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- builtins.object
-
- AllowedSeqposForGeomCst
- CovalentConnectionReplaceInfo
- EnzConstraintIO
- EnzConstraintParameters
- EnzCstTemplateRes
- EnzCstTemplateResAtoms
- EnzCstTemplateResCache
- EnzdesCstCache
- EnzdesCstParamCache
- EnzdesLoopInfo
- EnzdesLoopsFile
- EnzdesSeqRecoveryCache
- ExternalGeomSampler
- ExternalTransform
- GeomSampleInfo
- InvrotCollector
- InvrotTree
-
- TheozymeInvrotTree
- InvrotTreeNodeBase
-
- InvrotTarget
-
- SingleResidueInvrotTarget
- InvrotTreeNode
- LigandConformer
- MatchConstraintFileInfo
- MatchConstraintFileInfoList
- ResInteractions
-
- CstResInteractions
- rosetta.core.pose.datacache.CacheableObserver(builtins.object)
-
- EnzdesCacheableObserver
- rosetta.protocols.moves.Mover(builtins.object)
-
- AlignPoseToInvrotTreeMover
class AlignPoseToInvrotTreeMover(rosetta.protocols.moves.Mover) |
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small mover that takes an invrot tree
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- Method resolution order:
- AlignPoseToInvrotTreeMover
- rosetta.protocols.moves.Mover
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, invrot_tree : protocols::toolbox::match_enzdes_util::InvrotTree, seqpos : protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst) -> NoneType
2. __init__(handle, rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover) -> 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.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover, pose : rosetta.core.pose.Pose) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover, : rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover) -> rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover) -> str
- set_add_target_to_pose(...) from builtins.PyCapsule
- set_add_target_to_pose(self : rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover, setting : bool) -> NoneType
- set_geomcst_for_superposition_from_enz_io(...) from builtins.PyCapsule
- set_geomcst_for_superposition_from_enz_io(self : rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover, enzcst_io : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO) -> NoneType
- setup_foldtree_around_anchor_invrot(...) from builtins.PyCapsule
- setup_foldtree_around_anchor_invrot(self : rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover, pose : rosetta.core.pose.Pose, anchor_seqpos : int, first_target_seqpos : int) -> NoneType
sets up a foldtree such that
the anchor residue doesn't move,
i.e. a backward edge from anchor to 1
and a forward edge from anchor to seqpos
also need to setup the jumps at anchor res
- switch_residue_type_set(...) from builtins.PyCapsule
- switch_residue_type_set(self : rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover, residue : rosetta.core.conformation.Residue, desired_restype_set_name : str) -> rosetta.core.conformation.Residue
silly helper function to get the equivalent
of a certain residue in a new residue type set
note if the passed in residue is already of the
required residue type set, nothing changes, just
passes back input pointer
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
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class CovalentConnectionReplaceInfo(builtins.object) |
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helper class to allow for removal of covalent constraints
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo, resA_base_in : str, resB_base_in : str, resA_var_in : str, resB_var_in : str, Apos_in : int, Bpos_in : int, restype_set_in : rosetta.core.chemical.ResidueTypeSet) -> NoneType
2. __init__(self : rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo, other : rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo) -> 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.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo, : rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo) -> rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo
- remap_resid(...) from builtins.PyCapsule
- remap_resid(self : rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo, smap : rosetta.core.id.SequenceMapping) -> NoneType
- remove_covalent_connection_from_pose(...) from builtins.PyCapsule
- remove_covalent_connection_from_pose(self : rosetta.protocols.toolbox.match_enzdes_util.CovalentConnectionReplaceInfo, pose : rosetta.core.pose.Pose) -> NoneType
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class EnzConstraintIO(builtins.object) |
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, src_restype_set : rosetta.core.chemical.ResidueTypeSet) -> NoneType
2. __init__(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_constraints_to_pose(...) from builtins.PyCapsule
- add_constraints_to_pose(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose : rosetta.core.pose.Pose, scofx : rosetta.core.scoring.ScoreFunction, accept_blocks_missing_header : bool) -> NoneType
- add_constraints_to_pose_for_block_without_clearing_and_header_processing(...) from builtins.PyCapsule
- add_constraints_to_pose_for_block_without_clearing_and_header_processing(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose : rosetta.core.pose.Pose, scofx : rosetta.core.scoring.ScoreFunction, cst_block : int) -> NoneType
BE CAREFUL when using this function, it generates constraints
without clearing the internal data structures and reading in
the information in the pdb REMARKs
if you're unsure use the above one
- add_pregenerated_constraints_to_pose(...) from builtins.PyCapsule
- add_pregenerated_constraints_to_pose(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose : rosetta.core.pose.Pose, scofx : rosetta.core.scoring.ScoreFunction) -> NoneType
convenience function that will add constraints to the pose if they have
been previously generated. BE CAREFUL when using this function, it relies on the
pose having the same residue types at the same constrained positions as in the pose
that was originally used to generate the constraints. If in doubt, it's safer to
regenerate the constraints before adding (i.e. use the above add_constraints_to_pose
function.)
- allowed_res_name3_at_position(...) from builtins.PyCapsule
- allowed_res_name3_at_position(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose : rosetta.core.pose.Pose, seqpos : int) -> rosetta.utility.vector1_std_string
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO) -> rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO
- clear_active_pose_constraints_for_block(...) from builtins.PyCapsule
- clear_active_pose_constraints_for_block(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose : rosetta.core.pose.Pose, cst_block : int) -> NoneType
- contains_position(...) from builtins.PyCapsule
- contains_position(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose : rosetta.core.pose.Pose, seqpos : int) -> bool
are constraints specified for this position?
- enz_cst_params(...) from builtins.PyCapsule
- enz_cst_params(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, block : int) -> protocols::toolbox::match_enzdes_util::EnzConstraintParameters
- enz_cst_params_missing_in_pose(...) from builtins.PyCapsule
- enz_cst_params_missing_in_pose(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_std_shared_ptr_const_protocols_toolbox_match_enzdes_util_EnzConstraintParameters_t
- enz_cst_params_size(...) from builtins.PyCapsule
- enz_cst_params_size(rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO) -> int
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO) -> rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO
self pointers
2. get_self_ptr(rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO) -> rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO) -> rosetta.std.weak_ptr_const_protocols_toolbox_match_enzdes_util_EnzConstraintIO_t
2. get_self_weak_ptr(rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO) -> rosetta.std.weak_ptr_protocols_toolbox_match_enzdes_util_EnzConstraintIO_t
- is_backbone_only_cst(...) from builtins.PyCapsule
- is_backbone_only_cst(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose : rosetta.core.pose.Pose, seqpos : int) -> bool
are the constraints specified at this position
mediated through backbone interactions only?
- mcfi_list(...) from builtins.PyCapsule
- mcfi_list(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, block : int) -> protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList
- mcfi_lists_size(...) from builtins.PyCapsule
- mcfi_lists_size(rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO) -> int
- num_mcfi_lists(...) from builtins.PyCapsule
- num_mcfi_lists(rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO) -> int
- ordered_constrained_positions(...) from builtins.PyCapsule
- ordered_constrained_positions(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_unsigned_long
- process_pdb_header(...) from builtins.PyCapsule
- process_pdb_header(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose : rosetta.core.pose.Pose, accept_missing_blocks : bool) -> NoneType
- read_enzyme_cstfile(...) from builtins.PyCapsule
- read_enzyme_cstfile(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, fname : str) -> NoneType
- remap_resid(...) from builtins.PyCapsule
- remap_resid(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, smap : rosetta.core.id.SequenceMapping) -> NoneType
changing the constrained residues if the sequence length changes
- remove_constraints_from_pose(...) from builtins.PyCapsule
- remove_constraints_from_pose(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose : rosetta.core.pose.Pose, keep_covalent : bool, fail_on_constraints_missing : bool) -> NoneType
- remove_constraints_from_pose_for_block(...) from builtins.PyCapsule
- remove_constraints_from_pose_for_block(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose : rosetta.core.pose.Pose, cst_block : int, fail_on_constraints_missing : bool) -> NoneType
- remove_position_from_template_res(...) from builtins.PyCapsule
- remove_position_from_template_res(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose : rosetta.core.pose.Pose, pos : int) -> NoneType
- remove_position_from_template_res_for_block(...) from builtins.PyCapsule
- remove_position_from_template_res_for_block(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose : rosetta.core.pose.Pose, pos : int, cst_block : int) -> NoneType
- set_external_position_for_resA_in_parameter_block(...) from builtins.PyCapsule
- set_external_position_for_resA_in_parameter_block(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, cst_block : int, respos : int) -> NoneType
- set_external_position_for_resB_in_parameter_block(...) from builtins.PyCapsule
- set_external_position_for_resB_in_parameter_block(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, cst_block : int, respos : int) -> NoneType
- set_position_for_missing_res_in_parameter_block(...) from builtins.PyCapsule
- set_position_for_missing_res_in_parameter_block(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose : rosetta.core.pose.Pose, cst_block : int, respos : int) -> NoneType
- show_cst_definitions(...) from builtins.PyCapsule
- show_cst_definitions(rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO) -> NoneType
- target_downstream_res(...) from builtins.PyCapsule
- target_downstream_res(rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO) -> rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t
- update_pdb_remarks_for_backbone_params(...) from builtins.PyCapsule
- update_pdb_remarks_for_backbone_params(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, pose : rosetta.core.pose.Pose) -> NoneType
|
class EnzConstraintParameters(builtins.object) |
| |
class that holds all the parameters for one specific constraint
|
| |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters) -> NoneType
2. __init__(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters, other : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- allowed_res_name3_at_position(...) from builtins.PyCapsule
- allowed_res_name3_at_position(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters, pose : rosetta.core.pose.Pose, seqpos : int) -> rosetta.std.set_std_string_std_less_std_string_std_allocator_std_string_t
all residue names specified in the cstfile
returns an empty set if the constraints don't apply
to the specifed position
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters, : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters) -> rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters
- convert_GeomSampleInfo_to_FuncOP(...) from builtins.PyCapsule
- convert_GeomSampleInfo_to_FuncOP(gsi : protocols::toolbox::match_enzdes_util::GeomSampleInfo, ideal_val : float) -> rosetta.core.scoring.func.Func
- cst_block(...) from builtins.PyCapsule
- cst_block(rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters) -> int
- enz_io(...) from builtins.PyCapsule
- enz_io(rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters) -> rosetta.std.weak_ptr_const_protocols_toolbox_match_enzdes_util_EnzConstraintIO_t
- generate_pose_specific_data(...) from builtins.PyCapsule
- generate_pose_specific_data(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters, pose : rosetta.core.pose.Pose, scofx : rosetta.core.scoring.ScoreFunction) -> NoneType
- get_missing_template_other_res(...) from builtins.PyCapsule
- get_missing_template_other_res(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters, pose : rosetta.core.pose.Pose) -> protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
- get_missing_template_res(...) from builtins.PyCapsule
- get_missing_template_res(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters, pose : rosetta.core.pose.Pose) -> protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters) -> rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters
self pointers
2. get_self_ptr(rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters) -> rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters) -> rosetta.std.weak_ptr_const_protocols_toolbox_match_enzdes_util_EnzConstraintParameters_t
- init(...) from builtins.PyCapsule
- init(*args, **kwargs)
Overloaded function.
1. init(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters, cst_block : int, src_restype_set : rosetta.core.chemical.ResidueTypeSet, src_enz_io : rosetta.std.weak_ptr_const_protocols_toolbox_match_enzdes_util_EnzConstraintIO_t) -> NoneType
2. init(rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters) -> NoneType
- is_covalent(...) from builtins.PyCapsule
- is_covalent(rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters) -> bool
- is_empty(...) from builtins.PyCapsule
- is_empty(rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters) -> bool
- missing_in_pose(...) from builtins.PyCapsule
- missing_in_pose(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters, pose : rosetta.core.pose.Pose) -> bool
- nonconst_resA(...) from builtins.PyCapsule
- nonconst_resA(rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters) -> protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
- nonconst_resB(...) from builtins.PyCapsule
- nonconst_resB(rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters) -> protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
- remap_resid(...) from builtins.PyCapsule
- remap_resid(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters, smap : rosetta.core.id.SequenceMapping) -> NoneType
- remove_covalent_connections_from_pose(...) from builtins.PyCapsule
- remove_covalent_connections_from_pose(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters, pose : rosetta.core.pose.Pose) -> NoneType
- resA(...) from builtins.PyCapsule
- resA(rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters) -> protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
- resB(...) from builtins.PyCapsule
- resB(rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters) -> protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
- set_cst_block(...) from builtins.PyCapsule
- set_cst_block(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters, cst_block : int) -> NoneType
- set_external_position_for_resA(...) from builtins.PyCapsule
- set_external_position_for_resA(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters, pos : int) -> NoneType
- set_external_position_for_resB(...) from builtins.PyCapsule
- set_external_position_for_resB(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters, pos : int) -> NoneType
- set_mcfi(...) from builtins.PyCapsule
- set_mcfi(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters, mcfi : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo) -> NoneType
- show_definitions(...) from builtins.PyCapsule
- show_definitions(rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters) -> NoneType
- update_pdb_remarks(...) from builtins.PyCapsule
- update_pdb_remarks(self : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters, pose : rosetta.core.pose.Pose) -> bool
updates the pdb remarks according to what is in the
EnzCstTemplateRes member data. returns false in case any
error occured
|
class EnzCstTemplateRes(builtins.object) |
| |
helper class for class EnzConstraintParameters, gathers information
from cst input and pdb input
|
| |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes, src_restype_set : rosetta.core.chemical.ResidueTypeSet) -> NoneType
2. __init__(self : rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes, src_restype_set : rosetta.core.chemical.ResidueTypeSet, src_enzio_param : rosetta.std.weak_ptr_const_protocols_toolbox_match_enzdes_util_EnzConstraintParameters_t) -> NoneType
3. __init__(self : rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes, other : rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes, new_ref_param : rosetta.std.weak_ptr_const_protocols_toolbox_match_enzdes_util_EnzConstraintParameters_t) -> NoneType
4. __init__(self : rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes, : rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- allowed_res_types(...) from builtins.PyCapsule
- allowed_res_types(rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes) -> rosetta.utility.vector1_std_string
- allowed_res_types_pointers(...) from builtins.PyCapsule
- allowed_res_types_pointers(rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes) -> rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes, : rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes) -> rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes
- atom_inds_for_restype(...) from builtins.PyCapsule
- atom_inds_for_restype(self : rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes, template_atom : int, restype : rosetta.core.chemical.ResidueType) -> rosetta.utility.vector1_unsigned_long
- atom_inds_for_restype_begin(...) from builtins.PyCapsule
- atom_inds_for_restype_begin(rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes) -> std::_Rb_tree_const_iterator<std::pair<std::shared_ptr<core::chemical::ResidueType const> const, utility::vector1<utility::vector1<unsigned long, std::allocator<unsigned long> >, std::allocator<utility::vector1<unsigned long, std::allocator<unsigned long> > > > > >
Iterator to the map from ResidueType pointers (addresses) to the set of atoms
that are used to build from; this returns ResidueTypes in an indeterminant order
as they are going to be sorted based on where in memory the ResidueTypes happened
to be allocated.
- atom_inds_for_restype_end(...) from builtins.PyCapsule
- atom_inds_for_restype_end(rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes) -> std::_Rb_tree_const_iterator<std::pair<std::shared_ptr<core::chemical::ResidueType const> const, utility::vector1<utility::vector1<unsigned long, std::allocator<unsigned long> >, std::allocator<utility::vector1<unsigned long, std::allocator<unsigned long> > > > > >
End iterator to the map from ResidueType pointers to the set of atoms
that are used to build from.
- clear_all(...) from builtins.PyCapsule
- clear_all(rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes) -> NoneType
- compatible_restype(...) from builtins.PyCapsule
- compatible_restype(self : rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes, restype : rosetta.core.chemical.ResidueType) -> bool
- corresponding_res_block(...) from builtins.PyCapsule
- corresponding_res_block(rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes) -> int
- determine_atom_inds_for_restype(...) from builtins.PyCapsule
- determine_atom_inds_for_restype(self : rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes, restype : rosetta.core.chemical.ResidueType) -> NoneType
- find_in_pose_if_missing_from_header(...) from builtins.PyCapsule
- find_in_pose_if_missing_from_header(self : rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes, pose : rosetta.core.pose.Pose) -> bool
- get_pose_data(...) from builtins.PyCapsule
- get_pose_data(self : rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes, pose : rosetta.core.pose.Pose) -> NoneType
- get_template_atoms_at_pos(...) from builtins.PyCapsule
- get_template_atoms_at_pos(self : rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes, pose : rosetta.core.pose.Pose, seqpos : int) -> rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResAtoms
- identical_info_consistency_check(...) from builtins.PyCapsule
- identical_info_consistency_check(rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes) -> NoneType
- is_backbone(...) from builtins.PyCapsule
- is_backbone(rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes) -> bool
- param_index(...) from builtins.PyCapsule
- param_index(rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes) -> int
- rb_minimizable(...) from builtins.PyCapsule
- rb_minimizable(rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes) -> bool
- read_params(...) from builtins.PyCapsule
- read_params(self : rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes, line_stream : rosetta.std.basic_istringstream_char_std_char_traits_char_std_allocator_char_t) -> NoneType
- remap_resid(...) from builtins.PyCapsule
- remap_resid(self : rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes, smap : rosetta.core.id.SequenceMapping) -> NoneType
- residue_conformations_redundant(...) from builtins.PyCapsule
- residue_conformations_redundant(self : rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes, res1 : rosetta.core.conformation.Residue, res2 : rosetta.core.conformation.Residue) -> bool
checks whether the distance
between any of the template res atoms
of res1 and res2 is below a certain
cutoff.
- set_enzio_param(...) from builtins.PyCapsule
- set_enzio_param(self : rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes, src_enz_io_param : rosetta.std.weak_ptr_const_protocols_toolbox_match_enzdes_util_EnzConstraintParameters_t) -> NoneType
- set_external_position(...) from builtins.PyCapsule
- set_external_position(self : rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes, resnum : int) -> NoneType
- set_param_index(...) from builtins.PyCapsule
- set_param_index(self : rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes, index : int) -> NoneType
- show_params(...) from builtins.PyCapsule
- show_params(rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes) -> NoneType
|
class EnzCstTemplateResCache(builtins.object) |
| | |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResCache) -> NoneType
2. __init__(self : rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResCache, other : rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResCache) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_position_in_pose(...) from builtins.PyCapsule
- add_position_in_pose(self : rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResCache, seqpos : int) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResCache, : rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResCache) -> rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResCache
- contains_position(...) from builtins.PyCapsule
- contains_position(self : rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResCache, seqpos : int) -> bool
- not_in_pose(...) from builtins.PyCapsule
- not_in_pose(rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResCache) -> bool
- remap_resid(...) from builtins.PyCapsule
- remap_resid(self : rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResCache, smap : rosetta.core.id.SequenceMapping) -> NoneType
remapping sequence positions
- remove_seqpos(...) from builtins.PyCapsule
- remove_seqpos(self : rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResCache, seqpos : int) -> bool
- seqpos_map_begin(...) from builtins.PyCapsule
- seqpos_map_begin(rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResCache) -> std::_Rb_tree_const_iterator<std::pair<unsigned long const, std::shared_ptr<protocols::toolbox::match_enzdes_util::EnzCstTemplateResAtoms> > >
- seqpos_map_end(...) from builtins.PyCapsule
- seqpos_map_end(rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResCache) -> std::_Rb_tree_const_iterator<std::pair<unsigned long const, std::shared_ptr<protocols::toolbox::match_enzdes_util::EnzCstTemplateResAtoms> > >
- seqpos_map_size(...) from builtins.PyCapsule
- seqpos_map_size(rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResCache) -> int
- set_position_in_pose(...) from builtins.PyCapsule
- set_position_in_pose(self : rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateResCache, seqpos : int) -> NoneType
|
class EnzdesCacheableObserver(rosetta.core.pose.datacache.CacheableObserver) |
| | |
- Method resolution order:
- EnzdesCacheableObserver
- rosetta.core.pose.datacache.CacheableObserver
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver) -> 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.toolbox.match_enzdes_util.EnzdesCacheableObserver, : rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver) -> rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver) -> rosetta.core.pose.datacache.CacheableObserver
- create(...) from builtins.PyCapsule
- create(rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver) -> rosetta.core.pose.datacache.CacheableObserver
- cst_cache(...) from builtins.PyCapsule
- cst_cache(*args, **kwargs)
Overloaded function.
1. cst_cache(rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver) -> protocols::toolbox::match_enzdes_util::EnzdesCstCache
2. cst_cache(rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver) -> protocols::toolbox::match_enzdes_util::EnzdesCstCache
- enzdes_loops_file(...) from builtins.PyCapsule
- enzdes_loops_file(rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver) -> rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile
- erase_rigid_body_confs_for_lig(...) from builtins.PyCapsule
- erase_rigid_body_confs_for_lig(self : rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver, seqpos : int) -> NoneType
- get_seq_recovery_cache(...) from builtins.PyCapsule
- get_seq_recovery_cache(*args, **kwargs)
Overloaded function.
1. get_seq_recovery_cache(rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver) -> protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache
2. get_seq_recovery_cache(rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver) -> protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache
- is_attached(...) from builtins.PyCapsule
- is_attached(rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver) -> bool
- lig_rigid_body_confs(...) from builtins.PyCapsule
- lig_rigid_body_confs(rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver) -> rosetta.std.map_unsigned_long_utility_vector1_std_shared_ptr_const_core_conformation_Residue_std_allocator_std_shared_ptr_const_core_conformation_Residue_t
- remove_favor_native_constraints(...) from builtins.PyCapsule
- remove_favor_native_constraints(self : rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver, pose : rosetta.core.pose.Pose) -> NoneType
- set_cst_cache(...) from builtins.PyCapsule
- set_cst_cache(self : rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver, cst_cache : protocols::toolbox::match_enzdes_util::EnzdesCstCache) -> NoneType
- set_enzdes_loops_file(...) from builtins.PyCapsule
- set_enzdes_loops_file(self : rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver, loopfile_in : rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile) -> NoneType
- set_rigid_body_confs_for_lig(...) from builtins.PyCapsule
- set_rigid_body_confs_for_lig(self : rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver, seqpos : int, rg_confs : rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) -> NoneType
- set_seq_recovery_cache(...) from builtins.PyCapsule
- set_seq_recovery_cache(self : rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver, seq_recovery_cache : protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache) -> NoneType
- setup_favor_native_constraints(...) from builtins.PyCapsule
- setup_favor_native_constraints(self : rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask, native_pose : rosetta.core.pose.Pose) -> NoneType
Methods inherited from rosetta.core.pose.datacache.CacheableObserver:
- attach_to(...) from builtins.PyCapsule
- attach_to(self : rosetta.core.pose.datacache.CacheableObserver, pose : rosetta.core.pose.Pose) -> NoneType
attach to Pose/Conformation
Derived classes do not overload this method -- see attach_impl()
instead.
- detach_from(...) from builtins.PyCapsule
- detach_from(rosetta.core.pose.datacache.CacheableObserver) -> NoneType
detach from Pose/Conformation
Derived classes do not overload this method -- see
detach_impl() instead.
|
class EnzdesCstCache(builtins.object) |
| |
a simple class to store the pose specific
enzdes constraint information in the actual pose
|
| |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache, enz_cstio : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, num_cst_blocks : int) -> NoneType
2. __init__(self : rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache, other : rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache) -> 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.toolbox.match_enzdes_util.EnzdesCstCache, : rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache) -> rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache
- contains_position(...) from builtins.PyCapsule
- contains_position(self : rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache, seqpos : int) -> bool
- enzcst_io(...) from builtins.PyCapsule
- enzcst_io(rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache) -> rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO
- ncsts(...) from builtins.PyCapsule
- ncsts(rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache) -> int
- ordered_constrained_positions(...) from builtins.PyCapsule
- ordered_constrained_positions(self : rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_unsigned_long
returns all seqpos present in the cache in order of the params
which they are in.
note: ligands are explicityly put at the end of the vector
- param_cache(...) from builtins.PyCapsule
- param_cache(*args, **kwargs)
Overloaded function.
1. param_cache(self : rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache, cst_block : int) -> protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
2. param_cache(self : rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache, cst_block : int) -> protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
- remap_resid(...) from builtins.PyCapsule
- remap_resid(self : rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache, smap : rosetta.core.id.SequenceMapping) -> NoneType
remapping sequence positions
- set_param_cache(...) from builtins.PyCapsule
- set_param_cache(self : rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache, cst_block : int, param_cache : protocols::toolbox::match_enzdes_util::EnzdesCstParamCache) -> NoneType
|
class EnzdesCstParamCache(builtins.object) |
| | |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache) -> NoneType
2. __init__(self : rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache, other : rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- active_pose_constraints(...) from builtins.PyCapsule
- active_pose_constraints(*args, **kwargs)
Overloaded function.
1. active_pose_constraints(rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache) -> rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t
2. active_pose_constraints(rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache) -> rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache, : rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache) -> rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache
- clear_active_pose_constraints(...) from builtins.PyCapsule
- clear_active_pose_constraints(rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache) -> NoneType
- contains_position(...) from builtins.PyCapsule
- contains_position(self : rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache, seqpos : int) -> bool
- covalent_connections(...) from builtins.PyCapsule
- covalent_connections(rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache) -> rosetta.utility.vector1_std_shared_ptr_const_protocols_toolbox_match_enzdes_util_CovalentConnectionReplaceInfo_t
- missing_in_pose(...) from builtins.PyCapsule
- missing_in_pose(rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache) -> bool
- remap_resid(...) from builtins.PyCapsule
- remap_resid(self : rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache, smap : rosetta.core.id.SequenceMapping) -> NoneType
remapping sequence positions
- remove_seqpos_from_template_res(...) from builtins.PyCapsule
- remove_seqpos_from_template_res(self : rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache, seqpos : int) -> NoneType
- set_active_pose_constraints(...) from builtins.PyCapsule
- set_active_pose_constraints(self : rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache, constraints : rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t) -> NoneType
- set_position_for_missing_res(...) from builtins.PyCapsule
- set_position_for_missing_res(self : rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache, seqpos : int) -> NoneType
- template_res_cache(...) from builtins.PyCapsule
- template_res_cache(*args, **kwargs)
Overloaded function.
1. template_res_cache(self : rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache, index : int) -> protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache
2. template_res_cache(self : rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache, index : int) -> protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache
- template_res_cache_size(...) from builtins.PyCapsule
- template_res_cache_size(rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache) -> int
|
class ExternalGeomSampler(builtins.object) |
| |
The external geom sampler is a class that manages the data necessary
to construct the coordinates of the three atoms in the downstream partner.
The external geom sampler holds the data for the six degrees of freedom
that describe the downstream atoms relative to the upstream atoms.
The naming of the 6 atoms involved and the 6 degrees of freedom involved
is as follows:
Atoms U1, U2, and U3 are on the upstream partner.
Atoms D1, D2, and D3 are on the downstream partner.
The numbers indicate the distance the atoms have from the "break" between the upstream
and downstream partners.
DOF 1: "tor_U3D1" is the torsion between atoms U3, U2, U1 and D1.
DOF 2: "ang_U2D1" is angle between atoms U2, U1 and D1.
DOF 3: "dis_U1D1" is the distance between atoms U1 and D1.
DOF 4: "tor_U2D2" is the torsion between atoms U2, U1, D1 and D2.
DOF 5: "ang_U1D2" is the angle between atoms U1, D1 and D3
DOF 6: "tor_U1D3" is the torsion between atoms U1, D1, D2 and D3
This naming convention describes a parameter by three letters followed by two atom names.
The letter is "d" for distance, "a" for angle, and "t" for torsion. The two numbers
describe the end points of that parameter assuming a continuous span of numbers
between. E.g. t25 describes the geometry of 4 atoms starting at 2 and going to 5,
hitting atoms 3 and 4 along the way.
ASCII art:
Fig 1. The 6 atoms that define the geometry between the upstream partner
and the downstream partner. dis_U1D1 is the distance between atoms U1 and D1
U3
.
U2 --- U1
\ dis_U1D1
D1 --- D2
.
D3
Fig 2. The two angles
U3
.
U2 --- U1
ang_U2D1
.
ang_U1D2
D1 --- D2
.
D3
Fig 3. The three torsions
U3
\ tor_U3D1 tor_U3D1: torsion about U2-U1 axis starting at atom U3 and ending at D1
U2 --- U1
\ tor_U2D2 tor_U2D2: torsion about U1-D1 axis starting at atom U2 and ending at D2
D1 --- D2
tor_U1D3 \ tor_U1D3: torsion about D1-D2 axis starting at atom U1 and ending at D3
D3
There are three other parameters needed to construct the location
of atoms 4, 5 and 6 from atoms 1, 2 and 3, but these are not
considered DOFs as they are not allowed to vary.
They are:
Extra 1: the distance between atom D1 and atom D2
Extra 2: the distance between atom D2 and atom D3
Extra 3: the angle between atoms D1, D2 and D3.
These three parameters must be communicated to the ExternGeomSampler
through its functions set_dis_D1D2, set_dis_D2D3 and set_ang_D1D2D3.
The ExternalGeomSampler holds the set of samples for each of the
6 DOFs. For each sample, it precomputes a HomogeneousTransform
so that during the enumeration of all sample combinations the
coordinate computation requires matrix multiplication only: the
more expensive transcendental function evaluations evaluated before
coordinate construction begins, their results stored, and are thereby
avoided in the enumeration loops.
To build the coordinates of atoms D1, D2 and D3, given the sample id's
for the 6 DOFs as the 6-tuple [ i, j, k, l, m, n ]:
start with a coordinate frame at atom U1 s.t. the z axis lies on the
vector from atom U2 to atom U1, the y axis lies in the plane defined
atoms U1, U2 and U3, and the x axis is the cross-product of y and z.
Call the start frame "frame1."
frame2 is the product: frame1 * transform( HT_tor_U3D1, i );
frame3 is the product: frame2 * transform( HT_ang_U2D1, j );
frame4 is computed from frame3 by walking along frame3's z-axis by dis_U1D1_samples( k );
frame4.point() is the coordinate for atom 4.
frame5 is the product: frame4 * transform( HT_tor_U2D2, l );
frame6 is the product: frame5 * transform( HT_ang_U1D2, m );
frame6.point() is the coordinate for atom 5.
NOTE: transform( HT_ang_U1D2, m ) is the product of the z-axis
rotation by ang_U1D2_sample_[ m ] and the transformation HT along the
z-axis by the distance between atoms D1 and D2. The ExternalGeomSampler
pre-multiplies these matricies.
frame7 is the product: frame6 * transform( HT_tor_U1D3, n );
frame7.point() is the coordinate for atom 6.
NOTE: transform( HT_tor_U1D3, n ) is the product of three HTs:
the HT representing the z-axis rotation by tor_U1D3_sample_[ n ],
the HT representing the x-axis rotation by ( -1 * ( 180 - ang_D1D2D3 ) )
and the HT representing the z-axis translation by the
distance between atoms D2 and D3. The ExternalGeomSampler
pre-multiplies these matrices.
|
| |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler) -> NoneType
2. __init__(self : rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler, : rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- ang_U1D2_samples(...) from builtins.PyCapsule
- ang_U1D2_samples(rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler) -> rosetta.utility.vector1_double
- ang_U2D1_samples(...) from builtins.PyCapsule
- ang_U2D1_samples(rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler) -> rosetta.utility.vector1_double
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler, rhs : rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler) -> rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler
- dis_U1D1_samples(...) from builtins.PyCapsule
- dis_U1D1_samples(rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler) -> rosetta.utility.vector1_double
- flip_upstream_downstream_samples(...) from builtins.PyCapsule
- flip_upstream_downstream_samples(rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler) -> NoneType
convenience function if one wants to change the meaning of
upstream and downstream
- n_ang_U1D2_samples(...) from builtins.PyCapsule
- n_ang_U1D2_samples(rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler) -> int
- n_ang_U2D1_samples(...) from builtins.PyCapsule
- n_ang_U2D1_samples(rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler) -> int
- n_dis_U1D1_samples(...) from builtins.PyCapsule
- n_dis_U1D1_samples(rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler) -> int
- n_tor_U1D3_samples(...) from builtins.PyCapsule
- n_tor_U1D3_samples(rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler) -> int
- n_tor_U2D2_samples(...) from builtins.PyCapsule
- n_tor_U2D2_samples(rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler) -> int
- n_tor_U3D1_samples(...) from builtins.PyCapsule
- n_tor_U3D1_samples(rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler) -> int
Accessors
- precompute_transforms(...) from builtins.PyCapsule
- precompute_transforms(rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler) -> NoneType
Must be called after the samples are set, and the
internal geometry of the three downstream coordinates
(point 4, 5, and 6) are described. Does nothing if the transforms
are up to date.
- set_ang_D1D2D3(...) from builtins.PyCapsule
- set_ang_D1D2D3(self : rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler, ang_in_degrees : float) -> NoneType
- set_ang_U1D2_samples(...) from builtins.PyCapsule
- set_ang_U1D2_samples(*args, **kwargs)
Overloaded function.
1. set_ang_U1D2_samples(self : rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler, ang_U1D2_samples : rosetta.utility.vector1_double) -> NoneType
2. set_ang_U1D2_samples(self : rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler, ang_U1D2_samples : rosetta.std.list_double_std_allocator_double_t) -> NoneType
- set_ang_U2D1_samples(...) from builtins.PyCapsule
- set_ang_U2D1_samples(*args, **kwargs)
Overloaded function.
1. set_ang_U2D1_samples(self : rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler, ang_U2D1_samples : rosetta.utility.vector1_double) -> NoneType
2. set_ang_U2D1_samples(self : rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler, ang_U2D1_samples : rosetta.std.list_double_std_allocator_double_t) -> NoneType
- set_dis_D1D2(...) from builtins.PyCapsule
- set_dis_D1D2(self : rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler, distance : float) -> NoneType
- set_dis_D2D3(...) from builtins.PyCapsule
- set_dis_D2D3(self : rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler, distance : float) -> NoneType
- set_dis_U1D1_samples(...) from builtins.PyCapsule
- set_dis_U1D1_samples(*args, **kwargs)
Overloaded function.
1. set_dis_U1D1_samples(self : rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler, dis_U1D1_samples : rosetta.utility.vector1_double) -> NoneType
2. set_dis_U1D1_samples(self : rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler, dis_U1D1_samples : rosetta.std.list_double_std_allocator_double_t) -> NoneType
- set_tor_U1D3_samples(...) from builtins.PyCapsule
- set_tor_U1D3_samples(*args, **kwargs)
Overloaded function.
1. set_tor_U1D3_samples(self : rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler, tor_U1D3_samples : rosetta.utility.vector1_double) -> NoneType
2. set_tor_U1D3_samples(self : rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler, tor_U1D3_samples : rosetta.std.list_double_std_allocator_double_t) -> NoneType
- set_tor_U2D2_samples(...) from builtins.PyCapsule
- set_tor_U2D2_samples(*args, **kwargs)
Overloaded function.
1. set_tor_U2D2_samples(self : rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler, tor_U2D2_samples : rosetta.utility.vector1_double) -> NoneType
2. set_tor_U2D2_samples(self : rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler, tor_U2D2_samples : rosetta.std.list_double_std_allocator_double_t) -> NoneType
- set_tor_U3D1_samples(...) from builtins.PyCapsule
- set_tor_U3D1_samples(*args, **kwargs)
Overloaded function.
1. set_tor_U3D1_samples(self : rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler, tor_U3D1_samples : rosetta.utility.vector1_double) -> NoneType
Intialization routines
all initialization routines must be invoked before building may begin.
Once each has been called, the function precompute_transforms() must
be called.
2. set_tor_U3D1_samples(self : rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler, tor_U3D1_samples : rosetta.std.list_double_std_allocator_double_t) -> NoneType
- tor_U1D3_samples(...) from builtins.PyCapsule
- tor_U1D3_samples(rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler) -> rosetta.utility.vector1_double
- tor_U2D2_samples(...) from builtins.PyCapsule
- tor_U2D2_samples(rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler) -> rosetta.utility.vector1_double
- tor_U3D1_samples(...) from builtins.PyCapsule
- tor_U3D1_samples(rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler) -> rosetta.utility.vector1_double
- transform(...) from builtins.PyCapsule
- transform(self : rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler, id : rosetta.protocols.toolbox.match_enzdes_util.ExternalTransform, which_state : int) -> rosetta.numeric.HomogeneousTransform_double_t
- transforms_uptodate(...) from builtins.PyCapsule
- transforms_uptodate(rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler) -> bool
|
class GeomSampleInfo(builtins.object) |
| |
class that stores information of one geometric parameter line of the .cst file
i.e. angleA or torsionB
|
| |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo, tag : str) -> NoneType
2. __init__(self : rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo, ideal_val : float, tolerance : float, force_k : float, periodicity_ : float) -> NoneType
3. __init__(self : rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo, : rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo) -> 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.toolbox.match_enzdes_util.GeomSampleInfo, : rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo) -> rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo
- create_sample_vector(...) from builtins.PyCapsule
- create_sample_vector(rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo) -> rosetta.utility.vector1_double
creates an explicit sample vector from the input data
i.e. translates ideal value, tolerance, num_steps and periodicity
into a vector of values
- force_const(...) from builtins.PyCapsule
- force_const(rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo) -> float
- function_tag(...) from builtins.PyCapsule
- function_tag(rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo) -> str
- ideal_val(...) from builtins.PyCapsule
- ideal_val(rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo) -> float
- num_steps(...) from builtins.PyCapsule
- num_steps(rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo) -> int
- periodicity(...) from builtins.PyCapsule
- periodicity(rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo) -> float
- read_data(...) from builtins.PyCapsule
- read_data(self : rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo, line_stream : rosetta.std.basic_istringstream_char_std_char_traits_char_std_allocator_char_t) -> bool
data reading routine
- step_size(...) from builtins.PyCapsule
- step_size(rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo) -> float
- tag(...) from builtins.PyCapsule
- tag(rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo) -> str
- tolerance(...) from builtins.PyCapsule
- tolerance(rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo) -> float
|
class InvrotTarget(InvrotTreeNodeBase) |
| |
the 'root' target against which the inverse rotamers are built
abstract base class to allow for invrots being built against
any sort of entity
|
| |
- Method resolution order:
- InvrotTarget
- InvrotTreeNodeBase
- builtins.object
Methods defined here:
- __init__(self, /, *args, **kwargs)
- Initialize self. See help(type(self)) for accurate signature.
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- all_target_res(...) from builtins.PyCapsule
- all_target_res(rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget) -> rosetta.std.list_std_shared_ptr_const_core_conformation_Residue_std_allocator_std_shared_ptr_const_core_conformation_Residue_t
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget, : rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget) -> rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget
- generate_constraints(...) from builtins.PyCapsule
- generate_constraints(self : rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget, pose : rosetta.core.pose.Pose, geomcst_seqpos : rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst) -> rosetta.core.scoring.constraints.Constraint
generate constraints against a certain pose
- initialize_tree_nodes_from_enzcst_io(...) from builtins.PyCapsule
- initialize_tree_nodes_from_enzcst_io(self : rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget, enzcst_io : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO) -> bool
can initialize tree nodes according to
an enzcst io
note that this function presumes that
representative_target_res_for_geom_cst_ and
all_target_res_ have been set through calling the
generate_representative_target_res_for_geom_cst()
function as implemented by the child class
- target_res_for_geom_cst(...) from builtins.PyCapsule
- target_res_for_geom_cst(self : rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget, geom_cst : int) -> rosetta.core.conformation.Residue
Methods inherited from InvrotTreeNodeBase:
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) -> rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase
self pointers
2. get_self_ptr(rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) -> rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) -> rosetta.std.weak_ptr_const_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t
2. get_self_weak_ptr(rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) -> rosetta.std.weak_ptr_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t
- location_in_parent_node(...) from builtins.PyCapsule
- location_in_parent_node(rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) -> int
- parent_node(...) from builtins.PyCapsule
- parent_node(rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) -> rosetta.std.weak_ptr_const_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t
- set_location_in_parent_node(...) from builtins.PyCapsule
- set_location_in_parent_node(self : rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase, location : int) -> NoneType
|
class InvrotTree(builtins.object) |
| |
abstract base class for the inverse rotamer tree
is abstract so that in the future inverse rots could
be generated in different ways than throug the enz cst machinery
|
| |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(rosetta.protocols.toolbox.match_enzdes_util.InvrotTree) -> 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.toolbox.match_enzdes_util.InvrotTree, : rosetta.protocols.toolbox.match_enzdes_util.InvrotTree) -> rosetta.protocols.toolbox.match_enzdes_util.InvrotTree
- check_pose_tree_compatibility(...) from builtins.PyCapsule
- check_pose_tree_compatibility(self : rosetta.protocols.toolbox.match_enzdes_util.InvrotTree, pose : rosetta.core.pose.Pose) -> bool
important function 2:
after a chain/pose has been generated,
check whether it's compatible with
the inverse rotamers in the tree
this can change the pose again
- collect_all_inverse_rotamers(...) from builtins.PyCapsule
- collect_all_inverse_rotamers(rosetta.protocols.toolbox.match_enzdes_util.InvrotTree) -> rosetta.utility.vector1_std_shared_ptr_const_protocols_toolbox_match_enzdes_util_InvrotCollector_t
convenience access function
to the inverse rotamers in the tree
note: the returned invrots can contain
duplications, as every unique definition
of the tree is returned
- dump_invrots_tree_as_multimodel_pdbs(...) from builtins.PyCapsule
- dump_invrots_tree_as_multimodel_pdbs(self : rosetta.protocols.toolbox.match_enzdes_util.InvrotTree, filename_base : str) -> NoneType
visualization
this can lead to several files
being written, depending on the
ambiguities in the tree
- generate_inverse_rotamer_constraints(...) from builtins.PyCapsule
- generate_inverse_rotamer_constraints(self : rosetta.protocols.toolbox.match_enzdes_util.InvrotTree, pose : rosetta.core.pose.Pose, geomcst_seqpos : rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst) -> NoneType
the main function, generate the constraints
- generate_targets_and_inverse_rotamers(...) from builtins.PyCapsule
- generate_targets_and_inverse_rotamers(rosetta.protocols.toolbox.match_enzdes_util.InvrotTree) -> NoneType
important function 1:
populate the tree
should be called before folding a chain
obviously
see TheozymeInvrotTree below for example
- get_constraint_for_target_state(...) from builtins.PyCapsule
- get_constraint_for_target_state(self : rosetta.protocols.toolbox.match_enzdes_util.InvrotTree, target_state : int) -> rosetta.core.scoring.constraints.Constraint
- num_target_states(...) from builtins.PyCapsule
- num_target_states(rosetta.protocols.toolbox.match_enzdes_util.InvrotTree) -> int
|
class InvrotTreeNode(InvrotTreeNodeBase) |
| | |
- Method resolution order:
- InvrotTreeNode
- InvrotTreeNodeBase
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, parent : rosetta.std.weak_ptr_const_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t) -> NoneType
2. __init__(handle, rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNode) -> 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.toolbox.match_enzdes_util.InvrotTreeNode, : rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNode) -> rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNode
- generate_constraints(...) from builtins.PyCapsule
- generate_constraints(self : rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNode, pose : rosetta.core.pose.Pose, geomcst_seqpos : rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst) -> rosetta.core.scoring.constraints.Constraint
1. for each invrots/node pointer pair:
a.generate an ambigous constraint for the inverse rots
for each node pointer to child nodes (only if there are child nodes, of course)
b. call the generate_constraints function on the pointers to child nodes
c. package the ambig constraint generated for the inverse rots
and the constraints that come from the child nodes into one multicst
caveat: if the child nodes send up a multi constraint and not an ambiguous
constraint, 'unpackage' those multicst and generate a new multicst
containing this nodes ambigcst and the member_csts from the
child nodes' multicsts
2. if there is more than one invrots/node pointer pair,
throw all the generated multicsts into one ambig cst
3. return either the multicst (one pair) or the ambigcst
4. hope this works
- get_fixed_pt(...) from builtins.PyCapsule
- get_fixed_pt(self : rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNode, pose : rosetta.core.pose.Pose) -> rosetta.core.id.AtomID
this function returns the AtomID for an atom
in the pose that's supposed to stay fixed during
folding, i.e. the neighbor atom of the first target
needed to generate the right backbone_stub constraints
- initialize_from_enzcst_io(...) from builtins.PyCapsule
- initialize_from_enzcst_io(*args, **kwargs)
Overloaded function.
1. initialize_from_enzcst_io(self : rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNode, target_residue : rosetta.core.conformation.Residue, enzcst_io : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, invrot_geomcst : int) -> bool
generate invrots according to
an enzdes cstfile
returns true if it was possible to
build invrots, i.e. geometry correctly
defined in cstfile and no clashes with
any parent inverse rotamers
2. initialize_from_enzcst_io(self : rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNode, target_residue : rosetta.core.conformation.Residue, enzcst_io : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, invrot_geomcst : int, pose : rosetta.core.pose.Pose) -> bool
generate invrots according to
an enzdes cstfile
returns true if it was possible to
build invrots, i.e. geometry correctly
defined in cstfile and no clashes with
any parent inverse rotamers
- initialize_from_enzcst_io_and_invrots(...) from builtins.PyCapsule
- initialize_from_enzcst_io_and_invrots(*args, **kwargs)
Overloaded function.
1. initialize_from_enzcst_io_and_invrots(self : rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNode, all_invrots : rosetta.std.list_std_shared_ptr_const_core_conformation_Residue_std_allocator_std_shared_ptr_const_core_conformation_Residue_t, enzcst_io : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, invrot_geomcst : int) -> bool
2. initialize_from_enzcst_io_and_invrots(self : rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNode, all_invrots : rosetta.std.list_std_shared_ptr_const_core_conformation_Residue_std_allocator_std_shared_ptr_const_core_conformation_Residue_t, enzcst_io : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO, invrot_geomcst : int, pose : rosetta.core.pose.Pose) -> bool
- remove_invrots_clashing_with_parent_res(...) from builtins.PyCapsule
- remove_invrots_clashing_with_parent_res(self : rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNode, invrots : rosetta.std.list_std_shared_ptr_const_core_conformation_Residue_std_allocator_std_shared_ptr_const_core_conformation_Residue_t, covalent : bool) -> NoneType
Methods inherited from InvrotTreeNodeBase:
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) -> rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase
self pointers
2. get_self_ptr(rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) -> rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) -> rosetta.std.weak_ptr_const_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t
2. get_self_weak_ptr(rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) -> rosetta.std.weak_ptr_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t
- location_in_parent_node(...) from builtins.PyCapsule
- location_in_parent_node(rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) -> int
- parent_node(...) from builtins.PyCapsule
- parent_node(rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) -> rosetta.std.weak_ptr_const_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t
- set_location_in_parent_node(...) from builtins.PyCapsule
- set_location_in_parent_node(self : rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase, location : int) -> NoneType
|
class InvrotTreeNodeBase(builtins.object) |
| |
abstract base class for an inverse rotamer tree node.
Exists so that the target node (InvrotTreeTarget) and the different
geom cst nodes (InvrotTreeNode) have a common base class.
This is necessary so that a node can point at its parent
node in a tree without having to worry about whether that
is a target or a regular node
|
| |
Methods defined here:
- __init__(self, /, *args, **kwargs)
- Initialize self. See help(type(self)) for accurate signature.
- __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.toolbox.match_enzdes_util.InvrotTreeNodeBase, : rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) -> rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase
- generate_constraints(...) from builtins.PyCapsule
- generate_constraints(self : rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase, pose : rosetta.core.pose.Pose, geomcst_seqpos : rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst) -> rosetta.core.scoring.constraints.Constraint
nodes need to be able to generate constraints
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) -> rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase
self pointers
2. get_self_ptr(rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) -> rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) -> rosetta.std.weak_ptr_const_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t
2. get_self_weak_ptr(rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) -> rosetta.std.weak_ptr_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t
- location_in_parent_node(...) from builtins.PyCapsule
- location_in_parent_node(rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) -> int
- parent_node(...) from builtins.PyCapsule
- parent_node(rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) -> rosetta.std.weak_ptr_const_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t
- set_location_in_parent_node(...) from builtins.PyCapsule
- set_location_in_parent_node(self : rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase, location : int) -> NoneType
|
class LigandConformer(builtins.object) |
| | |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.toolbox.match_enzdes_util.LigandConformer) -> NoneType
2. __init__(self : rosetta.protocols.toolbox.match_enzdes_util.LigandConformer, : rosetta.protocols.toolbox.match_enzdes_util.LigandConformer) -> 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.toolbox.match_enzdes_util.LigandConformer, : rosetta.protocols.toolbox.match_enzdes_util.LigandConformer) -> rosetta.protocols.toolbox.match_enzdes_util.LigandConformer
- atom1_atom2_atom3_angle(...) from builtins.PyCapsule
- atom1_atom2_atom3_angle(rosetta.protocols.toolbox.match_enzdes_util.LigandConformer) -> float
Returns an angle in degrees between the three downstream atoms.
- atom1_atom2_distance(...) from builtins.PyCapsule
- atom1_atom2_distance(rosetta.protocols.toolbox.match_enzdes_util.LigandConformer) -> float
- atom2_atom3_distance(...) from builtins.PyCapsule
- atom2_atom3_distance(rosetta.protocols.toolbox.match_enzdes_util.LigandConformer) -> float
- collision_check_id_2_restype_id(...) from builtins.PyCapsule
- collision_check_id_2_restype_id(self : rosetta.protocols.toolbox.match_enzdes_util.LigandConformer, coll_check_id : int) -> int
- coordinate_in_D3_frame(...) from builtins.PyCapsule
- coordinate_in_D3_frame(self : rosetta.protocols.toolbox.match_enzdes_util.LigandConformer, restype_atomno : int, frame3 : rosetta.numeric.HomogeneousTransform_double_t) -> rosetta.numeric.xyzVector_double_t
- coordinate_in_global_frame(...) from builtins.PyCapsule
- coordinate_in_global_frame(self : rosetta.protocols.toolbox.match_enzdes_util.LigandConformer, restype_atomno : int, orientation_frame : rosetta.numeric.HomogeneousTransform_double_t) -> rosetta.numeric.xyzVector_double_t
- coordinates_from_orientation(...) from builtins.PyCapsule
- coordinates_from_orientation(self : rosetta.protocols.toolbox.match_enzdes_util.LigandConformer, orientation : rosetta.utility.fixedsizearray1_double_6_t, atom_indices : rosetta.utility.vector1_core_id_AtomID, atom_coords : rosetta.utility.vector1_numeric_xyzVector_double_t) -> NoneType
- frame_from_global_orientation(...) from builtins.PyCapsule
- frame_from_global_orientation(self : rosetta.protocols.toolbox.match_enzdes_util.LigandConformer, orientation : rosetta.utility.fixedsizearray1_double_6_t) -> rosetta.numeric.HomogeneousTransform_double_t
The orientation frame at orientation atom 3 given
orientation atom 3's xyz coordinates and the euler angles
describing the frame
- get_global_coords_as_FArray2D(...) from builtins.PyCapsule
- get_global_coords_as_FArray2D(self : rosetta.protocols.toolbox.match_enzdes_util.LigandConformer, coords : ObjexxFCL::FArray2D<double>, orientation_frame : rosetta.numeric.HomogeneousTransform_double_t, restype_atomnos : rosetta.utility.vector1_unsigned_long) -> NoneType
@ brief helper function to get the coordinates in 2D FArray format
- get_lig_restype(...) from builtins.PyCapsule
- get_lig_restype(rosetta.protocols.toolbox.match_enzdes_util.LigandConformer) -> rosetta.core.chemical.ResidueType
- global_orientation_from_frame3(...) from builtins.PyCapsule
- global_orientation_from_frame3(self : rosetta.protocols.toolbox.match_enzdes_util.LigandConformer, frame3 : rosetta.numeric.HomogeneousTransform_double_t) -> rosetta.utility.fixedsizearray1_double_6_t
The orientaton frame at orientation atom 3 given
the coordinate frame at D3 (this frame is called frame3)
- ignore_h_collisions(...) from builtins.PyCapsule
- ignore_h_collisions(self : rosetta.protocols.toolbox.match_enzdes_util.LigandConformer, setting : bool) -> NoneType
- initialize_from_residue(...) from builtins.PyCapsule
- initialize_from_residue(self : rosetta.protocols.toolbox.match_enzdes_util.LigandConformer, D1 : int, D2 : int, D3 : int, orientation_atom1 : int, orientation_atom2 : int, orientation_atom3 : int, residue : rosetta.core.conformation.Residue) -> NoneType
Specify the residue, with coordinates, that's being used as the downstream
partner. This class is meant to be used in conjuction with the ClassicMatchAglrotihm,
and therefore the initialization routines are specific for that algorithm. In this
initialization function, one must list atoms "D1, D2 and D3" in the convention of
describing the rigid-body orientation between three atoms of the upstream partner
(atoms U3, U2 & U1) and three atoms of the downstream partner (atoms D1, D2 & D3) in terms
of 2 angles, 1 distance, and 3 dihedrals. The user must also list the 3 atoms used to
define the orientation frame of the downstream ligand. It is essential to the
matching algorithm that the same three orientation atoms are used for all LigandConformers.
- move_atoms_to_collcheck_begin(...) from builtins.PyCapsule
- move_atoms_to_collcheck_begin(self : rosetta.protocols.toolbox.match_enzdes_util.LigandConformer, restype_atnos_to_move_early : rosetta.utility.vector1_unsigned_long) -> NoneType
- n_collision_check_atoms(...) from builtins.PyCapsule
- n_collision_check_atoms(rosetta.protocols.toolbox.match_enzdes_util.LigandConformer) -> int
- oatom1_oatom2_distance(...) from builtins.PyCapsule
- oatom1_oatom2_distance(rosetta.protocols.toolbox.match_enzdes_util.LigandConformer) -> float
returns the distance between orientation atom 1 and orientation atom 2
- oatom1_oatom2_oatom3_angle(...) from builtins.PyCapsule
- oatom1_oatom2_oatom3_angle(rosetta.protocols.toolbox.match_enzdes_util.LigandConformer) -> float
Returns an angle in degrees between the three orientation atoms.
- oatom2_oatom3_distance(...) from builtins.PyCapsule
- oatom2_oatom3_distance(rosetta.protocols.toolbox.match_enzdes_util.LigandConformer) -> float
returns the distance between orientation atom 2 and orientation atom 3
- restype_id_2_collision_check_id(...) from builtins.PyCapsule
- restype_id_2_collision_check_id(self : rosetta.protocols.toolbox.match_enzdes_util.LigandConformer, restype_atomno : int) -> int
|
class MatchConstraintFileInfo(builtins.object) |
| | |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(self : rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo, index : int, restype_set : rosetta.core.chemical.ResidueTypeSet) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- algorithm_inputs(...) from builtins.PyCapsule
- algorithm_inputs(rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo) -> rosetta.std.map_std_string_utility_vector1_std_string_std_allocator_std_string_t
holds information read from ALGORITHM_INFO blocks
in the input file
- allowed_res_name3s(...) from builtins.PyCapsule
- allowed_res_name3s(self : rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo, which_cstres : int) -> rosetta.utility.vector1_std_string
what type of amino acids/ligands make this
constraint
- allowed_restypes(...) from builtins.PyCapsule
- allowed_restypes(self : rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo, which_cstres : int) -> rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t
all chemically non-redundant restypes of the given restypes. Note -- now sorted by name!
- allowed_seqpos(...) from builtins.PyCapsule
- allowed_seqpos(rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo) -> rosetta.utility.vector1_unsigned_long
all positions where a residue for this geometry
can be placed
- ang_U1D2(...) from builtins.PyCapsule
- ang_U1D2(rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo) -> rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo
- ang_U2D1(...) from builtins.PyCapsule
- ang_U2D1(rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo) -> rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo, : rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo) -> rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo
- create_exgs(...) from builtins.PyCapsule
- create_exgs(rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo) -> rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler
returns ExternalGeomSampler only if the user has specified all six degrees of freedom,
otherwise null pointer is returned
- dis_U1D1(...) from builtins.PyCapsule
- dis_U1D1(rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo) -> rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo
- diversify_backbone_only_rotamers(...) from builtins.PyCapsule
- diversify_backbone_only_rotamers(self : rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo, rotamers : rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) -> NoneType
- downstream_res(...) from builtins.PyCapsule
- downstream_res(rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo) -> int
which one of the residues (1 or 2 ) in this block
is the upstream res. used for classic match algorithm
hardcoded 1 for now
- enz_cst_template_res(...) from builtins.PyCapsule
- enz_cst_template_res(self : rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo, template_res : int) -> rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes
- index(...) from builtins.PyCapsule
- index(rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo) -> int
- inverse_rotamers_against_residue(...) from builtins.PyCapsule
- inverse_rotamers_against_residue(*args, **kwargs)
Overloaded function.
1. inverse_rotamers_against_residue(self : rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo, target_template : int, target_conf : rosetta.core.conformation.Residue) -> rosetta.std.list_std_shared_ptr_const_core_conformation_Residue_std_allocator_std_shared_ptr_const_core_conformation_Residue_t
function that takes all rotamers for the ResidueType(s)
that interact with the target residues and places them according
according to the geometry specified
2. inverse_rotamers_against_residue(self : rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo, target_conf : rosetta.core.conformation.Residue, invrot_restype : rosetta.core.chemical.ResidueType, target_ats : rosetta.utility.vector1_unsigned_long, invrot_ats : rosetta.utility.vector1_unsigned_long, flip_exgs_upstream_downstream_samples : bool, backbone_interaction : bool) -> rosetta.std.list_std_shared_ptr_const_core_conformation_Residue_std_allocator_std_shared_ptr_const_core_conformation_Residue_t
- is_backbone(...) from builtins.PyCapsule
- is_backbone(self : rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo, which_cstres : int) -> bool
is this interaction a backbone interaction
- is_covalent(...) from builtins.PyCapsule
- is_covalent(rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo) -> bool
- native(...) from builtins.PyCapsule
- native(rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo) -> bool
- num_enz_cst_template_res(...) from builtins.PyCapsule
- num_enz_cst_template_res(rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo) -> int
- process_data(...) from builtins.PyCapsule
- process_data(rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo) -> NoneType
processes the read data
right now this only generates the template atomnos for every restype
- read_data(...) from builtins.PyCapsule
- read_data(self : rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo, data : rosetta.utility.io.izstream) -> bool
data reading routine
- template_atom_inds(...) from builtins.PyCapsule
- template_atom_inds(self : rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo, which_cstres : int, which_template_atom : int, restype : rosetta.core.chemical.ResidueType) -> rosetta.utility.vector1_unsigned_long
all atoms of restype to be used as template_atom
in the matcher/constraints
- tor_U1D3(...) from builtins.PyCapsule
- tor_U1D3(rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo) -> rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo
- tor_U2D2(...) from builtins.PyCapsule
- tor_U2D2(rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo) -> rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo
- tor_U3D1(...) from builtins.PyCapsule
- tor_U3D1(rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo) -> rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo
- upstream_res(...) from builtins.PyCapsule
- upstream_res(rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo) -> int
which one of the residues (1 or 2 ) in this block
is the upstream res. used for classic match algorithm
hardcoded 2 for now
|
class SingleResidueInvrotTarget(InvrotTarget) |
| | |
- Method resolution order:
- SingleResidueInvrotTarget
- InvrotTarget
- InvrotTreeNodeBase
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, single_res : rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) -> NoneType
2. __init__(handle, rosetta.protocols.toolbox.match_enzdes_util.SingleResidueInvrotTarget) -> 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.toolbox.match_enzdes_util.SingleResidueInvrotTarget, : rosetta.protocols.toolbox.match_enzdes_util.SingleResidueInvrotTarget) -> rosetta.protocols.toolbox.match_enzdes_util.SingleResidueInvrotTarget
Methods inherited from InvrotTarget:
- all_target_res(...) from builtins.PyCapsule
- all_target_res(rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget) -> rosetta.std.list_std_shared_ptr_const_core_conformation_Residue_std_allocator_std_shared_ptr_const_core_conformation_Residue_t
- generate_constraints(...) from builtins.PyCapsule
- generate_constraints(self : rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget, pose : rosetta.core.pose.Pose, geomcst_seqpos : rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst) -> rosetta.core.scoring.constraints.Constraint
generate constraints against a certain pose
- initialize_tree_nodes_from_enzcst_io(...) from builtins.PyCapsule
- initialize_tree_nodes_from_enzcst_io(self : rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget, enzcst_io : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO) -> bool
can initialize tree nodes according to
an enzcst io
note that this function presumes that
representative_target_res_for_geom_cst_ and
all_target_res_ have been set through calling the
generate_representative_target_res_for_geom_cst()
function as implemented by the child class
- target_res_for_geom_cst(...) from builtins.PyCapsule
- target_res_for_geom_cst(self : rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget, geom_cst : int) -> rosetta.core.conformation.Residue
Methods inherited from InvrotTreeNodeBase:
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) -> rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase
self pointers
2. get_self_ptr(rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) -> rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) -> rosetta.std.weak_ptr_const_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t
2. get_self_weak_ptr(rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) -> rosetta.std.weak_ptr_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t
- location_in_parent_node(...) from builtins.PyCapsule
- location_in_parent_node(rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) -> int
- parent_node(...) from builtins.PyCapsule
- parent_node(rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase) -> rosetta.std.weak_ptr_const_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t
- set_location_in_parent_node(...) from builtins.PyCapsule
- set_location_in_parent_node(self : rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase, location : int) -> NoneType
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class TheozymeInvrotTree(InvrotTree) |
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This class takes an EnzConstraintIO object
and generates a 3D model of the theozyme in it,
where inverse rotamers are generated for every block
in the cstfile. It gets complicated when ambiguous
interactions are specified and other residues are
interacting (possibly in ambiguous fashion) with
these ambiguous residues...
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- Method resolution order:
- TheozymeInvrotTree
- InvrotTree
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(self : handle, enzcst_io : rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO) -> 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.toolbox.match_enzdes_util.TheozymeInvrotTree, : rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree) -> rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree
- check_pose_tree_compatibility(...) from builtins.PyCapsule
- check_pose_tree_compatibility(self : rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree, pose : rosetta.core.pose.Pose) -> bool
- generate_targets_and_inverse_rotamers(...) from builtins.PyCapsule
- generate_targets_and_inverse_rotamers(rosetta.protocols.toolbox.match_enzdes_util.TheozymeInvrotTree) -> NoneType
this function generates the 'target' for the inverse rotamers,
i.e. in the case of enzdes, simply the coordinates for the ligand
if in the future somebody wants to use this to build inverse rotamers
against a protein, this function can be reimplemented.
called from the constructor, is this really the best idea?
Methods inherited from InvrotTree:
- collect_all_inverse_rotamers(...) from builtins.PyCapsule
- collect_all_inverse_rotamers(rosetta.protocols.toolbox.match_enzdes_util.InvrotTree) -> rosetta.utility.vector1_std_shared_ptr_const_protocols_toolbox_match_enzdes_util_InvrotCollector_t
convenience access function
to the inverse rotamers in the tree
note: the returned invrots can contain
duplications, as every unique definition
of the tree is returned
- dump_invrots_tree_as_multimodel_pdbs(...) from builtins.PyCapsule
- dump_invrots_tree_as_multimodel_pdbs(self : rosetta.protocols.toolbox.match_enzdes_util.InvrotTree, filename_base : str) -> NoneType
visualization
this can lead to several files
being written, depending on the
ambiguities in the tree
- generate_inverse_rotamer_constraints(...) from builtins.PyCapsule
- generate_inverse_rotamer_constraints(self : rosetta.protocols.toolbox.match_enzdes_util.InvrotTree, pose : rosetta.core.pose.Pose, geomcst_seqpos : rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst) -> NoneType
the main function, generate the constraints
- get_constraint_for_target_state(...) from builtins.PyCapsule
- get_constraint_for_target_state(self : rosetta.protocols.toolbox.match_enzdes_util.InvrotTree, target_state : int) -> rosetta.core.scoring.constraints.Constraint
- num_target_states(...) from builtins.PyCapsule
- num_target_states(rosetta.protocols.toolbox.match_enzdes_util.InvrotTree) -> int
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