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Rosetta
2020.50
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Classes | |
class | CCDLoopClosureMover |
Close a loop (protein or otherwise) using bi-directional Cyclic Coordinate Descent. More... | |
class | CCDLoopClosureMoverCreator |
CCDLoopClosureMoverCreator allows the MoverFactory to create a CCDLoopClosureMover instance. More... | |
class | FASelectSlidingWindowLoopClosure |
class | LoopClosure |
class | RamaCheck1B |
class | RamaCheck2B |
class | RamaCheckBase |
class | ShortLoopClosure |
class | SlidingWindowLoopClosure |
class | WidthFirstSlidingWindowLoopClosure |
Typedefs | |
using | Matrix = numeric::xyzMatrix< Real > |
typedef utility::pointer::shared_ptr < CCDLoopClosureMover > | CCDLoopClosureMoverOP |
typedef utility::pointer::shared_ptr < CCDLoopClosureMover const > | CCDLoopClosureMoverCOP |
typedef utility::pointer::shared_ptr < CcdMover > | CcdMoverOP |
typedef utility::pointer::shared_ptr < CcdMover const > | CcdMoverCOP |
typedef utility::pointer::shared_ptr < LoopClosure > | LoopClosureOP |
typedef utility::pointer::shared_ptr < LoopClosure const > | LoopClosureCOP |
typedef utility::pointer::shared_ptr < RamaCheckBase > | RamaCheckBaseOP |
typedef utility::pointer::shared_ptr < RamaCheckBase const > | RamaCheckBaseCOP |
typedef utility::pointer::shared_ptr < RamaCheck1B > | RamaCheck1BOP |
typedef utility::pointer::shared_ptr < RamaCheck1B const > | RamaCheck1BCOP |
typedef utility::pointer::shared_ptr < RamaCheck2B > | RamaCheck2BOP |
typedef utility::pointer::shared_ptr < RamaCheck2B const > | RamaCheck2BCOP |
typedef utility::pointer::shared_ptr < ShortLoopClosure > | ShortLoopClosureOP |
typedef utility::pointer::shared_ptr < ShortLoopClosure const > | ShortLoopClosureCOP |
typedef utility::pointer::shared_ptr < SlidingWindowLoopClosure > | SlidingWindowLoopClosureOP |
typedef utility::pointer::shared_ptr < SlidingWindowLoopClosure const > | SlidingWindowLoopClosureCOP |
typedef utility::pointer::shared_ptr < FASelectSlidingWindowLoopClosure > | FASelectSlidingWindowLoopClosureOP |
typedef utility::pointer::shared_ptr < FASelectSlidingWindowLoopClosure const > | FASelectSlidingWindowLoopClosureCOP |
Enumerations | |
enum | ChainDirection { forward = 1, backward, n_chain_directions = backward } |
enum | SecondaryStructureType { helix = 1, strand, coil, n_secondary_structure_types = coil } |
Functions | |
static basic::Tracer | TR ("protocols.loops.loop_closure.ccd.ccd_closure") |
void | load_coords_and_torsions (pose::Pose const &pose, utility::vector1< utility::vector1< core::Vector > > &coords, utility::vector1< utility::vector1< core::Angle > > &torsions) |
void | get_overlap_pos (utility::vector1< utility::vector1< core::Vector > > const &coords, utility::vector1< utility::vector1< core::Angle > > const &torsions, core::uint const cutpoint, core::uint const direction, core::Angle const bond_angle1, core::Length const bond_length, core::Angle const bond_angle2, Matrix &M) |
Distance | compute_single_direction_deviation (vector1< vector1< Vector > > const &coords, vector1< vector1< Angle > > const &torsions, int const cutpoint, core::uint const direction, Angle const ideal_theta_lower, Length const bond_length, Angle const bond_angle2, Matrix const &F) |
std::pair< core::Real, core::Real > | get_deviation (core::pose::Pose const &pose, core::uint const cutpoint) |
std::ostream & | operator<< (std::ostream &os, CCDLoopClosureMover const &mover) |
static basic::Tracer | tr ("protocols.loops.loop_closure.ccd.LoopClosure") |
static basic::Tracer | TR ("protocols.loops.loop_closure.ccd.RamaCheck") |
std::ostream & | operator<< (std::ostream &os, RamaCheckBase const &rama_check) |
static basic::Tracer | tr ("protocols.loops.loop_closure.ccd.ShortLoopClosure") |
static basic::Tracer | tr ("protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure") |
std::string const | VDW_FRAG_STORE ("closure_loop_vdw") |
std::string const | SCORE_FRAG_STORE ("closure_loop_score") |
std::string const | RMSD_FRAG_STORE ("closure_loop_rmsd") |
const Real | REALLY_BAD_SCORE (1000000000.0) |
static basic::Tracer | tr ("protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure") |
Variables | |
std::string const | VDW_FRAG_STORE |
std::string const | SCORE_FRAG_STORE |
std::string const | RMSD_FRAG_STORE |
typedef utility::pointer::shared_ptr< CCDLoopClosureMover const > protocols::loops::loop_closure::ccd::CCDLoopClosureMoverCOP |
typedef utility::pointer::shared_ptr< CCDLoopClosureMover > protocols::loops::loop_closure::ccd::CCDLoopClosureMoverOP |
typedef utility::pointer::shared_ptr< CcdMover const > protocols::loops::loop_closure::ccd::CcdMoverCOP |
typedef utility::pointer::shared_ptr< CcdMover > protocols::loops::loop_closure::ccd::CcdMoverOP |
typedef utility::pointer::shared_ptr< FASelectSlidingWindowLoopClosure const > protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosureCOP |
typedef utility::pointer::shared_ptr< FASelectSlidingWindowLoopClosure > protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosureOP |
typedef utility::pointer::shared_ptr< LoopClosure const > protocols::loops::loop_closure::ccd::LoopClosureCOP |
typedef utility::pointer::shared_ptr< LoopClosure > protocols::loops::loop_closure::ccd::LoopClosureOP |
using protocols::loops::loop_closure::ccd::Matrix = typedef numeric::xyzMatrix<Real> |
typedef utility::pointer::shared_ptr< RamaCheck1B const > protocols::loops::loop_closure::ccd::RamaCheck1BCOP |
typedef utility::pointer::shared_ptr< RamaCheck1B > protocols::loops::loop_closure::ccd::RamaCheck1BOP |
typedef utility::pointer::shared_ptr< RamaCheck2B const > protocols::loops::loop_closure::ccd::RamaCheck2BCOP |
typedef utility::pointer::shared_ptr< RamaCheck2B > protocols::loops::loop_closure::ccd::RamaCheck2BOP |
typedef utility::pointer::shared_ptr< RamaCheckBase const > protocols::loops::loop_closure::ccd::RamaCheckBaseCOP |
typedef utility::pointer::shared_ptr< RamaCheckBase > protocols::loops::loop_closure::ccd::RamaCheckBaseOP |
typedef utility::pointer::shared_ptr< ShortLoopClosure const > protocols::loops::loop_closure::ccd::ShortLoopClosureCOP |
typedef utility::pointer::shared_ptr< ShortLoopClosure > protocols::loops::loop_closure::ccd::ShortLoopClosureOP |
typedef utility::pointer::shared_ptr< SlidingWindowLoopClosure const > protocols::loops::loop_closure::ccd::SlidingWindowLoopClosureCOP |
typedef utility::pointer::shared_ptr< SlidingWindowLoopClosure > protocols::loops::loop_closure::ccd::SlidingWindowLoopClosureOP |
Distance protocols::loops::loop_closure::ccd::compute_single_direction_deviation | ( | vector1< vector1< Vector > > const & | coords, |
vector1< vector1< Angle > > const & | torsions, | ||
int const | cutpoint, | ||
core::uint const | direction, | ||
Angle const | ideal_theta_lower, | ||
Length const | bond_length, | ||
Angle const | bond_angle2, | ||
Matrix const & | F | ||
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References protocols::simple_filters::coords(), core::chemical::element::F, get_overlap_pos(), and core::scoring::electron_density::square().
Referenced by get_deviation().
std::pair< core::Real, core::Real > protocols::loops::loop_closure::ccd::get_deviation | ( | core::pose::Pose const & | pose, |
core::uint const | cutpoint | ||
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References compute_single_direction_deviation(), protocols::simple_filters::coords(), core::chemical::AtomICoor::d(), core::chemical::element::F, core::chemical::ResidueConnection::icoor(), load_coords_and_torsions(), core::conformation::Residue::lower_connect(), core::conformation::Residue::mainchain_atoms(), core::pose::Pose::residue(), core::chemical::AtomICoor::theta(), and core::conformation::Residue::upper_connect().
void protocols::loops::loop_closure::ccd::get_overlap_pos | ( | utility::vector1< utility::vector1< core::Vector > > const & | coords, |
utility::vector1< utility::vector1< core::Angle > > const & | torsions, | ||
core::uint const | cutpoint, | ||
core::uint const | direction, | ||
core::Angle const | bond_angle1, | ||
core::Length const | bond_length, | ||
core::Angle const | bond_angle2, | ||
Matrix & | M | ||
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References core::scoring::packstat::old::angles, protocols::simple_filters::coords(), and core::kinematics::distance().
Referenced by compute_single_direction_deviation().
void protocols::loops::loop_closure::ccd::load_coords_and_torsions | ( | pose::Pose const & | pose, |
utility::vector1< utility::vector1< core::Vector > > & | coords, | ||
utility::vector1< utility::vector1< core::Angle > > & | torsions | ||
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<coords> | an array of coordinates of the main-chain atoms for every residue in the Pose |
<torsions> | an array of values for the main-chain torsion angles for every residue in the Pose |
References protocols::simple_filters::coords(), core::pose::Pose::residue(), core::pose::Pose::size(), and protocols::kinmatch::xyz().
Referenced by get_deviation().
std::ostream & protocols::loops::loop_closure::ccd::operator<< | ( | std::ostream & | os, |
RamaCheckBase const & | rama_check | ||
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std::ostream & protocols::loops::loop_closure::ccd::operator<< | ( | std::ostream & | os, |
CCDLoopClosureMover const & | mover | ||
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const Real protocols::loops::loop_closure::ccd::REALLY_BAD_SCORE | ( | 1000000000. | 0 | ) |
std::string const protocols::loops::loop_closure::ccd::RMSD_FRAG_STORE | ( | "closure_loop_rmsd" | ) |
std::string const protocols::loops::loop_closure::ccd::SCORE_FRAG_STORE | ( | "closure_loop_score" | ) |
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Referenced by protocols::loops::loop_closure::ccd::RamaCheckBase::accept_new_conformation(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::adjust_residue_to_minimize_deviation(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::apply(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::calculate_ccd_angle(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::close_loop_in_single_direction(), protocols::loops::loop_closure::ccd::RamaCheckBase::initialize_starting_rama_scores(), and protocols::loops::loop_closure::ccd::RamaCheckBase::total_net_change_in_rama_score_over_range().
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Referenced by protocols::loops::loop_closure::ccd::ShortLoopClosure::apply(), protocols::loops::loop_closure::ccd::LoopClosure::apply(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::apply(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::determine_loop(), protocols::loops::loop_closure::ccd::LoopClosure::do_frag_cycles(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::generate_window_list(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::process_fragments(), protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::sample_loops(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::sample_loops(), protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::select_final_loop(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::select_final_loop(), protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::set_defaults(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::set_defaults(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::setup_frag_scorefxn(), and protocols::loops::loop_closure::ccd::ShortLoopClosure::ShortLoopClosure().
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std::string const protocols::loops::loop_closure::ccd::VDW_FRAG_STORE | ( | "closure_loop_vdw" | ) |
std::string const protocols::loops::loop_closure::ccd::RMSD_FRAG_STORE |
std::string const protocols::loops::loop_closure::ccd::SCORE_FRAG_STORE |
std::string const protocols::loops::loop_closure::ccd::VDW_FRAG_STORE |