ncbb¶

oop

Bindings for protocols::ncbb namespace

class pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc¶

Bases: pyrosetta.rosetta.core.optimization.Multifunc

class for fitting a length of secondary structure keeping the same dihedrals

__call__(self: pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc, vars: pyrosetta.rosetta.utility.vector1_double) → float¶

Calculate function value (rms squared)

C++: protocols::ncbb::SecStructMinimizeMultiFunc::operator()(const class utility::vector1<double, class std::allocator<double> > &) const –> double

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn_in: pyrosetta.rosetta.core.scoring.ScoreFunction, min_map: pyrosetta.rosetta.core.optimization.MinimizerMap, alpha_beta_pattern: str, dihedral_pattern: str) -> None
__init__(self: pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc, arg0: pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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

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

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> >

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

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> >

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

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

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

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

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

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

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

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: protocols::simple_moves::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::simple_moves::TaskAwareMinMover>, class std::shared_ptr<class core::scoring::ScoreFunction>, class std::shared_ptr<class protocols::moves::MonteCarlo>) –> void

pyrosetta.rosetta.protocols.ncbb.setup_filter_stats() → None¶: C++: protocols::ncbb::setup_filter_stats() –> void

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