CartesianddG

Bindings for protocols::ddg::CartesianddG namespace

class pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet

Bases: pybind11_builtins.pybind11_object

add_fragments(self: pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet, resnum: int, fragset: pyrosetta.rosetta.core.fragment.FragSet) None

C++: protocols::ddg::CartesianddG::MutationSet::add_fragments(unsigned long, class std::shared_ptr<class core::fragment::FragSet>) –> void

add_score(self: pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet, score: float) None

C++: protocols::ddg::CartesianddG::MutationSet::add_score(double) –> void

add_wildtypes(self: pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::ddg::CartesianddG::MutationSet::add_wildtypes(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet, : pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet) pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet

C++: protocols::ddg::CartesianddG::MutationSet::operator=(const class protocols::ddg::CartesianddG::MutationSet &) –> class protocols::ddg::CartesianddG::MutationSet &

generate_tag(self: pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet) str

C++: protocols::ddg::CartesianddG::MutationSet::generate_tag() –> std::string

get_aa(self: pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet, index: int) pyrosetta.rosetta.core.chemical.AA

C++: protocols::ddg::CartesianddG::MutationSet::get_aa(unsigned long) –> enum core::chemical::AA

get_fragments(self: pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet) pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_core_fragment_FragSet_t

C++: protocols::ddg::CartesianddG::MutationSet::get_fragments() –> class std::map<unsigned long, class std::shared_ptr<class core::fragment::FragSet>, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class std::shared_ptr<class core::fragment::FragSet> > > >

get_mutation_pairs(self: pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet) pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_std_string_t

C++: protocols::ddg::CartesianddG::MutationSet::get_mutation_pairs() –> class utility::vector1<struct std::pair<unsigned long, std::string >, class std::allocator<struct std::pair<unsigned long, std::string > > >

get_mutations(self: pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet) pyrosetta.rosetta.utility.vector1_core_chemical_AA

C++: protocols::ddg::CartesianddG::MutationSet::get_mutations() –> class utility::vector1<enum core::chemical::AA, class std::allocator<enum core::chemical::AA> >

get_prolines(self: pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet) pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::ddg::CartesianddG::MutationSet::get_prolines() –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

get_resnum(self: pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet, index: int) int

C++: protocols::ddg::CartesianddG::MutationSet::get_resnum(unsigned long) –> unsigned long

get_resnums(self: pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet) pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::ddg::CartesianddG::MutationSet::get_resnums() –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

has_proline(self: pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet) bool

C++: protocols::ddg::CartesianddG::MutationSet::has_proline() –> bool

is_converged(self: pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet, n_to_check: int, cutoff: float) bool

C++: protocols::ddg::CartesianddG::MutationSet::is_converged(const unsigned long, const double) –> bool

is_same(self: pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet, otherset: pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet) bool

C++: protocols::ddg::CartesianddG::MutationSet::is_same(class protocols::ddg::CartesianddG::MutationSet) –> bool

iterations(self: pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet) int

C++: protocols::ddg::CartesianddG::MutationSet::iterations() –> unsigned long

set_tag(self: pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet, newtag: str) None

C++: protocols::ddg::CartesianddG::MutationSet::set_tag(std::string) –> void

subtract_iterations(self: pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet, n_sub: int) None

C++: protocols::ddg::CartesianddG::MutationSet::subtract_iterations(unsigned long) –> void

pyrosetta.rosetta.protocols.ddg.CartesianddG.break_any_disulfide(pose: pyrosetta.rosetta.core.pose.Pose, res: int) None

if the residue is part of a disulfide bond break it.

C++: protocols::ddg::CartesianddG::break_any_disulfide(class core::pose::Pose &, const unsigned long) –> void

pyrosetta.rosetta.protocols.ddg.CartesianddG.extract_element(context_pose: pyrosetta.rosetta.core.pose.Pose, peptide_pose: pyrosetta.rosetta.core.pose.Pose, mutations: pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet, neighbors_to_extract: int) None

Trim the two input poses to match the context of the structure and the peptide around the target mutation respectively.

C++: protocols::ddg::CartesianddG::extract_element(class core::pose::Pose &, class core::pose::Pose &, class protocols::ddg::CartesianddG::MutationSet, const unsigned long) –> void

pyrosetta.rosetta.protocols.ddg.CartesianddG.extracted_score(pose: pyrosetta.rosetta.core.pose.Pose, mutations: pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet, score_fxn: pyrosetta.rosetta.core.scoring.ScoreFunction, n_nbrs_to_extract: int) float

Extract the neighbors around the mutation(s) and calculate the score ignoring the local electrostatic and hydrogen bonding.

C++: protocols::ddg::CartesianddG::extracted_score(class core::pose::Pose &, class protocols::ddg::CartesianddG::MutationSet, class std::shared_ptr<class core::scoring::ScoreFunction>, const unsigned long) –> double

pyrosetta.rosetta.protocols.ddg.CartesianddG.find_interface_jump(pose: pyrosetta.rosetta.core.pose.Pose, interface_ddg: int) int

Finds the jump that corresponds to the interface

C++: protocols::ddg::CartesianddG::find_interface_jump(class core::pose::Pose &, const unsigned long) –> unsigned long

pyrosetta.rosetta.protocols.ddg.CartesianddG.interface_separate_and_score(mutations: pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet, work_pose: pyrosetta.rosetta.core.pose.Pose, score_fxn: pyrosetta.rosetta.core.scoring.ScoreFunction, neighbors: pyrosetta.rosetta.utility.vector1_unsigned_long, bbnbrs: int, interface_ddg: int, flex_bb: bool, cartesian: bool, ofp: pyrosetta.rosetta.utility.io.ozstream) None

Separates the two interfaces and then runs the optimazation calcuations and writes the results.

C++: protocols::ddg::CartesianddG::interface_separate_and_score(class protocols::ddg::CartesianddG::MutationSet, class core::pose::Pose &, class std::shared_ptr<class core::scoring::ScoreFunction>, class utility::vector1<unsigned long, class std::allocator<unsigned long> >, const unsigned long, const unsigned long, bool, bool, class utility::io::ozstream &) –> void

pyrosetta.rosetta.protocols.ddg.CartesianddG.involves_prolines(pose: pyrosetta.rosetta.core.pose.Pose, mutations: pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet) pyrosetta.rosetta.utility.vector1_unsigned_long

Return a list of any residues in the mutation set that will involve proline.

C++: protocols::ddg::CartesianddG::involves_prolines(class core::pose::Pose &, class protocols::ddg::CartesianddG::MutationSet) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.ddg.CartesianddG.min_pack_min_element(pose: pyrosetta.rosetta.core.pose.Pose, min_resis: pyrosetta.rosetta.utility.vector1_unsigned_long, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

Cartesian Minimizer the residues in the set

C++: protocols::ddg::CartesianddG::min_pack_min_element(class core::pose::Pose &, class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

pyrosetta.rosetta.protocols.ddg.CartesianddG.mutate_pose(pose: pyrosetta.rosetta.core.pose.Pose, mutations: pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet, score_fxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

Mutate the pose to the residues specified in the mutation set.

C++: protocols::ddg::CartesianddG::mutate_pose(class core::pose::Pose &, class protocols::ddg::CartesianddG::MutationSet, class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

pyrosetta.rosetta.protocols.ddg.CartesianddG.mutate_sequence(sequence: str, mutations: pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet) None

Mutate the one letter sequence to match the mutation set

C++: protocols::ddg::CartesianddG::mutate_sequence(std::string &, class protocols::ddg::CartesianddG::MutationSet) –> void

pyrosetta.rosetta.protocols.ddg.CartesianddG.optimize_structure(*args, **kwargs)

Overloaded function.

  1. optimize_structure(mutations: pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet, fa_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, neighbors: pyrosetta.rosetta.utility.vector1_unsigned_long, flex_bb: bool) -> None

  2. optimize_structure(mutations: pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet, fa_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, neighbors: pyrosetta.rosetta.utility.vector1_unsigned_long, flex_bb: bool, cartesian: bool) -> None

  3. optimize_structure(mutations: pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet, fa_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, neighbors: pyrosetta.rosetta.utility.vector1_unsigned_long, flex_bb: bool, cartesian: bool, bbnbrs: int) -> None

C++: protocols::ddg::CartesianddG::optimize_structure(class protocols::ddg::CartesianddG::MutationSet, class std::shared_ptr<class core::scoring::ScoreFunction>, class core::pose::Pose &, class utility::vector1<unsigned long, class std::allocator<unsigned long> >, const bool, const bool, const unsigned long) –> void

pyrosetta.rosetta.protocols.ddg.CartesianddG.run(pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::ddg::CartesianddG::run(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.ddg.CartesianddG.sample_fragments(pose: pyrosetta.rosetta.core.pose.Pose, mutations: pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, bbnbrs: int, ncycles: int) None

C++: protocols::ddg::CartesianddG::sample_fragments(class core::pose::Pose &, class protocols::ddg::CartesianddG::MutationSet &, class std::shared_ptr<class core::scoring::ScoreFunction>, const unsigned long, const unsigned long) –> void