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docking Namespace Reference

Namespaces

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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")
 
FileOptionKey const recover_sidechains ("docking:recover_sidechains")
 
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")
 
StringOptionKey const docking_low_res_score ("docking:docking_low_res_score")
 
BooleanOptionKey const randomize1 ("docking:randomize1")
 
BooleanOptionKey const randomize2 ("docking:randomize2")
 
BooleanOptionKey const use_ellipsoidal_randomization ("docking:use_ellipsoidal_randomization")
 
BooleanOptionKey const spin ("docking:spin")
 
RealVectorOptionKey const tilt ("docking:tilt")
 
StringOptionKey const tilt1_center ("docking:tilt1_center")
 
StringOptionKey const tilt2_center ("docking:tilt2_center")
 
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 dock_mcm_first_cycles ("docking:dock_mcm_first_cycles")
 
IntegerOptionKey const dock_mcm_second_cycles ("docking:dock_mcm_second_cycles")
 
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")
 
RealOptionKey const minimization_threshold ("docking:minimization_threshold")
 
RealOptionKey const temperature ("docking:temperature")
 
IntegerOptionKey const repack_period ("docking:repack_period")
 
BooleanOptionKey const extra_rottrial ("docking:extra_rottrial")
 
BooleanOptionKey const dock_rtmin ("docking:dock_rtmin")
 
BooleanOptionKey const sc_min ("docking:sc_min")
 
BooleanOptionKey const norepack1 ("docking:norepack1")
 
BooleanOptionKey const norepack2 ("docking:norepack2")
 
IntegerVectorOptionKey const bb_min_res ("docking:bb_min_res")
 
IntegerVectorOptionKey const sc_min_res ("docking:sc_min_res")
 
BooleanOptionKey const dock_ppk ("docking:dock_ppk")
 
IntegerOptionKey const max_repeats ("docking:max_repeats")
 
RealVectorOptionKey const dock_lowres_filter ("docking:dock_lowres_filter")
 
RealOptionKey const SymDock_lowres_filter ("docking:SymDock_lowres_filter")
 
IntegerVectorOptionKey const multibody ("docking:multibody")
 
BooleanOptionKey const ignore_default_docking_task ("docking:ignore_default_docking_task")
 
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")
 
RealOptionKey const docklowres_trans_magnitude ("docking:docklowres_trans_magnitude")
 
RealOptionKey const docklowres_rot_magnitude ("docking:docklowres_rot_magnitude")
 
BooleanOptionKey const enable_pymol_viewer ("docking:enable_pymol_viewer")
 
BooleanOptionKey const SymDock_reduce_motif_dock_weights ("docking:SymDock_reduce_motif_dock_weights")
 
RealOptionKey const SymDock_fa_rep_max ("docking:SymDock_fa_rep_max")
 
RealOptionKey const SymDock_fa_sol_max ("docking:SymDock_fa_sol_max")
 

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('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 = protocols.docking.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

IntegerVectorOptionKey const docking::bb_min_res ( "docking:bb_min_res"  )
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"  )
IntegerOptionKey const docking::dock_mcm_first_cycles ( "docking:dock_mcm_first_cycles"  )
RealOptionKey const docking::dock_mcm_rot_magnitude ( "docking:dock_mcm_rot_magnitude"  )
IntegerOptionKey const docking::dock_mcm_second_cycles ( "docking:dock_mcm_second_cycles"  )
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::docking_low_res_score ( "docking:docking_low_res_score"  )
RealOptionKey const docking::docklowres_rot_magnitude ( "docking:docklowres_rot_magnitude"  )
RealOptionKey const docking::docklowres_trans_magnitude ( "docking:docklowres_trans_magnitude"  )
BooleanOptionKey const docking::enable_pymol_viewer ( "docking:enable_pymol_viewer"  )
StringOptionKey const docking::ensemble1 ( "docking:ensemble1"  )
StringOptionKey const docking::ensemble2 ( "docking:ensemble2"  )
BooleanOptionKey const docking::extra_rottrial ( "docking:extra_rottrial"  )
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::ignore_default_docking_task ( "docking:ignore_default_docking_task"  )
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"  )
RealOptionKey const docking::minimization_threshold ( "docking:minimization_threshold"  )
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"  )
FileOptionKey const docking::recover_sidechains ( "docking:recover_sidechains"  )
IntegerOptionKey const docking::repack_period ( "docking:repack_period"  )
BooleanOptionKey const docking::sc_min ( "docking:sc_min"  )
IntegerVectorOptionKey const docking::sc_min_res ( "docking:sc_min_res"  )
BooleanOptionKey const docking::spin ( "docking:spin"  )
RealOptionKey const docking::SymDock_fa_rep_max ( "docking:SymDock_fa_rep_max"  )
RealOptionKey const docking::SymDock_fa_sol_max ( "docking:SymDock_fa_sol_max"  )
RealOptionKey const docking::SymDock_lowres_filter ( "docking:SymDock_lowres_filter"  )
BooleanOptionKey const docking::SymDock_reduce_motif_dock_weights ( "docking:SymDock_reduce_motif_dock_weights"  )
RealOptionKey const docking::temperature ( "docking:temperature"  )
RealVectorOptionKey const docking::tilt ( "docking:tilt"  )
StringOptionKey const docking::tilt1_center ( "docking:tilt1_center"  )
StringOptionKey const docking::tilt2_center ( "docking:tilt2_center"  )
RealOptionKey const docking::uniform_trans ( "docking:uniform_trans"  )
BooleanOptionKey const docking::use_ellipsoidal_randomization ( "docking:use_ellipsoidal_randomization"  )
BooleanOptionKey const docking::use_legacy_protocol ( "docking:use_legacy_protocol"  )
BooleanOptionKey const docking::view ( "docking:view"  )

Variable Documentation

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