pmut_scan¶
Bindings for protocols::pmut_scan namespace
- class pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver¶
Bases:
PointMutScanDriver
this subclass of Ron’s PointMutScanDriver exists to tweak one aspect of his code: instead of looking for total-energy-stabilizing mutations, it looks for binding-energy-DEstabilizing point & pair mutations.
- assign(self: pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver, : pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver) pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver ¶
C++: protocols::pmut_scan::AlterSpecDisruptionDriver::operator=(const class protocols::pmut_scan::AlterSpecDisruptionDriver &) –> class protocols::pmut_scan::AlterSpecDisruptionDriver &
- calculate_neighbor_table(self: pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver, pose: pyrosetta.rosetta.core.pose.Pose, neighbors: pyrosetta.rosetta.utility.vector1_utility_vector1_bool_std_allocator_bool_t) None ¶
C++: protocols::pmut_scan::PointMutScanDriver::calculate_neighbor_table(class core::pose::Pose &, class utility::vector1<class utility::vector1<bool, class std::allocator<bool> >, class std::allocator<class utility::vector1<bool, class std::allocator<bool> > > > &) –> void
- fill_mutations_list(self: pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver) None ¶
C++: protocols::pmut_scan::PointMutScanDriver::fill_mutations_list() –> void
- get_scorefxn(self: pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
accessor for scorefxn_ now that it is private member data
C++: protocols::pmut_scan::PointMutScanDriver::get_scorefxn() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>
- go(self: pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver) None ¶
C++: protocols::pmut_scan::PointMutScanDriver::go() –> void
- make_specific_mutant(*args, **kwargs)¶
Overloaded function.
make_specific_mutant(self: pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver, mutant_poses: pyrosetta.rosetta.utility.vector1_core_pose_Pose, native_poses: pyrosetta.rosetta.utility.vector1_core_pose_Pose, m: protocols::pmut_scan::Mutant) -> None
make_specific_mutant(self: pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver, mutant_poses: pyrosetta.rosetta.utility.vector1_core_pose_Pose, native_poses: pyrosetta.rosetta.utility.vector1_core_pose_Pose, m: protocols::pmut_scan::Mutant, mutation_string: str) -> None
make_specific_mutant(self: pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver, mutant_poses: pyrosetta.rosetta.utility.vector1_core_pose_Pose, native_poses: pyrosetta.rosetta.utility.vector1_core_pose_Pose, m: protocols::pmut_scan::Mutant, mutation_string: str, mutation_string_PDB_numbering: str) -> None
C++: protocols::pmut_scan::PointMutScanDriver::make_specific_mutant(class utility::vector1<class core::pose::Pose, class std::allocator<class core::pose::Pose> > &, class utility::vector1<class core::pose::Pose, class std::allocator<class core::pose::Pose> > &, class protocols::pmut_scan::Mutant &, std::string, std::string) –> void
- n_mutants(self: pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver) int ¶
C++: protocols::pmut_scan::PointMutScanDriver::n_mutants() const –> unsigned long
- read_in_structures(self: pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver) None ¶
C++: protocols::pmut_scan::PointMutScanDriver::read_in_structures() –> void
- reject_mutant(self: pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver, mutant: protocols::pmut_scan::Mutant, pose: pyrosetta.rosetta.core.pose.Pose) bool ¶
offers a chance for child classes to inject mutant selection logic
C++: protocols::pmut_scan::AlterSpecDisruptionDriver::reject_mutant(const class protocols::pmut_scan::Mutant &, const class core::pose::Pose &) –> bool
- score(self: pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver, pose: pyrosetta.rosetta.core.pose.Pose) float ¶
return a score that is a ddG of binding, rather than a ddG of the interface. It returns a reversed value because this class wants to find DEstabilizing mutations.
C++: protocols::pmut_scan::AlterSpecDisruptionDriver::score(class core::pose::Pose &) –> double
- set_ddG_cutoff(self: pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver, threshold: float) None ¶
C++: protocols::pmut_scan::PointMutScanDriver::set_ddG_cutoff(double) –> void
- class pyrosetta.rosetta.protocols.pmut_scan.Mutant¶
Bases:
pybind11_object
- add_mutation(self: pyrosetta.rosetta.protocols.pmut_scan.Mutant, md: pyrosetta.rosetta.protocols.pmut_scan.MutationData) None ¶
C++: protocols::pmut_scan::Mutant::add_mutation(class protocols::pmut_scan::MutationData) –> void
- n_mutations(self: pyrosetta.rosetta.protocols.pmut_scan.Mutant) int ¶
C++: protocols::pmut_scan::Mutant::n_mutations() const –> unsigned long
- pop_mutation(self: pyrosetta.rosetta.protocols.pmut_scan.Mutant) pyrosetta.rosetta.protocols.pmut_scan.MutationData ¶
C++: protocols::pmut_scan::Mutant::pop_mutation() –> class protocols::pmut_scan::MutationData
- class pyrosetta.rosetta.protocols.pmut_scan.MutationData¶
Bases:
pybind11_object
- mut_residue(self: pyrosetta.rosetta.protocols.pmut_scan.MutationData) str ¶
C++: protocols::pmut_scan::MutationData::mut_residue() const –> char
- mutation_string(self: pyrosetta.rosetta.protocols.pmut_scan.MutationData) str ¶
C++: protocols::pmut_scan::MutationData::mutation_string() const –> std::string
- mutation_string_PDB_numbering(self: pyrosetta.rosetta.protocols.pmut_scan.MutationData) str ¶
C++: protocols::pmut_scan::MutationData::mutation_string_PDB_numbering() const –> std::string
- pdb_chain(self: pyrosetta.rosetta.protocols.pmut_scan.MutationData) str ¶
C++: protocols::pmut_scan::MutationData::pdb_chain() const –> char
- pose_resnum(self: pyrosetta.rosetta.protocols.pmut_scan.MutationData) int ¶
C++: protocols::pmut_scan::MutationData::pose_resnum() const –> unsigned long
- print_mutation_data(self: pyrosetta.rosetta.protocols.pmut_scan.MutationData, md: pyrosetta.rosetta.protocols.pmut_scan.MutationData) None ¶
C++: protocols::pmut_scan::MutationData::print_mutation_data(class protocols::pmut_scan::MutationData &) –> void
- class pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver¶
Bases:
pybind11_object
- assign(self: pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver, : pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver) pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver ¶
C++: protocols::pmut_scan::PointMutScanDriver::operator=(const class protocols::pmut_scan::PointMutScanDriver &) –> class protocols::pmut_scan::PointMutScanDriver &
- calculate_neighbor_table(self: pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver, pose: pyrosetta.rosetta.core.pose.Pose, neighbors: pyrosetta.rosetta.utility.vector1_utility_vector1_bool_std_allocator_bool_t) None ¶
C++: protocols::pmut_scan::PointMutScanDriver::calculate_neighbor_table(class core::pose::Pose &, class utility::vector1<class utility::vector1<bool, class std::allocator<bool> >, class std::allocator<class utility::vector1<bool, class std::allocator<bool> > > > &) –> void
- fill_mutations_list(self: pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver) None ¶
C++: protocols::pmut_scan::PointMutScanDriver::fill_mutations_list() –> void
- get_scorefxn(self: pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
accessor for scorefxn_ now that it is private member data
C++: protocols::pmut_scan::PointMutScanDriver::get_scorefxn() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>
- go(self: pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver) None ¶
C++: protocols::pmut_scan::PointMutScanDriver::go() –> void
- make_specific_mutant(*args, **kwargs)¶
Overloaded function.
make_specific_mutant(self: pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver, mutant_poses: pyrosetta.rosetta.utility.vector1_core_pose_Pose, native_poses: pyrosetta.rosetta.utility.vector1_core_pose_Pose, m: protocols::pmut_scan::Mutant) -> None
make_specific_mutant(self: pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver, mutant_poses: pyrosetta.rosetta.utility.vector1_core_pose_Pose, native_poses: pyrosetta.rosetta.utility.vector1_core_pose_Pose, m: protocols::pmut_scan::Mutant, mutation_string: str) -> None
make_specific_mutant(self: pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver, mutant_poses: pyrosetta.rosetta.utility.vector1_core_pose_Pose, native_poses: pyrosetta.rosetta.utility.vector1_core_pose_Pose, m: protocols::pmut_scan::Mutant, mutation_string: str, mutation_string_PDB_numbering: str) -> None
C++: protocols::pmut_scan::PointMutScanDriver::make_specific_mutant(class utility::vector1<class core::pose::Pose, class std::allocator<class core::pose::Pose> > &, class utility::vector1<class core::pose::Pose, class std::allocator<class core::pose::Pose> > &, class protocols::pmut_scan::Mutant &, std::string, std::string) –> void
- n_mutants(self: pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver) int ¶
C++: protocols::pmut_scan::PointMutScanDriver::n_mutants() const –> unsigned long
- read_in_structures(self: pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver) None ¶
C++: protocols::pmut_scan::PointMutScanDriver::read_in_structures() –> void
- reject_mutant(self: pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver, : protocols::pmut_scan::Mutant, : pyrosetta.rosetta.core.pose.Pose) bool ¶
offers a chance for child classes to inject mutant selection logic
C++: protocols::pmut_scan::PointMutScanDriver::reject_mutant(const class protocols::pmut_scan::Mutant &, const class core::pose::Pose &) –> bool
- score(self: pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver, pose: pyrosetta.rosetta.core.pose.Pose) float ¶
score the pose for the purposes of determining if a mutation is “good” or not. In the base implementation, it’s just a scorefunction call, but in child implementations it may be fancier (for example, calculating a binding energy instead)
C++: protocols::pmut_scan::PointMutScanDriver::score(class core::pose::Pose &) –> double
- set_ddG_cutoff(self: pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver, threshold: float) None ¶
C++: protocols::pmut_scan::PointMutScanDriver::set_ddG_cutoff(double) –> void