|
| | evaluate_beta_mutants.score_fxn = core.scoring.get_score_function() |
| |
| | evaluate_beta_mutants.Pose = core.import_pose.pose_from_file( pose, sys.argv[1], core.import_pose.PDB_file ) |
| |
| | evaluate_beta_mutants.is_1ycr |
| |
| | evaluate_beta_mutants.is_mdm4 |
| |
| | evaluate_beta_mutants.chm = rosetta.core.chemical.ChemicalManager.get_instance() |
| |
| | evaluate_beta_mutants.restype_set = chm.residue_type_set('fa_standard').get_self_ptr() |
| |
| int | evaluate_beta_mutants.leu_pos = 96 if is_mdm4 else ( 88 if is_1ycr else 91 ) |
| |
| int | evaluate_beta_mutants.trp_pos = leu_pos + 3 |
| |
| int | evaluate_beta_mutants.phe_pos = leu_pos + 6 |
| |
| | evaluate_beta_mutants.leu = pose.residue(leu_pos) |
| |
| | evaluate_beta_mutants.trp = pose.residue(trp_pos) |
| |
| | evaluate_beta_mutants.phe = pose.residue(phe_pos) |
| |
| | evaluate_beta_mutants.trp_mm = kinematics.MoveMap() |
| |
| | evaluate_beta_mutants.trp_min = protocols.minimization_packing.MinMover(trp_mm, score_fxn, "lbfgs_armijo_nonmonotone", 0.001, True) |
| |
| | evaluate_beta_mutants.leu_mm = kinematics.MoveMap() |
| |
| | evaluate_beta_mutants.leu_min = protocols.minimization_packing.MinMover(leu_mm, score_fxn, "lbfgs_armijo_nonmonotone", 0.001, True) |
| |
| | evaluate_beta_mutants.phe_mm = kinematics.MoveMap() |
| |
| | evaluate_beta_mutants.phe_min = protocols.minimization_packing.MinMover(phe_mm, score_fxn, "lbfgs_armijo_nonmonotone", 0.001, True) |
| |
| | evaluate_beta_mutants.file = sys.argv[1] |
| |
| def | evaluate_beta_mutants.b53_8_score = score_ensemble(pose, score_fxn, "native_"+file) |
| |
| | evaluate_beta_mutants.b53_12_pose = Pose(pose) |
| |
| | evaluate_beta_mutants.tfm_rt = restype_set.name_map("B3F:B3F-CE1-trifluoromethylated") |
| |
| | evaluate_beta_mutants.tfm = ResidueFactory.create_residue(tfm_rt, pose.residue(trp_pos), pose.conformation()) |
| |
| def | evaluate_beta_mutants.b53_12_score = score_ensemble(b53_12_pose, score_fxn, "meta_trifluoromethyl_phe_"+file) |
| |
| | evaluate_beta_mutants.b53_12b_pose = Pose(pose) |
| |
| | evaluate_beta_mutants.tfmb_rt = restype_set.name_map("B3F:B3F-CE2-trifluoromethylated") |
| |
| | evaluate_beta_mutants.tfmb = ResidueFactory.create_residue(tfmb_rt, pose.residue(trp_pos), pose.conformation()) |
| |
| def | evaluate_beta_mutants.b53_12b_score = score_ensemble(b53_12b_pose, score_fxn, "meta_trifluoromethyl_pheb_"+file) |
| |
| | evaluate_beta_mutants.b53_13_pose = Pose(pose) |
| |
| | evaluate_beta_mutants.ch2_rt = restype_set.name_map("B3W:B3W-CH2-chlorinated") |
| |
| | evaluate_beta_mutants.ch2 = ResidueFactory.create_residue(ch2_rt, pose.residue(trp_pos), pose.conformation()) |
| |
| def | evaluate_beta_mutants.b53_13_score = score_ensemble(b53_13_pose, score_fxn, "chloro_trp_"+file) |
| |
| | evaluate_beta_mutants.b53_14_pose = Pose(pose) |
| |
| | evaluate_beta_mutants.phe2_rt = restype_set.name_map("B3F") |
| |
| | evaluate_beta_mutants.phe2 = ResidueFactory.create_residue(phe2_rt, pose.residue(trp_pos), pose.conformation()) |
| |
| def | evaluate_beta_mutants.b53_14_score = score_ensemble(b53_14_pose, score_fxn, "phe_"+file) |
| |
| | evaluate_beta_mutants.b53_15_pose = Pose(pose) |
| |
| | evaluate_beta_mutants.mcl_rt = restype_set.name_map("B3F:B3F-CE1-chlorinated") |
| |
| | evaluate_beta_mutants.mcl = ResidueFactory.create_residue(mcl_rt, pose.residue(trp_pos), pose.conformation()) |
| |
| def | evaluate_beta_mutants.b53_15_score = score_ensemble(b53_15_pose, score_fxn, "meta_chloro_phe_"+file) |
| |
| | evaluate_beta_mutants.b53_16_pose = Pose(pose) |
| |
| | evaluate_beta_mutants.mpcl_rt = restype_set.name_map("B3F:B3F-CE1-chlorinated:B3F-CZ-chlorinated") |
| |
| | evaluate_beta_mutants.mpcl = ResidueFactory.create_residue(mpcl_rt, pose.residue(trp_pos), pose.conformation()) |
| |
| def | evaluate_beta_mutants.b53_16_score = score_ensemble(b53_16_pose, score_fxn, "meta_para_dichloro_phe_"+file) |
| |
| | evaluate_beta_mutants.b53_17_pose = Pose(b53_12_pose) |
| |
| | evaluate_beta_mutants.ile_rt = restype_set.name_map( "B3I" ) |
| |
| | evaluate_beta_mutants.ile = ResidueFactory.create_residue( ile_rt, pose.residue(leu_pos), pose.conformation() ) |
| |
| def | evaluate_beta_mutants.b53_17_score = score_ensemble(b53_17_pose, score_fxn, "ile_"+file) |
| |
| | evaluate_beta_mutants.b53_18_pose = Pose(b53_16_pose) |
| |
| | evaluate_beta_mutants.fp_rt = restype_set.name_map("B3F:B3F-CZ-fluorinated") |
| |
| | evaluate_beta_mutants.fp = ResidueFactory.create_residue(fp_rt, pose.residue(phe_pos), pose.conformation()) |
| |
| def | evaluate_beta_mutants.b53_18_score = score_ensemble(b53_18_pose, score_fxn, "para_fluoro_phe_"+file) |
| |
