Rosetta 3.3
Namespaces | Functions | Variables
docking Namespace Reference

Namespaces

namespace  ligand
namespace  symmetry

Functions

BooleanOptionKey const kick_relax ("docking:kick_relax")
BooleanOptionKey const docking ("docking")
BooleanOptionKey const view ("docking:view")
BooleanOptionKey const no_filters ("docking:no_filters")
StringVectorOptionKey const design_chains ("docking:design_chains")
StringOptionKey const partners ("docking:partners")
BooleanOptionKey const docking_local_refine ("docking:docking_local_refine")
BooleanOptionKey const low_res_protocol_only ("docking:low_res_protocol_only")
BooleanOptionKey const randomize1 ("docking:randomize1")
BooleanOptionKey const randomize2 ("docking:randomize2")
BooleanOptionKey const spin ("docking:spin")
RealVectorOptionKey const dock_pert ("docking:dock_pert")
RealOptionKey const uniform_trans ("docking:uniform_trans")
BooleanOptionKey const center_at_interface ("docking:center_at_interface")
IntegerOptionKey const docking_centroid_outer_cycles ("docking:docking_centroid_outer_cycles")
IntegerOptionKey const docking_centroid_inner_cycles ("docking:docking_centroid_inner_cycles")
BooleanOptionKey const dock_min ("docking:dock_min")
StringOptionKey const flexible_bb_docking ("docking:flexible_bb_docking")
RealOptionKey const flexible_bb_docking_interface_dist ("docking:flexible_bb_docking_interface_dist")
StringOptionKey const ensemble1 ("docking:ensemble1")
StringOptionKey const ensemble2 ("docking:ensemble2")
RealOptionKey const dock_mcm_trans_magnitude ("docking:dock_mcm_trans_magnitude")
RealOptionKey const dock_mcm_rot_magnitude ("docking:dock_mcm_rot_magnitude")
BooleanOptionKey const dock_rtmin ("docking:dock_rtmin")
BooleanOptionKey const sc_min ("docking:sc_min")
BooleanOptionKey const norepack1 ("docking:norepack1")
BooleanOptionKey const norepack2 ("docking:norepack2")
BooleanOptionKey const dock_ppk ("docking:dock_ppk")
IntegerOptionKey const max_repeats ("docking:max_repeats")
RealVectorOptionKey const dock_lowres_filter ("docking:dock_lowres_filter")
IntegerVectorOptionKey const multibody ("docking:multibody")
StringOptionKey const low_patch ("docking:low_patch")
StringOptionKey const high_patch ("docking:high_patch")
StringOptionKey const high_min_patch ("docking:high_min_patch")
StringOptionKey const pack_patch ("docking:pack_patch")
BooleanOptionKey const use_legacy_protocol ("docking:use_legacy_protocol")

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 = SwitchResidueTypeSetMover('centroid')
tuple to_fullatom = SwitchResidueTypeSetMover('fa_standard')
tuple recover_sidechains = ReturnSidechainMover(starting_p)
tuple randomize1 = RigidBodyRandomizeMover(p, dock_jump, partner_upstream)
tuple randomize2 = RigidBodyRandomizeMover(p, dock_jump, 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()

Function Documentation

BooleanOptionKey const docking::center_at_interface ( "docking:center_at_interface"  )
StringVectorOptionKey const docking::design_chains ( "docking:design_chains"  )
RealVectorOptionKey const docking::dock_lowres_filter ( "docking:dock_lowres_filter"  )
RealOptionKey const docking::dock_mcm_rot_magnitude ( "docking:dock_mcm_rot_magnitude"  )
RealOptionKey const docking::dock_mcm_trans_magnitude ( "docking:dock_mcm_trans_magnitude"  )
BooleanOptionKey const docking::dock_min ( "docking:dock_min"  )
RealVectorOptionKey const docking::dock_pert ( "docking:dock_pert"  )
BooleanOptionKey const docking::dock_ppk ( "docking:dock_ppk"  )
BooleanOptionKey const docking::dock_rtmin ( "docking:dock_rtmin"  )
BooleanOptionKey const docking::docking ( "docking"  )
IntegerOptionKey const docking::docking_centroid_inner_cycles ( "docking:docking_centroid_inner_cycles"  )
IntegerOptionKey const docking::docking_centroid_outer_cycles ( "docking:docking_centroid_outer_cycles"  )
BooleanOptionKey const docking::docking_local_refine ( "docking:docking_local_refine"  )
StringOptionKey const docking::ensemble1 ( "docking:ensemble1"  )
StringOptionKey const docking::ensemble2 ( "docking:ensemble2"  )
StringOptionKey const docking::flexible_bb_docking ( "docking:flexible_bb_docking"  )
RealOptionKey const docking::flexible_bb_docking_interface_dist ( "docking:flexible_bb_docking_interface_dist"  )
StringOptionKey const docking::high_min_patch ( "docking:high_min_patch"  )
StringOptionKey const docking::high_patch ( "docking:high_patch"  )
BooleanOptionKey const docking::kick_relax ( "docking:kick_relax"  )
StringOptionKey const docking::low_patch ( "docking:low_patch"  )
BooleanOptionKey const docking::low_res_protocol_only ( "docking:low_res_protocol_only"  )
IntegerOptionKey const docking::max_repeats ( "docking:max_repeats"  )
IntegerVectorOptionKey const docking::multibody ( "docking:multibody"  )
BooleanOptionKey const docking::no_filters ( "docking:no_filters"  )
BooleanOptionKey const docking::norepack1 ( "docking:norepack1"  )
BooleanOptionKey const docking::norepack2 ( "docking:norepack2"  )
StringOptionKey const docking::pack_patch ( "docking:pack_patch"  )
StringOptionKey const docking::partners ( "docking:partners"  )
BooleanOptionKey const docking::randomize1 ( "docking:randomize1"  )
BooleanOptionKey const docking::randomize2 ( "docking:randomize2"  )
BooleanOptionKey const docking::sc_min ( "docking:sc_min"  )
BooleanOptionKey const docking::spin ( "docking:spin"  )
RealOptionKey const docking::uniform_trans ( "docking:uniform_trans"  )

Referenced by main().

BooleanOptionKey const docking::use_legacy_protocol ( "docking:use_legacy_protocol"  )
BooleanOptionKey const docking::view ( "docking:view"  )

Variable Documentation

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

Referenced by main().

tuple docking::dock_prot = DockingProtocol()
tuple docking::docking_lowres = DockingLowRes( scorefxn_low, dock_jump )
tuple docking::jd = PyJobDistributor("dock_output", 20, scorefxn_high)

Referenced by ca_to_allatom_main().

tuple docking::p = Pose()
tuple docking::randomize1 = RigidBodyRandomizeMover(p, dock_jump, partner_upstream)

Referenced by add_rosetta_options_0().

tuple docking::randomize2 = RigidBodyRandomizeMover(p, dock_jump, partner_downstream)

Referenced by add_rosetta_options_0(), and main().

tuple docking::recover_sidechains = ReturnSidechainMover(starting_p)
tuple docking::scorefxn_high = create_score_function('docking')
tuple docking::scorefxn_high_min = create_score_function_ws_patch('docking','docking_min')
tuple docking::scorefxn_low = create_score_function('interchain_cen')
tuple docking::slide_into_contact = DockingSlideIntoContact( dock_jump )
tuple docking::spin = RigidBodySpinMover( dock_jump )
tuple docking::starting_p = Pose()
tuple docking::to_centroid = SwitchResidueTypeSetMover('centroid')
tuple docking::to_fullatom = SwitchResidueTypeSetMover('fa_standard')
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