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- builtins.object
-
- InterfaceData
- InterfaceRegion
- PeptideDeriverEntryType
- PeptideDeriverOutputter
-
- PeptideDeriverBasicStreamOutputter
- PeptideDeriverMarkdownStreamOutputter
- PeptideDeriverOutputterContainer
- PeptideDeriverPoseOutputter
- PeptideDeriverReportFormat
- PerResidueInterfaceData
- rosetta.protocols.filters.Filter(builtins.object)
-
- PeptideDeriverFilter
- rosetta.protocols.filters.FilterCreator(builtins.object)
-
- PeptideDeriverFilterCreator
- rosetta.protocols.moves.Mover(builtins.object)
-
- InterfaceAnalyzerMover
- LoopAnalyzerMover
- PackStatMover
- rosetta.protocols.moves.MoverCreator(builtins.object)
-
- InterfaceAnalyzerMoverCreator
class InterfaceAnalyzerMover(rosetta.protocols.moves.Mover) |
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Class for analyzing interfaces of a pose. Many metrics are calculated and accessible after the apply method.
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- Method resolution order:
- InterfaceAnalyzerMover
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
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2. __init__(handle, int) -> NoneType
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3. __init__(handle, int, bool) -> NoneType
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4. __init__(handle, int, bool, rosetta.core.scoring.ScoreFunction) -> NoneType
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5. __init__(handle, int, bool, rosetta.core.scoring.ScoreFunction, bool) -> NoneType
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6. __init__(handle, int, bool, rosetta.core.scoring.ScoreFunction, bool, bool) -> NoneType
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7. __init__(handle, int, bool, rosetta.core.scoring.ScoreFunction, bool, bool, bool) -> NoneType
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8. __init__(self : handle, interface_jump : int, tracer : bool, sf : rosetta.core.scoring.ScoreFunction, compute_packstat : bool, pack_input : bool, pack_separated : bool, use_jobname : bool) -> NoneType
9. __init__(handle, rosetta.std.set_int_std_less_int_std_allocator_int_t) -> NoneType
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10. __init__(handle, rosetta.std.set_int_std_less_int_std_allocator_int_t, bool) -> NoneType
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11. __init__(handle, rosetta.std.set_int_std_less_int_std_allocator_int_t, bool, rosetta.core.scoring.ScoreFunction) -> NoneType
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12. __init__(handle, rosetta.std.set_int_std_less_int_std_allocator_int_t, bool, rosetta.core.scoring.ScoreFunction, bool) -> NoneType
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13. __init__(handle, rosetta.std.set_int_std_less_int_std_allocator_int_t, bool, rosetta.core.scoring.ScoreFunction, bool, bool) -> NoneType
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14. __init__(handle, rosetta.std.set_int_std_less_int_std_allocator_int_t, bool, rosetta.core.scoring.ScoreFunction, bool, bool, bool) -> NoneType
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15. __init__(self : handle, fixed_chains : rosetta.std.set_int_std_less_int_std_allocator_int_t, tracer : bool, sf : rosetta.core.scoring.ScoreFunction, compute_packstat : bool, pack_input : bool, pack_separated : bool, use_jobname : bool) -> NoneType
16. __init__(handle, str) -> NoneType
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17. __init__(handle, str, bool) -> NoneType
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18. __init__(handle, str, bool, rosetta.core.scoring.ScoreFunction) -> NoneType
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19. __init__(handle, str, bool, rosetta.core.scoring.ScoreFunction, bool) -> NoneType
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20. __init__(handle, str, bool, rosetta.core.scoring.ScoreFunction, bool, bool) -> NoneType
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21. __init__(handle, str, bool, rosetta.core.scoring.ScoreFunction, bool, bool, bool) -> NoneType
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22. __init__(self : handle, dock_chains : str, tracer : bool, sf : rosetta.core.scoring.ScoreFunction, compute_packstat : bool, pack_input : bool, pack_separated : bool, use_jobname : bool) -> NoneType
23. __init__(handle, rosetta.protocols.analysis.InterfaceAnalyzerMover) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_score_info_to_pose(...) from builtins.PyCapsule
- add_score_info_to_pose(self : rosetta.protocols.analysis.InterfaceAnalyzerMover, pose : rosetta.core.pose.Pose) -> NoneType
Add all the scoring data normally output via job to the pose instead. Can't add this to method due to const apply.
Use after you have used the apply for the class.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.analysis.InterfaceAnalyzerMover, pose : rosetta.core.pose.Pose) -> NoneType
apply function will calculate data about the input pose. It is not intended to modify the pose itself (conformation and energies objects) although it may toss data into the DataCache or a Job object.
- apply_const(...) from builtins.PyCapsule
- apply_const(self : rosetta.protocols.analysis.InterfaceAnalyzerMover, pose : rosetta.core.pose.Pose) -> NoneType
Apply method for const pose. Used by InterfaceFeatures reporter
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.analysis.InterfaceAnalyzerMover, : rosetta.protocols.analysis.InterfaceAnalyzerMover) -> rosetta.protocols.analysis.InterfaceAnalyzerMover
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.analysis.InterfaceAnalyzerMover) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.analysis.InterfaceAnalyzerMover) -> rosetta.protocols.moves.Mover
- get_all_data(...) from builtins.PyCapsule
- get_all_data(rosetta.protocols.analysis.InterfaceAnalyzerMover) -> rosetta.protocols.analysis.InterfaceData
Get all interface data.
- get_all_per_residue_data(...) from builtins.PyCapsule
- get_all_per_residue_data(rosetta.protocols.analysis.InterfaceAnalyzerMover) -> rosetta.protocols.analysis.PerResidueInterfaceData
Get all per residue interface data.
- get_centroid_dG(...) from builtins.PyCapsule
- get_centroid_dG(rosetta.protocols.analysis.InterfaceAnalyzerMover) -> float
- get_chain_groups(...) from builtins.PyCapsule
- get_chain_groups(rosetta.protocols.analysis.InterfaceAnalyzerMover) -> rosetta.utility.vector1_std_pair_std_set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_std_set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t
- get_complex_energy(...) from builtins.PyCapsule
- get_complex_energy(rosetta.protocols.analysis.InterfaceAnalyzerMover) -> float
- get_complexed_sasa(...) from builtins.PyCapsule
- get_complexed_sasa(rosetta.protocols.analysis.InterfaceAnalyzerMover) -> float
- get_crossterm_interface_energy(...) from builtins.PyCapsule
- get_crossterm_interface_energy(rosetta.protocols.analysis.InterfaceAnalyzerMover) -> float
- get_crossterm_interface_energy_ratio(...) from builtins.PyCapsule
- get_crossterm_interface_energy_ratio(rosetta.protocols.analysis.InterfaceAnalyzerMover) -> float
- get_fixed_chains(...) from builtins.PyCapsule
- get_fixed_chains(rosetta.protocols.analysis.InterfaceAnalyzerMover) -> rosetta.std.set_int_std_less_int_std_allocator_int_t
- get_gly_interface_energy(...) from builtins.PyCapsule
- get_gly_interface_energy(rosetta.protocols.analysis.InterfaceAnalyzerMover) -> float
Return the interface energy of an all glycine interface (like bb-bb energies)
- get_interface_dG(...) from builtins.PyCapsule
- get_interface_dG(rosetta.protocols.analysis.InterfaceAnalyzerMover) -> float
- get_interface_delta_hbond_unsat(...) from builtins.PyCapsule
- get_interface_delta_hbond_unsat(rosetta.protocols.analysis.InterfaceAnalyzerMover) -> int
- get_interface_delta_sasa(...) from builtins.PyCapsule
- get_interface_delta_sasa(rosetta.protocols.analysis.InterfaceAnalyzerMover) -> float
- get_interface_packstat(...) from builtins.PyCapsule
- get_interface_packstat(rosetta.protocols.analysis.InterfaceAnalyzerMover) -> float
- get_interface_set(...) from builtins.PyCapsule
- get_interface_set(rosetta.protocols.analysis.InterfaceAnalyzerMover) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t
Get the residues at the interface in question
- get_multichain_constructor(...) from builtins.PyCapsule
- get_multichain_constructor(rosetta.protocols.analysis.InterfaceAnalyzerMover) -> bool
Return boolean if a multichain (fixedchain) constructor was used
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.analysis.InterfaceAnalyzerMover) -> str
- get_num_interface_residues(...) from builtins.PyCapsule
- get_num_interface_residues(rosetta.protocols.analysis.InterfaceAnalyzerMover) -> int
- get_pack_input(...) from builtins.PyCapsule
- get_pack_input(rosetta.protocols.analysis.InterfaceAnalyzerMover) -> bool
- get_per_residue_energy(...) from builtins.PyCapsule
- get_per_residue_energy(rosetta.protocols.analysis.InterfaceAnalyzerMover) -> float
return the average per residue interface energy
- get_pymol_sel_hbond_unsat(...) from builtins.PyCapsule
- get_pymol_sel_hbond_unsat(rosetta.protocols.analysis.InterfaceAnalyzerMover) -> str
- get_pymol_sel_interface(...) from builtins.PyCapsule
- get_pymol_sel_interface(rosetta.protocols.analysis.InterfaceAnalyzerMover) -> str
- get_pymol_sel_packing(...) from builtins.PyCapsule
- get_pymol_sel_packing(rosetta.protocols.analysis.InterfaceAnalyzerMover) -> str
- get_separated_interface_energy(...) from builtins.PyCapsule
- get_separated_interface_energy(rosetta.protocols.analysis.InterfaceAnalyzerMover) -> float
- get_separated_interface_energy_ratio(...) from builtins.PyCapsule
- get_separated_interface_energy_ratio(rosetta.protocols.analysis.InterfaceAnalyzerMover) -> float
- get_side1_nres(...) from builtins.PyCapsule
- get_side1_nres(rosetta.protocols.analysis.InterfaceAnalyzerMover) -> int
- get_side1_score(...) from builtins.PyCapsule
- get_side1_score(rosetta.protocols.analysis.InterfaceAnalyzerMover) -> float
- get_side2_nres(...) from builtins.PyCapsule
- get_side2_nres(rosetta.protocols.analysis.InterfaceAnalyzerMover) -> int
- get_side2_score(...) from builtins.PyCapsule
- get_side2_score(rosetta.protocols.analysis.InterfaceAnalyzerMover) -> float
- get_total_Hbond_E(...) from builtins.PyCapsule
- get_total_Hbond_E(rosetta.protocols.analysis.InterfaceAnalyzerMover) -> float
- get_use_centroid_dG(...) from builtins.PyCapsule
- get_use_centroid_dG(rosetta.protocols.analysis.InterfaceAnalyzerMover) -> bool
- init_on_new_input(...) from builtins.PyCapsule
- init_on_new_input(self : rosetta.protocols.analysis.InterfaceAnalyzerMover, pose : rosetta.core.pose.Pose) -> NoneType
Explicitly initialize settings on apply - not at the constructor, since this can hold state, and some protocols use apply multiple times.
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.analysis.InterfaceAnalyzerMover) -> bool
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.analysis.InterfaceAnalyzerMover) -> bool
- report_data(...) from builtins.PyCapsule
- report_data(rosetta.protocols.analysis.InterfaceAnalyzerMover) -> NoneType
Print data to tracer or scorefile if tracer is not set (default).
- set_calc_hbond_sasaE(...) from builtins.PyCapsule
- set_calc_hbond_sasaE(self : rosetta.protocols.analysis.InterfaceAnalyzerMover, calc_hbond_sasaE : bool) -> NoneType
- set_compute_interface_delta_hbond_unsat(...) from builtins.PyCapsule
- set_compute_interface_delta_hbond_unsat(self : rosetta.protocols.analysis.InterfaceAnalyzerMover, IDHU : bool) -> NoneType
- set_compute_interface_energy(...) from builtins.PyCapsule
- set_compute_interface_energy(self : rosetta.protocols.analysis.InterfaceAnalyzerMover, iface_en : bool) -> NoneType
- set_compute_interface_sc(...) from builtins.PyCapsule
- set_compute_interface_sc(self : rosetta.protocols.analysis.InterfaceAnalyzerMover, compute_interface_sc : bool) -> NoneType
- set_compute_packstat(...) from builtins.PyCapsule
- set_compute_packstat(self : rosetta.protocols.analysis.InterfaceAnalyzerMover, compute_packstat : bool) -> NoneType
- set_compute_separated_sasa(...) from builtins.PyCapsule
- set_compute_separated_sasa(self : rosetta.protocols.analysis.InterfaceAnalyzerMover, compute_separated_sasa : bool) -> NoneType
- set_defaults(...) from builtins.PyCapsule
- set_defaults(rosetta.protocols.analysis.InterfaceAnalyzerMover) -> NoneType
////////////////////////////////////////////////
- set_interface_jump(...) from builtins.PyCapsule
- set_interface_jump(self : rosetta.protocols.analysis.InterfaceAnalyzerMover, interface_jump : int) -> NoneType
- set_pack_input(...) from builtins.PyCapsule
- set_pack_input(self : rosetta.protocols.analysis.InterfaceAnalyzerMover, pack_input : bool) -> NoneType
Repack the interface of the complex before separation.
- set_pack_separated(...) from builtins.PyCapsule
- set_pack_separated(self : rosetta.protocols.analysis.InterfaceAnalyzerMover, pack_separated : bool) -> NoneType
Repack the interface of the complex after separation.
- set_scorefunction(...) from builtins.PyCapsule
- set_scorefunction(self : rosetta.protocols.analysis.InterfaceAnalyzerMover, sf : rosetta.core.scoring.ScoreFunction) -> NoneType
- set_skip_reporting(...) from builtins.PyCapsule
- set_skip_reporting(self : rosetta.protocols.analysis.InterfaceAnalyzerMover, skip_reporting : bool) -> NoneType
- set_use_centroid_dG(...) from builtins.PyCapsule
- set_use_centroid_dG(self : rosetta.protocols.analysis.InterfaceAnalyzerMover, use_centroid : bool) -> NoneType
- set_use_jobname(...) from builtins.PyCapsule
- set_use_jobname(self : rosetta.protocols.analysis.InterfaceAnalyzerMover, use_jobname : bool) -> NoneType
- set_use_resfile(...) from builtins.PyCapsule
- set_use_resfile(self : rosetta.protocols.analysis.InterfaceAnalyzerMover, use_resfile : bool) -> NoneType
- set_use_tracer(...) from builtins.PyCapsule
- set_use_tracer(self : rosetta.protocols.analysis.InterfaceAnalyzerMover, tracer : bool) -> NoneType
Methods inherited from rosetta.protocols.moves.Mover:
- clear_info(...) from builtins.PyCapsule
- clear_info(rosetta.protocols.moves.Mover) -> NoneType
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options.
Do this recursively!
If you use movers within your mover, call their register_options in your register_options() method.
2. register_options() -> NoneType
3. register_options() -> NoneType
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
7. register_options() -> NoneType
8. register_options() -> NoneType
9. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
10. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
11. register_options() -> NoneType
Associates relevant options with the SnugDock class
12. register_options() -> NoneType
Associates relevant options with the SnugDockProtocol class
13. register_options() -> NoneType
Register the options used by this mover with the global options
system.
14. register_options() -> NoneType
15. register_options() -> NoneType
Associate relevant options with the TemperedDocking class.
16. register_options() -> NoneType
17. register_options() -> NoneType
18. register_options() -> NoneType
Associates relevant options with the TemperedDocking class.
19. register_options() -> NoneType
20. register_options() -> NoneType
Associates relevant options with the ConstraintSetMover class
21. register_options() -> NoneType
22. register_options() -> NoneType
Associates relevant options with the DockingInitialPerturbation class
23. register_options() -> NoneType
Associates relevant options with the DockingProtocol class
24. register_options() -> NoneType
Associates relevant options with the TemperedDocking class
25. register_options() -> NoneType
26. register_options() -> NoneType
27. register_options() -> NoneType
28. register_options() -> NoneType
register options
29. register_options() -> NoneType
30. register_options() -> NoneType
Registers applicable options
31. register_options() -> NoneType
Register options with the option system.
32. register_options() -> NoneType
33. register_options() -> NoneType
34. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
35. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycleContainer class
36. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
37. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
38. register_options() -> NoneType
39. register_options() -> NoneType
Register options with the option system.
40. register_options() -> NoneType
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
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class InterfaceData(builtins.object) |
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All interface data. Unless otherwise specified, they refer specifically to the interface
All vectors correspond to InterfaceRegion enums
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : rosetta.protocols.analysis.InterfaceData, : rosetta.protocols.analysis.InterfaceData) -> NoneType
2. __init__(rosetta.protocols.analysis.InterfaceData) -> 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.analysis.InterfaceData, : rosetta.protocols.analysis.InterfaceData) -> rosetta.protocols.analysis.InterfaceData
Data descriptors defined here:
- aromatic_dG_fraction
- aromatic_dSASA_fraction
- aromatic_nres
- centroid_dG
- complex_total_energy
- complexed_SASA
- complexed_interface_score
- crossterm_interface_energy
- crossterm_interface_energy_dSASA_ratio
- dG
- dG_dSASA_ratio
- dSASA
- dSASA_sc
- delta_unsat_hbonds
- dhSASA
- dhSASA_rel_by_charge
- dhSASA_sc
- gly_dG
- hbond_E_fraction
- interface_hbonds
- interface_nres
- interface_residues
- interface_to_surface_fraction
- packstat
- pymol_sel_hbond_unsat
- pymol_sel_interface
- pymol_sel_packing
- sc_value
- separated_SASA
- separated_interface_score
- separated_total_energy
- ss_helix_nres
- ss_loop_nres
- ss_sheet_nres
- total_hb_E
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class LoopAnalyzerMover(rosetta.protocols.moves.Mover) |
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- Method resolution order:
- LoopAnalyzerMover
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle, rosetta.protocols.loops.Loops) -> NoneType
doc
2. __init__(self : handle, loops : rosetta.protocols.loops.Loops, tracer : bool) -> NoneType
3. __init__(handle) -> NoneType
4. __init__(handle, rosetta.protocols.analysis.LoopAnalyzerMover) -> 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.analysis.LoopAnalyzerMover, input_pose : rosetta.core.pose.Pose) -> NoneType
apply function will calculate data about the input pose. It is not intended to modify the pose itself (conformation and energies objects) although it may toss data into the DataCache or a Job object.
- get_chainbreak_scores(...) from builtins.PyCapsule
- get_chainbreak_scores(rosetta.protocols.analysis.LoopAnalyzerMover) -> rosetta.utility.vector1_double
Return the vector of chainbreak scores
- get_max_chainbreak(...) from builtins.PyCapsule
- get_max_chainbreak(rosetta.protocols.analysis.LoopAnalyzerMover) -> float
- get_max_omega(...) from builtins.PyCapsule
- get_max_omega(rosetta.protocols.analysis.LoopAnalyzerMover) -> float
- get_max_pbond(...) from builtins.PyCapsule
- get_max_pbond(rosetta.protocols.analysis.LoopAnalyzerMover) -> float
- get_max_rama(...) from builtins.PyCapsule
- get_max_rama(rosetta.protocols.analysis.LoopAnalyzerMover) -> float
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.analysis.LoopAnalyzerMover) -> str
- get_total_score(...) from builtins.PyCapsule
- get_total_score(rosetta.protocols.analysis.LoopAnalyzerMover) -> float
Return the total score found from the last apply call
Methods inherited from rosetta.protocols.moves.Mover:
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.moves.Mover, other : rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- clear_info(...) from builtins.PyCapsule
- clear_info(rosetta.protocols.moves.Mover) -> NoneType
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Return a clone of the Mover object.
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Generates a new Mover object freshly created with the default ctor.
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options.
Do this recursively!
If you use movers within your mover, call their register_options in your register_options() method.
2. register_options() -> NoneType
3. register_options() -> NoneType
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
7. register_options() -> NoneType
8. register_options() -> NoneType
9. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
10. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
11. register_options() -> NoneType
Associates relevant options with the SnugDock class
12. register_options() -> NoneType
Associates relevant options with the SnugDockProtocol class
13. register_options() -> NoneType
Register the options used by this mover with the global options
system.
14. register_options() -> NoneType
15. register_options() -> NoneType
Associate relevant options with the TemperedDocking class.
16. register_options() -> NoneType
17. register_options() -> NoneType
18. register_options() -> NoneType
Associates relevant options with the TemperedDocking class.
19. register_options() -> NoneType
20. register_options() -> NoneType
Associates relevant options with the ConstraintSetMover class
21. register_options() -> NoneType
22. register_options() -> NoneType
Associates relevant options with the DockingInitialPerturbation class
23. register_options() -> NoneType
Associates relevant options with the DockingProtocol class
24. register_options() -> NoneType
Associates relevant options with the TemperedDocking class
25. register_options() -> NoneType
26. register_options() -> NoneType
27. register_options() -> NoneType
28. register_options() -> NoneType
register options
29. register_options() -> NoneType
30. register_options() -> NoneType
Registers applicable options
31. register_options() -> NoneType
Register options with the option system.
32. register_options() -> NoneType
33. register_options() -> NoneType
34. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
35. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycleContainer class
36. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
37. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
38. register_options() -> NoneType
39. register_options() -> NoneType
Register options with the option system.
40. register_options() -> NoneType
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
each use.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for
that one input pose).
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
|
class PackStatMover(rosetta.protocols.moves.Mover) |
| | |
- Method resolution order:
- PackStatMover
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.analysis.PackStatMover) -> 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.analysis.PackStatMover, pose : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.analysis.PackStatMover, : rosetta.protocols.analysis.PackStatMover) -> rosetta.protocols.analysis.PackStatMover
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.analysis.PackStatMover) -> str
Methods inherited from rosetta.protocols.moves.Mover:
- clear_info(...) from builtins.PyCapsule
- clear_info(rosetta.protocols.moves.Mover) -> NoneType
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Return a clone of the Mover object.
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
Generates a new Mover object freshly created with the default ctor.
- get_additional_output(...) from builtins.PyCapsule
- get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
fpd
Mechanism by which a mover may return multiple output poses from a single input pose.
- get_current_job(...) from builtins.PyCapsule
- get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
- get_current_tag(...) from builtins.PyCapsule
- get_current_tag(rosetta.protocols.moves.Mover) -> str
A tag is a unique identifier used to identify structures produced
by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag )
sets the tag. This functionality is not intended for use with the 2008 job distributor.
- get_input_pose(...) from builtins.PyCapsule
- get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_last_move_status(...) from builtins.PyCapsule
- get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
- get_native_pose(...) from builtins.PyCapsule
- get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.moves.Mover) -> str
- info(...) from builtins.PyCapsule
- info(*args, **kwargs)
Overloaded function.
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
non-const accessor
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
const accessor
- last_proposal_density_ratio(...) from builtins.PyCapsule
- last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
- name(...) from builtins.PyCapsule
- name() -> str
- register_options(...) from builtins.PyCapsule
- register_options(*args, **kwargs)
Overloaded function.
1. register_options() -> NoneType
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options.
Do this recursively!
If you use movers within your mover, call their register_options in your register_options() method.
2. register_options() -> NoneType
3. register_options() -> NoneType
4. register_options() -> NoneType
5. register_options() -> NoneType
6. register_options() -> NoneType
7. register_options() -> NoneType
8. register_options() -> NoneType
9. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
10. register_options() -> NoneType
Associates relevant options with the AntibodyModeler class
11. register_options() -> NoneType
Associates relevant options with the SnugDock class
12. register_options() -> NoneType
Associates relevant options with the SnugDockProtocol class
13. register_options() -> NoneType
Register the options used by this mover with the global options
system.
14. register_options() -> NoneType
15. register_options() -> NoneType
Associate relevant options with the TemperedDocking class.
16. register_options() -> NoneType
17. register_options() -> NoneType
18. register_options() -> NoneType
Associates relevant options with the TemperedDocking class.
19. register_options() -> NoneType
20. register_options() -> NoneType
Associates relevant options with the ConstraintSetMover class
21. register_options() -> NoneType
22. register_options() -> NoneType
Associates relevant options with the DockingInitialPerturbation class
23. register_options() -> NoneType
Associates relevant options with the DockingProtocol class
24. register_options() -> NoneType
Associates relevant options with the TemperedDocking class
25. register_options() -> NoneType
26. register_options() -> NoneType
27. register_options() -> NoneType
28. register_options() -> NoneType
register options
29. register_options() -> NoneType
30. register_options() -> NoneType
Registers applicable options
31. register_options() -> NoneType
Register options with the option system.
32. register_options() -> NoneType
33. register_options() -> NoneType
34. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
35. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycleContainer class
36. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
37. register_options() -> NoneType
Associates relevant options with the LoopRefineInnerCycle class
38. register_options() -> NoneType
39. register_options() -> NoneType
Register options with the option system.
40. register_options() -> NoneType
- reinitialize_for_each_job(...) from builtins.PyCapsule
- reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
each use.
- reinitialize_for_new_input(...) from builtins.PyCapsule
- reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for
that one input pose).
- reset_status(...) from builtins.PyCapsule
- reset_status(rosetta.protocols.moves.Mover) -> NoneType
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
- set_current_job(...) from builtins.PyCapsule
- set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
////////////////////////////end Job Distributor interface////////////////////////////////////////
- set_current_tag(...) from builtins.PyCapsule
- set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
- set_input_pose(...) from builtins.PyCapsule
- set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for poses contained for rms
- set_native_pose(...) from builtins.PyCapsule
- set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
- set_type(...) from builtins.PyCapsule
- set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
- test_move(...) from builtins.PyCapsule
- test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
: Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
- type(...) from builtins.PyCapsule
- type(*args, **kwargs)
Overloaded function.
1. type(rosetta.protocols.moves.Mover) -> str
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType
|
class PeptideDeriverBasicStreamOutputter(PeptideDeriverOutputter) |
| |
outputs a Peptiderive report to a stream in a basic, easily parsable format
|
| |
- Method resolution order:
- PeptideDeriverBasicStreamOutputter
- PeptideDeriverOutputter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, out : rosetta.utility.io.orstream, prefix : str) -> NoneType
2. __init__(handle, rosetta.protocols.analysis.PeptideDeriverBasicStreamOutputter) -> 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.analysis.PeptideDeriverBasicStreamOutputter, : rosetta.protocols.analysis.PeptideDeriverBasicStreamOutputter) -> rosetta.protocols.analysis.PeptideDeriverBasicStreamOutputter
- begin_receptor_partner_pair(...) from builtins.PyCapsule
- begin_receptor_partner_pair(self : rosetta.protocols.analysis.PeptideDeriverBasicStreamOutputter, receptor_chain_letter : str, partner_chain_letter : str, total_isc : float, options_string : str) -> NoneType
- begin_structure(...) from builtins.PyCapsule
- begin_structure(self : rosetta.protocols.analysis.PeptideDeriverBasicStreamOutputter, : rosetta.core.pose.Pose, : str) -> NoneType
- chain_pair_pose_prepared(...) from builtins.PyCapsule
- chain_pair_pose_prepared(self : rosetta.protocols.analysis.PeptideDeriverBasicStreamOutputter, : rosetta.core.pose.Pose) -> NoneType
- end_receptor_partner_pair(...) from builtins.PyCapsule
- end_receptor_partner_pair(rosetta.protocols.analysis.PeptideDeriverBasicStreamOutputter) -> NoneType
- end_structure(...) from builtins.PyCapsule
- end_structure(rosetta.protocols.analysis.PeptideDeriverBasicStreamOutputter) -> NoneType
- peptide_entry(...) from builtins.PyCapsule
- peptide_entry(self : rosetta.protocols.analysis.PeptideDeriverBasicStreamOutputter, : rosetta.core.pose.Pose, entry_type : rosetta.protocols.analysis.PeptideDeriverEntryType, pep_start : int, linear_isc : float, binding_contribution_fraction : float, disulfide_info : str, was_cyclic_pep_modeled : bool, : rosetta.core.pose.Pose, cyclic_isc : float) -> NoneType
- peptide_length(...) from builtins.PyCapsule
- peptide_length(self : rosetta.protocols.analysis.PeptideDeriverBasicStreamOutputter, pep_length : int) -> NoneType
|
class PeptideDeriverFilter(rosetta.protocols.filters.Filter) |
| |
implementation of the Peptiderive protocol - given a pose, it
evaluates the binding energy of linear stretches, of given lengths,
and indicates which of these contributes more than others to the
interaction energy. It also reports on and optionally models
cyclizable peptides.
Data is either output to a log (using report()) or passed to the given
PeptideDeriverOutputter (using derive_peptide()).
When calling report(), the output format is determined by a list of flags:
- is_dump_peptide_pose
- is_dump_cyclic_poses
- is_dump_prepared_pose
- is_dump_report_file
- is_report_gzip
See each flag's documentation for their effect. These flags are settable
via command-line or RosettaScripts options, and may also be set
programmatically. These only affect the output coming from report(), since
report() uses these to determine which PeptideDeriverOutputter instances
it passes to derive_peptide().
When calling derive_peptide(), however, it is up to the consumer to provide
the PeptideDeriverOutputter instance of choice. Naturally, it may use any
of the subclasses provided in this file:
- PeptideDeriverOutputterContainer
- PeptideDeriverBasicStreamOutputter
- PeptideDeriverMarkdownStreamOutputter
- PeptideDeriverPoseOutputter
Note: the PeptideDeriverFilter doesn't actually filter anything, so it
might have been better to suffix it with -Reporter, but wasn't so not to
confuse it with the FeatureReporter class hierarchy.
|
| |
- Method resolution order:
- PeptideDeriverFilter
- rosetta.protocols.filters.Filter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.analysis.PeptideDeriverFilter) -> 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.analysis.PeptideDeriverFilter, pose : rosetta.core.pose.Pose) -> bool
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.analysis.PeptideDeriverFilter, rhs : rosetta.protocols.analysis.PeptideDeriverFilter) -> rosetta.protocols.analysis.PeptideDeriverFilter
assignment operator
- build_receptor_peptide_pose(...) from builtins.PyCapsule
- build_receptor_peptide_pose(self : rosetta.protocols.analysis.PeptideDeriverFilter, receptor_pose : rosetta.core.pose.Pose, partner_pose : rosetta.core.pose.Pose, peptide_start : int, peptide_end : int, jump_id : int) -> rosetta.core.pose.Pose
- calculate_interface_score(...) from builtins.PyCapsule
- calculate_interface_score(self : rosetta.protocols.analysis.PeptideDeriverFilter, pose : rosetta.core.pose.Pose, jump_id : int) -> float
Calculate the interface score, i.e. addition to energy
resulting from the complex coming together.
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.analysis.PeptideDeriverFilter) -> rosetta.protocols.filters.Filter
- derive_peptide(...) from builtins.PyCapsule
- derive_peptide(*args, **kwargs)
Overloaded function.
1. derive_peptide(self : rosetta.protocols.analysis.PeptideDeriverFilter, output : rosetta.protocols.analysis.PeptideDeriverOutputter, pose : rosetta.core.pose.Pose, first_chain_index : int, second_chain_index : int, both_ways : bool) -> NoneType
overload of PeptideDeriverFilter::derive_peptide() which accepts
a many-chain pose and chain indices, rather than single-chain poses.
2. derive_peptide(self : rosetta.protocols.analysis.PeptideDeriverFilter, output : rosetta.protocols.analysis.PeptideDeriverOutputter, receptor_pose : rosetta.core.pose.Pose, partner_pose : rosetta.core.pose.Pose, total_isc : float) -> NoneType
The core of the filter: calculate and output a table of the
energetic contribution of each linear segment of the
pep_chain_pose chain (going through it with a sliding window),
together with other interesting data.
- fresh_instance(...) from builtins.PyCapsule
- fresh_instance(rosetta.protocols.analysis.PeptideDeriverFilter) -> rosetta.protocols.filters.Filter
- get_is_do_minimize(...) from builtins.PyCapsule
- get_is_do_minimize(rosetta.protocols.analysis.PeptideDeriverFilter) -> bool
- get_is_dump_cyclic_poses(...) from builtins.PyCapsule
- get_is_dump_cyclic_poses(rosetta.protocols.analysis.PeptideDeriverFilter) -> bool
- get_is_dump_peptide_pose(...) from builtins.PyCapsule
- get_is_dump_peptide_pose(rosetta.protocols.analysis.PeptideDeriverFilter) -> bool
- get_is_dump_prepared_pose(...) from builtins.PyCapsule
- get_is_dump_prepared_pose(rosetta.protocols.analysis.PeptideDeriverFilter) -> bool
- get_is_dump_report_file(...) from builtins.PyCapsule
- get_is_dump_report_file(rosetta.protocols.analysis.PeptideDeriverFilter) -> bool
- get_is_report_gzip(...) from builtins.PyCapsule
- get_is_report_gzip(rosetta.protocols.analysis.PeptideDeriverFilter) -> bool
- get_is_skip_zero_isc(...) from builtins.PyCapsule
- get_is_skip_zero_isc(rosetta.protocols.analysis.PeptideDeriverFilter) -> bool
- get_optimize_cyclic_threshold(...) from builtins.PyCapsule
- get_optimize_cyclic_threshold(rosetta.protocols.analysis.PeptideDeriverFilter) -> float
- get_pep_lengths(...) from builtins.PyCapsule
- get_pep_lengths(rosetta.protocols.analysis.PeptideDeriverFilter) -> rosetta.utility.vector1_unsigned_long
- get_report_format(...) from builtins.PyCapsule
- get_report_format(rosetta.protocols.analysis.PeptideDeriverFilter) -> rosetta.protocols.analysis.PeptideDeriverReportFormat
- get_restrict_partners_to_chains(...) from builtins.PyCapsule
- get_restrict_partners_to_chains(rosetta.protocols.analysis.PeptideDeriverFilter) -> rosetta.utility.vector1_char
- get_restrict_receptors_to_chains(...) from builtins.PyCapsule
- get_restrict_receptors_to_chains(rosetta.protocols.analysis.PeptideDeriverFilter) -> rosetta.utility.vector1_char
- get_scorefxn_deriver(...) from builtins.PyCapsule
- get_scorefxn_deriver(rosetta.protocols.analysis.PeptideDeriverFilter) -> rosetta.core.scoring.ScoreFunction
- name(...) from builtins.PyCapsule
- name(rosetta.protocols.analysis.PeptideDeriverFilter) -> str
- parse_report_format_string(...) from builtins.PyCapsule
- parse_report_format_string(value : str) -> rosetta.protocols.analysis.PeptideDeriverReportFormat
- prepare_pose(...) from builtins.PyCapsule
- prepare_pose(self : rosetta.protocols.analysis.PeptideDeriverFilter, output : rosetta.protocols.analysis.PeptideDeriverOutputter, pose : rosetta.core.pose.Pose) -> NoneType
Prepare pose before derivation, by minimizing it and finding disulfides
- set_is_do_minimize(...) from builtins.PyCapsule
- set_is_do_minimize(self : rosetta.protocols.analysis.PeptideDeriverFilter, value : bool) -> NoneType
- set_is_dump_cyclic_poses(...) from builtins.PyCapsule
- set_is_dump_cyclic_poses(self : rosetta.protocols.analysis.PeptideDeriverFilter, value : bool) -> NoneType
- set_is_dump_peptide_pose(...) from builtins.PyCapsule
- set_is_dump_peptide_pose(self : rosetta.protocols.analysis.PeptideDeriverFilter, value : bool) -> NoneType
- set_is_dump_prepared_pose(...) from builtins.PyCapsule
- set_is_dump_prepared_pose(self : rosetta.protocols.analysis.PeptideDeriverFilter, value : bool) -> NoneType
- set_is_dump_report_file(...) from builtins.PyCapsule
- set_is_dump_report_file(self : rosetta.protocols.analysis.PeptideDeriverFilter, value : bool) -> NoneType
- set_is_report_gzip(...) from builtins.PyCapsule
- set_is_report_gzip(self : rosetta.protocols.analysis.PeptideDeriverFilter, value : bool) -> NoneType
- set_is_skip_zero_isc(...) from builtins.PyCapsule
- set_is_skip_zero_isc(self : rosetta.protocols.analysis.PeptideDeriverFilter, value : bool) -> NoneType
- set_optimize_cyclic_threshold(...) from builtins.PyCapsule
- set_optimize_cyclic_threshold(self : rosetta.protocols.analysis.PeptideDeriverFilter, value : float) -> NoneType
- set_pep_lengths(...) from builtins.PyCapsule
- set_pep_lengths(self : rosetta.protocols.analysis.PeptideDeriverFilter, values : rosetta.utility.vector1_unsigned_long) -> NoneType
- set_report_format(...) from builtins.PyCapsule
- set_report_format(self : rosetta.protocols.analysis.PeptideDeriverFilter, value : rosetta.protocols.analysis.PeptideDeriverReportFormat) -> NoneType
- set_restrict_partners_to_chains(...) from builtins.PyCapsule
- set_restrict_partners_to_chains(self : rosetta.protocols.analysis.PeptideDeriverFilter, values : rosetta.utility.vector1_char) -> NoneType
- set_restrict_receptors_to_chains(...) from builtins.PyCapsule
- set_restrict_receptors_to_chains(self : rosetta.protocols.analysis.PeptideDeriverFilter, values : rosetta.utility.vector1_char) -> NoneType
- set_scorefxn_deriver(...) from builtins.PyCapsule
- set_scorefxn_deriver(self : rosetta.protocols.analysis.PeptideDeriverFilter, value : rosetta.core.scoring.ScoreFunction) -> NoneType
Methods inherited from rosetta.protocols.filters.Filter:
- clear(...) from builtins.PyCapsule
- clear(rosetta.protocols.filters.Filter) -> NoneType
used to clear internal variables if needed. Using fresh_instance is preferred since it's a pure virtual
- get_type(...) from builtins.PyCapsule
- get_type(rosetta.protocols.filters.Filter) -> str
- get_user_defined_name(...) from builtins.PyCapsule
- get_user_defined_name(rosetta.protocols.filters.Filter) -> str
- report_sm(...) from builtins.PyCapsule
- report_sm(self : rosetta.protocols.filters.Filter, : rosetta.core.pose.Pose) -> float
- score(...) from builtins.PyCapsule
- score(self : rosetta.protocols.filters.Filter, pose : rosetta.core.pose.Pose) -> float
- set_user_defined_name(...) from builtins.PyCapsule
- set_user_defined_name(self : rosetta.protocols.filters.Filter, name : str) -> NoneType
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class PeptideDeriverMarkdownStreamOutputter(PeptideDeriverOutputter) |
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outputs a Markdown formatted Peptiderive report to a stream
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- Method resolution order:
- PeptideDeriverMarkdownStreamOutputter
- PeptideDeriverOutputter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(self : handle, out : rosetta.utility.io.orstream, prefix : str) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- begin_receptor_partner_pair(...) from builtins.PyCapsule
- begin_receptor_partner_pair(self : rosetta.protocols.analysis.PeptideDeriverMarkdownStreamOutputter, receptor_chain_letter : str, partner_chain_letter : str, total_isc : float, options_string : str) -> NoneType
- begin_structure(...) from builtins.PyCapsule
- begin_structure(self : rosetta.protocols.analysis.PeptideDeriverMarkdownStreamOutputter, pose : rosetta.core.pose.Pose, : str) -> NoneType
- chain_pair_pose_prepared(...) from builtins.PyCapsule
- chain_pair_pose_prepared(self : rosetta.protocols.analysis.PeptideDeriverMarkdownStreamOutputter, : rosetta.core.pose.Pose) -> NoneType
- end_receptor_partner_pair(...) from builtins.PyCapsule
- end_receptor_partner_pair(rosetta.protocols.analysis.PeptideDeriverMarkdownStreamOutputter) -> NoneType
- end_structure(...) from builtins.PyCapsule
- end_structure(rosetta.protocols.analysis.PeptideDeriverMarkdownStreamOutputter) -> NoneType
- peptide_entry(...) from builtins.PyCapsule
- peptide_entry(self : rosetta.protocols.analysis.PeptideDeriverMarkdownStreamOutputter, pose : rosetta.core.pose.Pose, entry_type : rosetta.protocols.analysis.PeptideDeriverEntryType, pep_start : int, linear_isc : float, binding_contribution_fraction : float, disulfide_info : str, was_cyclic_pep_modeled : bool, : rosetta.core.pose.Pose, cyclic_isc : float) -> NoneType
- peptide_length(...) from builtins.PyCapsule
- peptide_length(self : rosetta.protocols.analysis.PeptideDeriverMarkdownStreamOutputter, pep_length : int) -> NoneType
Methods inherited from PeptideDeriverOutputter:
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.analysis.PeptideDeriverOutputter, : rosetta.protocols.analysis.PeptideDeriverOutputter) -> rosetta.protocols.analysis.PeptideDeriverOutputter
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class PeptideDeriverOutputter(builtins.object) |
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an abstract base class for handling calculation outputs from
PeptideDeriverFilter
Since PeptideDeriverFilter might have a set of outputs for each residue,
for each chain in each chain-pair, outputting is quite elaborate. This is
an attempt to decouple the calculation from the representation of results.
Representation of results is delegated to implementors of this class.
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.analysis.PeptideDeriverOutputter) -> NoneType
2. __init__(rosetta.protocols.analysis.PeptideDeriverOutputter, rosetta.protocols.analysis.PeptideDeriverOutputter) -> 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.analysis.PeptideDeriverOutputter, : rosetta.protocols.analysis.PeptideDeriverOutputter) -> rosetta.protocols.analysis.PeptideDeriverOutputter
- begin_receptor_partner_pair(...) from builtins.PyCapsule
- begin_receptor_partner_pair(self : rosetta.protocols.analysis.PeptideDeriverOutputter, receptor_chain_letter : str, partner_chain_letter : str, total_isc : float, options_string : str) -> NoneType
called by PeptideDeriverFilter when calculation commences on a receptor-partner pair
- begin_structure(...) from builtins.PyCapsule
- begin_structure(self : rosetta.protocols.analysis.PeptideDeriverOutputter, : rosetta.core.pose.Pose, : str) -> NoneType
called by PeptideDeriverFilter when processing of a strucuture (possibly multi-chain) starts
- chain_pair_pose_prepared(...) from builtins.PyCapsule
- chain_pair_pose_prepared(self : rosetta.protocols.analysis.PeptideDeriverOutputter, pose : rosetta.core.pose.Pose) -> NoneType
called by PeptideDeriverFilter when a chain-pair pose is prepared (minimized and disulfide-bridge resolved)
- end_receptor_partner_pair(...) from builtins.PyCapsule
- end_receptor_partner_pair(rosetta.protocols.analysis.PeptideDeriverOutputter) -> NoneType
called by PeptideDeriverFilter when calculation concludes for a receptor-partner pair (for all the different peptide lengths)
- end_structure(...) from builtins.PyCapsule
- end_structure(rosetta.protocols.analysis.PeptideDeriverOutputter) -> NoneType
called by PeptideDeriverFilter when processing of a strucuture (all chain-pairs considered) ends
- peptide_entry(...) from builtins.PyCapsule
- peptide_entry(self : rosetta.protocols.analysis.PeptideDeriverOutputter, pose : rosetta.core.pose.Pose, entry_type : rosetta.protocols.analysis.PeptideDeriverEntryType, pep_start : int, linear_isc : float, binding_contribution_fraction : float, disulfide_info : str, was_cyclic_pep_modeled : bool, cyclic_pose : rosetta.core.pose.Pose, cyclic_isc : float) -> NoneType
called by PeptideDeriverFilter for each 'peptide' entry that should be output.
besides the peptides for each sliding window, this is being called for the 'best' peptides (
PeptideDeriverEntryType)
- peptide_length(...) from builtins.PyCapsule
- peptide_length(self : rosetta.protocols.analysis.PeptideDeriverOutputter, pep_length : int) -> NoneType
called by PeptideDeriverFilter when calculation commences for
the specified peptide length
this is called for every peptide length specified to
PeptideDeriverFilter, per each call to
PeptideDeriverOutputter::begin_receptor_partner_pair()
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class PeptideDeriverOutputterContainer(PeptideDeriverOutputter) |
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a container class which holds a list of PeptideDeriverOutputter instances and delegates calls to those.
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- Method resolution order:
- PeptideDeriverOutputterContainer
- PeptideDeriverOutputter
- 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.analysis.PeptideDeriverOutputterContainer, : rosetta.protocols.analysis.PeptideDeriverOutputterContainer) -> rosetta.protocols.analysis.PeptideDeriverOutputterContainer
- begin_receptor_partner_pair(...) from builtins.PyCapsule
- begin_receptor_partner_pair(self : rosetta.protocols.analysis.PeptideDeriverOutputterContainer, receptor_chain_letter : str, partner_chain_letter : str, total_isc : float, options_string : str) -> NoneType
- begin_structure(...) from builtins.PyCapsule
- begin_structure(self : rosetta.protocols.analysis.PeptideDeriverOutputterContainer, pose : rosetta.core.pose.Pose, : str) -> NoneType
- chain_pair_pose_prepared(...) from builtins.PyCapsule
- chain_pair_pose_prepared(self : rosetta.protocols.analysis.PeptideDeriverOutputterContainer, pose : rosetta.core.pose.Pose) -> NoneType
- clear(...) from builtins.PyCapsule
- clear(rosetta.protocols.analysis.PeptideDeriverOutputterContainer) -> NoneType
clear all outputters in the list.
- end_receptor_partner_pair(...) from builtins.PyCapsule
- end_receptor_partner_pair(rosetta.protocols.analysis.PeptideDeriverOutputterContainer) -> NoneType
- end_structure(...) from builtins.PyCapsule
- end_structure(rosetta.protocols.analysis.PeptideDeriverOutputterContainer) -> NoneType
- peptide_entry(...) from builtins.PyCapsule
- peptide_entry(self : rosetta.protocols.analysis.PeptideDeriverOutputterContainer, pose : rosetta.core.pose.Pose, entry_type : rosetta.protocols.analysis.PeptideDeriverEntryType, pep_start : int, linear_isc : float, binding_contribution_fraction : float, disulfide_info : str, was_cyclic_pep_modeled : bool, cyclic_pose : rosetta.core.pose.Pose, cyclic_isc : float) -> NoneType
- peptide_length(...) from builtins.PyCapsule
- peptide_length(self : rosetta.protocols.analysis.PeptideDeriverOutputterContainer, pep_length : int) -> NoneType
- push_back(...) from builtins.PyCapsule
- push_back(self : rosetta.protocols.analysis.PeptideDeriverOutputterContainer, item : rosetta.protocols.analysis.PeptideDeriverOutputter) -> NoneType
add an outputter to the list.
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class PeptideDeriverPoseOutputter(PeptideDeriverOutputter) |
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outputs poses at different points of the Peptiderive protocol, according to the given set of options
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| |
- Method resolution order:
- PeptideDeriverPoseOutputter
- PeptideDeriverOutputter
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(self : handle, is_dump_best_peptide_pose : bool, is_dump_prepared_pose : bool, is_dump_cyclic_poses : bool, scorefxn : rosetta.core.scoring.ScoreFunction) -> 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.analysis.PeptideDeriverPoseOutputter, : rosetta.protocols.analysis.PeptideDeriverPoseOutputter) -> rosetta.protocols.analysis.PeptideDeriverPoseOutputter
- begin_receptor_partner_pair(...) from builtins.PyCapsule
- begin_receptor_partner_pair(self : rosetta.protocols.analysis.PeptideDeriverPoseOutputter, receptor_chain_letter : str, partner_chain_letter : str, : float, : str) -> NoneType
- begin_structure(...) from builtins.PyCapsule
- begin_structure(self : rosetta.protocols.analysis.PeptideDeriverPoseOutputter, : rosetta.core.pose.Pose, : str) -> NoneType
- chain_pair_pose_prepared(...) from builtins.PyCapsule
- chain_pair_pose_prepared(self : rosetta.protocols.analysis.PeptideDeriverPoseOutputter, pose : rosetta.core.pose.Pose) -> NoneType
- end_receptor_partner_pair(...) from builtins.PyCapsule
- end_receptor_partner_pair(rosetta.protocols.analysis.PeptideDeriverPoseOutputter) -> NoneType
- end_structure(...) from builtins.PyCapsule
- end_structure(rosetta.protocols.analysis.PeptideDeriverPoseOutputter) -> NoneType
- peptide_entry(...) from builtins.PyCapsule
- peptide_entry(self : rosetta.protocols.analysis.PeptideDeriverPoseOutputter, pose : rosetta.core.pose.Pose, entry_type : rosetta.protocols.analysis.PeptideDeriverEntryType, : int, : float, : float, disulfide_info : str, was_cyclic_pep_modeled : bool, cyclic_pose : rosetta.core.pose.Pose, : float) -> NoneType
- peptide_length(...) from builtins.PyCapsule
- peptide_length(self : rosetta.protocols.analysis.PeptideDeriverPoseOutputter, pep_length : int) -> NoneType
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