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.

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver, pdb_file_names: pyrosetta.rosetta.utility.vector1_std_string, double_mutant_scan: bool, list_file: str, output_mutant_structures: bool) -> None
__init__(self: pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver, arg0: pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver) -> None
__init__(self: pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver, arg0: pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver) -> None

_pybind11_conduit_v1_()¶

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

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.pmut_scan.Mutant) -> None
__init__(self: pyrosetta.rosetta.protocols.pmut_scan.Mutant, arg0: pyrosetta.rosetta.protocols.pmut_scan.Mutant) -> None

_pybind11_conduit_v1_()¶

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

__init__(self: pyrosetta.rosetta.protocols.pmut_scan.MutationData, wt_residue: str, mut_residue: str, pose_resnum: int, pdb_resnum: int, icode: str, chain: str) → None¶

_pybind11_conduit_v1_()¶

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

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver, pdb_file_names: pyrosetta.rosetta.utility.vector1_std_string, double_mutant_scan: bool, list_file: str, output_mutant_structures: bool) -> None
__init__(self: pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver, arg0: pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver) -> None
__init__(self: pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver, arg0: pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver) -> None

_pybind11_conduit_v1_()¶

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