docking Namespace Reference

Namespaces
	ligand

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")
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")

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::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')