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How to use unbind method in lisa

Best Python code snippet using lisa_python

bind_unbind.py

Source:bind_unbind.py

1from pyrosetta import *2from pyrosetta import PyMOLMover3from pyrosetta.toolbox import cleanATOM4from pyrosetta.toolbox import get_secstruct5from pyrosetta.teaching import *6from pyrosetta.toolbox import get_hbonds7from pyrosetta.toolbox import mutate_residue8from pyrosetta.rosetta.protocols.relax import *9from pyrosetta.rosetta.protocols.simple_moves import *10from pyrosetta.rosetta.core.fragment import *11from pyrosetta.rosetta.protocols.moves import *12from pyrosetta.rosetta.protocols.rigid import *13from pyrosetta.rosetta.protocols.docking import *14import sys15init()1617def main():18    pose=pose_from_pdb("Folding_WT_8.pdb")19    scorefxn = get_fa_scorefxn()20    dumpfile = 'Folding_WT_8_bind_unbind.pdb'21    newfile=open("dg.txt", "w")22    bind_score=float(scorefxn(pose))23    setup_foldtree(pose, 'ABCDEF_OPMTUV', Vector1([1]))24    trans_mover = RigidBodyTransMover(pose, 1)25    trans_mover.step_size(100)26    trans_mover.apply(pose)27    unbind_score=float(scorefxn(pose))28    ddg_bind = bind_score-unbind_score29    newfile.write(str(ddg_bind))30    newfile.write('\n')31    pose.dump_pdb(dumpfile)32    #####################################################33    pose=pose_from_pdb("Folding_Output_P1411Y.pdb")34    scorefxn = get_fa_scorefxn()35    dumpfile = 'Folding_Output_P1411Y_bind_unbind.pdb'36    bind_score=float(scorefxn(pose))37    setup_foldtree(pose, 'ABCDEF_OPMTUV', Vector1([1]))38    trans_mover = RigidBodyTransMover(pose, 1)39    trans_mover.step_size(100)40    trans_mover.apply(pose)41    unbind_score=float(scorefxn(pose))42    ddg_bind = bind_score-unbind_score43    newfile.write(str(ddg_bind))44    newfile.write('\n')45    pose.dump_pdb(dumpfile)46    #####################################################47    pose=pose_from_pdb("Folding_Output_S1412P.pdb")48    scorefxn = get_fa_scorefxn()49    dumpfile = 'Folding_Output_S1412P_bind_unbind.pdb'50    bind_score=float(scorefxn(pose))51    setup_foldtree(pose, 'ABCDEF_OPMTUV', Vector1([1]))52    trans_mover = RigidBodyTransMover(pose, 1)53    trans_mover.step_size(100)54    trans_mover.apply(pose)55    unbind_score=float(scorefxn(pose))56    ddg_bind = bind_score-unbind_score57    newfile.write(str(ddg_bind))58    newfile.write('\n')59    pose.dump_pdb(dumpfile)60    #####################################################61    pose=pose_from_pdb("Folding_Output_G1413W.pdb")62    scorefxn = get_fa_scorefxn()63    dumpfile = 'Folding_Output_G1413W_bind_unbind.pdb'64    bind_score=float(scorefxn(pose))65    setup_foldtree(pose, 'ABCDEF_OPMTUV', Vector1([1]))66    trans_mover = RigidBodyTransMover(pose, 1)67    trans_mover.step_size(100)68    trans_mover.apply(pose)69    unbind_score=float(scorefxn(pose))70    ddg_bind = bind_score-unbind_score71    newfile.write(str(ddg_bind))72    newfile.write('\n')73    pose.dump_pdb(dumpfile)74    #####################################################75    pose=pose_from_pdb("Folding_Output_V1414W.pdb")76    scorefxn = get_fa_scorefxn()77    dumpfile = 'Folding_Output_V1414W_bind_unbind.pdb'78    bind_score=float(scorefxn(pose))79    setup_foldtree(pose, 'ABCDEF_OPMTUV', Vector1([1]))80    trans_mover = RigidBodyTransMover(pose, 1)81    trans_mover.step_size(100)82    trans_mover.apply(pose)83    unbind_score=float(scorefxn(pose))84    ddg_bind = bind_score-unbind_score85    newfile.write(str(ddg_bind))86    newfile.write('\n')87    pose.dump_pdb(dumpfile)88    #####################################################89    pose=pose_from_pdb("Folding_Output_F1415G.pdb")90    scorefxn = get_fa_scorefxn()91    dumpfile = 'Folding_Output_F1415G_bind_unbind.pdb'92    bind_score=float(scorefxn(pose))93    setup_foldtree(pose, 'ABCDEF_OPMTUV', Vector1([1]))94    trans_mover = RigidBodyTransMover(pose, 1)95    trans_mover.step_size(100)96    trans_mover.apply(pose)97    unbind_score=float(scorefxn(pose))98    ddg_bind = bind_score-unbind_score99    newfile.write(str(ddg_bind))100    newfile.write('\n')101    pose.dump_pdb(dumpfile)102    #####################################################103    pose=pose_from_pdb("Folding_Output_T1416R.pdb")104    scorefxn = get_fa_scorefxn()105    dumpfile = 'Folding_Output_T1416R_bind_unbind.pdb'106    bind_score=float(scorefxn(pose))107    setup_foldtree(pose, 'ABCDEF_OPMTUV', Vector1([1]))108    trans_mover = RigidBodyTransMover(pose, 1)109    trans_mover.step_size(100)110    trans_mover.apply(pose)111    unbind_score=float(scorefxn(pose))112    ddg_bind = bind_score-unbind_score113    newfile.write(str(ddg_bind))114    newfile.write('\n')115    pose.dump_pdb(dumpfile)116    #####################################################117    pose=pose_from_pdb("Folding_Output_F1417G.pdb")118    scorefxn = get_fa_scorefxn()119    dumpfile = 'Folding_Output_F1417G_bind_unbind.pdb'120    bind_score=float(scorefxn(pose))121    setup_foldtree(pose, 'ABCDEF_OPMTUV', Vector1([1]))122    trans_mover = RigidBodyTransMover(pose, 1)123    trans_mover.step_size(100)124    trans_mover.apply(pose)125    unbind_score=float(scorefxn(pose))126    ddg_bind = bind_score-unbind_score127    newfile.write(str(ddg_bind))128    newfile.write('\n')129    pose.dump_pdb(dumpfile)130    #####################################################131    pose=pose_from_pdb("Folding_Output_G1418Y.pdb")132    scorefxn = get_fa_scorefxn()133    dumpfile = 'Folding_Output_G1418Y_bind_unbind.pdb'134    bind_score=float(scorefxn(pose))135    setup_foldtree(pose, 'ABCDEF_OPMTUV', Vector1([1]))136    trans_mover = RigidBodyTransMover(pose, 1)137    trans_mover.step_size(100)138    trans_mover.apply(pose)139    unbind_score=float(scorefxn(pose))140    ddg_bind = bind_score-unbind_score141    newfile.write(str(ddg_bind))142    newfile.write('\n')143    pose.dump_pdb(dumpfile)144    #####################################################145    pose=pose_from_pdb("Folding_Output_P1411M.pdb")146    scorefxn = get_fa_scorefxn()147    dumpfile = 'Folding_Output_P1411M_bind_unbind.pdb'148    bind_score=float(scorefxn(pose))149    setup_foldtree(pose, 'ABCDEF_OPMTUV', Vector1([1]))150    trans_mover = RigidBodyTransMover(pose, 1)151    trans_mover.step_size(100)152    trans_mover.apply(pose)153    unbind_score=float(scorefxn(pose))154    ddg_bind = bind_score-unbind_score155    newfile.write(str(ddg_bind))156    newfile.write('\n')157    pose.dump_pdb(dumpfile)158    #####################################################159    pose=pose_from_pdb("Folding_Output_S1412M.pdb")160    scorefxn = get_fa_scorefxn()161    dumpfile = 'Folding_Output_S1412M_bind_unbind.pdb'162    bind_score=float(scorefxn(pose))163    setup_foldtree(pose, 'ABCDEF_OPMTUV', Vector1([1]))164    trans_mover = RigidBodyTransMover(pose, 1)165    trans_mover.step_size(100)166    trans_mover.apply(pose)167    unbind_score=float(scorefxn(pose))168    ddg_bind = bind_score-unbind_score169    newfile.write(str(ddg_bind))170    newfile.write('\n')171    pose.dump_pdb(dumpfile)172    #####################################################173    pose=pose_from_pdb("Folding_Output_G1413M.pdb")174    scorefxn = get_fa_scorefxn()175    dumpfile = 'Folding_Output_G1413M_bind_unbind.pdb'176    bind_score=float(scorefxn(pose))177    setup_foldtree(pose, 'ABCDEF_OPMTUV', Vector1([1]))178    trans_mover = RigidBodyTransMover(pose, 1)179    trans_mover.step_size(100)180    trans_mover.apply(pose)181    unbind_score=float(scorefxn(pose))182    ddg_bind = bind_score-unbind_score183    newfile.write(str(ddg_bind))184    newfile.write('\n')185    pose.dump_pdb(dumpfile)186    #####################################################187    pose=pose_from_pdb("Folding_Output_V1414I.pdb")188    scorefxn = get_fa_scorefxn()189    dumpfile = 'Folding_Output_V1414I_bind_unbind.pdb'190    bind_score=float(scorefxn(pose))191    setup_foldtree(pose, 'ABCDEF_OPMTUV', Vector1([1]))192    trans_mover = RigidBodyTransMover(pose, 1)193    trans_mover.step_size(100)194    trans_mover.apply(pose)195    unbind_score=float(scorefxn(pose))196    ddg_bind = bind_score-unbind_score197    newfile.write(str(ddg_bind))198    newfile.write('\n')199    pose.dump_pdb(dumpfile)200    #####################################################201    pose=pose_from_pdb("Folding_Output_F1415M.pdb")202    scorefxn = get_fa_scorefxn()203    dumpfile = 'Folding_Output_F1415M_bind_unbind.pdb'204    bind_score=float(scorefxn(pose))205    setup_foldtree(pose, 'ABCDEF_OPMTUV', Vector1([1]))206    trans_mover = RigidBodyTransMover(pose, 1)207    trans_mover.step_size(100)208    trans_mover.apply(pose)209    unbind_score=float(scorefxn(pose))210    ddg_bind = bind_score-unbind_score211    newfile.write(str(ddg_bind))212    newfile.write('\n')213    pose.dump_pdb(dumpfile)214    #####################################################215    pose=pose_from_pdb("Folding_Output_T1416M.pdb")216    scorefxn = get_fa_scorefxn()217    dumpfile = 'Folding_Output_T1416M_bind_unbind.pdb'218    bind_score=float(scorefxn(pose))219    setup_foldtree(pose, 'ABCDEF_OPMTUV', Vector1([1]))220    trans_mover = RigidBodyTransMover(pose, 1)221    trans_mover.step_size(100)222    trans_mover.apply(pose)223    unbind_score=float(scorefxn(pose))224    ddg_bind = bind_score-unbind_score225    newfile.write(str(ddg_bind))226    newfile.write('\n')227    pose.dump_pdb(dumpfile)228    #####################################################229    pose=pose_from_pdb("Folding_Output_F1417Y.pdb")230    scorefxn = get_fa_scorefxn()231    dumpfile = 'Folding_Output_F1417Y_bind_unbind.pdb'232    bind_score=float(scorefxn(pose))233    setup_foldtree(pose, 'ABCDEF_OPMTUV', Vector1([1]))234    trans_mover = RigidBodyTransMover(pose, 1)235    trans_mover.step_size(100)236    trans_mover.apply(pose)237    unbind_score=float(scorefxn(pose))238    ddg_bind = bind_score-unbind_score239    newfile.write(str(ddg_bind))240    newfile.write('\n')241    pose.dump_pdb(dumpfile)242    #####################################################243    pose=pose_from_pdb("Folding_Output_G1418A.pdb")244    scorefxn = get_fa_scorefxn()245    dumpfile = 'Folding_Output_G1418A_bind_unbind.pdb'246    bind_score=float(scorefxn(pose))247    setup_foldtree(pose, 'ABCDEF_OPMTUV', Vector1([1]))248    trans_mover = RigidBodyTransMover(pose, 1)249    trans_mover.step_size(100)250    trans_mover.apply(pose)251    unbind_score=float(scorefxn(pose))252    ddg_bind = bind_score-unbind_score253    newfile.write(str(ddg_bind))254    newfile.write('\n')255    pose.dump_pdb(dumpfile)256    newfile.close()
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