protocols::backrub Namespace Reference

Classes
class	BackrubMover
	class for applying backrub moves to arbitrary protein segments More...
class	BackrubMoverCreator
class	BackrubProtocol
class	BackrubProtocolCreator
class	BackrubSegment
	a class for holind information about individual backrub segments More...
class	BackrubSidechainMover
class	BackrubSidechainMoverCreator

Typedefs
typedef utility::pointer::shared_ptr< BackrubMover >	BackrubMoverOP
typedef utility::pointer::shared_ptr< BackrubMover const >	BackrubMoverCOP
typedef utility::pointer::shared_ptr< BackrubProtocol >	BackrubProtocolOP
typedef utility::pointer::shared_ptr< BackrubProtocol const >	BackrubProtocolCOP
typedef utility::pointer::shared_ptr< BackrubSidechainMover >	BackrubSidechainMoverOP
typedef utility::pointer::shared_ptr< BackrubSidechainMover const >	BackrubSidechainMoverCOP

Functions
void	init_backrub_mover_with_options (BackrubMover &mover)
int	tree_distance (kinematics::tree::AtomCOP ancestor, kinematics::tree::AtomCOP descendent)
	calculate the number of atom tree bonds between the two atoms possibly move this into the Atom class More...
core::Size	connected_mainchain_atomids (Pose const &pose, core::id::AtomID atomid, utility::vector1< core::id::AtomID > &atomids)
void	backrub_rotation_constants (core::kinematics::tree::AtomCOP PM2_atom, core::kinematics::tree::AtomCOP PM1_atom, core::kinematics::tree::AtomCOP P_atom, core::kinematics::tree::AtomCOP PP1_atom, core::kinematics::tree::AtomCOP PP2_atom, core::kinematics::tree::AtomCOP REF_atom, utility::vector0< Real > &constants, core::Real const alpha_min, core::Real const alpha_max, numeric::IntervalSet< core::Real > *tau_intervals)
void	backrub_rotation_angles (utility::vector0< Real > const &constants, Real const tau, Real &bondange, Real &torsion1, Real &torsion2)
void	backrub_rotation_constants (core::kinematics::tree::AtomCOP PM2_atom, core::kinematics::tree::AtomCOP PM1_atom, core::kinematics::tree::AtomCOP P_atom, core::kinematics::tree::AtomCOP PP1_atom, core::kinematics::tree::AtomCOP PP2_atom, core::kinematics::tree::AtomCOP REF_atom, utility::vector0< core::Real > &constants, core::Real const alpha_min=0, core::Real const alpha_max=numeric::NumericTraits< core::Real >::pi(), numeric::IntervalSet< core::Real > *tau_intervals=nullptr)
	calculate constants necessary for calculating internal angles/derivatives More...
void	backrub_rotation_angles (utility::vector0< core::Real > const &constants, core::Real const tau, core::Real &bondange, core::Real &torsion1, core::Real &torsion2)
	calculate internal coordinate values for any tau value More...
bool	read_fold_tree_from_file (core::kinematics::FoldTree &foldtree, std::string const &filepath)
bool	read_fold_tree_from_file (core::pose::Pose &pose, std::string const &filepath)
void	append_fold_tree_to_file (core::kinematics::FoldTree const &foldtree, std::string file_path)
utility::vector1< core::Size >	positions_incompatible_with_task (core::pose::Pose &pose, core::pack::task::PackerTask &packertask)
utility::vector1< core::Size >	get_pivot_residues_from_movemap (core::kinematics::MoveMapCOP movemap)

Typedef Documentation

BackrubMoverCOP

typedef utility::pointer::shared_ptr< BackrubMover const > protocols::backrub::BackrubMoverCOP

BackrubMoverOP

typedef utility::pointer::shared_ptr< BackrubMover > protocols::backrub::BackrubMoverOP

BackrubProtocolCOP

typedef utility::pointer::shared_ptr< BackrubProtocol const > protocols::backrub::BackrubProtocolCOP

BackrubProtocolOP

typedef utility::pointer::shared_ptr< BackrubProtocol > protocols::backrub::BackrubProtocolOP

BackrubSidechainMoverCOP

typedef utility::pointer::shared_ptr< BackrubSidechainMover const > protocols::backrub::BackrubSidechainMoverCOP

BackrubSidechainMoverOP

typedef utility::pointer::shared_ptr< BackrubSidechainMover > protocols::backrub::BackrubSidechainMoverOP

Function Documentation

append_fold_tree_to_file()

void protocols::backrub::append_fold_tree_to_file	(	core::kinematics::FoldTree const &	foldtree,
		std::string	file_path
	)

References core::conformation::membrane::out, and protocols::TR().

Referenced by protocols::backrub::BackrubProtocol::apply().

backrub_rotation_angles() [1/2]

void protocols::backrub::backrub_rotation_angles	(	utility::vector0< core::Real > const &	constants,
		core::Real const	tau,
		core::Real &	bondange,
		core::Real &	torsion1,
		core::Real &	torsion2
	)

calculate internal coordinate values for any tau value

backrub_rotation_angles() [2/2]

void protocols::backrub::backrub_rotation_angles	(	utility::vector0< Real > const &	constants,
		Real const	tau,
		Real &	bondange,
		Real &	torsion1,
		Real &	torsion2
	)

tau is the angular displacement

Referenced by protocols::backrub::BackrubMover::rotate_segment().

backrub_rotation_constants() [1/2]

void protocols::backrub::backrub_rotation_constants	(	core::kinematics::tree::AtomCOP	PM2_atom,
		core::kinematics::tree::AtomCOP	PM1_atom,
		core::kinematics::tree::AtomCOP	P_atom,
		core::kinematics::tree::AtomCOP	PP1_atom,
		core::kinematics::tree::AtomCOP	PP2_atom,
		core::kinematics::tree::AtomCOP	REF_atom,
		utility::vector0< core::Real > &	constants,
		core::Real const	alpha_min = 0,
		core::Real const	alpha_max = numeric::NumericTraits< core::Real >::pi(),
		numeric::IntervalSet< core::Real > *	tau_intervals = nullptr
	)

calculate constants necessary for calculating internal angles/derivatives

backrub_rotation_constants() [2/2]

void protocols::backrub::backrub_rotation_constants	(	core::kinematics::tree::AtomCOP	PM2_atom,
		core::kinematics::tree::AtomCOP	PM1_atom,
		core::kinematics::tree::AtomCOP	P_atom,
		core::kinematics::tree::AtomCOP	PP1_atom,
		core::kinematics::tree::AtomCOP	PP2_atom,
		core::kinematics::tree::AtomCOP	REF_atom,
		utility::vector0< Real > &	constants,
		core::Real const	alpha_min,
		core::Real const	alpha_max,
		numeric::IntervalSet< core::Real > *	tau_intervals
	)

PM1 & PM2 are the parent and grandparent atoms (respectively) of the pivot atom, P. PP1 and PP2 are the child and grandchiled atoms (respectively) of the pivot atom. PM2 and PP2 are optional and may be NULL. REF is the other (reference) pivot atom that defines the rotation axis.

The first 9 constants returned represent A1-A3, B1-B3, & C1-C3 as described in Betancourt 2005. The last 6 constants allow calculation of the signs of phi and psi. They could be called B4-B6 & C4-C6. For a given tau angle, phi is negative if the following is true:

B4 < B5 * cos(B6 + tau)

Similarly, psi is negative if the following is true:

C4 < C5 * cos(C6 + tau)

References core::chemical::element::C, protocols::frag_picker::CA, core::chemical::element::N, core::chemical::element::U, core::chemical::element::V, and core::chemical::element::W.

Referenced by protocols::backrub::BackrubMover::random_angle(), and protocols::backrub::BackrubMover::rotate_segment().

connected_mainchain_atomids()

core::Size protocols::backrub::connected_mainchain_atomids	(	Pose const &	pose,
		core::id::AtomID	atomid,
		utility::vector1< core::id::AtomID > &	atomids
	)

References core::conformation::Residue::actual_residue_connection(), core::id::AtomID::atomno(), core::conformation::Residue::connection_incomplete(), core::chemical::ResConnID::connid(), core::chemical::ResidueType::mainchain_atoms(), core::conformation::Residue::mainchain_atoms(), core::conformation::Residue::n_possible_residue_connections(), core::chemical::ResConnID::resid(), core::pose::Pose::residue(), core::conformation::Residue::residue_connect_atom_index(), core::pose::Pose::residue_type(), core::id::AtomID::rsd(), and core::conformation::Residue::seqpos().

Referenced by protocols::backrub::BackrubMover::add_mainchain_segments().

get_pivot_residues_from_movemap()

utility::vector1< core::Size > protocols::backrub::get_pivot_residues_from_movemap

(

core::kinematics::MoveMapCOP

movemap

)

References core::id::BB.

Referenced by protocols::backrub::BackrubMover::set_movemap(), and protocols::backrub::BackrubProtocol::set_movemap().

init_backrub_mover_with_options()

void protocols::backrub::init_backrub_mover_with_options

(

BackrubMover &

mover

)

References protocols::backrub::BackrubMover::set_max_atoms(), protocols::backrub::BackrubMover::set_min_atoms(), protocols::backrub::BackrubMover::set_movemap(), protocols::backrub::BackrubMover::set_pivot_atoms(), and protocols::backrub::BackrubMover::set_pivot_residues().

Referenced by protocols::backrub::BackrubMover::init_with_options().

positions_incompatible_with_task()

utility::vector1< core::Size > protocols::backrub::positions_incompatible_with_task	(	core::pose::Pose &	pose,
		core::pack::task::PackerTask &	packertask
	)

References core::pack::task::ResidueLevelTask::allowed_residue_types_begin(), core::pack::task::ResidueLevelTask::allowed_residue_types_end(), core::chemical::ResidueTypeBase::name(), core::pack::task::PackerTask::pack_residue(), core::pack::task::PackerTask::residue_task(), core::pose::Pose::residue_type(), core::pose::Pose::size(), and core::pack::task::PackerTask::total_residue().

Referenced by protocols::backrub::BackrubProtocol::apply().

read_fold_tree_from_file() [1/2]

bool protocols::backrub::read_fold_tree_from_file	(	core::kinematics::FoldTree &	foldtree,
		std::string const &	filepath
	)

References protocols::TR().

Referenced by protocols::backrub::BackrubProtocol::apply(), and read_fold_tree_from_file().

read_fold_tree_from_file() [2/2]

bool protocols::backrub::read_fold_tree_from_file	(	core::pose::Pose &	pose,
		std::string const &	filepath
	)

References core::pose::Pose::fold_tree(), core::kinematics::FoldTree::nres(), read_fold_tree_from_file(), core::pose::Pose::size(), and protocols::TR().

tree_distance()

int protocols::backrub::tree_distance	(	kinematics::tree::AtomCOP	ancestor,
		kinematics::tree::AtomCOP	descendent
	)

calculate the number of atom tree bonds between the two atoms possibly move this into the Atom class

References core::kinematics::tree::Atom::parent().

Referenced by protocols::backrub::BackrubMover::add_segment().