|
| | vancomycin.scorefxn = get_score_function() |
| |
| | vancomycin.chm = rosetta.core.chemical.ChemicalManager.get_instance() |
| |
| | vancomycin.restype_set_cap = chm.residue_type_set('fa_standard').get_self_ptr() |
| |
| | vancomycin.dleu_type = residue_set_cap.name_map("DLEU:NtermProteinMethylated") |
| |
| | vancomycin.V01_type = residue_set_cap.name_map("DV01:aryl-O-conjugated") |
| |
| | vancomycin.asn_type = residue_set_cap.name_map("ASN") |
| |
| | vancomycin.V02_type = residue_set_cap.name_map("DV02:aryl-O-conjugated:phg_cd1_conjugation:phg_cd2_conjugation") |
| |
| | vancomycin.V02_type2 = residue_set_cap.name_map("DV02:phg_cd1_conjugation") |
| |
| | vancomycin.V04_type = residue_set_cap.name_map("V04:aryl-O-conjugated") |
| |
| | vancomycin.V03_type = residue_set_cap.name_map("V03:CtermProteinFull:aryl-C-conjugated") |
| |
| | vancomycin.dleu = Residue(dleu_type, True) |
| |
| | vancomycin.V01 = Residue(V01_type, True) |
| |
| | vancomycin.asn = Residue(asn_type, True) |
| |
| | vancomycin.V02 = Residue(V02_type, True) |
| |
| | vancomycin.V022 = Residue(V02_type2, True) |
| |
| | vancomycin.V04 = Residue(V04_type, True) |
| |
| | vancomycin.V03 = Residue(V03_type, True) |
| |
| | vancomycin.vancomycin = Pose() |
| |
| | vancomycin.translate = protocols.rigid.RigidBodyTransMover(vancomycin, 1) |
| |
| int | vancomycin.ii = i + 1 |
| |
| | vancomycin.pert_mm = kinematics.MoveMap() |
| |
| | vancomycin.min_mover = minimization_packing.MinMover(pert_mm, scorefxn, "lbfgs_armijo_nonmonotone", 0.0001, True) |
| |
| | vancomycin.f = vancomycin.fold_tree() |
| |
| | vancomycin.task = TaskFactory.create_packer_task(vancomycin) |
| |
| int | vancomycin.i = ii + 1 |
| |
| | vancomycin.pack = PackRotamersMover(scorefxn, task) |
| |
| | vancomycin.vanc2 = Pose() |
| |
| | vancomycin.trans2 = protocols.rigid.RigidBodyTransMover(vanc2, 1) |
| |
| | vancomycin.dharm = core.scoring.func.CircularHarmonicFunc(-71.5 * 3.14159 / 180, 0.02) |
| |
| | vancomycin.dharm2 = core.scoring.func.CircularHarmonicFunc(176.9 * 3.14159 / 180, 0.02) |
| |
| | vancomycin.dharm3 = core.scoring.func.CircularHarmonicFunc(60 * 3.14159 / 180, 0.02) |
| |
| | vancomycin.harm = core.scoring.func.HarmonicFunc(1.31, 0.02) |
| |
| | vancomycin.aharm2 = core.scoring.func.CircularHarmonicFunc(120 * 3.14159 / 180, 0.02) |
| |
| | vancomycin.OZ4 = core.id.AtomID(vanc2.residue(2).type().atom_index("OZ"), 2) |
| |
| | vancomycin.C18 = core.id.AtomID(vanc2.residue(4).type().atom_index("C1"), 4) |
| |
| | vancomycin.C28 = core.id.AtomID(vanc2.residue(4).type().atom_index("C2"), 4) |
| |
| | vancomycin.O28 = core.id.AtomID(vanc2.residue(4).type().atom_index("O2"), 4) |
| |
| | vancomycin.C19 = core.id.AtomID(vanc2.residue(5).type().atom_index("C1"), 5) |
| |
| | vancomycin.O58 = core.id.AtomID(vanc2.residue(4).type().atom_index("O5"), 4) |
| |
| | vancomycin.O59 = core.id.AtomID(vanc2.residue(5).type().atom_index("O5"), 5) |
| |
| | vancomycin.C58 = core.id.AtomID(vanc2.residue(4).type().atom_index("C5"), 4) |
| |
| | vancomycin.C59 = core.id.AtomID(vanc2.residue(5).type().atom_index("C5"), 5) |
| |
| | vancomycin.CE = core.id.AtomID(vanc2.residue(2).type().atom_index("CE"), 2) |
| |
| | vancomycin.pert_mm2 = kinematics.MoveMap() |
| |
| | vancomycin.min_mover2 = minimization_packing.MinMover(pert_mm2, scorefxn, "lbfgs_armijo_nonmonotone", 0.0001, True) |
| |
| | vancomycin.f2 = vanc2.fold_tree() |
| |
| | vancomycin.task2 = TaskFactory.create_packer_task(vanc2) |
| |
| | vancomycin.pack2 = PackRotamersMover(scorefxn, task2) |
| |
