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- builtins.object
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- ImplicitFastClashCheck
- Interface
- rosetta.basic.datacache.CacheableData(builtins.object)
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- InterfaceInfo
- ResidualDipolarCouplingRigidSegments
- rosetta.utility.SingletonBase_protocols_scoring_InterchainPotential_t(builtins.object)
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- InterchainPotential
class ImplicitFastClashCheck(builtins.object) |
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : rosetta.protocols.scoring.ImplicitFastClashCheck, pose_in : rosetta.core.pose.Pose, clash_dis : float) -> NoneType
2. __init__(self : rosetta.protocols.scoring.ImplicitFastClashCheck, pose_in : rosetta.core.pose.Pose, clash_dis : float, ignore : rosetta.utility.vector1_unsigned_long) -> NoneType
3. __init__(self : rosetta.protocols.scoring.ImplicitFastClashCheck, poses_in : rosetta.utility.vector1_core_pose_Pose, clash_dis : float, ignore : rosetta.utility.vector1_unsigned_long) -> NoneType
4. __init__(self : rosetta.protocols.scoring.ImplicitFastClashCheck, : rosetta.protocols.scoring.ImplicitFastClashCheck) -> 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.scoring.ImplicitFastClashCheck, : rosetta.protocols.scoring.ImplicitFastClashCheck) -> rosetta.protocols.scoring.ImplicitFastClashCheck
- clash_check(...) from builtins.PyCapsule
- clash_check(*args, **kwargs)
Overloaded function.
1. clash_check(self : rosetta.protocols.scoring.ImplicitFastClashCheck, pp : rosetta.numeric.xyzVector_double_t) -> bool
2. clash_check(self : rosetta.protocols.scoring.ImplicitFastClashCheck, pp : rosetta.numeric.xyzVector_double_t, resno : int) -> bool
- clash_check_test(...) from builtins.PyCapsule
- clash_check_test(self : rosetta.protocols.scoring.ImplicitFastClashCheck, pp : rosetta.numeric.xyzVector_double_t) -> bool
- clash_check_trimer(...) from builtins.PyCapsule
- clash_check_trimer(self : rosetta.protocols.scoring.ImplicitFastClashCheck, pose : rosetta.core.pose.Pose, refrsd : int) -> bool
- clash_count(...) from builtins.PyCapsule
- clash_count(self : rosetta.protocols.scoring.ImplicitFastClashCheck, pp : rosetta.numeric.xyzVector_double_t) -> int
- dump_debug_pdb(...) from builtins.PyCapsule
- dump_debug_pdb(*args, **kwargs)
Overloaded function.
1. dump_debug_pdb(self : rosetta.protocols.scoring.ImplicitFastClashCheck, out : rosetta.utility.io.ozstream, stub : rosetta.core.kinematics.Stub) -> NoneType
2. dump_debug_pdb(self : rosetta.protocols.scoring.ImplicitFastClashCheck, out : rosetta.utility.io.ozstream, stub : rosetta.core.kinematics.Stub, chain : str) -> NoneType
3. dump_debug_pdb(self : rosetta.protocols.scoring.ImplicitFastClashCheck, fname : str, stub : rosetta.core.kinematics.Stub) -> NoneType
4. dump_debug_pdb(self : rosetta.protocols.scoring.ImplicitFastClashCheck, fname : str, stub : rosetta.core.kinematics.Stub, chain : str) -> NoneType
- init_clash_check(...) from builtins.PyCapsule
- init_clash_check(self : rosetta.protocols.scoring.ImplicitFastClashCheck, poses : rosetta.utility.vector1_core_pose_Pose, neighbor_cutoff : float, ignore : rosetta.utility.vector1_unsigned_long) -> NoneType
- size(...) from builtins.PyCapsule
- size(rosetta.protocols.scoring.ImplicitFastClashCheck) -> int
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class InterchainPotential(rosetta.utility.SingletonBase_protocols_scoring_InterchainPotential_t) |
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Singleton class to hold the interface-derived statistics for residue-pair
scores at protein/protein interfaces.
This previously derived from the EnvPairPotential, which is in no way
necessary because the two classes have nothing in common; rather, the
InterchainPairEnergy and InterchainEnvEnergy classes can hold a pointer to both
the InterchainPotential and the EnvPairPotential.
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- Method resolution order:
- InterchainPotential
- rosetta.utility.SingletonBase_protocols_scoring_InterchainPotential_t
- 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.
- compute_interface(...) from builtins.PyCapsule
- compute_interface(self : rosetta.protocols.scoring.InterchainPotential, pose : rosetta.core.pose.Pose) -> NoneType
- evaluate_contact_score(...) from builtins.PyCapsule
- evaluate_contact_score(self : rosetta.protocols.scoring.InterchainPotential, pose : rosetta.core.pose.Pose, contact_score : float) -> NoneType
- evaluate_env_score(...) from builtins.PyCapsule
- evaluate_env_score(self : rosetta.protocols.scoring.InterchainPotential, pose : rosetta.core.pose.Pose, rsd : rosetta.core.conformation.Residue, env_score : float) -> NoneType
- evaluate_pair_and_vdw_score(...) from builtins.PyCapsule
- evaluate_pair_and_vdw_score(self : rosetta.protocols.scoring.InterchainPotential, pose : rosetta.core.pose.Pose, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pair_score : float, vdw_score : float) -> NoneType
- finalize(...) from builtins.PyCapsule
- finalize(self : rosetta.protocols.scoring.InterchainPotential, pose : rosetta.core.pose.Pose) -> NoneType
- interface_from_pose(...) from builtins.PyCapsule
- interface_from_pose(self : rosetta.protocols.scoring.InterchainPotential, : rosetta.core.pose.Pose) -> protocols::scoring::InterfaceInfo
- nonconst_interface_from_pose(...) from builtins.PyCapsule
- nonconst_interface_from_pose(self : rosetta.protocols.scoring.InterchainPotential, : rosetta.core.pose.Pose) -> protocols::scoring::InterfaceInfo
Methods inherited from rosetta.utility.SingletonBase_protocols_scoring_InterchainPotential_t:
- get_instance(...) from builtins.PyCapsule
- get_instance() -> protocols::scoring::InterchainPotential
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class Interface(builtins.object) |
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.scoring.Interface) -> NoneType
2. __init__(self : rosetta.protocols.scoring.Interface, jump_number_in : int) -> NoneType
3. __init__(self : rosetta.protocols.scoring.Interface, partner : ObjexxFCL::FArray1D<bool>) -> NoneType
4. __init__(self : rosetta.protocols.scoring.Interface, : rosetta.protocols.scoring.Interface) -> 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.scoring.Interface, : rosetta.protocols.scoring.Interface) -> rosetta.protocols.scoring.Interface
- calculate(...) from builtins.PyCapsule
- calculate(self : rosetta.protocols.scoring.Interface, pose : rosetta.core.pose.Pose) -> NoneType
- center(...) from builtins.PyCapsule
- center(self : rosetta.protocols.scoring.Interface, pose : rosetta.core.pose.Pose) -> rosetta.numeric.xyzVector_double_t
- closest_interface_residue(...) from builtins.PyCapsule
- closest_interface_residue(self : rosetta.protocols.scoring.Interface, pose : rosetta.core.pose.Pose, src_rsd : int, distance : float) -> int
- contact_list(...) from builtins.PyCapsule
- contact_list(rosetta.protocols.scoring.Interface) -> rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t
The contact_list is pose.total_residue() long, each element
(contact_list_[i]) contains a list of residues from the other partner that
interacts with residue i. This is calculated in protein_calculate, and
used by Interface.is_pair() function as well as the interchain_vdw,
interchain_env, and interchain_pair scoring components.
- distance(...) from builtins.PyCapsule
- distance(self : rosetta.protocols.scoring.Interface, distance_in : float) -> NoneType
- interface_nres(...) from builtins.PyCapsule
- interface_nres(rosetta.protocols.scoring.Interface) -> int
returns the total number of residues on both sides of the interface for
a given jump
- is_interface(...) from builtins.PyCapsule
- is_interface(*args, **kwargs)
Overloaded function.
1. is_interface(self : rosetta.protocols.scoring.Interface, rsd : rosetta.core.conformation.Residue) -> bool
2. is_interface(self : rosetta.protocols.scoring.Interface, position : int) -> bool
- is_pair(...) from builtins.PyCapsule
- is_pair(self : rosetta.protocols.scoring.Interface, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue) -> bool
returns whether the rsd1 and rsd2 are considered a contact pair
based on contact_list_ array
- jump(...) from builtins.PyCapsule
- jump(self : rosetta.protocols.scoring.Interface, jump_number : int) -> NoneType
- jump_id(...) from builtins.PyCapsule
- jump_id(rosetta.protocols.scoring.Interface) -> int
- pair_list(...) from builtins.PyCapsule
- pair_list(rosetta.protocols.scoring.Interface) -> rosetta.utility.vector1_utility_vector1_int_std_allocator_int_t
Get two lists containing the residues on each side of the interface
You might expect something called pair_list() to output pairs or somehow
relate to the is_pair function, but it does not.
It returns a two element list.
- The first element is a list of all residues on the lower partner of the
interface.
- The second element is a list of all the residues in the interface on the
upper partner.
Both lists are sorted by residue number, so the indices of one list have
no relationship to the other list.
rename this to something more logical & give it a better return type
make a function that returns a vector1<pair<Size,Size> > containing
all interacting pairs. This would be easy to implement.
- print(...) from builtins.PyCapsule
- print(self : rosetta.protocols.scoring.Interface, pose : rosetta.core.pose.Pose) -> NoneType
- set_pack(...) from builtins.PyCapsule
- set_pack(self : rosetta.protocols.scoring.Interface, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> NoneType
- set_symmetric_pack(...) from builtins.PyCapsule
- set_symmetric_pack(self : rosetta.protocols.scoring.Interface, pose : rosetta.core.pose.Pose, task : rosetta.core.pack.task.PackerTask) -> NoneType
- show(...) from builtins.PyCapsule
- show(self : rosetta.protocols.scoring.Interface, pose : rosetta.core.pose.Pose) -> NoneType
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class InterfaceInfo(rosetta.basic.datacache.CacheableData) |
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/////////////////////////////////////////////////////////////////////////////////////////////////
Keep track of the interface information
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- Method resolution order:
- InterfaceInfo
- rosetta.basic.datacache.CacheableData
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, rb_jump_in : int) -> NoneType
3. __init__(self : handle, rb_jump_in : rosetta.utility.vector1_unsigned_long) -> NoneType
4. __init__(handle, rosetta.protocols.scoring.InterfaceInfo) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_jump(...) from builtins.PyCapsule
- add_jump(self : rosetta.protocols.scoring.InterfaceInfo, jump_in : int) -> NoneType
Adds another jump to the interface calculation, for example
for multi-body docking
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.scoring.InterfaceInfo, : rosetta.protocols.scoring.InterfaceInfo) -> rosetta.protocols.scoring.InterfaceInfo
- calculate(...) from builtins.PyCapsule
- calculate(self : rosetta.protocols.scoring.InterfaceInfo, pose : rosetta.core.pose.Pose) -> NoneType
Calculates the interface for all jumps specified in
rb_jump_
- calculated(...) from builtins.PyCapsule
- calculated(*args, **kwargs)
Overloaded function.
1. calculated(rosetta.protocols.scoring.InterfaceInfo) -> bool
Returns if interface calculation is up to date
2. calculated(rosetta.protocols.scoring.InterfaceInfo) -> bool
Returns if interface calculation is up to date
- clear_jumps(...) from builtins.PyCapsule
- clear_jumps(rosetta.protocols.scoring.InterfaceInfo) -> NoneType
Removes all jumps from the interface calculation
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.scoring.InterfaceInfo) -> rosetta.basic.datacache.CacheableData
- closest_interface_residue(...) from builtins.PyCapsule
- closest_interface_residue(self : rosetta.protocols.scoring.InterfaceInfo, pose : rosetta.core.pose.Pose, src_rsd : int, distance : float) -> int
- distance(...) from builtins.PyCapsule
- distance(self : rosetta.protocols.scoring.InterfaceInfo, distance_in : float) -> NoneType
Sets the distance cutoff for interface calculations
- initialize(...) from builtins.PyCapsule
- initialize(rosetta.protocols.scoring.InterfaceInfo) -> NoneType
Sets up InterfaceInfo members such as interface_list_
based on variables from construction
- interface(...) from builtins.PyCapsule
- interface(self : rosetta.protocols.scoring.InterfaceInfo, interface_num : int) -> rosetta.protocols.scoring.Interface
- interface_nres(...) from builtins.PyCapsule
- interface_nres(self : rosetta.protocols.scoring.InterfaceInfo, jump_num : int) -> int
Returns the number of resides at the interface defined
by jump_num
- is_interface(...) from builtins.PyCapsule
- is_interface(self : rosetta.protocols.scoring.InterfaceInfo, rsd : rosetta.core.conformation.Residue) -> bool
Returns whether a residue is at any of the interfaces
- is_pair(...) from builtins.PyCapsule
- is_pair(self : rosetta.protocols.scoring.InterfaceInfo, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue) -> bool
Returns whether the two residues are considered a
residue pair at any of the interfaces
- num_jump(...) from builtins.PyCapsule
- num_jump(rosetta.protocols.scoring.InterfaceInfo) -> int
Returns the number of jumps that are being used
in interface calculations
Methods inherited from rosetta.basic.datacache.CacheableData:
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData
self pointers
2. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_const_basic_datacache_CacheableData_t
2. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_basic_datacache_CacheableData_t
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