pmut_scan

Bindings for protocols::pmut_scan namespace

class pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver

Bases: pyrosetta.rosetta.protocols.pmut_scan.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.

__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.

1. __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
2. __init__(self: pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver, arg0: pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver) -> 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).

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.

1. 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
2. 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
3. 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 &, class std::basic_string<char>, class std::basic_string<char>) –> void

mutants_begin(self: pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver) → __gnu_cxx::__normal_iterator<protocols::pmut_scan::Mutant const*, std::vector<protocols::pmut_scan::Mutant, std::allocator<protocols::pmut_scan::Mutant> > >

C++: protocols::pmut_scan::PointMutScanDriver::mutants_begin() const –> class __gnu_cxx::__normal_iterator<const class protocols::pmut_scan::Mutant *, class std::vector<class protocols::pmut_scan::Mutant, class std::allocator<class protocols::pmut_scan::Mutant> > >

mutants_end(self: pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver) → __gnu_cxx::__normal_iterator<protocols::pmut_scan::Mutant const*, std::vector<protocols::pmut_scan::Mutant, std::allocator<protocols::pmut_scan::Mutant> > >

C++: protocols::pmut_scan::PointMutScanDriver::mutants_end() const –> class __gnu_cxx::__normal_iterator<const class protocols::pmut_scan::Mutant *, class std::vector<class protocols::pmut_scan::Mutant, class std::allocator<class protocols::pmut_scan::Mutant> > >

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