r1,
		core::Real const &	omega1,
		core::Real const &	z1,
		utility::vector1< core::Real > const &	delta_omega1,
		utility::vector1< core::Real > const &	delta_z1
	)

References utility::io::ozstream::open(), and runtime_assert_string_msg.