Bindings for protocols::protein_interface_design namespace

Modules
		rosetta.protocols.protein_interface_design.filters rosetta.protocols.protein_interface_design.movers

Classes
		builtins.object DockDesignFilterFactory FavorNativeResidue FavorNonNativeResidue PatchdockReader ReportPSSMDifferences ReportSequenceDifferences Revert Transformation rosetta.protocols.jd2.JobInputterCreator(builtins.object) ParserJobInputterCreator rosetta.protocols.jd2.PDBJobInputter(rosetta.protocols.jd2.JobInputter) ParserJobInputter   class DockDesignFilterFactory(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.protein_interface_design.DockDesignFilterFactory) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_type(...) from builtins.PyCapsule add_type(*args, **kwargs) Overloaded function.   1. add_type(self : rosetta.protocols.protein_interface_design.DockDesignFilterFactory,  : rosetta.protocols.filters.Filter) -> NoneType   add a Filter prototype, using its default type name as the map key   2. add_type(self : rosetta.protocols.protein_interface_design.DockDesignFilterFactory,  : str,  : rosetta.protocols.filters.Filter) -> NoneType   add a Filter prototype, using an arbitrary type name as the map key assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.protein_interface_design.DockDesignFilterFactory,  : rosetta.protocols.protein_interface_design.DockDesignFilterFactory) -> rosetta.protocols.protein_interface_design.DockDesignFilterFactory newFilter(...) from builtins.PyCapsule newFilter(self : rosetta.protocols.protein_interface_design.DockDesignFilterFactory,  : str) -> rosetta.protocols.filters.Filter   return new Filter by key lookup in dock_design_filter_map_   class FavorNativeResidue(builtins.object)     class FavorNativeResidue changes a pose object so that its residue identities at the initialization of FavorNativeResidue are kept in memory. If the res_type_constraint score term is set to a value other than 0, an energy bonus will be assigned if the residue doesn't change. This is useful e.g., in design based on a native scaffold where we want a barrier to mutation.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.protocols.protein_interface_design.FavorNativeResidue, pose : rosetta.core.pose.Pose, native_residue_bonus : float) -> NoneType   2. __init__(self : rosetta.protocols.protein_interface_design.FavorNativeResidue, pose : rosetta.core.pose.Pose, native_residue_bonus : rosetta.utility.vector1_double) -> NoneType   3. __init__(self : rosetta.protocols.protein_interface_design.FavorNativeResidue,  : rosetta.protocols.protein_interface_design.FavorNativeResidue) -> 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.protein_interface_design.FavorNativeResidue,  : rosetta.protocols.protein_interface_design.FavorNativeResidue) -> rosetta.protocols.protein_interface_design.FavorNativeResidue   class FavorNonNativeResidue(builtins.object)     class FavorNonNativeResidue changes a pose object so that its residue identities at the initialization of FavorNonNativeResidue are kept in memory. If the res_type_constraint score term is set to a value other than 0, an energy bonus will be assigned if the residue changes. This is useful if we want to encourage mutation.  A negative score would discourage mutation.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.protocols.protein_interface_design.FavorNonNativeResidue, pose : rosetta.core.pose.Pose, native_residue_bonus : float) -> NoneType   2. __init__(self : rosetta.protocols.protein_interface_design.FavorNonNativeResidue, pose : rosetta.core.pose.Pose, native_residue_bonus : rosetta.utility.vector1_double) -> NoneType   3. __init__(self : rosetta.protocols.protein_interface_design.FavorNonNativeResidue,  : rosetta.protocols.protein_interface_design.FavorNonNativeResidue) -> 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.protein_interface_design.FavorNonNativeResidue,  : rosetta.protocols.protein_interface_design.FavorNonNativeResidue) -> rosetta.protocols.protein_interface_design.FavorNonNativeResidue   class ParserJobInputter(rosetta.protocols.jd2.PDBJobInputter)       Method resolution order: ParserJobInputter rosetta.protocols.jd2.PDBJobInputter rosetta.protocols.jd2.JobInputter builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.protocols.protein_interface_design.ParserJobInputter) -> 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.protein_interface_design.ParserJobInputter,  : rosetta.protocols.protein_interface_design.ParserJobInputter) -> rosetta.protocols.protein_interface_design.ParserJobInputter pose_from_job(...) from builtins.PyCapsule pose_from_job(self : rosetta.protocols.protein_interface_design.ParserJobInputter, pose : rosetta.core.pose.Pose, job : rosetta.protocols.jd2.Job) -> NoneType   this function is responsible for filling the pose reference with the pose indicated by the job.  The Job object (within its InnerJob) contains a PoseCOP.  This function needs to either fill the pose reference from the InnerJob or, on first demand of a pose from that InnerJob, instantiate the pose, hand off a COP to the InnerJob, and fill the reference.  This implementation uses pose_from_pdb Methods inherited from rosetta.protocols.jd2.PDBJobInputter: fill_jobs(...) from builtins.PyCapsule fill_jobs(self : rosetta.protocols.jd2.PDBJobInputter, jobs : rosetta.protocols.jd2.JobsContainer) -> NoneType   this function determines what jobs exist from -s/-l input_source(...) from builtins.PyCapsule input_source(rosetta.protocols.jd2.PDBJobInputter) -> rosetta.protocols.jd2.JobInputterInputSource.Enum   Return the type of input source that the PDBJobInputter is currently   using.      Always PDB_FILE. Methods inherited from rosetta.protocols.jd2.JobInputter: get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.protocols.jd2.JobInputter   Get self const owning pointers.   2. get_self_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.protocols.jd2.JobInputter   Get self owning pointers. get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.std.weak_ptr_const_protocols_jd2_JobInputter_t   Get self const weak pointers.   2. get_self_weak_ptr(rosetta.protocols.jd2.JobInputter) -> rosetta.std.weak_ptr_protocols_jd2_JobInputter_t   Get self weak pointers. job_inputter_input_source_to_string(...) from builtins.PyCapsule job_inputter_input_source_to_string(source : rosetta.protocols.jd2.JobInputterInputSource.Enum) -> str   call this with input_source() to get the input source of a  particular job inputter update_jobs_list(...) from builtins.PyCapsule update_jobs_list(self : rosetta.protocols.jd2.JobInputter, jobs : protocols::jd2::JobsContainer) -> NoneType   This function is only called by certain JobInputters to update the jobs list after it has already been created.      An example case would be the LargeNstructJobInputter, which uses this function to load additional jobs after the first N have started to come back. updates_jobs_list(...) from builtins.PyCapsule updates_jobs_list(rosetta.protocols.jd2.JobInputter) -> bool   Does this type of JobInputter update the jobs list?      False by default.  Override this function in derived classes to make it true.   class ParserJobInputterCreator(rosetta.protocols.jd2.JobInputterCreator)       Method resolution order: ParserJobInputterCreator rosetta.protocols.jd2.JobInputterCreator builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(handle) -> 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.protein_interface_design.ParserJobInputterCreator,  : rosetta.protocols.protein_interface_design.ParserJobInputterCreator) -> rosetta.protocols.protein_interface_design.ParserJobInputterCreator create_JobInputter(...) from builtins.PyCapsule create_JobInputter(rosetta.protocols.protein_interface_design.ParserJobInputterCreator) -> rosetta.protocols.jd2.JobInputter keyname(...) from builtins.PyCapsule keyname(rosetta.protocols.protein_interface_design.ParserJobInputterCreator) -> str   class PatchdockReader(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.protein_interface_design.PatchdockReader) -> NoneType   2. __init__(self : rosetta.protocols.protein_interface_design.PatchdockReader,  : rosetta.protocols.protein_interface_design.PatchdockReader) -> 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.protein_interface_design.PatchdockReader,  : rosetta.protocols.protein_interface_design.PatchdockReader) -> rosetta.protocols.protein_interface_design.PatchdockReader clear_internals(...) from builtins.PyCapsule clear_internals(rosetta.protocols.protein_interface_design.PatchdockReader) -> NoneType from_entry(...) from builtins.PyCapsule from_entry(*args, **kwargs) Overloaded function.   1. from_entry(self : rosetta.protocols.protein_interface_design.PatchdockReader, f : int) -> NoneType   2. from_entry(rosetta.protocols.protein_interface_design.PatchdockReader) -> int number_of_patchdock_entries(...) from builtins.PyCapsule number_of_patchdock_entries(rosetta.protocols.protein_interface_design.PatchdockReader) -> int patchdock_entry_num(...) from builtins.PyCapsule patchdock_entry_num(*args, **kwargs) Overloaded function.   1. patchdock_entry_num(rosetta.protocols.protein_interface_design.PatchdockReader) -> int   2. patchdock_entry_num(self : rosetta.protocols.protein_interface_design.PatchdockReader, s : int) -> NoneType patchdock_fname(...) from builtins.PyCapsule patchdock_fname(*args, **kwargs) Overloaded function.   1. patchdock_fname(rosetta.protocols.protein_interface_design.PatchdockReader) -> str   2. patchdock_fname(self : rosetta.protocols.protein_interface_design.PatchdockReader, s : str) -> NoneType random_entry(...) from builtins.PyCapsule random_entry(*args, **kwargs) Overloaded function.   1. random_entry(rosetta.protocols.protein_interface_design.PatchdockReader) -> bool   2. random_entry(self : rosetta.protocols.protein_interface_design.PatchdockReader, b : bool) -> NoneType read_patchdock(...) from builtins.PyCapsule read_patchdock(self : rosetta.protocols.protein_interface_design.PatchdockReader, input_tag : str, native_tag : str) -> NoneType read_patchdock_entry(...) from builtins.PyCapsule read_patchdock_entry(rosetta.protocols.protein_interface_design.PatchdockReader) -> rosetta.protocols.protein_interface_design.Transformation read_poses(...) from builtins.PyCapsule read_poses(*args, **kwargs) Overloaded function.   1. read_poses(self : rosetta.protocols.protein_interface_design.PatchdockReader, input_pose : rosetta.core.pose.Pose, input_tag : str) -> NoneType   if no native is read   2. read_poses(self : rosetta.protocols.protein_interface_design.PatchdockReader, input_pose : rosetta.core.pose.Pose, native_pose : rosetta.core.pose.Pose, input_tag : str, native_tag : str) -> NoneType   reads input and native poses from file. If patchdock flags are used will read the patchdock transformation  and transform the input pose accordingly to_entry(...) from builtins.PyCapsule to_entry(*args, **kwargs) Overloaded function.   1. to_entry(self : rosetta.protocols.protein_interface_design.PatchdockReader, t : int) -> NoneType   2. to_entry(rosetta.protocols.protein_interface_design.PatchdockReader) -> int transform_pose(...) from builtins.PyCapsule transform_pose(self : rosetta.protocols.protein_interface_design.PatchdockReader, pose : rosetta.core.pose.Pose, chain : int, t : rosetta.protocols.protein_interface_design.Transformation) -> NoneType   class ReportPSSMDifferences(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.protein_interface_design.ReportPSSMDifferences) -> NoneType   2. __init__(self : rosetta.protocols.protein_interface_design.ReportPSSMDifferences, init : rosetta.protocols.protein_interface_design.ReportPSSMDifferences) -> 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.protein_interface_design.ReportPSSMDifferences,  : rosetta.protocols.protein_interface_design.ReportPSSMDifferences) -> rosetta.protocols.protein_interface_design.ReportPSSMDifferences calculate(...) from builtins.PyCapsule calculate(self : rosetta.protocols.protein_interface_design.ReportPSSMDifferences, pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> float load_pssm_data(...) from builtins.PyCapsule load_pssm_data(self : rosetta.protocols.protein_interface_design.ReportPSSMDifferences, native_filename : str) -> bool pssm_(...) from builtins.PyCapsule pssm_(rosetta.protocols.protein_interface_design.ReportPSSMDifferences) -> rosetta.utility.vector1_std_pair_core_chemical_AA_utility_vector1_double_std_allocator_double_t res_name1(...) from builtins.PyCapsule res_name1(rosetta.protocols.protein_interface_design.ReportPSSMDifferences) -> rosetta.std.map_unsigned_long_std_string   class ReportSequenceDifferences(builtins.object)     Class ReportSequenceDifferences takes in two poses and provides information on the sequence changes between them, including the residue energies associated with those changes.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.protocols.protein_interface_design.ReportSequenceDifferences, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType   2. __init__(self : rosetta.protocols.protein_interface_design.ReportSequenceDifferences, init : rosetta.protocols.protein_interface_design.ReportSequenceDifferences) -> 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.protein_interface_design.ReportSequenceDifferences,  : rosetta.protocols.protein_interface_design.ReportSequenceDifferences) -> rosetta.protocols.protein_interface_design.ReportSequenceDifferences calculate(...) from builtins.PyCapsule calculate(self : rosetta.protocols.protein_interface_design.ReportSequenceDifferences, pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose) -> NoneType get_res_energy(...) from builtins.PyCapsule get_res_energy(self : rosetta.protocols.protein_interface_design.ReportSequenceDifferences, num : int) -> rosetta.std.map_unsigned_long_double res_name1(...) from builtins.PyCapsule res_name1(rosetta.protocols.protein_interface_design.ReportSequenceDifferences) -> rosetta.std.map_unsigned_long_std_string res_name2(...) from builtins.PyCapsule res_name2(rosetta.protocols.protein_interface_design.ReportSequenceDifferences) -> rosetta.std.map_unsigned_long_std_string   class Revert(builtins.object)     class Revert takes in 'wt' and 'designed' poses and attempts to revert all substitutions in the design to their wt identities. Each substitution is tried separately in the context of the designed protein and reversions that don't adversely affect ddg are made. If the energy of the residue in the design is higher than 0, but the reversion did not succeed, Revert will attempt an Ala substitution.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.protein_interface_design.Revert, rosetta.core.scoring.ScoreFunction, float) -> NoneType   doc   2. __init__(self : rosetta.protocols.protein_interface_design.Revert, scorefxn : rosetta.core.scoring.ScoreFunction, ddg_tolerance : float, ddg_cycles : int) -> NoneType   3. __init__(self : rosetta.protocols.protein_interface_design.Revert, init : rosetta.protocols.protein_interface_design.Revert) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.protein_interface_design.Revert, pose_wt : rosetta.core.pose.Pose, pose_des : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.protein_interface_design.Revert,  : rosetta.protocols.protein_interface_design.Revert) -> rosetta.protocols.protein_interface_design.Revert   class Transformation(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.protocols.protein_interface_design.Transformation) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. Data descriptors defined here: alpha beta gamma translation

Functions
		MinimizeInterface(...) method of builtins.PyCapsule instance MinimizeInterface(*args, **kwargs) Overloaded function.   1. MinimizeInterface(pose : rosetta.core.pose.Pose, scorefxn : rosetta.core.scoring.ScoreFunction, min_bb : rosetta.utility.vector1_bool, min_sc : rosetta.utility.vector1_bool, min_rb : rosetta.utility.vector1_bool, optimize_foldtree : bool, target_residues : rosetta.utility.vector1_unsigned_long) -> NoneType   utility function for minimizing sidechain in rigid-body dof, the interface sc, and bb in the entire protein.   2. MinimizeInterface(pose : rosetta.core.pose.Pose, scorefxn : rosetta.core.scoring.ScoreFunction, min_bb : rosetta.utility.vector1_bool, min_sc : rosetta.utility.vector1_bool, min_rb : rosetta.utility.vector1_bool, optimize_foldtree : bool, target_residues : rosetta.utility.vector1_unsigned_long, simultaneous_minimization : bool) -> NoneType   utility function for minimizing sidechain in rigid-body dof, the interface sc, and bb in the entire protein. SymMinimizeInterface(...) method of builtins.PyCapsule instance SymMinimizeInterface(*args, **kwargs) Overloaded function.   1. SymMinimizeInterface(pose : rosetta.core.pose.Pose, scorefxn : rosetta.core.scoring.ScoreFunction, min_bb : rosetta.utility.vector1_bool, min_sc : rosetta.utility.vector1_bool, min_rb : rosetta.utility.vector1_bool) -> NoneType   2. SymMinimizeInterface(pose : rosetta.core.pose.Pose, scorefxn : rosetta.core.scoring.ScoreFunction, min_bb : rosetta.utility.vector1_bool, min_sc : rosetta.utility.vector1_bool, min_rb : rosetta.utility.vector1_bool, simultaneous_minimization : bool) -> NoneType best_bbcst_residues(...) method of builtins.PyCapsule instance best_bbcst_residues(pose : rosetta.core.pose.Pose, chain : int, n_return : int) -> rosetta.utility.vector1_unsigned_long   evaluate backbone_stub_constraints for each residue in a chain and return a vector with the top n_return residue numbers by cst score  note that this function is NOT guaranteed to return n_return residues! It will return the best n<=n_return best_cutpoint(...) method of builtins.PyCapsule instance best_cutpoint(pose : rosetta.core.pose.Pose, prev_u : int, prev_d : int, u : int, d : int) -> int   utility function for stub_based_atom_tree. tries to find an optimal cutpoint in a pose given two different boundaries. find_lowest_constraint_energy_residue(...) method of builtins.PyCapsule instance find_lowest_constraint_energy_residue(pose : rosetta.core.pose.Pose, chain : int, resi : int, lowest_energy : float) -> NoneType find_nearest_residue(...) method of builtins.PyCapsule instance find_nearest_residue(*args, **kwargs) Overloaded function.   1. find_nearest_residue(pose : rosetta.core.pose.Pose, target_chain : int, res : int) -> int   find nearest residue on target_chain to res   2. find_nearest_residue(pose : rosetta.core.pose.Pose, target_chain : int, res : int, atom : str) -> int   find nearest residue on target_chain to res get_bbcsts(...) method of builtins.PyCapsule instance get_bbcsts(pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t hbonded(...) method of builtins.PyCapsule instance hbonded(*args, **kwargs) Overloaded function.   1. hbonded(pose : rosetta.core.pose.Pose, target_residue : int, binders : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t, bb : bool, sc : bool, energy_thres : float) -> rosetta.std.list_unsigned_long_std_allocator_unsigned_long_t   utility function for finding hbonding partners among a list of potential binder residues to a specific target   2. hbonded(pose : rosetta.core.pose.Pose, target_residue : int, binders : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t, bb : bool, sc : bool, energy_thres : float, bb_bb : bool) -> rosetta.std.list_unsigned_long_std_allocator_unsigned_long_t   utility function for finding hbonding partners among a list of potential binder residues to a specific target   3. hbonded(pose : rosetta.core.pose.Pose, target_residue : int, binders : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t, bb : bool, sc : bool, energy_thres : float, bb_bb : bool, sfxn : rosetta.core.scoring.ScoreFunction) -> rosetta.std.list_unsigned_long_std_allocator_unsigned_long_t   utility function for finding hbonding partners among a list of potential binder residues to a specific target hbonded_atom(...) method of builtins.PyCapsule instance hbonded_atom(*args, **kwargs) Overloaded function.   1. hbonded_atom(pose : rosetta.core.pose.Pose, target_residue : int, target_atom : str, binders : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t, bb : bool, sc : bool, energy_thres : float) -> rosetta.std.list_unsigned_long_std_allocator_unsigned_long_t   utility function for finding hbonding partners among a list of potential binder residues to a specific target   2. hbonded_atom(pose : rosetta.core.pose.Pose, target_residue : int, target_atom : str, binders : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t, bb : bool, sc : bool, energy_thres : float, bb_bb : bool) -> rosetta.std.list_unsigned_long_std_allocator_unsigned_long_t   utility function for finding hbonding partners among a list of potential binder residues to a specific target   3. hbonded_atom(pose : rosetta.core.pose.Pose, target_residue : int, target_atom : str, binders : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t, bb : bool, sc : bool, energy_thres : float, bb_bb : bool, sfxn : rosetta.core.scoring.ScoreFunction) -> rosetta.std.list_unsigned_long_std_allocator_unsigned_long_t   utility function for finding hbonding partners among a list of potential binder residues to a specific target make_hotspot_foldtree(...) method of builtins.PyCapsule instance make_hotspot_foldtree(pose : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree optimal_connection_point(...) method of builtins.PyCapsule instance optimal_connection_point(residue_type : str) -> str   what is the optimal connection point for an atom tree, given a residue type (puts the connection point  at the beginning of a functional group remove_coordinate_constraints_from_pose(...) method of builtins.PyCapsule instance remove_coordinate_constraints_from_pose(pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t   removes ALL coordinate constraints from a pose. returns the constraints that were removed star_fold_tree(...) method of builtins.PyCapsule instance star_fold_tree(pose : rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree sum_total_residue_energy(...) method of builtins.PyCapsule instance sum_total_residue_energy(pose : rosetta.core.pose.Pose, resid : int) -> float