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- builtins.object
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- BranchAngleOptimizer
- BranchCoef1
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- BranchCoef2
- BranchParam1
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- BranchParam2
class BranchAngleOptimizer(builtins.object) |
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : rosetta.protocols.branch_angle.BranchAngleOptimizer, mm_bondangle_library : rosetta.core.scoring.mm.MMBondAngleLibrary) -> NoneType
2. __init__(rosetta.protocols.branch_angle.BranchAngleOptimizer) -> NoneType
3. __init__(self : rosetta.protocols.branch_angle.BranchAngleOptimizer, src : rosetta.protocols.branch_angle.BranchAngleOptimizer) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- bond_angle_residue_type_param_set(...) from builtins.PyCapsule
- bond_angle_residue_type_param_set(*args, **kwargs)
Overloaded function.
1. bond_angle_residue_type_param_set(rosetta.protocols.branch_angle.BranchAngleOptimizer) -> rosetta.core.scoring.mm.MMBondAngleResidueTypeParamSet
2. bond_angle_residue_type_param_set(rosetta.protocols.branch_angle.BranchAngleOptimizer) -> rosetta.core.scoring.mm.MMBondAngleResidueTypeParamSet
3. bond_angle_residue_type_param_set(self : rosetta.protocols.branch_angle.BranchAngleOptimizer, param_set : rosetta.core.scoring.mm.MMBondAngleResidueTypeParamSet) -> NoneType
set input MMBondAngleResidueTypeParamSet, sharing with the input
4. bond_angle_residue_type_param_set(self : rosetta.protocols.branch_angle.BranchAngleOptimizer, param_set : rosetta.core.scoring.mm.MMBondAngleResidueTypeParamSet) -> NoneType
set input MMBondAngleResidueTypeParamSet, making a copy
- initialized(...) from builtins.PyCapsule
- initialized(rosetta.protocols.branch_angle.BranchAngleOptimizer) -> bool
- num_coef1(...) from builtins.PyCapsule
- num_coef1(rosetta.protocols.branch_angle.BranchAngleOptimizer) -> int
get number of single branching atom coefficients
- num_coef2(...) from builtins.PyCapsule
- num_coef2(rosetta.protocols.branch_angle.BranchAngleOptimizer) -> int
get number of double branching atom coefficients
- num_undefined_coef1(...) from builtins.PyCapsule
- num_undefined_coef1(rosetta.protocols.branch_angle.BranchAngleOptimizer) -> int
get number of undefined single branching atom coefficients
- num_undefined_coef2(...) from builtins.PyCapsule
- num_undefined_coef2(rosetta.protocols.branch_angle.BranchAngleOptimizer) -> int
get number of undefined double branching atom coefficients
- optimize_angles(...) from builtins.PyCapsule
- optimize_angles(*args, **kwargs)
Overloaded function.
1. optimize_angles(self : rosetta.protocols.branch_angle.BranchAngleOptimizer, pose : rosetta.core.pose.Pose, main_atomid1 : rosetta.core.id.AtomID, center_atomid : rosetta.core.id.AtomID, main_atomid2 : rosetta.core.id.AtomID) -> int
optimize angles branching off the defined mainchain
2. optimize_angles(self : rosetta.protocols.branch_angle.BranchAngleOptimizer, pose : rosetta.core.pose.Pose, main_atomid1 : rosetta.core.id.AtomID, center_atomid : rosetta.core.id.AtomID, main_atomid2 : rosetta.core.id.AtomID, optimize_for_minimum : bool) -> int
optimize angles branching off the defined mainchain
- overall_params(...) from builtins.PyCapsule
- overall_params(self : rosetta.protocols.branch_angle.BranchAngleOptimizer, pose : rosetta.core.pose.Pose, main_atomid1 : rosetta.core.id.AtomID, center_atomid : rosetta.core.id.AtomID, main_atomid2 : rosetta.core.id.AtomID, Ktheta : float, theta0 : float, energy0 : float) -> int
get overall bond angle parameters for the defined mainchian
- param1(...) from builtins.PyCapsule
- param1(self : rosetta.protocols.branch_angle.BranchAngleOptimizer, pose : rosetta.core.pose.Pose, main_atomid1 : rosetta.core.id.AtomID, center_atomid : rosetta.core.id.AtomID, main_atomid2 : rosetta.core.id.AtomID, branch_atomid1 : rosetta.core.id.AtomID) -> protocols::branch_angle::BranchParam1
get single branching atom bond angle parameters
- param2(...) from builtins.PyCapsule
- param2(self : rosetta.protocols.branch_angle.BranchAngleOptimizer, pose : rosetta.core.pose.Pose, main_atomid1 : rosetta.core.id.AtomID, center_atomid : rosetta.core.id.AtomID, main_atomid2 : rosetta.core.id.AtomID, branch_atomid1 : rosetta.core.id.AtomID, branch_atomid2 : rosetta.core.id.AtomID) -> protocols::branch_angle::BranchParam2
get double branching atom bond angle parameters
- read_coef1(...) from builtins.PyCapsule
- read_coef1(self : rosetta.protocols.branch_angle.BranchAngleOptimizer, filename : str) -> bool
read single branching atom coefficients from a file
- read_coef1_default(...) from builtins.PyCapsule
- read_coef1_default(rosetta.protocols.branch_angle.BranchAngleOptimizer) -> NoneType
read single branching atom coefficients from default database file
- read_coef1_user(...) from builtins.PyCapsule
- read_coef1_user(rosetta.protocols.branch_angle.BranchAngleOptimizer) -> bool
read single branching atom coefficients from user database file
- read_coef2(...) from builtins.PyCapsule
- read_coef2(self : rosetta.protocols.branch_angle.BranchAngleOptimizer, filename : str) -> bool
read double branching atom coefficients from a file
- read_coef2_default(...) from builtins.PyCapsule
- read_coef2_default(rosetta.protocols.branch_angle.BranchAngleOptimizer) -> NoneType
read double branching atom coefficients from default database file
- read_coef2_user(...) from builtins.PyCapsule
- read_coef2_user(rosetta.protocols.branch_angle.BranchAngleOptimizer) -> bool
read double branching atom coefficients from user database file
- read_database(...) from builtins.PyCapsule
- read_database(rosetta.protocols.branch_angle.BranchAngleOptimizer) -> NoneType
read known parameters from the database
- read_undefined_coef1(...) from builtins.PyCapsule
- read_undefined_coef1(*args, **kwargs)
Overloaded function.
1. read_undefined_coef1(self : rosetta.protocols.branch_angle.BranchAngleOptimizer, filename : str) -> bool
read parameters for undefined single branching atom coefficients from a file
2. read_undefined_coef1(rosetta.protocols.branch_angle.BranchAngleOptimizer) -> bool
read single branching atom undefined coefficients from the database file
- read_undefined_coef2(...) from builtins.PyCapsule
- read_undefined_coef2(*args, **kwargs)
Overloaded function.
1. read_undefined_coef2(self : rosetta.protocols.branch_angle.BranchAngleOptimizer, filename : str) -> bool
read parameters for undefined double branching atom coefficients from a file
2. read_undefined_coef2(rosetta.protocols.branch_angle.BranchAngleOptimizer) -> bool
read double branching atom undefined coefficients from the database file
- tolerance(...) from builtins.PyCapsule
- tolerance(*args, **kwargs)
Overloaded function.
1. tolerance(rosetta.protocols.branch_angle.BranchAngleOptimizer) -> float
2. tolerance(self : rosetta.protocols.branch_angle.BranchAngleOptimizer, tolerance : float) -> NoneType
- write_database(...) from builtins.PyCapsule
- write_database(rosetta.protocols.branch_angle.BranchAngleOptimizer) -> NoneType
write undefined parameters to the database
- write_undefined_coef1(...) from builtins.PyCapsule
- write_undefined_coef1(*args, **kwargs)
Overloaded function.
1. write_undefined_coef1(self : rosetta.protocols.branch_angle.BranchAngleOptimizer, filename : str) -> bool
write parameters for undefined single branching atom coefficients to a file
2. write_undefined_coef1(rosetta.protocols.branch_angle.BranchAngleOptimizer) -> bool
write single branching atom undefined coefficients to the database file
- write_undefined_coef2(...) from builtins.PyCapsule
- write_undefined_coef2(*args, **kwargs)
Overloaded function.
1. write_undefined_coef2(self : rosetta.protocols.branch_angle.BranchAngleOptimizer, filename : str) -> bool
write parameters for undefined double branching atom coefficients to a file
2. write_undefined_coef2(rosetta.protocols.branch_angle.BranchAngleOptimizer) -> bool
write double branching atom undefined coefficients to the database file
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class BranchCoef1(builtins.object) |
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a class to store coefficients for branching angle optimization around a
single atom atom with three bonded neighbors
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : rosetta.protocols.branch_angle.BranchCoef1, overall_Ktheta : float, overall_theta0 : float, overall_energy0 : float, b1_torsion_offset_A : float, b1_torsion_offset_B : float, b1_torsion_offset_C : float, b1_bond_angle_A : float, b1_bond_angle_B : float, b1_bond_angle_C : float) -> NoneType
2. __init__(self : rosetta.protocols.branch_angle.BranchCoef1, : rosetta.protocols.branch_angle.BranchCoef1) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- b1_bond_angle_A(...) from builtins.PyCapsule
- b1_bond_angle_A(rosetta.protocols.branch_angle.BranchCoef1) -> float
get branching atom 1 bond angle A coefficient (angle^0)
- b1_bond_angle_B(...) from builtins.PyCapsule
- b1_bond_angle_B(rosetta.protocols.branch_angle.BranchCoef1) -> float
get branching atom 1 bond angle B coefficient (angle^1)
- b1_bond_angle_C(...) from builtins.PyCapsule
- b1_bond_angle_C(rosetta.protocols.branch_angle.BranchCoef1) -> float
get branching atom 1 bond angle C coefficient (angle^2)
- b1_torsion_offset_A(...) from builtins.PyCapsule
- b1_torsion_offset_A(rosetta.protocols.branch_angle.BranchCoef1) -> float
get branching atom 1 torsion offset A coefficient (angle^0)
- b1_torsion_offset_B(...) from builtins.PyCapsule
- b1_torsion_offset_B(rosetta.protocols.branch_angle.BranchCoef1) -> float
get branching atom 1 torsion offset B coefficient (angle^1)
- b1_torsion_offset_C(...) from builtins.PyCapsule
- b1_torsion_offset_C(rosetta.protocols.branch_angle.BranchCoef1) -> float
get branching atom 1 torsion offset C coefficient (angle^2)
- evaluate(...) from builtins.PyCapsule
- evaluate(self : rosetta.protocols.branch_angle.BranchCoef1, m2_bond_angle : float, b1_torsion_offset : float, b1_bond_angle : float) -> NoneType
calculate single branching angles for a main chain bond angle
- overall_Ktheta(...) from builtins.PyCapsule
- overall_Ktheta(rosetta.protocols.branch_angle.BranchCoef1) -> float
get overall Ktheta parameter
- overall_energy0(...) from builtins.PyCapsule
- overall_energy0(rosetta.protocols.branch_angle.BranchCoef1) -> float
get overall energy0 parameter
- overall_theta0(...) from builtins.PyCapsule
- overall_theta0(rosetta.protocols.branch_angle.BranchCoef1) -> float
get overall theta0 parameter
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class BranchCoef2(BranchCoef1) |
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a class to store coefficients for branching angle optimization around a
single atom atom with three bonded neighbors
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- Method resolution order:
- BranchCoef2
- BranchCoef1
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(self : rosetta.protocols.branch_angle.BranchCoef2, overall_Ktheta : float, overall_theta0 : float, overall_energy0 : float, b1_torsion_offset_A : float, b1_torsion_offset_B : float, b1_torsion_offset_C : float, b1_bond_angle_A : float, b1_bond_angle_B : float, b1_bond_angle_C : float, b2_torsion_offset_A : float, b2_torsion_offset_B : float, b2_torsion_offset_C : float, b2_bond_angle_A : float, b2_bond_angle_B : float, b2_bond_angle_C : float) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- b2_bond_angle_A(...) from builtins.PyCapsule
- b2_bond_angle_A(rosetta.protocols.branch_angle.BranchCoef2) -> float
get branching atom 2 bond angle A coefficient (angle^0)
- b2_bond_angle_B(...) from builtins.PyCapsule
- b2_bond_angle_B(rosetta.protocols.branch_angle.BranchCoef2) -> float
get branching atom 2 bond angle B coefficient (angle^1)
- b2_bond_angle_C(...) from builtins.PyCapsule
- b2_bond_angle_C(rosetta.protocols.branch_angle.BranchCoef2) -> float
get branching atom 2 bond angle C coefficient (angle^2)
- b2_torsion_offset_A(...) from builtins.PyCapsule
- b2_torsion_offset_A(rosetta.protocols.branch_angle.BranchCoef2) -> float
get branching atom 2 torsion offset A coefficient (angle^0)
- b2_torsion_offset_B(...) from builtins.PyCapsule
- b2_torsion_offset_B(rosetta.protocols.branch_angle.BranchCoef2) -> float
get branching atom 2 torsion offset B coefficient (angle^1)
- b2_torsion_offset_C(...) from builtins.PyCapsule
- b2_torsion_offset_C(rosetta.protocols.branch_angle.BranchCoef2) -> float
get branching atom 2 torsion offset C coefficient (angle^2)
- evaluate(...) from builtins.PyCapsule
- evaluate(self : rosetta.protocols.branch_angle.BranchCoef2, m2_bond_angle : float, b1_torsion_offset : float, b1_bond_angle : float, b2_torsion_offset : float, b2_bond_angle : float) -> NoneType
calculate single branching angles for a main chain bond angle
Methods inherited from BranchCoef1:
- b1_bond_angle_A(...) from builtins.PyCapsule
- b1_bond_angle_A(rosetta.protocols.branch_angle.BranchCoef1) -> float
get branching atom 1 bond angle A coefficient (angle^0)
- b1_bond_angle_B(...) from builtins.PyCapsule
- b1_bond_angle_B(rosetta.protocols.branch_angle.BranchCoef1) -> float
get branching atom 1 bond angle B coefficient (angle^1)
- b1_bond_angle_C(...) from builtins.PyCapsule
- b1_bond_angle_C(rosetta.protocols.branch_angle.BranchCoef1) -> float
get branching atom 1 bond angle C coefficient (angle^2)
- b1_torsion_offset_A(...) from builtins.PyCapsule
- b1_torsion_offset_A(rosetta.protocols.branch_angle.BranchCoef1) -> float
get branching atom 1 torsion offset A coefficient (angle^0)
- b1_torsion_offset_B(...) from builtins.PyCapsule
- b1_torsion_offset_B(rosetta.protocols.branch_angle.BranchCoef1) -> float
get branching atom 1 torsion offset B coefficient (angle^1)
- b1_torsion_offset_C(...) from builtins.PyCapsule
- b1_torsion_offset_C(rosetta.protocols.branch_angle.BranchCoef1) -> float
get branching atom 1 torsion offset C coefficient (angle^2)
- overall_Ktheta(...) from builtins.PyCapsule
- overall_Ktheta(rosetta.protocols.branch_angle.BranchCoef1) -> float
get overall Ktheta parameter
- overall_energy0(...) from builtins.PyCapsule
- overall_energy0(rosetta.protocols.branch_angle.BranchCoef1) -> float
get overall energy0 parameter
- overall_theta0(...) from builtins.PyCapsule
- overall_theta0(rosetta.protocols.branch_angle.BranchCoef1) -> float
get overall theta0 parameter
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class BranchParam1(builtins.object) |
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a class to store bond angle energy parameters around a single atom atom with three bonded neighbors
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.branch_angle.BranchParam1, float, float, float, float, float, float) -> NoneType
doc
2. __init__(self : rosetta.protocols.branch_angle.BranchParam1, m1_m2_Ktheta : float, m1_m2_theta0 : float, m1_b1_Ktheta : float, m1_b1_theta0 : float, m2_b1_Ktheta : float, m2_b1_theta0 : float, tolerance : float) -> NoneType
3. __init__(self : rosetta.protocols.branch_angle.BranchParam1, : rosetta.protocols.branch_angle.BranchParam1) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- m1_b1_Ktheta(...) from builtins.PyCapsule
- m1_b1_Ktheta(rosetta.protocols.branch_angle.BranchParam1) -> float
get Ktheta for mainchain atom 1 - branching atom 1 angle
- m1_b1_theta0(...) from builtins.PyCapsule
- m1_b1_theta0(rosetta.protocols.branch_angle.BranchParam1) -> float
get theta0 for mainchain atom 1 - branching atom 1 angle
- m1_m2_Ktheta(...) from builtins.PyCapsule
- m1_m2_Ktheta(rosetta.protocols.branch_angle.BranchParam1) -> float
get Ktheta for mainchain atom 1 - mainchain atom 1 angle
- m1_m2_theta0(...) from builtins.PyCapsule
- m1_m2_theta0(rosetta.protocols.branch_angle.BranchParam1) -> float
get theta0 for mainchain atom 1 - mainchain atom 1 angle
- m2_b1_Ktheta(...) from builtins.PyCapsule
- m2_b1_Ktheta(rosetta.protocols.branch_angle.BranchParam1) -> float
get Ktheta for mainchain atom 2 - branching atom 1 angle
- m2_b1_theta0(...) from builtins.PyCapsule
- m2_b1_theta0(rosetta.protocols.branch_angle.BranchParam1) -> float
get theta0 for mainchain atom 2 - branching atom 1 angle
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class BranchParam2(BranchParam1) |
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a class to store bond angle energy parameters around a single atom atom with four bonded neighbors
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- Method resolution order:
- BranchParam2
- BranchParam1
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.branch_angle.BranchParam2, float, float, float, float, float, float, float, float, float, float, float, float) -> NoneType
doc
2. __init__(self : rosetta.protocols.branch_angle.BranchParam2, m1_m2_Ktheta : float, m1_m2_theta0 : float, m1_b1_Ktheta : float, m1_b1_theta0 : float, m2_b1_Ktheta : float, m2_b1_theta0 : float, m1_b2_Ktheta : float, m1_b2_theta0 : float, m2_b2_Ktheta : float, m2_b2_theta0 : float, b1_b2_Ktheta : float, b1_b2_theta0 : float, tolerance : float) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- b1_b2_Ktheta(...) from builtins.PyCapsule
- b1_b2_Ktheta(rosetta.protocols.branch_angle.BranchParam2) -> float
get Ktheta for branching atom 1 - branching atom 2 angle
- b1_b2_theta0(...) from builtins.PyCapsule
- b1_b2_theta0(rosetta.protocols.branch_angle.BranchParam2) -> float
get theta0 for branching atom 1 - branching atom 2 angle
- m1_b2_Ktheta(...) from builtins.PyCapsule
- m1_b2_Ktheta(rosetta.protocols.branch_angle.BranchParam2) -> float
get Ktheta for mainchain atom 1 - branching atom 2 angle
- m1_b2_theta0(...) from builtins.PyCapsule
- m1_b2_theta0(rosetta.protocols.branch_angle.BranchParam2) -> float
get theta0 for mainchain atom 1 - branching atom 2 angle
- m2_b2_Ktheta(...) from builtins.PyCapsule
- m2_b2_Ktheta(rosetta.protocols.branch_angle.BranchParam2) -> float
get Ktheta for mainchain atom 2 - branching atom 2 angle
- m2_b2_theta0(...) from builtins.PyCapsule
- m2_b2_theta0(rosetta.protocols.branch_angle.BranchParam2) -> float
get theta0 for mainchain atom 2 - branching atom 2 angle
Methods inherited from BranchParam1:
- m1_b1_Ktheta(...) from builtins.PyCapsule
- m1_b1_Ktheta(rosetta.protocols.branch_angle.BranchParam1) -> float
get Ktheta for mainchain atom 1 - branching atom 1 angle
- m1_b1_theta0(...) from builtins.PyCapsule
- m1_b1_theta0(rosetta.protocols.branch_angle.BranchParam1) -> float
get theta0 for mainchain atom 1 - branching atom 1 angle
- m1_m2_Ktheta(...) from builtins.PyCapsule
- m1_m2_Ktheta(rosetta.protocols.branch_angle.BranchParam1) -> float
get Ktheta for mainchain atom 1 - mainchain atom 1 angle
- m1_m2_theta0(...) from builtins.PyCapsule
- m1_m2_theta0(rosetta.protocols.branch_angle.BranchParam1) -> float
get theta0 for mainchain atom 1 - mainchain atom 1 angle
- m2_b1_Ktheta(...) from builtins.PyCapsule
- m2_b1_Ktheta(rosetta.protocols.branch_angle.BranchParam1) -> float
get Ktheta for mainchain atom 2 - branching atom 1 angle
- m2_b1_theta0(...) from builtins.PyCapsule
- m2_b1_theta0(rosetta.protocols.branch_angle.BranchParam1) -> float
get theta0 for mainchain atom 2 - branching atom 1 angle
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