docking Namespace Reference

Variables
tuple	p = Pose()
tuple	starting_p = Pose()
tuple	dock_prot = DockingProtocol()
int	dock_jump = 1
tuple	scorefxn_low = create_score_function('interchain_cen')
tuple	scorefxn_high = create_score_function('docking')
tuple	scorefxn_high_min = create_score_function_ws_patch('docking','docking_min')
tuple	to_centroid = protocols.simple_moves.SwitchResidueTypeSetMover('centroid')
tuple	to_fullatom = protocols.simple_moves.SwitchResidueTypeSetMover('fa_standard')
tuple	recover_sidechains = protocols.simple_moves.ReturnSidechainMover(starting_p)
tuple	randomize1 = RigidBodyRandomizeMover(p, dock_jump, rigid.partner_upstream)
tuple	randomize2 = RigidBodyRandomizeMover(p, dock_jump, rigid.partner_downstream)
tuple	dock_pert = RigidBodyPerturbMover(dock_jump, 3, 8)
tuple	spin = RigidBodySpinMover( dock_jump )
tuple	slide_into_contact = DockingSlideIntoContact( dock_jump )
tuple	docking_lowres = DockingLowRes( scorefxn_low, dock_jump )
tuple	docking_highres = DockingHighRes( scorefxn_high_min, dock_jump )
tuple	jd = PyJobDistributor("dock_output", 20, scorefxn_high)
tuple	starting_p_centroid = Pose()

Variable Documentation

int docking.dock_jump = 1

Definition at line 18 of file docking.py.

tuple docking.dock_pert = RigidBodyPerturbMover(dock_jump, 3, 8)

Definition at line 35 of file docking.py.

Referenced by main().

tuple docking.dock_prot = DockingProtocol()

Definition at line 16 of file docking.py.

tuple docking.docking_highres = DockingHighRes( scorefxn_high_min, dock_jump )

Definition at line 43 of file docking.py.

tuple docking.docking_lowres = DockingLowRes( scorefxn_low, dock_jump )

Definition at line 40 of file docking.py.

tuple docking.jd = PyJobDistributor("dock_output", 20, scorefxn_high)

Definition at line 46 of file docking.py.

tuple docking.p = Pose()

Definition at line 9 of file docking.py.

Referenced by utility.down_cast(), ObjexxFCL::format.F(), basic::resource_manager::locator::FileStream.FileStream(), ObjexxFCL.fixed_Fstring_of(), ObjexxFCL.fixed_string_of(), ObjexxFCL.general_Fstring_of(), ObjexxFCL.general_string_of(), numeric::interpolation::spline::SplineGenerator.get_interpolator(), get_max_and_intervals(), numeric.hsv_to_rgb(), numeric::geometry::hashing::SixDOffsetTree.init(), numeric::fourier.kf_bfly_generic(), numeric::fourier.kf_factor(), numeric::fourier.kf_work(), numeric::statistics.kl_divergence(), list_repr(), numeric::geometry::hashing::SixDOffsetTree.lookup(), main(), minimize_with_constraints(), numeric.operator<<(), utility.operator<<(), numeric::sphericalVector< typename >.operator=(), numeric::xyzTriple< typename >.operator=(), numeric::xyzVector< core::Real >.operator=(), ObjexxFCL::CArrayP< typename >.Proxy(), basic::sampling::orientations::QuaternionGrid.QuaternionGrid(), numeric.read_probabilities_or_die(), numeric::MathNTensor< Real >.replace_layer(), numeric::geometry::BoundingBox< Vector >.reset(), myMC.roll(), ObjexxFCL.scientific_Fstring_of(), ObjexxFCL.scientific_string_of(), numeric::geometry::BoundingBox< Vector >.set_lower(), set_repr(), numeric::geometry::BoundingBox< Vector >.set_upper(), numeric::fourier::SHT.setup_Pmls(), sigmoid_train(), numeric::interpolation::spline.spline_second_derivative(), utility.strip(), svm_load_model(), svm_predict_values(), svm_save_model(), svm_train(), utility::json_spirit.to_str(), numeric::interpolation::spline::PolycubicSpline.train(), numeric::kinematic_closure.triaxialCoefficients(), and numeric::kinematic_closure::radians.triaxialCoefficients().

tuple docking.randomize1 = RigidBodyRandomizeMover(p, dock_jump, rigid.partner_upstream)

Definition at line 33 of file docking.py.

tuple docking.randomize2 = RigidBodyRandomizeMover(p, dock_jump, rigid.partner_downstream)

Definition at line 34 of file docking.py.

Referenced by main().

tuple docking.recover_sidechains = protocols.simple_moves.ReturnSidechainMover(starting_p)

Definition at line 30 of file docking.py.

tuple docking.scorefxn_high = create_score_function('docking')

Definition at line 22 of file docking.py.

tuple docking.scorefxn_high_min = create_score_function_ws_patch('docking','docking_min')

Definition at line 23 of file docking.py.

tuple docking.scorefxn_low = create_score_function('interchain_cen')

Definition at line 21 of file docking.py.

tuple docking.slide_into_contact = DockingSlideIntoContact( dock_jump )

Definition at line 37 of file docking.py.

tuple docking.spin = RigidBodySpinMover( dock_jump )

Definition at line 36 of file docking.py.

tuple docking.starting_p = Pose()

Definition at line 12 of file docking.py.

tuple docking.starting_p_centroid = Pose()

Definition at line 53 of file docking.py.

tuple docking.to_centroid = protocols.simple_moves.SwitchResidueTypeSetMover('centroid')

Definition at line 28 of file docking.py.

tuple docking.to_fullatom = protocols.simple_moves.SwitchResidueTypeSetMover('fa_standard')

Definition at line 29 of file docking.py.