orn_macrocycle Namespace Reference

Functions
def	add_orn_cst (pose, res1, res2)

Variables
	pose = Pose()
	score_fxn = core.scoring.get_score_function()
	chm = rosetta.core.chemical.ChemicalManager.get_instance()
	rts = chm.residue_type_set('fa_standard').get_self_ptr()
	ala_type = rts.name_map("ALA")
	orn_type = rts.name_map("ORN:NtermProteinFull:N-conjugated")
	ala = Residue(ala_type, True)
	orn = Residue(orn_type, True)
	new_orn = ResidueFactory.create_residue(orn_type, pose.residue(1), pose.conformation())
	new_ala = ResidueFactory.create_residue( ala_type, pose.residue( 12 ), pose.conformation() )
	new_orn2 = ResidueFactory.create_residue( orn_type, pose.residue( 7 ), pose.conformation() )
	new_ala2 = ResidueFactory.create_residue( ala_type, pose.residue( 6 ), pose.conformation() )
	nres = pose.size()
	mm = core.kinematics.MoveMap()
	minM = protocols.simple_moves.MinMover(mm, score_fxn, "lbfgs_armijo_nonmonotone", 0.01, True)
	pert_sequence = protocols.moves.SequenceMover()
	Initial MC. More...
	pert_mc = protocols.moves.MonteCarlo(pose, score_fxn, 0.2)
	pert_pep_mm = core.kinematics.MoveMap()
	pert_pep_small = protocols.simple_moves.SmallMover(pert_pep_mm, 0.2, 1)
	pert_pep_shear = protocols.simple_moves.ShearMover(pert_pep_mm, 0.2, 1)
	pert_pep_random = protocols.moves.RandomMover()
	pert_pep_repeat = protocols.moves.RepeatMover(pert_pep_random, 100)
	pert_trial = protocols.moves.TrialMover(pert_sequence, pert_mc)
float	wt = 0.01

Function Documentation

add_orn_cst()

def orn_macrocycle.add_orn_cst	(		pose,
			res1,
			res2
	)

References basic.init().

Variable Documentation

ala

orn_macrocycle.ala = Residue(ala_type, True)

Referenced by add_pep_buffer_res(), A3BHbsCreatorMover.apply(), collect_stats(), design_hits(), dock(), gen_pep_bb_sequential(), MatchBase.init(), main(), A3BHbsCreatorMover.make_a3b_pose(), run(), run_3bpy(), run_diiron_glu(), run_m8(), run_pep_prep(), run_tyr_his(), run_zn2his(), and RunPepSpec().

ala_type

orn_macrocycle.ala_type = rts.name_map("ALA")

chm

orn_macrocycle.chm = rosetta.core.chemical.ChemicalManager.get_instance()

minM

orn_macrocycle.minM = protocols.simple_moves.MinMover(mm, score_fxn, "lbfgs_armijo_nonmonotone", 0.01, True)

mm

orn_macrocycle.mm = core.kinematics.MoveMap()

new_ala

orn_macrocycle.new_ala = ResidueFactory.create_residue( ala_type, pose.residue( 12 ), pose.conformation() )

new_ala2

orn_macrocycle.new_ala2 = ResidueFactory.create_residue( ala_type, pose.residue( 6 ), pose.conformation() )

new_orn

orn_macrocycle.new_orn = ResidueFactory.create_residue(orn_type, pose.residue(1), pose.conformation())

new_orn2

orn_macrocycle.new_orn2 = ResidueFactory.create_residue( orn_type, pose.residue( 7 ), pose.conformation() )

nres

orn_macrocycle.nres = pose.size()

orn

orn_macrocycle.orn = Residue(orn_type, True)

orn_type

orn_macrocycle.orn_type = rts.name_map("ORN:NtermProteinFull:N-conjugated")

pert_mc

orn_macrocycle.pert_mc = protocols.moves.MonteCarlo(pose, score_fxn, 0.2)

Referenced by DougsDockDesignMinimizeMagicMover.apply(), A3BHbsDockDesignMinimizeMover.apply(), CovalentPeptidomimeticDockDesign.apply(), CovalentPeptidomimeticCreator.apply(), MikeLinkerMover.apply(), TrizaolamerDockDesignMinimizeMover.apply(), and A3BHbsCreatorMover.do_mc().

pert_pep_mm

orn_macrocycle.pert_pep_mm = core.kinematics.MoveMap()

Referenced by DougsDockDesignMinimizeMagicMover.apply(), A3BPeptideBuilder.apply(), TrizaolamerDockDesignMinimizeMover.apply(), HbsDesignMover.apply(), OopDesignMover.apply(), and PeptoidDesignMover.apply().

pert_pep_random

orn_macrocycle.pert_pep_random = protocols.moves.RandomMover()

Referenced by DougsDockDesignMinimizeMagicMover.apply(), A3BHbsDockDesignMinimizeMover.apply(), A3BPeptideBuilder.apply(), MikeLinkerMover.apply(), TrizaolamerDockDesignMinimizeMover.apply(), OopDesignMover.apply(), and A3BHbsCreatorMover.do_mc().

pert_pep_repeat

orn_macrocycle.pert_pep_repeat = protocols.moves.RepeatMover(pert_pep_random, 100)

Referenced by DougsDockDesignMinimizeMagicMover.apply(), A3BHbsDockDesignMinimizeMover.apply(), MikeLinkerMover.apply(), TrizaolamerDockDesignMinimizeMover.apply(), OopDesignMover.apply(), and A3BHbsCreatorMover.do_mc().

pert_pep_shear

orn_macrocycle.pert_pep_shear = protocols.simple_moves.ShearMover(pert_pep_mm, 0.2, 1)

Referenced by DougsDockDesignMinimizeMagicMover.apply(), MikeLinkerMover.apply(), and TrizaolamerDockDesignMinimizeMover.apply().

pert_pep_small

orn_macrocycle.pert_pep_small = protocols.simple_moves.SmallMover(pert_pep_mm, 0.2, 1)

Referenced by DougsDockDesignMinimizeMagicMover.apply(), MikeLinkerMover.apply(), TrizaolamerDockDesignMinimizeMover.apply(), and OopDesignMover.apply().

pert_sequence

orn_macrocycle.pert_sequence = protocols.moves.SequenceMover()

Initial MC.

Referenced by DougsDockDesignMinimizeMagicMover.apply(), PeptiodMovieMover.apply(), A3BHbsDockDesignMinimizeMover.apply(), MikeLinkerMover.apply(), TrizaolamerDockDesignMinimizeMover.apply(), HbsDesignMover.apply(), OopDesignMover.apply(), PeptoidDesignMover.apply(), and A3BHbsCreatorMover.do_mc().

pert_trial

orn_macrocycle.pert_trial = protocols.moves.TrialMover(pert_sequence, pert_mc)

Referenced by DougsDockDesignMinimizeMagicMover.apply(), PeptiodMovieMover.apply(), A3BHbsDockDesignMinimizeMover.apply(), A3BPeptideBuilder.apply(), MikeLinkerMover.apply(), TrizaolamerDockDesignMinimizeMover.apply(), HbsDesignMover.apply(), OopDesignMover.apply(), PeptoidDesignMover.apply(), aramid_main(), and A3BHbsCreatorMover.do_mc().

pose

orn_macrocycle.pose = Pose()

rts

orn_macrocycle.rts = chm.residue_type_set('fa_standard').get_self_ptr()

score_fxn

orn_macrocycle.score_fxn = core.scoring.get_score_function()

wt

float orn_macrocycle.wt = 0.01

Referenced by PoseWrap.add_apcs_local(), InterfaceDDGMover.apply(), TriazoleCreator.apply(), calc_ddg(), correlation(), dna_dr_loop_test(), gradual_minimization(), harvest_scores(), TCDock.init(), main(), InterfaceDDGMover.mutate_and_relax(), print_ddgs(), print_verbose_ddgs(), read_in_mutations(), PoseWrap.replace_scattach_res(), MinPackMin.set_density_wt(), sicdock_thread_num(), numeric::fourier::SHT.sph_standardize(), superimpose_pose(), and TCDock.TCDock().