ncbb¶
Bindings for protocols::ncbb namespace
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class
pyrosetta.rosetta.protocols.ncbb.
SecStructMinimizeMultiFunc
¶ Bases:
pyrosetta.rosetta.core.optimization.Multifunc
class for fitting a length of secondary structure keeping the same dihedrals
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abort_min
(self: pyrosetta.rosetta.core.optimization.Multifunc, : pyrosetta.rosetta.utility.vector1_double) → bool¶ - Christophe added the following to allow premature end of minimization
- If you want to abort the minimizer under specific circonstances overload this function and return true if you want to stop, false if you want to continue. FOR THE MOMENT, ONLY IN DFPMIN!
C++: core::optimization::Multifunc::abort_min(const class utility::vector1<double, class std::allocator<double> > &) const –> bool
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dfunc
(self: pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double) → None¶ Calculate function value derivatives
C++: protocols::ncbb::SecStructMinimizeMultiFunc::dfunc(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &) const –> void
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dofs_to_vars
(self: pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc, dofs: pyrosetta.rosetta.utility.vector1_double) → pyrosetta.rosetta.utility.vector1_double¶ give short set of torsions from full dofs
C++: protocols::ncbb::SecStructMinimizeMultiFunc::dofs_to_vars(const class utility::vector1<double, class std::allocator<double> > &) const –> class utility::vector1<double, class std::allocator<double> >
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dump
(self: pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc, vars: pyrosetta.rosetta.utility.vector1_double, vars2: pyrosetta.rosetta.utility.vector1_double) → None¶ Error state reached – derivative does not match gradient
C++: protocols::ncbb::SecStructMinimizeMultiFunc::dump(const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &) const –> void
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vars_to_dofs
(self: pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc, vars: pyrosetta.rosetta.utility.vector1_double) → pyrosetta.rosetta.utility.vector1_double¶ give full dofs from short set of torsions
C++: protocols::ncbb::SecStructMinimizeMultiFunc::vars_to_dofs(const class utility::vector1<double, class std::allocator<double> > &) const –> class utility::vector1<double, class std::allocator<double> >
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pyrosetta.rosetta.protocols.ncbb.
add_attributes_for_common_options
(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None¶ C++: protocols::ncbb::add_attributes_for_common_options(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void
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pyrosetta.rosetta.protocols.ncbb.
calculate_statistics
(pose: pyrosetta.rosetta.core.pose.Pose, score_fxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶ Calculate various statistics, and add them to the current JD2 job
C++: protocols::ncbb::calculate_statistics(const class core::pose::Pose &, class std::shared_ptr<class core::scoring::ScoreFunction>) –> void
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pyrosetta.rosetta.protocols.ncbb.
count_uniq_char
(pattern: str, num: int, uniqs: pyrosetta.rosetta.utility.vector1_char) → None¶ C++: protocols::ncbb::count_uniq_char(class std::basic_string<char>, unsigned long &, class utility::vector1<char, class std::allocator<char> > &) –> void
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pyrosetta.rosetta.protocols.ncbb.
final_design_min
(pose: pyrosetta.rosetta.core.pose.Pose, score_fxn_: pyrosetta.rosetta.core.scoring.ScoreFunction, desn_tf: pyrosetta.rosetta.core.pack.task.TaskFactory) → None¶ C++: protocols::ncbb::final_design_min(class core::pose::Pose &, class std::shared_ptr<class core::scoring::ScoreFunction>, class std::shared_ptr<class core::pack::task::TaskFactory>) –> void
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pyrosetta.rosetta.protocols.ncbb.
get_number_dihedrals
(uniqs: pyrosetta.rosetta.utility.vector1_char, dihedral_pattern: str, alpha_beta_pattern: str) → int¶ C++: protocols::ncbb::get_number_dihedrals(class utility::vector1<char, class std::allocator<char> >, const class std::basic_string<char> &, const class std::basic_string<char> &) –> unsigned long
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pyrosetta.rosetta.protocols.ncbb.
give_dihedral_index
(n: int, uniqs: pyrosetta.rosetta.utility.vector1_char, dihedral_pattern: str, alpha_beta_pattern: str) → int¶ C++: protocols::ncbb::give_dihedral_index(unsigned long, class utility::vector1<char, class std::allocator<char> >, class std::basic_string<char>, class std::basic_string<char>) –> unsigned long
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pyrosetta.rosetta.protocols.ncbb.
init_common_options
(tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap, score_fxn_: pyrosetta.rosetta.core.scoring.ScoreFunction, mc_temp_: float, pert_mc_temp_: float, pert_dock_rot_mag_: float, pert_dock_trans_mag_: float, pert_pep_small_temp_: float, pert_pep_small_H_: float, pert_pep_small_L_: float, pert_pep_small_E_: float, pert_pep_shear_temp_: float, pert_pep_shear_H_: float, pert_pep_shear_L_: float, pert_pep_shear_E_: float, pert_pep_num_rep_: int, pert_num_: int, dock_design_loop_num_: int, no_design_: bool, final_design_min_: bool, use_soft_rep_: bool, mc_initial_pose_: bool, pymol_: bool, keep_history_: bool) → None¶ C++: protocols::ncbb::init_common_options(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &, class std::shared_ptr<class core::scoring::ScoreFunction>, double &, double &, double &, double &, double &, double &, double &, double &, double &, double &, double &, double &, unsigned long &, unsigned long &, unsigned long &, bool &, bool &, bool &, bool &, bool &, bool &) –> void
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pyrosetta.rosetta.protocols.ncbb.
ncbb_design_main_loop
(loop_num: int, pert_num: int, pose: pyrosetta.rosetta.core.pose.Pose, pert_trial: pyrosetta.rosetta.protocols.moves.TrialMover, designable_positions: pyrosetta.rosetta.utility.vector1_unsigned_long, pep_start: int, pep_end: int, desn_ta_min: pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover, score_fxn: pyrosetta.rosetta.core.scoring.ScoreFunction, mc: pyrosetta.rosetta.protocols.moves.MonteCarlo) → None¶ C++: protocols::ncbb::ncbb_design_main_loop(unsigned long, unsigned long, class core::pose::Pose, class std::shared_ptr<class protocols::moves::TrialMover>, class utility::vector1<unsigned long, class std::allocator<unsigned long> >, unsigned long, unsigned long, class std::shared_ptr<class protocols::minimization_packing::TaskAwareMinMover>, class std::shared_ptr<class core::scoring::ScoreFunction>, class std::shared_ptr<class protocols::moves::MonteCarlo>) –> void
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pyrosetta.rosetta.protocols.ncbb.
setup_filter_stats
() → None¶ C++: protocols::ncbb::setup_filter_stats() –> void
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pyrosetta.rosetta.protocols.ncbb.
setup_pert_foldtree
(pose: pyrosetta.rosetta.core.pose.Pose) → None¶ C++: protocols::ncbb::setup_pert_foldtree(class core::pose::Pose &) –> void