Bindings for protocols::pmut_scan namespace

Classes
		builtins.object Mutant MutationData PointMutScanDriver AlterSpecDisruptionDriver   class AlterSpecDisruptionDriver(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.     Method resolution order: AlterSpecDisruptionDriver PointMutScanDriver builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, pdb_file_names : rosetta.utility.vector1_std_string, double_mutant_scan : bool, list_file : str, output_mutant_structures : bool) -> NoneType   2. __init__(handle, rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver,  : rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver) -> rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver reject_mutant(...) from builtins.PyCapsule reject_mutant(self : rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver, mutant : protocols::pmut_scan::Mutant, pose : rosetta.core.pose.Pose) -> bool   offers a chance for child classes to inject mutant selection logic score(...) from builtins.PyCapsule score(self : rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver, pose : 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. Methods inherited from PointMutScanDriver: calculate_neighbor_table(...) from builtins.PyCapsule calculate_neighbor_table(self : rosetta.protocols.pmut_scan.PointMutScanDriver, pose : rosetta.core.pose.Pose, neighbors : rosetta.utility.vector1_utility_vector1_bool_std_allocator_bool_t) -> NoneType fill_mutations_list(...) from builtins.PyCapsule fill_mutations_list(rosetta.protocols.pmut_scan.PointMutScanDriver) -> NoneType get_scorefxn(...) from builtins.PyCapsule get_scorefxn(rosetta.protocols.pmut_scan.PointMutScanDriver) -> rosetta.core.scoring.ScoreFunction   accessor for scorefxn_ now that it is private member data go(...) from builtins.PyCapsule go(rosetta.protocols.pmut_scan.PointMutScanDriver) -> NoneType make_specific_mutant(...) from builtins.PyCapsule make_specific_mutant(*args, **kwargs) Overloaded function.   1. make_specific_mutant(self : rosetta.protocols.pmut_scan.PointMutScanDriver, mutant_poses : rosetta.utility.vector1_core_pose_Pose, native_poses : rosetta.utility.vector1_core_pose_Pose, m : protocols::pmut_scan::Mutant) -> NoneType   2. make_specific_mutant(self : rosetta.protocols.pmut_scan.PointMutScanDriver, mutant_poses : rosetta.utility.vector1_core_pose_Pose, native_poses : rosetta.utility.vector1_core_pose_Pose, m : protocols::pmut_scan::Mutant, mutation_string : str) -> NoneType   3. make_specific_mutant(self : rosetta.protocols.pmut_scan.PointMutScanDriver, mutant_poses : rosetta.utility.vector1_core_pose_Pose, native_poses : rosetta.utility.vector1_core_pose_Pose, m : protocols::pmut_scan::Mutant, mutation_string : str, mutation_string_PDB_numbering : str) -> NoneType mutants_begin(...) from builtins.PyCapsule mutants_begin(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> > > mutants_end(...) from builtins.PyCapsule mutants_end(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> > > n_mutants(...) from builtins.PyCapsule n_mutants(rosetta.protocols.pmut_scan.PointMutScanDriver) -> int read_in_structures(...) from builtins.PyCapsule read_in_structures(rosetta.protocols.pmut_scan.PointMutScanDriver) -> NoneType set_ddG_cutoff(...) from builtins.PyCapsule set_ddG_cutoff(self : rosetta.protocols.pmut_scan.PointMutScanDriver, threshold : float) -> NoneType   class Mutant(builtins.object)       Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(self : rosetta.protocols.pmut_scan.Mutant, m_other : rosetta.protocols.pmut_scan.Mutant) -> bool __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.pmut_scan.Mutant) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.protocols.pmut_scan.Mutant) -> str add_mutation(...) from builtins.PyCapsule add_mutation(self : rosetta.protocols.pmut_scan.Mutant, md : rosetta.protocols.pmut_scan.MutationData) -> NoneType mutations_begin(...) from builtins.PyCapsule mutations_begin(rosetta.protocols.pmut_scan.Mutant) -> __gnu_cxx::__normal_iterator<protocols::pmut_scan::MutationData const*, std::vector<protocols::pmut_scan::MutationData, std::allocator<protocols::pmut_scan::MutationData> > > mutations_end(...) from builtins.PyCapsule mutations_end(rosetta.protocols.pmut_scan.Mutant) -> __gnu_cxx::__normal_iterator<protocols::pmut_scan::MutationData const*, std::vector<protocols::pmut_scan::MutationData, std::allocator<protocols::pmut_scan::MutationData> > > n_mutations(...) from builtins.PyCapsule n_mutations(rosetta.protocols.pmut_scan.Mutant) -> int pop_mutation(...) from builtins.PyCapsule pop_mutation(rosetta.protocols.pmut_scan.Mutant) -> rosetta.protocols.pmut_scan.MutationData   class MutationData(builtins.object)       Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(self : rosetta.protocols.pmut_scan.MutationData, md_other : rosetta.protocols.pmut_scan.MutationData) -> bool __init__(...) from builtins.PyCapsule __init__(self : rosetta.protocols.pmut_scan.MutationData, wt_residue : str, mut_residue : str, pose_resnum : int, pdb_resnum : int, icode : str, chain : str) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.protocols.pmut_scan.MutationData) -> str mut_residue(...) from builtins.PyCapsule mut_residue(rosetta.protocols.pmut_scan.MutationData) -> str mutation_string(...) from builtins.PyCapsule mutation_string(rosetta.protocols.pmut_scan.MutationData) -> str mutation_string_PDB_numbering(...) from builtins.PyCapsule mutation_string_PDB_numbering(rosetta.protocols.pmut_scan.MutationData) -> str pdb_chain(...) from builtins.PyCapsule pdb_chain(rosetta.protocols.pmut_scan.MutationData) -> str pose_resnum(...) from builtins.PyCapsule pose_resnum(rosetta.protocols.pmut_scan.MutationData) -> int print_mutation_data(...) from builtins.PyCapsule print_mutation_data(self : rosetta.protocols.pmut_scan.MutationData, md : rosetta.protocols.pmut_scan.MutationData) -> NoneType   class PointMutScanDriver(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, pdb_file_names : rosetta.utility.vector1_std_string, double_mutant_scan : bool, list_file : str, output_mutant_structures : bool) -> NoneType   2. __init__(handle, rosetta.protocols.pmut_scan.PointMutScanDriver) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.pmut_scan.PointMutScanDriver,  : rosetta.protocols.pmut_scan.PointMutScanDriver) -> rosetta.protocols.pmut_scan.PointMutScanDriver calculate_neighbor_table(...) from builtins.PyCapsule calculate_neighbor_table(self : rosetta.protocols.pmut_scan.PointMutScanDriver, pose : rosetta.core.pose.Pose, neighbors : rosetta.utility.vector1_utility_vector1_bool_std_allocator_bool_t) -> NoneType fill_mutations_list(...) from builtins.PyCapsule fill_mutations_list(rosetta.protocols.pmut_scan.PointMutScanDriver) -> NoneType get_scorefxn(...) from builtins.PyCapsule get_scorefxn(rosetta.protocols.pmut_scan.PointMutScanDriver) -> rosetta.core.scoring.ScoreFunction   accessor for scorefxn_ now that it is private member data go(...) from builtins.PyCapsule go(rosetta.protocols.pmut_scan.PointMutScanDriver) -> NoneType make_specific_mutant(...) from builtins.PyCapsule make_specific_mutant(*args, **kwargs) Overloaded function.   1. make_specific_mutant(self : rosetta.protocols.pmut_scan.PointMutScanDriver, mutant_poses : rosetta.utility.vector1_core_pose_Pose, native_poses : rosetta.utility.vector1_core_pose_Pose, m : protocols::pmut_scan::Mutant) -> NoneType   2. make_specific_mutant(self : rosetta.protocols.pmut_scan.PointMutScanDriver, mutant_poses : rosetta.utility.vector1_core_pose_Pose, native_poses : rosetta.utility.vector1_core_pose_Pose, m : protocols::pmut_scan::Mutant, mutation_string : str) -> NoneType   3. make_specific_mutant(self : rosetta.protocols.pmut_scan.PointMutScanDriver, mutant_poses : rosetta.utility.vector1_core_pose_Pose, native_poses : rosetta.utility.vector1_core_pose_Pose, m : protocols::pmut_scan::Mutant, mutation_string : str, mutation_string_PDB_numbering : str) -> NoneType mutants_begin(...) from builtins.PyCapsule mutants_begin(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> > > mutants_end(...) from builtins.PyCapsule mutants_end(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> > > n_mutants(...) from builtins.PyCapsule n_mutants(rosetta.protocols.pmut_scan.PointMutScanDriver) -> int read_in_structures(...) from builtins.PyCapsule read_in_structures(rosetta.protocols.pmut_scan.PointMutScanDriver) -> NoneType reject_mutant(...) from builtins.PyCapsule reject_mutant(self : rosetta.protocols.pmut_scan.PointMutScanDriver,  : protocols::pmut_scan::Mutant,  : rosetta.core.pose.Pose) -> bool   offers a chance for child classes to inject mutant selection logic score(...) from builtins.PyCapsule score(self : rosetta.protocols.pmut_scan.PointMutScanDriver, pose : 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) set_ddG_cutoff(...) from builtins.PyCapsule set_ddG_cutoff(self : rosetta.protocols.pmut_scan.PointMutScanDriver, threshold : float) -> NoneType