Symmetrical Docking Example

Thank you very much for your answer.



I'm trying to do symmetry docking of two identical monomers, so  based on the article "Modeling Symmetric Macromolecular Structures in Rosetta3"  I created symmetry definition files using make_symmdef_file.pl.



I have also created a modified script based on D100_Docking.py, but

calling "protocols.docking.setup_foldtree(pose, '_', jmp_arr)" consumes 32 GB of ram quickly, while calling D100_Docking.py does not. Does symmetry docking consume more RAM?

@hlp.timeit

# Create a symmetric pose.

def symmetrize_pose(self, pose):

print('

n')

print('Pose is ', pose)

pose.dump_pdb('Pre_Symmetric_pose_test.pdb')

# pose_symm_data = core.conformation.symmetry.SymmData(pose.n_residue(),

#                                                      pose.num_jump())



pose_symm_data = core.conformation.symmetry.SymmData(pose.total_residue(),

pose.num_jump())

pose_symm_data.read_symmetry_data_from_file(self.symmetry_dat_file)

symmetric_pose = core.pose.symmetry.make_symmetric_pose(pose, pose_symm_data)



pose.dump_pdb('Symmetric_pose_test.pdb')



# Many other useful utility funtions are in core.pose.symmetry.

# init(extra_options="-mute all")

init("-symmetry:symmetry_definition {0}".format(symmetry_dat_file))





job_output = self.job_output + '_proc:1'



# 1. creates a pose from the desired PDB file

pose = Pose()

pose_from_file(pose, pdb_filename)





# TODO symmetrize pose

self.symmetrize_pose(pose)



print('Curr Pose ', pose)



# 2. setup the docking FoldTree

# using this method, the jump number 1 is automatically set to be the

#    inter-body jump

dock_jump = 1





# TODO This consumes a lot of ram

# protocols.docking.setup_foldtree(pose, partners, Vector1([dock_jump]))



# protocols.docking.setup_foldtree(pose, partners, Vector1([dock_jump]))



jmp_arr = utility.vector1_int()

# jmp_arr = utility.vector1_ulong()

jmp_arr.append(1)

protocols.docking.setup_foldtree(pose, '_', jmp_arr)



# # 3. create centroid <--> fullatom conversion Movers

to_centroid = SwitchResidueTypeSetMover('centroid')

to_fullatom = SwitchResidueTypeSetMover('fa_standard')

# recover_sidechains = protocols.simple_moves.ReturnSidechainMover(pose)

# 4. convert to centroid

to_centroid.apply(pose)



# 5. create a (centroid) test pose

test_pose = Pose()

test_pose.assign(pose)



# TODO 6. create ScoreFunctions for symmetrical docking

sym_sfxn = core.scoring.symmetry.SymmetricScoreFunction()



# # 6. create ScoreFunctions for centroid and fullatom docking

scorefxn_low = create_score_function('interchain_cen')

# scorefxn_high = create_score_function('docking')

#

# # PyRosetta3: scorefxn_high_min = create_score_function_ws_patch('docking', 'docking_min')

# scorefxn_high_min = create_score_function('docking', 'docking_min')

#

# # 7. create Movers for producing an initial perturbation of the structure

dock_pert = RigidBodyPerturbMover(dock_jump, translation, rotation)

# this Mover randomizes a pose's partners (rotation)

spin = RigidBodySpinMover(dock_jump)

# this Mover uses the axis defined by the inter-body jump (jump 1) to move

#    the docking partners close together

slide_into_contact = protocols.docking.DockingSlideIntoContact(dock_jump)



mytask = TaskFactory.create_packer_task(pose)

mytask.initialize_from_command_line()

# parse_resfile(pose, mytask, resfile)



# TODO sympack

# Create a symmetric pack rotamers mover.

# sym_packer = protocols.simple_moves.symmetry.SymPackRotamersMover(sym_sfxn,

#                                                                   task)

sym_packer = protocols.simple_moves.symmetry.SymPackRotamersMover(sym_sfxn,

mytask)





# 8. setup the MinMover

# the MoveMap can set jumps (by jump number) as degrees of freedom

movemap = MoveMap()

movemap.set_jump(dock_jump, True)



# the MinMover can minimize score based on a jump degree of freedom, this

#    will find the distance between the docking partners which minimizes

#    the score

# TODO

# minmover = protocols.simple_moves.MinMover()

# TODO symMover

# Create a symmetric min mover.

sym_min_mover = protocols.simple_moves.symmetry.SymMinMover()



move_map = MoveMap()

core.pose.symmetry.make_symmetric_movemap(pose, move_map)



sym_min_mover.movemap(movemap)

# minmover.score_function(scorefxn_high_min)

sym_min_mover.score_function(sym_sfxn)



# 9. create a SequenceMover for the perturbation step

perturb = protocols.moves.SequenceMover()

# perturb.add_mover(randomize_upstream)

# perturb.add_mover(randomize_downstream)



# TODO TESTING PHASE

perturb.add_mover(dock_pert)

# # perturb.add_mover(spin)

perturb.add_mover(slide_into_contact)

perturb.add_mover(to_fullatom)

# perturb.add_mover(recover_sidechains)

perturb.add_mover(sym_min_mover)





dock_prot = protocols.docking.DockingLowRes()  # contains many docking functions

dock_prot.set_movable_jumps(Vector1([1]))  # set the jump to jump 1

dock_prot.set_lowres_scorefxn(scorefxn_low)

# dock_prot.set_highres_scorefxn(scorefxn_high_min)

dock_prot.set_highres_scorefxn(sym_sfxn)



# 11. setup the PyJobDistributor

# jd = PyJobDistributor(job_output, jobs, scorefxn_high)

jd = PyJobDistributor(job_output, jobs, sym_sfxn)

temp_pose = Pose()  # a temporary pose to export to PyMOL

temp_pose.assign(pose)

# to_fullatom.apply(temp_pose)  # the original pose was fullatom

# recover_sidechains.apply(temp_pose)  # with these sidechains

jd.native_pose = temp_pose  # for RMSD comparison





# 13. perform protein-protein docking

counter = 0  # for pretty output to PyMOL

while not jd.job_complete:

# a. set necessary variables for this trajectory

# -reset the test pose to original (centroid) structure

try:

test_pose.assign(pose)

# -change the pose name, for pretty output to PyMOL

counter += 1

test_pose.pdb_info().name(job_output + '_' + str(counter))



# b. perturb the structure for this trajectory

perturb.apply(test_pose)



# c. perform docking



# THIS consumes too much ram

dock_prot.apply(test_pose)



to_fullatom.apply(test_pose)  # ensure the output is fullatom

test_pose.pdb_info().name(job_output + '_' + str(counter) + '_fa')

jd.output_decoy(test_pose)



print("DONE RUNNING")

except RuntimeError:

print('ERROR:NAN occurred in H-bonding calculations!')

Thank you very much for your answer.



I'm trying to do symmetry docking of two identical monomers, so  based on the article "Modeling Symmetric Macromolecular Structures in Rosetta3"  I created symmetry definition files using make_symmdef_file.pl.



I have also created a modified script based on D100_Docking.py, but

calling "protocols.docking.setup_foldtree(pose, '_', jmp_arr)" consumes 32 GB of ram quickly, while calling D100_Docking.py does not. Does symmetry docking consume more RAM?

@hlp.timeit

# Create a symmetric pose.

def symmetrize_pose(self, pose):

print('

n')

print('Pose is ', pose)

pose.dump_pdb('Pre_Symmetric_pose_test.pdb')

# pose_symm_data = core.conformation.symmetry.SymmData(pose.n_residue(),

#                                                      pose.num_jump())



pose_symm_data = core.conformation.symmetry.SymmData(pose.total_residue(),

pose.num_jump())

pose_symm_data.read_symmetry_data_from_file(self.symmetry_dat_file)

symmetric_pose = core.pose.symmetry.make_symmetric_pose(pose, pose_symm_data)



pose.dump_pdb('Symmetric_pose_test.pdb')



# Many other useful utility funtions are in core.pose.symmetry.

# init(extra_options="-mute all")

init("-symmetry:symmetry_definition {0}".format(symmetry_dat_file))





job_output = self.job_output + '_proc:1'



# 1. creates a pose from the desired PDB file

pose = Pose()

pose_from_file(pose, pdb_filename)





# TODO symmetrize pose

self.symmetrize_pose(pose)



print('Curr Pose ', pose)



# 2. setup the docking FoldTree

# using this method, the jump number 1 is automatically set to be the

#    inter-body jump

dock_jump = 1





# TODO This consumes a lot of ram

# protocols.docking.setup_foldtree(pose, partners, Vector1([dock_jump]))



# protocols.docking.setup_foldtree(pose, partners, Vector1([dock_jump]))



jmp_arr = utility.vector1_int()

# jmp_arr = utility.vector1_ulong()

jmp_arr.append(1)

protocols.docking.setup_foldtree(pose, '_', jmp_arr)



# # 3. create centroid <--> fullatom conversion Movers

to_centroid = SwitchResidueTypeSetMover('centroid')

to_fullatom = SwitchResidueTypeSetMover('fa_standard')

# recover_sidechains = protocols.simple_moves.ReturnSidechainMover(pose)

# 4. convert to centroid

to_centroid.apply(pose)



# 5. create a (centroid) test pose

test_pose = Pose()

test_pose.assign(pose)



# TODO 6. create ScoreFunctions for symmetrical docking

sym_sfxn = core.scoring.symmetry.SymmetricScoreFunction()



# # 6. create ScoreFunctions for centroid and fullatom docking

scorefxn_low = create_score_function('interchain_cen')

# scorefxn_high = create_score_function('docking')

#

# # PyRosetta3: scorefxn_high_min = create_score_function_ws_patch('docking', 'docking_min')

# scorefxn_high_min = create_score_function('docking', 'docking_min')

#

# # 7. create Movers for producing an initial perturbation of the structure

dock_pert = RigidBodyPerturbMover(dock_jump, translation, rotation)

# this Mover randomizes a pose's partners (rotation)

spin = RigidBodySpinMover(dock_jump)

# this Mover uses the axis defined by the inter-body jump (jump 1) to move

#    the docking partners close together

slide_into_contact = protocols.docking.DockingSlideIntoContact(dock_jump)



mytask = TaskFactory.create_packer_task(pose)

mytask.initialize_from_command_line()

# parse_resfile(pose, mytask, resfile)



# TODO sympack

# Create a symmetric pack rotamers mover.

# sym_packer = protocols.simple_moves.symmetry.SymPackRotamersMover(sym_sfxn,

#                                                                   task)

sym_packer = protocols.simple_moves.symmetry.SymPackRotamersMover(sym_sfxn,

mytask)





# 8. setup the MinMover

# the MoveMap can set jumps (by jump number) as degrees of freedom

movemap = MoveMap()

movemap.set_jump(dock_jump, True)



# the MinMover can minimize score based on a jump degree of freedom, this

#    will find the distance between the docking partners which minimizes

#    the score

# TODO

# minmover = protocols.simple_moves.MinMover()

# TODO symMover

# Create a symmetric min mover.

sym_min_mover = protocols.simple_moves.symmetry.SymMinMover()



move_map = MoveMap()

core.pose.symmetry.make_symmetric_movemap(pose, move_map)



sym_min_mover.movemap(movemap)

# minmover.score_function(scorefxn_high_min)

sym_min_mover.score_function(sym_sfxn)



# 9. create a SequenceMover for the perturbation step

perturb = protocols.moves.SequenceMover()

# perturb.add_mover(randomize_upstream)

# perturb.add_mover(randomize_downstream)



# TODO TESTING PHASE

perturb.add_mover(dock_pert)

# # perturb.add_mover(spin)

perturb.add_mover(slide_into_contact)

perturb.add_mover(to_fullatom)

# perturb.add_mover(recover_sidechains)

perturb.add_mover(sym_min_mover)





dock_prot = protocols.docking.DockingLowRes()  # contains many docking functions

dock_prot.set_movable_jumps(Vector1([1]))  # set the jump to jump 1

dock_prot.set_lowres_scorefxn(scorefxn_low)

# dock_prot.set_highres_scorefxn(scorefxn_high_min)

dock_prot.set_highres_scorefxn(sym_sfxn)



# 11. setup the PyJobDistributor

# jd = PyJobDistributor(job_output, jobs, scorefxn_high)

jd = PyJobDistributor(job_output, jobs, sym_sfxn)

temp_pose = Pose()  # a temporary pose to export to PyMOL

temp_pose.assign(pose)

# to_fullatom.apply(temp_pose)  # the original pose was fullatom

# recover_sidechains.apply(temp_pose)  # with these sidechains

jd.native_pose = temp_pose  # for RMSD comparison





# 13. perform protein-protein docking

counter = 0  # for pretty output to PyMOL

while not jd.job_complete:

# a. set necessary variables for this trajectory

# -reset the test pose to original (centroid) structure

try:

test_pose.assign(pose)

# -change the pose name, for pretty output to PyMOL

counter += 1

test_pose.pdb_info().name(job_output + '_' + str(counter))



# b. perturb the structure for this trajectory

perturb.apply(test_pose)



# c. perform docking



# THIS consumes too much ram

dock_prot.apply(test_pose)



to_fullatom.apply(test_pose)  # ensure the output is fullatom

test_pose.pdb_info().name(job_output + '_' + str(counter) + '_fa')

jd.output_decoy(test_pose)



print("DONE RUNNING")

except RuntimeError:

print('ERROR:NAN occurred in H-bonding calculations!')

Thank you very much for your answer.



I'm trying to do symmetry docking of two identical monomers, so  based on the article "Modeling Symmetric Macromolecular Structures in Rosetta3"  I created symmetry definition files using make_symmdef_file.pl.



I have also created a modified script based on D100_Docking.py, but

calling "protocols.docking.setup_foldtree(pose, '_', jmp_arr)" consumes 32 GB of ram quickly, while calling D100_Docking.py does not. Does symmetry docking consume more RAM?

@hlp.timeit

# Create a symmetric pose.

def symmetrize_pose(self, pose):

print('

n')

print('Pose is ', pose)

pose.dump_pdb('Pre_Symmetric_pose_test.pdb')

# pose_symm_data = core.conformation.symmetry.SymmData(pose.n_residue(),

#                                                      pose.num_jump())



pose_symm_data = core.conformation.symmetry.SymmData(pose.total_residue(),

pose.num_jump())

pose_symm_data.read_symmetry_data_from_file(self.symmetry_dat_file)

symmetric_pose = core.pose.symmetry.make_symmetric_pose(pose, pose_symm_data)



pose.dump_pdb('Symmetric_pose_test.pdb')



# Many other useful utility funtions are in core.pose.symmetry.

# init(extra_options="-mute all")

init("-symmetry:symmetry_definition {0}".format(symmetry_dat_file))





job_output = self.job_output + '_proc:1'



# 1. creates a pose from the desired PDB file

pose = Pose()

pose_from_file(pose, pdb_filename)





# TODO symmetrize pose

self.symmetrize_pose(pose)



print('Curr Pose ', pose)



# 2. setup the docking FoldTree

# using this method, the jump number 1 is automatically set to be the

#    inter-body jump

dock_jump = 1





# TODO This consumes a lot of ram

# protocols.docking.setup_foldtree(pose, partners, Vector1([dock_jump]))



# protocols.docking.setup_foldtree(pose, partners, Vector1([dock_jump]))



jmp_arr = utility.vector1_int()

# jmp_arr = utility.vector1_ulong()

jmp_arr.append(1)

protocols.docking.setup_foldtree(pose, '_', jmp_arr)



# # 3. create centroid <--> fullatom conversion Movers

to_centroid = SwitchResidueTypeSetMover('centroid')

to_fullatom = SwitchResidueTypeSetMover('fa_standard')

# recover_sidechains = protocols.simple_moves.ReturnSidechainMover(pose)

# 4. convert to centroid

to_centroid.apply(pose)



# 5. create a (centroid) test pose

test_pose = Pose()

test_pose.assign(pose)



# TODO 6. create ScoreFunctions for symmetrical docking

sym_sfxn = core.scoring.symmetry.SymmetricScoreFunction()



# # 6. create ScoreFunctions for centroid and fullatom docking

scorefxn_low = create_score_function('interchain_cen')

# scorefxn_high = create_score_function('docking')

#

# # PyRosetta3: scorefxn_high_min = create_score_function_ws_patch('docking', 'docking_min')

# scorefxn_high_min = create_score_function('docking', 'docking_min')

#

# # 7. create Movers for producing an initial perturbation of the structure

dock_pert = RigidBodyPerturbMover(dock_jump, translation, rotation)

# this Mover randomizes a pose's partners (rotation)

spin = RigidBodySpinMover(dock_jump)

# this Mover uses the axis defined by the inter-body jump (jump 1) to move

#    the docking partners close together

slide_into_contact = protocols.docking.DockingSlideIntoContact(dock_jump)



mytask = TaskFactory.create_packer_task(pose)

mytask.initialize_from_command_line()

# parse_resfile(pose, mytask, resfile)



# TODO sympack

# Create a symmetric pack rotamers mover.

# sym_packer = protocols.simple_moves.symmetry.SymPackRotamersMover(sym_sfxn,

#                                                                   task)

sym_packer = protocols.simple_moves.symmetry.SymPackRotamersMover(sym_sfxn,

mytask)





# 8. setup the MinMover

# the MoveMap can set jumps (by jump number) as degrees of freedom

movemap = MoveMap()

movemap.set_jump(dock_jump, True)



# the MinMover can minimize score based on a jump degree of freedom, this

#    will find the distance between the docking partners which minimizes

#    the score

# TODO

# minmover = protocols.simple_moves.MinMover()

# TODO symMover

# Create a symmetric min mover.

sym_min_mover = protocols.simple_moves.symmetry.SymMinMover()



move_map = MoveMap()

core.pose.symmetry.make_symmetric_movemap(pose, move_map)



sym_min_mover.movemap(movemap)

# minmover.score_function(scorefxn_high_min)

sym_min_mover.score_function(sym_sfxn)



# 9. create a SequenceMover for the perturbation step

perturb = protocols.moves.SequenceMover()

# perturb.add_mover(randomize_upstream)

# perturb.add_mover(randomize_downstream)



# TODO TESTING PHASE

perturb.add_mover(dock_pert)

# # perturb.add_mover(spin)

perturb.add_mover(slide_into_contact)

perturb.add_mover(to_fullatom)

# perturb.add_mover(recover_sidechains)

perturb.add_mover(sym_min_mover)





dock_prot = protocols.docking.DockingLowRes()  # contains many docking functions

dock_prot.set_movable_jumps(Vector1([1]))  # set the jump to jump 1

dock_prot.set_lowres_scorefxn(scorefxn_low)

# dock_prot.set_highres_scorefxn(scorefxn_high_min)

dock_prot.set_highres_scorefxn(sym_sfxn)



# 11. setup the PyJobDistributor

# jd = PyJobDistributor(job_output, jobs, scorefxn_high)

jd = PyJobDistributor(job_output, jobs, sym_sfxn)

temp_pose = Pose()  # a temporary pose to export to PyMOL

temp_pose.assign(pose)

# to_fullatom.apply(temp_pose)  # the original pose was fullatom

# recover_sidechains.apply(temp_pose)  # with these sidechains

jd.native_pose = temp_pose  # for RMSD comparison





# 13. perform protein-protein docking

counter = 0  # for pretty output to PyMOL

while not jd.job_complete:

# a. set necessary variables for this trajectory

# -reset the test pose to original (centroid) structure

try:

test_pose.assign(pose)

# -change the pose name, for pretty output to PyMOL

counter += 1

test_pose.pdb_info().name(job_output + '_' + str(counter))



# b. perturb the structure for this trajectory

perturb.apply(test_pose)



# c. perform docking



# THIS consumes too much ram

dock_prot.apply(test_pose)



to_fullatom.apply(test_pose)  # ensure the output is fullatom

test_pose.pdb_info().name(job_output + '_' + str(counter) + '_fa')

jd.output_decoy(test_pose)



print("DONE RUNNING")

except RuntimeError:

print('ERROR:NAN occurred in H-bonding calculations!')