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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::Sizepositions_incompatible_with_task (core::pose::Pose &pose, core::pack::task::PackerTask &packertask)
 
utility::vector1< core::Sizeget_pivot_residues_from_movemap (core::kinematics::MoveMapCOP movemap)
 

Typedef Documentation

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

Function Documentation

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

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().

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

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().

core::Size protocols::backrub::connected_mainchain_atomids ( Pose const &  pose,
core::id::AtomID  atomid,
utility::vector1< core::id::AtomID > &  atomids 
)
utility::vector1< core::Size > protocols::backrub::get_pivot_residues_from_movemap ( core::kinematics::MoveMapCOP  movemap)
void protocols::backrub::init_backrub_mover_with_options ( BackrubMover &  mover)
utility::vector1< core::Size > protocols::backrub::positions_incompatible_with_task ( core::pose::Pose pose,
core::pack::task::PackerTask packertask 
)
bool protocols::backrub::read_fold_tree_from_file ( core::kinematics::FoldTree foldtree,
std::string const &  filepath 
)
bool protocols::backrub::read_fold_tree_from_file ( core::pose::Pose pose,
std::string const &  filepath 
)
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().