Functions
def	evaluate_interface (pose, score_fxn)

def	score_ensemble (pose, score_fxn, name, ntrials=3)

Variables
	score_fxn = core.scoring.get_score_function()

	Pose = core.import_pose.pose_from_file( pose, sys.argv[1], core.import_pose.PDB_file )

	is_1ycr

	is_mdm4

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

	restype_set = chm.residue_type_set('fa_standard').get_self_ptr()

int	leu_pos = 96 if is_mdm4 else ( 88 if is_1ycr else 91 )

int	trp_pos = leu_pos + 3

int	phe_pos = leu_pos + 6

	leu = pose.residue(leu_pos)

	trp = pose.residue(trp_pos)

	phe = pose.residue(phe_pos)

	trp_mm = kinematics.MoveMap()

	trp_min = protocols.minimization_packing.MinMover(trp_mm, score_fxn, "lbfgs_armijo_nonmonotone", 0.001, True)

	leu_mm = kinematics.MoveMap()

	leu_min = protocols.minimization_packing.MinMover(leu_mm, score_fxn, "lbfgs_armijo_nonmonotone", 0.001, True)

	phe_mm = kinematics.MoveMap()

	phe_min = protocols.minimization_packing.MinMover(phe_mm, score_fxn, "lbfgs_armijo_nonmonotone", 0.001, True)

	file = sys.argv[1]

def	b53_8_score = score_ensemble(pose, score_fxn, "native_"+file)

	b53_12_pose = Pose(pose)

	tfm_rt = restype_set.name_map("B3F:B3F-CE1-trifluoromethylated")

	tfm = ResidueFactory.create_residue(tfm_rt, pose.residue(trp_pos), pose.conformation())

def	b53_12_score = score_ensemble(b53_12_pose, score_fxn, "meta_trifluoromethyl_phe_"+file)

	b53_12b_pose = Pose(pose)

	tfmb_rt = restype_set.name_map("B3F:B3F-CE2-trifluoromethylated")

	tfmb = ResidueFactory.create_residue(tfmb_rt, pose.residue(trp_pos), pose.conformation())

def	b53_12b_score = score_ensemble(b53_12b_pose, score_fxn, "meta_trifluoromethyl_pheb_"+file)

	b53_13_pose = Pose(pose)

	ch2_rt = restype_set.name_map("B3W:B3W-CH2-chlorinated")

	ch2 = ResidueFactory.create_residue(ch2_rt, pose.residue(trp_pos), pose.conformation())

def	b53_13_score = score_ensemble(b53_13_pose, score_fxn, "chloro_trp_"+file)

	b53_14_pose = Pose(pose)

	phe2_rt = restype_set.name_map("B3F")

	phe2 = ResidueFactory.create_residue(phe2_rt, pose.residue(trp_pos), pose.conformation())

def	b53_14_score = score_ensemble(b53_14_pose, score_fxn, "phe_"+file)

	b53_15_pose = Pose(pose)

	mcl_rt = restype_set.name_map("B3F:B3F-CE1-chlorinated")

	mcl = ResidueFactory.create_residue(mcl_rt, pose.residue(trp_pos), pose.conformation())

def	b53_15_score = score_ensemble(b53_15_pose, score_fxn, "meta_chloro_phe_"+file)

	b53_16_pose = Pose(pose)

	mpcl_rt = restype_set.name_map("B3F:B3F-CE1-chlorinated:B3F-CZ-chlorinated")

	mpcl = ResidueFactory.create_residue(mpcl_rt, pose.residue(trp_pos), pose.conformation())

def	b53_16_score = score_ensemble(b53_16_pose, score_fxn, "meta_para_dichloro_phe_"+file)

	b53_17_pose = Pose(b53_12_pose)

	ile_rt = restype_set.name_map( "B3I" )

	ile = ResidueFactory.create_residue( ile_rt, pose.residue(leu_pos), pose.conformation() )

def	b53_17_score = score_ensemble(b53_17_pose, score_fxn, "ile_"+file)

	b53_18_pose = Pose(b53_16_pose)

	fp_rt = restype_set.name_map("B3F:B3F-CZ-fluorinated")

	fp = ResidueFactory.create_residue(fp_rt, pose.residue(phe_pos), pose.conformation())

def	b53_18_score = score_ensemble(b53_18_pose, score_fxn, "para_fluoro_phe_"+file)

Function Documentation

◆ evaluate_interface()

def evaluate_beta_mutants.evaluate_interface	(	pose,
		score_fxn
	)

References score_fxn, and oop_conformations.scorefxn.

Referenced by score_ensemble().

◆ score_ensemble()

def evaluate_beta_mutants.score_ensemble	(	pose,
		score_fxn,
		name,
		ntrials = `3`
	)

References evaluate_interface(), run_backbone.float, and sum().

Variable Documentation

◆ b53_12_pose

evaluate_beta_mutants.b53_12_pose = Pose(pose)

◆ b53_12_score

def evaluate_beta_mutants.b53_12_score = score_ensemble(b53_12_pose, score_fxn, "meta_trifluoromethyl_phe_"+file)

◆ b53_12b_pose

evaluate_beta_mutants.b53_12b_pose = Pose(pose)

◆ b53_12b_score

def evaluate_beta_mutants.b53_12b_score = score_ensemble(b53_12b_pose, score_fxn, "meta_trifluoromethyl_pheb_"+file)

◆ b53_13_pose

evaluate_beta_mutants.b53_13_pose = Pose(pose)

◆ b53_13_score

def evaluate_beta_mutants.b53_13_score = score_ensemble(b53_13_pose, score_fxn, "chloro_trp_"+file)

◆ b53_14_pose

evaluate_beta_mutants.b53_14_pose = Pose(pose)

◆ b53_14_score

def evaluate_beta_mutants.b53_14_score = score_ensemble(b53_14_pose, score_fxn, "phe_"+file)

◆ b53_15_pose

evaluate_beta_mutants.b53_15_pose = Pose(pose)

◆ b53_15_score

def evaluate_beta_mutants.b53_15_score = score_ensemble(b53_15_pose, score_fxn, "meta_chloro_phe_"+file)

◆ b53_16_pose

evaluate_beta_mutants.b53_16_pose = Pose(pose)

◆ b53_16_score

def evaluate_beta_mutants.b53_16_score = score_ensemble(b53_16_pose, score_fxn, "meta_para_dichloro_phe_"+file)

◆ b53_17_pose

evaluate_beta_mutants.b53_17_pose = Pose(b53_12_pose)

◆ b53_17_score

def evaluate_beta_mutants.b53_17_score = score_ensemble(b53_17_pose, score_fxn, "ile_"+file)

◆ b53_18_pose

evaluate_beta_mutants.b53_18_pose = Pose(b53_16_pose)

◆ b53_18_score

def evaluate_beta_mutants.b53_18_score = score_ensemble(b53_18_pose, score_fxn, "para_fluoro_phe_"+file)

◆ b53_8_score

def evaluate_beta_mutants.b53_8_score = score_ensemble(pose, score_fxn, "native_"+file)

◆ ch2

evaluate_beta_mutants.ch2 = ResidueFactory.create_residue(ch2_rt, pose.residue(trp_pos), pose.conformation())

Referenced by dock(), dumpsym2(), dumpsym6(), BruteFunGroupTK.place_c(), KinFunGroupTK.place_c(), and run().

◆ ch2_rt

evaluate_beta_mutants.ch2_rt = restype_set.name_map("B3W:B3W-CH2-chlorinated")

◆ chm

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

◆ file

evaluate_beta_mutants.file = sys.argv[1]

Referenced by ui::task::TaskView.action_output_save_as(), ui::task::Task.add_file(), detail.assert_fail(), utility.cond_exit(), utility::file.create_temp_filename(), BinderFrontendAction.CreateASTConsumer(), dna_chain_check(), dostuff(), utility.exit(), utility.exit_handler(), utility.exit_with_user_fixable_issue(), extract_pdb_id(), filebase(), handle_assert_failure(), hbond_stats(), numeric::interpolation::Histogram< X, Y >.Histogram(), ui::task::TaskView.index_to_file(), ui::task::File.init_from_local_file(), load_checkpoint(), mp_ddG.main(), main(), make_templates.makeFile(), ui::widgets::PoseEditor.on_action_open_pose_triggered(), ui::task::ProjectView.on_action_open_project_triggered(), ui::task::TaskView.on_export_all_files_clicked(), ui::task::JobSubmit.on_flags_from_file_clicked(), ui::task::TaskView.on_output_clicked(), ui::task::TaskView.on_output_doubleClicked(), ui::task.open_file_viewer(), ui::network::PathArgument.operator QString(), ui::viewers.parse_score_file(), ui::task::TaskView.preview_file(), mp_ddG.print_ddG_breakdown(), mp_ddG.print_score_labels_to_file(), DB_Builder.read_data_file(), readFile(), ui::task::Task.rename_input_file(), rescore_test(), protocols::abinitio::Application.run(), utility.save_crash_report(), utility.save_crash_report_to_file(), ui::task.save_project(), sequence_tolerance_mf_main(), protocols::abinitio::JumpSpecificAbrelax.setup_fold(), basic::options.start_files(), ui::task::TaskSyncer_TaskStrategy.task_files_upload(), apps::pilot::frankdt.write_segments_to_file(), options_class.writeToFile(), and zf_test().

◆ fp

evaluate_beta_mutants.fp = ResidueFactory.create_residue(fp_rt, pose.residue(phe_pos), pose.conformation())

Referenced by numeric::kinematic_closure.buildsturm(), numeric::kinematic_closure.evalpoly(), detail.format_float(), numeric::nls.lm_lmpar(), numeric::kinematic_closure.modrf(), posewrap_from_command_line(), select_string(), svm_load_model(), and svm_save_model().

◆ fp_rt

evaluate_beta_mutants.fp_rt = restype_set.name_map("B3F:B3F-CZ-fluorinated")

◆ ile

evaluate_beta_mutants.ile = ResidueFactory.create_residue( ile_rt, pose.residue(leu_pos), pose.conformation() )

Referenced by run().

◆ ile_rt

evaluate_beta_mutants.ile_rt = restype_set.name_map( "B3I" )

◆ is_1ycr

evaluate_beta_mutants.is_1ycr

◆ is_mdm4

evaluate_beta_mutants.is_mdm4

◆ leu

evaluate_beta_mutants.leu = pose.residue(leu_pos)

◆ leu_min

evaluate_beta_mutants.leu_min = protocols.minimization_packing.MinMover(leu_mm, score_fxn, "lbfgs_armijo_nonmonotone", 0.001, True)

◆ leu_mm

evaluate_beta_mutants.leu_mm = kinematics.MoveMap()

◆ leu_pos

int evaluate_beta_mutants.leu_pos = 96 if is_mdm4 else ( 88 if is_1ycr else 91 )

◆ mcl

evaluate_beta_mutants.mcl = ResidueFactory.create_residue(mcl_rt, pose.residue(trp_pos), pose.conformation())

◆ mcl_rt

evaluate_beta_mutants.mcl_rt = restype_set.name_map("B3F:B3F-CE1-chlorinated")

◆ mpcl

evaluate_beta_mutants.mpcl = ResidueFactory.create_residue(mpcl_rt, pose.residue(trp_pos), pose.conformation())

◆ mpcl_rt

evaluate_beta_mutants.mpcl_rt = restype_set.name_map("B3F:B3F-CE1-chlorinated:B3F-CZ-chlorinated")

◆ phe

evaluate_beta_mutants.phe = pose.residue(phe_pos)

◆ phe2

evaluate_beta_mutants.phe2 = ResidueFactory.create_residue(phe2_rt, pose.residue(trp_pos), pose.conformation())

◆ phe2_rt

evaluate_beta_mutants.phe2_rt = restype_set.name_map("B3F")

◆ phe_min

evaluate_beta_mutants.phe_min = protocols.minimization_packing.MinMover(phe_mm, score_fxn, "lbfgs_armijo_nonmonotone", 0.001, True)

◆ phe_mm

evaluate_beta_mutants.phe_mm = kinematics.MoveMap()

◆ phe_pos

int evaluate_beta_mutants.phe_pos = leu_pos + 6

◆ Pose

evaluate_beta_mutants.Pose = core.import_pose.pose_from_file( pose, sys.argv[1], core.import_pose.PDB_file )

◆ restype_set

evaluate_beta_mutants.restype_set = chm.residue_type_set('fa_standard').get_self_ptr()

◆ score_fxn

evaluate_beta_mutants.score_fxn = core.scoring.get_score_function()

Referenced by evaluate_interface().

◆ tfm

evaluate_beta_mutants.tfm = ResidueFactory.create_residue(tfm_rt, pose.residue(trp_pos), pose.conformation())

◆ tfm_rt

evaluate_beta_mutants.tfm_rt = restype_set.name_map("B3F:B3F-CE1-trifluoromethylated")

◆ tfmb

evaluate_beta_mutants.tfmb = ResidueFactory.create_residue(tfmb_rt, pose.residue(trp_pos), pose.conformation())

◆ tfmb_rt

evaluate_beta_mutants.tfmb_rt = restype_set.name_map("B3F:B3F-CE2-trifluoromethylated")

◆ trp

evaluate_beta_mutants.trp = pose.residue(trp_pos)

◆ trp_min

evaluate_beta_mutants.trp_min = protocols.minimization_packing.MinMover(trp_mm, score_fxn, "lbfgs_armijo_nonmonotone", 0.001, True)

◆ trp_mm

evaluate_beta_mutants.trp_mm = kinematics.MoveMap()

◆ trp_pos

int evaluate_beta_mutants.trp_pos = leu_pos + 3

Functions

Variables