def set_up_pack_mover(self, pose, scorefxn, res_list=None):
task_pack = pyrosetta.standard_packer_task(pose)
task_pack.restrict_to_repacking()
task_pack.temporarily_fix_everything()
if res_list is None:
for i in range(1, 1+len(pose.sequence())):
task_pack.temporarily_set_pack_residue(i, True)
else:
for i in res_list:
task_pack.temporarily_set_pack_residue(i, True)
self.packmover = pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover(scorefxn, task_pack)
return None
def mutate_residue(pack_or_pose,
mutant_position,
mutant_aa,
pack_radius=0.,
pack_scorefxn=None):
"""Replace the residue at a single position in a Pose with a new amino acid
and repack any residues within user-defined radius of selected residue's
center using.
Args:
pack_or_pose (pyrosetta.rosetta.core.pose.Pose OR pyrosetta.distributed.packed_pose.PackedPose):
the `Pose` instance to use.
mutant_position (int): Pose-numbered position of the residue to mutate.
mutant_aa (str): The single letter name for the desired amino acid.
pack_radius (float): Radius used to define neighboring residues.
pack_scorefxn (pyrosetta.ScoreFunction): `ScoreFunction` to use when repacking the `Pose`.
Defaults to the standard `ScoreFunction`.
"""
import pyrosetta
import pyrosetta.distributed.packed_pose as packed_pose
wpose = packed_pose.to_pose(pack_or_pose)
if not wpose.is_fullatom():
raise IOError("mutate_residue only works with fullatom poses")
# create a standard scorefxn by default
if not pack_scorefxn:
pack_scorefxn = pyrosetta.get_score_function()
# the numbers 1-20 correspond individually to the 20 proteogenic amino acids
from pyrosetta.rosetta.core.chemical import aa_from_oneletter_code
mutant_aa = int(aa_from_oneletter_code(mutant_aa))
aa_bool = pyrosetta.Vector1([aa == mutant_aa for aa in range(1, 21)])
# mutation is performed by using a PackerTask with only the mutant
# amino acid available during design
task = pyrosetta.standard_packer_task(wpose)
task.nonconst_residue_task(mutant_position).restrict_absent_canonical_aas(
aa_bool)
# prevent residues from packing by setting the per-residue "options" of the PackerTask
task = restrict_non_nbrs_from_repacking(wpose, mutant_position, task,
pack_radius)
# apply the mutation and pack nearby residues
from pyrosetta.rosetta.protocols.minimization_packing import PackRotamersMover
packer = PackRotamersMover(pack_scorefxn, task)
packer.apply(wpose)
def sample_refinement(pdb_filename,
kT=1.0,
smallmoves=3,
shearmoves=5,
backbone_angle_max=7,
cycles=9,
jobs=1,
job_output='refine_output'):
"""
Performs fullatom structural refinement on the input <pdb_filename> by
perturbing backbone torsion angles with a maximum perturbation of
<backbone_angle_max> for <cycles> trials of
<smallmoves> perturbations of a random residue's phi or psi and
<shearmoves> perturbations of a random residue's phi and the preceding
residue's psi followed by gradient based backbone torsion angle
minimization and sidechain packing with an acceptance criteria scaled
by <kT>. <jobs> trajectories are performed, continually exporting
structures to a PyMOL instance.
Output structures are named <job_output>_(job#).pdb.
"""
# 1. create a pose from the desired PDB file
pose = Pose()
pose_from_file(pose, pdb_filename)
# 2. create a reference copy of the pose in fullatom
starting_pose = Pose()
starting_pose.assign(pose)
# 3. create a standard ScoreFunction
#### implement the desired ScoreFunction here
scorefxn = get_fa_scorefxn() # create_score_function('standard')
#### If you wish to use the ClassRelax protocol, uncomment the following
#### line and comment-out the protocol setup below
#refinement = protocols.relax.ClassicRelax( scorefxn )
#### Setup custom high-resolution refinement protocol
#### backbone refinement protocol
# 4. create a MoveMap, all backbone torsions free
movemap = MoveMap()
movemap.set_bb(True)
# 5. create a SmallMover
# a SmallMover perturbs a random (free in the MoveMap) residue's phi or psi
# torsion angle for an input number of times and accepts of rejects this
# change based on the Metropolis Criteria using the "rama" ScoreType and
# the parameter kT
# set the maximum angle to backbone_angle_max, apply it smallmoves times
smallmover = protocols.simple_moves.SmallMover(movemap, kT, smallmoves)
# angle_max is secondary structure dependent, however secondary structure
# has not been evaulated in this protocol, thus they are all set
# to the same value0
smallmover.angle_max(backbone_angle_max) # sets all at once
#### use the overloaded version of the SmallMover.angle_max method if you
#### want to use secondary structure biased moves
#smallmover.angle_max('H', backbone_angle_max)
#smallmover.angle_max('E', backbone_angle_max)
#smallmover.angle_max('L', backbone_angle_max)
# 6. create a ShearMover
# a ShearMover is identical to a SmallMover except that the angles perturbed
# are instead a random (free in the MoveMap) residue's phi and the
# preceding residue's psi, this reduces the downstream structural change
# set the maximum angle to backbone_angle_max, apply it shearmoves times
shearmover = protocols.simple_moves.ShearMover(movemap, kT, shearmoves)
# same angle_max restictions as SmallMover
shearmover.angle_max(backbone_angle_max)
#### use the overloaded version of the SmallMover.angle_max method if you
#### want to use secondary structure biased moves
#shearmover.angle_max('H', backbone_angle_max)
#shearmover.angle_max('E', backbone_angle_max)
#shearmover.angle_max('L', backbone_angle_max)
# 7. create a MinMover, for backbone torsion minimization
minmover = protocols.minimization_packing.MinMover()
minmover.movemap(movemap)
minmover.score_function(scorefxn)
#### sidechain refinement protocol, simple packing
# 8. setup a PackRotamersMover
to_pack = standard_packer_task(starting_pose)
to_pack.restrict_to_repacking() # prevents design, packing only
to_pack.or_include_current(True) # considers the original sidechains
packmover = protocols.minimization_packing.PackRotamersMover(
scorefxn, to_pack)
#### assess the new structure
# 9. create a PyMOLMover
pymover = PyMOLMover()
# uncomment the line below to load structures into successive states
#pymover.keep_history(True)
#### the PyMOLMover slows down the protocol SIGNIFICANTLY but provides
#### very informative displays
#### the keep_history flag (when True) tells the PyMOLMover to store new
#### structures into successive states, for a single trajectory, this
#### allows you to see intermediate changes (depending on where the
#### PyMOLMover is applied), when using a JobDistributor or otherwise
#### displaying multiple trajectories with a single protocol, the output
#### can get confusing to interpret, by changing the pose's PDBInfo.name
#### the structure will load into a new PyMOL state
#### try uncommenting the lines below to see different output
#pymover.update_energy(True) # see the total score in color
# 10. export the original structure, and scores, to PyMOL
pymover.apply(pose)
scorefxn(pose)
pymover.send_energy(pose)
# 11. setup a RepeatMover on a TrialMover of a SequenceMover (wow!)
# -setup a TrialMover
# a. create a SequenceMover of the previous moves
#### add any other moves you desire
combined_mover = SequenceMover()
combined_mover.add_mover(smallmover)
combined_mover.add_mover(shearmover)
combined_mover.add_mover(minmover)
combined_mover.add_mover(packmover)
#### explore the protocol using the PyMOLMover, try viewing structures
#### before they are accepted or rejected
combined_mover.add_mover(pymover)
# b. create a MonteCarlo object to define success/failure
mc = MonteCarlo(pose, scorefxn, kT) # must reset for each trajectory!
# c. create the TrialMover
trial = TrialMover(combined_mover, mc)
#### explore the protocol using the PyMOLMover, try viewing structures
#### after acceptance/rejection, comment-out the lines below
#original_trial = TrialMover(combined_mover, mc)
#trial = SequenceMover()
#trial.add_mover(original_trial)
#trial.add_mover(pymover)
#### for each trajectory, try cycles number of applications
# -create the RepeatMover
refinement = RepeatMover(trial, cycles)
####
# 12. create a (Py)JobDistributor
jd = PyJobDistributor(job_output, jobs, scorefxn)
jd.native_pose = starting_pose
# 13. store the score evaluations for output
# printing the scores as they are produced would be difficult to read,
# Rosetta produces a lot of verbose output when running
scores = [0] * (jobs + 1)
scores[0] = scorefxn(starting_pose)
# 14. perform the refinement protocol
counter = 0 # for exporting to PyMOL
while not jd.job_complete:
# a. set necessary variables for the new trajectory
# -reload the starting pose
pose.assign(starting_pose)
# -change the pose's PDBInfo.name, for the PyMOLMover
counter += 1
pose.pdb_info().name(job_output + '_' + str(counter))
# -reset the MonteCarlo object (sets lowest_score to that of p)
mc.reset(pose)
#### if you create a custom protocol, you may have additional
#### variables to reset, such as kT
#### if you create a custom protocol, this section will most likely
#### change, many protocols exist as single Movers or can be
#### chained together in a sequence (see above) so you need
#### only apply the final Mover
# b. apply the refinement protocol
refinement.apply(pose)
####
# c. output the lowest scoring decoy structure for this trajectory
# -recover and output the decoy structure to a PDB file
mc.recover_low(pose)
jd.output_decoy(pose)
# -export the final structure to PyMOL for each trajectory
pose.pdb_info().name(job_output + '_' + str(counter) + '_final')
pymover.apply(pose)
pymover.send_energy(pose) # see the total score in color
# -store the final score for this trajectory
scores[counter] = scorefxn(pose)
# 15. output the score evaluations
print('Original Score\t:\t', scores[0])
for i in range(1, len(scores)): # print out the job scores
print(job_output + '_' + str(i) + '\t:\t', scores[i])
return scores # for other protocols
pr.init('-extra_res_fa inputs/AZC.params -ex1 -ex2')
pose = pr.pose_from_pdb('TEV_solo.pdb')
print("emd182::Building score function")
sf = pr.rosetta.core.scoring.ScoreFunction()
sf.add_weights_from_file('ref2015')
print("emd182::Setting up and making a mutation")
res_mut = 30
mutater = pr.rosetta.protocols.simple_moves.MutateResidue()
mutater.set_target(res_mut)
mutater.set_res_name('AZC')
mutater.apply(pose)
print("emd182::Making Packertask and restricting to repacking")
packer_task = pr.standard_packer_task(pose)
packer_task.restrict_to_repacking()
packer_task.set_bump_check(False)
pack_mover = PackRotamersMover(sf, packer_task)
rsf = RotamerSetFactory()
rs = rsf.create_rotamer_set(pose)
rs.set_resid(res_mut)
sf(pose)
packer_graph = pr.rosetta.core.pack.create_packer_graph(pose, sf, packer_task)
rs.build_rotamers(pose, sf, packer_task, packer_graph)
print(rs.rotamer(1).name(), rs.num_rotamers())
short_pose = pr.rosetta.core.pose.Pose()
short_pose.detached_copy(pose)
for i in range(1, rs.num_rotamers() + 1):
def mutate_residue(pose,
mutant_position,
mutant_aa,
pack_radius=0.0,
pack_scorefxn=''):
"""
Replaces the residue at <mutant_position> in <pose> with <mutant_aa>
and repack any residues within <pack_radius> Angstroms of the mutating
residue's center (nbr_atom) using <pack_scorefxn>
note: <mutant_aa> is the single letter name for the desired ResidueType
example:
mutate_residue(pose, 30, A)
See also:
Pose
PackRotamersMover
MutateResidue
pose_from_sequence
"""
#### a MutateResidue Mover exists similar to this except it does not pack
#### the area around the mutant residue (no pack_radius feature)
#mutator = MutateResidue(mutant_position, mutant_aa)
#mutator.apply(test_pose)
if pose.is_fullatom() == False:
IOError('mutate_residue only works with fullatom poses')
# create a standard scorefxn by default
if not pack_scorefxn:
pack_scorefxn = rosetta.core.scoring.get_score_function()
task = pyrosetta.standard_packer_task(pose)
# the Vector1 of booleans (a specific object) is needed for specifying the
# mutation, this demonstrates another more direct method of setting
# PackerTask options for design
aa_bool = rosetta.utility.vector1_bool()
# PyRosetta uses several ways of tracking amino acids (ResidueTypes)
# the numbers 1-20 correspond individually to the 20 proteogenic amino acids
# aa_from_oneletter returns the integer representation of an amino acid
# from its one letter code
# convert mutant_aa to its integer representation
mutant_aa = rosetta.core.chemical.aa_from_oneletter_code(mutant_aa)
# mutation is performed by using a PackerTask with only the mutant
# amino acid available during design
# to do this, construct a Vector1 of booleans indicating which amino acid
# (by its numerical designation, see above) to allow
for i in range(1, 21):
# in Python, logical expression are evaluated with priority, thus the
# line below appends to aa_bool the truth (True or False) of the
# statement i == mutant_aa
aa_bool.append(i == int(mutant_aa))
# modify the mutating residue's assignment in the PackerTask using the
# Vector1 of booleans across the proteogenic amino acids
task.nonconst_residue_task(mutant_position).restrict_absent_canonical_aas(
aa_bool)
# prevent residues from packing by setting the per-residue "options" of
# the PackerTask
restrict_non_nbrs_from_repacking(pose, mutant_position, task, pack_radius)
# apply the mutation and pack nearby residues
#print task
packer = rosetta.protocols.simple_moves.PackRotamersMover(
pack_scorefxn, task)
packer.apply(pose)
initial_pose = pose_from_pdb(clean_name)
print initial_pose
print toolbox.get_secstruct(initial_pose)
#Set up ScoreFunction
sf = get_fa_scorefxn()
#Set up MoveMap.
mm = MoveMap()
#change these for more or less flexability
mm.set_bb(True)
mm.set_chi(True)
#Pack and minimize initial pose to remove clashes.
pre_pre_packing_score = sf(initial_pose)
print "1"
task = standard_packer_task(initial_pose)
task.restrict_to_repacking()
task.or_include_current(True)
print "2"
pack_rotamers_mover = protocols.simple_moves.RotamerTrialsMover(sf, task)
pack_rotamers_mover.apply(initial_pose)
print "3"
min_mover = protocols.simple_moves.MinMover()
print "4"
min_mover.movemap(mm)
print "5"
min_mover.score_function(sf)
print "6"
min_mover.min_type('dfpmin_armijo_nonmonotone')
def packer_task(pose, PDB_out=False):
"""
Demonstrates the syntax necessary for basic usage of the PackerTask object
performs demonstrative sidechain packing and selected design
using <pose> and writes structures to PDB files if <PDB_out>
is True
"""
# create a copy of the pose
test_pose = Pose()
test_pose.assign(pose)
# this object is contained in PyRosetta v2.0 and above
pymover = PyMOLMover()
# create a standard ScoreFunction
scorefxn = get_fa_scorefxn(
) # create_score_function_ws_patch('standard', 'score12')
############
# PackerTask
# a PackerTask encodes preferences and options for sidechain packing, an
# effective Rosetta methodology for changing sidechain conformations, and
# design (mutation)
# a PackerTask stores information on a per-residue basis
# each residue may be packed or designed
# PackerTasks are handled slightly differently in PyRosetta
####pose_packer = PackerTask() # this line will not work properly
pose_packer = standard_packer_task(test_pose)
# the pose argument tells the PackerTask how large it should be
# sidechain packing "optimizes" a pose's sidechain conformations by cycling
# through (Dunbrack) rotamers (sets of chi angles) at a specific residue
# and selecting the rotamer which achieves the lowest score,
# enumerating all possibilities for all sidechains simultaneously is
# impractically expensive so the residues to be packed are individually
# optimized in a "random" order
# packing options include:
# -"freezing" the residue, preventing it from changing conformation
# -including the original sidechain conformation when determining the
# lowest scoring conformation
pose_packer.restrict_to_repacking() # turns off design
pose_packer.or_include_current(True) # considers original conformation
print(pose_packer)
# packing and design can be performed by a PackRotamersMover, it requires
# a ScoreFunction, for optimizing the sidechains and a PackerTask,
# setting the packing and design options
packmover = protocols.minimization_packing.PackRotamersMover(
scorefxn, pose_packer)
scorefxn(pose) # to prevent verbose output on the next line
print('\nPre packing score:', scorefxn(test_pose))
test_pose.pdb_info().name('original') # for PyMOLMover
pymover.apply(test_pose)
packmover.apply(test_pose)
print('Post packing score:', scorefxn(test_pose))
test_pose.pdb_info().name('packed') # for PyMOLMover
pymover.apply(test_pose)
if PDB_out:
test_pose.dump_pdb('packed.pdb')
# since the PackerTask specifies how the sidechains change, it has been
# extended to include sidechain constitutional changes allowing
# protein design, this method of design is very similar to sidechain
# packing; all rotamers of the possible mutants at a single residue
# are considered and the lowest scoring conformation is selected
# design options include:
# -allow all amino acids
# -allow all amino acids except cysteine
# -allow specific amino acids
# -prevent specific amino acids
# -allow polar amino acids only
# -prevent polar amino acids
# -allow only the native amino acid
# the myriad of packing and design options can be set manually or, more
# commonly, using a specific file format known as a resfile
# resfile syntax is explained at:
# http://www.rosettacommons.org/manuals/archive/rosetta3.1_user_guide/file_resfiles.html
# manually setting deign options is tedious, the methods below are handy
# for creating resfiles
# mutate the "middle" residues
center = test_pose.total_residue() // 2
specific_design = {}
for i in range(center - 2, center + 3):
specific_design[i] = 'ALLAA'
# write a resfile to perform these mutations
generate_resfile_from_pose(test_pose,
'sample_resfile',
False,
specific=specific_design)
# setup the design PackerTask, use the generated resfile
pose_design = standard_packer_task(test_pose)
rosetta.core.pack.task.parse_resfile(test_pose, pose_design,
'sample_resfile')
print(pose_design)
# prepare a new structure
test_pose.assign(pose)
# perform design
designmover = protocols.minimization_packing.PackRotamersMover(
scorefxn, pose_design)
print(
'\nDesign with all proteogenic amino acids at (pose numbered)\
residues', center - 2, 'to', center + 2)
print('Pre-design score:', scorefxn(test_pose))
print( 'Pre-design sequence: ...' + \
test_pose.sequence()[center - 5:center + 4] + '...' )
designmover.apply(test_pose) # perform design
print('\nPost-design score:', scorefxn(test_pose))
print( 'Post-design sequence: ...' + \
test_pose.sequence()[center - 5:center + 4] + '...' )
test_pose.pdb_info().name('designed') # for PyMOLMover
pymover.apply(test_pose)
if PDB_out:
test_pose.dump_pdb('designed.pdb')
def mutate(pdb_name, n_muts=100):
OUT = open(mydir + '/data/deltas.txt', 'w')
#takes name of pdb file without the extention
init(extra_options='-mute basic -mute core')
# Constants
PACK_RADIUS = 10.0
#Amino acids, notice there is no C
AAs = ("A", "D", "E", "F", "G", "H", "I", "K", "L", "M", "N", "P", "Q",
"R", "S", "T", "V", "W", "Y")
#Number of mutations to accept
max_accept_mut = 600
#Population size
N = 100
#Beta (temp term)
beta = 1
pdb = pdb_name + ".pdb"
cleanATOM(pdb)
pdb_clean_name = pdb_name + '.clean.pdb'
initial_pose = pose_from_pdb(pdb_clean_name)
#Set up ScoreFunction
sf = get_fa_scorefxn()
#Set up MoveMap.
mm = MoveMap()
#change these for more or less flexability
mm.set_bb(True)
mm.set_chi(True)
#Pack and minimize initial pose to remove clashes.
pre_pre_packing_score = sf(initial_pose)
task = standard_packer_task(initial_pose)
task.restrict_to_repacking()
task.or_include_current(True)
pack_rotamers_mover = RotamerTrialsMover(sf, task)
pack_rotamers_mover.apply(initial_pose)
min_mover = MinMover()
min_mover.movemap(mm)
min_mover.score_function(sf)
min_mover.min_type('dfpmin_armijo_nonmonotone')
min_mover.apply(initial_pose)
post_pre_packing_score = sf(initial_pose)
#Set threshold for selection
threshold = pre_pre_packing_score / 2
#number of residues to select from
n_res = initial_pose.total_residue()
max_accept_mut = 1500
#start sim
i = 0
gen = 0
columns = ['Number', 'Selection', 'P_fix', 'P_fix_MH']
print >> OUT, '\t'.join(columns)
while i < max_accept_mut:
#update the number of generations that have pased
gen += 1
#pick a place to mutate
mut_location = random.randint(1, n_res)
#get the amino acid at that position
res = initial_pose.residue(mut_location)
#don't mess with C, just choose again
if res.name1() == 'C':
mut_location = random.randint(1, n_res)
#get the amino acid at that position
res = initial_pose.residue(mut_location)
#choose the amino acid to mutate to
new_mut_key = random.randint(0, len(AAs) - 1)
proposed_res = AAs[new_mut_key]
#don't bother mutating to the same amino acid it just takes more time
if proposed_res == res.name1():
new_mut_key = random.randint(0, len(AAs) - 1)
proposed_res = AAs[new_mut_key]
#make the mutation
mutant_pose = mutate_residue(initial_pose, mut_location, proposed_res,
PACK_RADIUS, sf)
#score mutant
variant_score = sf(mutant_pose)
probability = calc_prob_fix(variant_score, post_pre_packing_score, N,
beta, threshold)
probability_mh = calc_prob_mh(variant_score, post_pre_packing_score, N,
beta, threshold)
f_i = calc_x_fix(post_pre_packing_score, beta, threshold)
f_j = calc_x_fix(variant_score, beta, threshold)
s = math.log(f_j) - math.log(f_i)
#test to see if mutation is accepted
if np.isnan(probability) == True:
continue
rndm = random.random()
if (i < 100):
if (rndm < probability):
initial_pose = mutant_pose
post_pre_packing_score = variant_score
else:
continue
# Assuming 100 burn in phase, take this if out if you want to store everything
else:
data = [str(i), str(s), str(probability), str(probability_mh)]
print >> OUT, '\t'.join(data)
#save name and energy change
#data.append(variant_name + "," + str(variant_score) + "," + str(variant_score - post_pre_packing_score) + "," + str(probability) + "," + str(gen) + "\n")
#pdb_name=str(i)+".pdb"
#mutant_pose.dump_pdb(pdb_name)
print i, s, probability, rndm
#update number of accepts
i += 1
OUT.close()
def apply( self, pose ):
'''
This is an adjustable 3ay4-glycan modeling protocol (as of my PyRosetta-3's most recent abilities 9/26/16). Use all the adjustable arguments to figure out what the best protocol actually is
:param pose: Pose
'''
#################
#### IMPORTS ####
#################
from os import popen
from random import choice
from rosetta.protocols.simple_moves import MinMover
from pyrosetta import MonteCarlo, standard_packer_task
from rosetta.protocols.simple_moves import RotamerTrialsMover
from rosetta.core.scoring import fa_atr, fa_rep
#from antibody_functions import native_Fc_glycan_nums_except_core_GlcNAc # shouldn't need this as a MoveMap is passed to create this class
from native_3ay4_glycan_modeling_protocol_functions import native_3ay4_Fc_glycan_LCM_reset, \
add_constraints_to_pose, get_ramp_score_weight, get_ramp_angle_max, \
native_3ay4_Fc_glycan_random_reset, get_res_nums_within_radius_of_residue_list, \
SugarSmallMover
########################################
#### COPY POSES AND MAKE VISUALIZER ####
########################################
# get the working and native pose (for this particular script, they are the same thing)
native_pose = pose.clone()
working_pose = pose.clone()
self.decoy_name = working_pose.pdb_info().name()
self.native_pose = native_pose.clone()
###############################
#### GET MOVEABLE RESIDUES ####
###############################
# get the moveable residues from passed MoveMap
# moveable means the BackBone in the MoveMap was set to True and it is a carbohydrate
moveable_residues = [ res_num for res_num in range( 1, working_pose.size() + 1 ) if self.mm.get_bb( res_num ) and working_pose.residue( res_num ).is_carbohydrate() ]
###################
#### LCM RESET ####
###################
# reset the glycan using the data from the default.table used for the LinkageConformerMover
if self.LCM_reset:
working_pose.assign( native_3ay4_Fc_glycan_LCM_reset( mm = self.mm,
input_pose = working_pose,
use_population_ideal_LCM_reset = self.use_population_ideal_LCM_reset ) )
if self.verbose:
print "score of LCM reset:", self.watch_sf( working_pose )
##########################
#### OR, RANDOM RESET ####
##########################
# reset the glycan to random values from -180 to 180
if self.random_reset:
working_pose.assign( native_3ay4_Fc_glycan_random_reset( mm = self.mm,
input_pose = working_pose ) )
if self.verbose:
print "score of random reset:", self.watch_sf( working_pose )
######################################################
#### SPIN CARB OF PROTEIN-CARBOHYDRATE CONNECTION ####
######################################################
# the intent of this spin is to set the carbohydrate involved in the protein-carbohydrate connection into
# a reasonable starting position after the reset. This is because current LCM data found in the default.table
# was collected for surface glycans. These data are not reflective of the glycans found in the Ig system
# use the MoveMap to see which residues have a parent connection to a protein
if self.spin_carb_connected_to_prot:
from native_3ay4_glycan_modeling_protocol_functions import spin_carbs_connected_to_prot
# the spin takes residue 216 and 440 of 3ay4 and assigns either 180, 60, or -60 to omega1 and omega2 individually
# can sample within +/- 15 of those three values as well, if specified
working_pose.assign( spin_carbs_connected_to_prot( self.mm,
input_pose = working_pose,
spin_using_ideal_omegas = self.spin_using_ideal_omegas) )
if self.verbose:
print "score of core GlcNAc spin:", self.watch_sf( working_pose )
#########################################
#### HARDCODED OMEGA RESET TO NATIVE ####
#########################################
# reset the native omega torsion, if desired
# hardcoded for now as this is not something that would be done in a real protocol
if self.set_native_omega:
working_pose.set_omega( 221, native_pose.omega( 221 ) )
working_pose.set_omega( 445, native_pose.omega( 445 ) )
if self.verbose:
print "score of omega branch reset:", self.watch_sf( working_pose )
########################################
#### HARDCODED CORE RESET TO NATIVE ####
########################################
# reset the native torsions for the core GlcNAcs, if desired
# hardcoded for now as this is not something that would be done in a real protocol
if self.set_native_core:
from rosetta.core.id import omega2_dihedral
from rosetta.core.pose.carbohydrates import get_glycosidic_torsion, set_glycosidic_torsion
# reset the phi, psi, omega, and omega2 torsions of residues 216 and 440 (core GlcNAc to ASN-69)
# 216
working_pose.set_phi( 216, native_pose.phi( 216 ) )
working_pose.set_psi( 216, native_pose.psi( 216 ) )
working_pose.set_omega( 216, native_pose.omega( 216 ) )
set_glycosidic_torsion( omega2_dihedral, working_pose, 216,
get_glycosidic_torsion( omega2_dihedral, native_pose, 216 ) )
# 440
working_pose.set_phi( 440, native_pose.phi( 440 ) )
working_pose.set_psi( 440, native_pose.psi( 440 ) )
working_pose.set_omega( 440, native_pose.omega( 440 ) )
set_glycosidic_torsion( omega2_dihedral, working_pose, 440,
get_glycosidic_torsion( omega2_dihedral, native_pose, 440 ) )
if self.verbose:
print "score of core GlcNAc reset:", self.watch_sf( working_pose )
###################################################
#### HARDCODED CORE RESET TO IgG FC STATISTICS ####
###################################################
# reset the torsions for the core GlcNAcs to values seen in IgG Fcs, if desired
# hardcoded for now as this is not something that would be done in a real protocol
if self.set_native_core_omegas_to_stats:
from rosetta.core.id import omega2_dihedral
from rosetta.core.pose.carbohydrates import set_glycosidic_torsion
from rosetta.numeric.random import gaussian
from native_3ay4_glycan_modeling_protocol_functions import calc_mean_degrees, calc_stddev_degrees
# compile the data I have found from native crystal structures
# subtracting 360 from positive numbers because...I think that's how I should do this
phi_data = []
psi_data = []
omega1_data = [ -154.566, -162.504, # 3ay4 - IgG1 Fc G2 to FcgRIIIa
-163.850, 176.923, # 3ave - IgG1 Fc no paper, but it comes out as G0F2
-164.387, -146.038, # 5d4q - IgG1 Fc G2F1 ( check )
-146.449, -146.340, # 5d6d - IgG1 Fc G2F2 to FcgRIIIa ( check )
-166.996, -171.113 # 1h3x - IgG1 Fc G0F2
]
omega1_data = [ deg - 360 if deg > 0 else deg for deg in omega1_data ]
omega2_data = [ 59.198, 59.055, # 3ay4
53.823, 47.082, # 3ave
48.590, 63.976, # 5d4q
64.005, 63.988, # 5d6d
45.997, 59.196 # 1h3x
]
omega2_data = [ deg - 360 if deg > 0 else deg for deg in omega2_data ]
# pick a number within a gaussian distribution (I think??) of the torsions
# mean + ( stddev * gaussian() )
# not doing it the SmallMover way because I would want to be able to sample out more than 1 standard deviation
# SmallMover way would be periodic_range( mean_torsion - torsion_stddev * rg().uniform(), 360.0 )
# mean
base_omega1 = calc_mean_degrees( omega1_data )
base_omega2 = calc_mean_degrees( omega2_data )
# standard deviation
omega1_stddev = calc_stddev_degrees( omega1_data )
omega2_stddev = calc_stddev_degrees( omega2_data )
# 216
new_omega1_216 = base_omega1 + ( omega1_stddev * gaussian() )
new_omega2_216 = base_omega2 + ( omega2_stddev * gaussian() )
# 440
new_omega1_440 = base_omega1 + ( omega1_stddev * gaussian() )
new_omega2_440 = base_omega2 + ( omega2_stddev * gaussian() )
# reset the omega1 and omega2 torsions of residues 216 and 440 (core GlcNAc to ASN-69)
# 216
working_pose.set_omega( 216, new_omega1_216 )
set_glycosidic_torsion( int( omega2_dihedral ), working_pose, 216, new_omega2_216 )
# 440
working_pose.set_omega( 440, new_omega1_440 )
set_glycosidic_torsion( int( omega2_dihedral ), working_pose, 440, new_omega2_440 )
if self.verbose:
print "score of core GlcNAc reset using IgG Fc statistics:", self.watch_sf( working_pose )
############################################
#### VISUALIZE AND STORE THE RESET POSE ####
############################################
# visualize the pose that has had all components of reset completed
try:
if self.pmm_name is not None:
working_pose.pdb_info().name( self.pmm_name )
self.pmm.apply( working_pose )
working_pose.pdb_info().name( self.decoy_name )
else:
self.pmm.apply( working_pose )
except:
pass
# store a copy of the reset pose object
# storing it here so that all types of resets could have been done, including the reset back to natives
self.reset_pose = working_pose.clone()
# dump the reset pose, if desired
if self.dump_reset_pose:
reset_name = self.reset_pose.pdb_info().name().split( ".pdb" )[0] + "_reset.pdb"
self.reset_pose.dump_file( reset_name )
# zip the dump file, if desired
if self.zip_dump_poses:
os.popen( "gzip %s" %reset_name )
#########################
#### ADD CONSTRAINTS ####
#########################
if self.constraint_file is not None:
from rosetta.core.scoring import atom_pair_constraint
try:
# set the constraints from the constraint_file
working_pose.assign( add_constraints_to_pose( self.constraint_file, working_pose ) )
# add atom_pair_constraint to the ScoreFunction, if needed
self.sf.set_weight_if_zero( atom_pair_constraint, 1.0 )
except:
print "\nThere was something wrong with your constraint file. Are you sure it exists? Are you sure you used the correct names for the constraints?\n"
sys.exit()
############################
#### MIN MOVER CREATION ####
############################
# make the MinMover from the passed MoveMap
# if desired
if self.minimize_each_round:
# if needed
if self.min_mover is None:
self.min_mover = MinMover()
self.min_mover.movemap( self.mm )
self.min_mover.score_function( self.sf )
self.min_mover.min_type( "dfpmin_strong_wolfe" )
self.min_mover.tolerance( 0.01 )
self.min_mover.nb_list( True )
######################################
#### PACK ROTAMERS MOVER CREATION ####
######################################
# make the PackerRotamersMover from the passed MoveMap
# if desired
if self.pack_after_x_rounds > 0:
# if needed
if self.pack_rotamers_mover is None:
# make the packer task
# default of standard_packer_task is to set packing for residues to True
task = standard_packer_task( working_pose )
task.or_include_current( True )
task.restrict_to_repacking()
# get all the protein residues within 8A of the moveable_residues
# this uses the nbr_atom to determine if a residue is nearby or not, hence why I'm using a big distance like 8A
# nbr_atom seems to be basically the same as C4 in sugars
# this should include the Tyr if core GlcNAc is moveable in 3ay4
nearby_protein_residues = get_res_nums_within_radius_of_residue_list( moveable_residues, working_pose,
radius = 8,
include_res_nums = False )
# create a list of residue numbers that can be packed
# meaning, the moveable carbohydrate residues and the residues around them
packable_residues = moveable_residues
packable_residues.extend( nearby_protein_residues )
packable_residues = set( packable_residues )
# turn off packing for all residues that are NOT_packable_residues
# this is a new set with elements in pose.size() but not in packable_residues ( disjoint, s - t )
# meaning, all residue numbers in pose.size() that are not packable need to be NOT packed
NOT_packable_residues = list( set( range( 1, working_pose.size() + 1 ) ) - packable_residues )
[ task.nonconst_residue_task( res_num ).prevent_repacking() for res_num in NOT_packable_residues ]
# make the pack_rotamers_mover
pack_rotamers_mover = RotamerTrialsMover( self.sf, task )
# attach the task and the mover to the protocol object
self.packer_task = task
self.pack_rotamers_mover = pack_rotamers_mover
####################################
#### MAKE THE MONTECARLO OBJECT ####
####################################
# create the MonteCarlo object, if needed
if self.mc is None:
self.mc = MonteCarlo( working_pose, self.sf, self.kT )
self.mc.reset_scorefxn( working_pose, self.sf )
########################################
#### MAKE AND APPLY THE SUGAR MOVER ####
########################################
# for as many trials as specified
num_mc_accepts = 0
num_mc_checks = 0
mc_acceptance = -1
for trial_num in range( 1, self.trials + 1 ):
# print current score
if self.verbose:
print "\nstarting score:", self.watch_sf( working_pose )
####################################
#### RAMP WITH ANGLE MAX UPDATE ####
####################################
if self.ramp_angle_max:
# skip ramping on the first trial because the passed angle_max should be the angle_max used
if trial_num !=1:
# by the end of the protocol our angle_max should be angle_min
# angle_min is 6.0 by default which is the angle_max for loop residues in the BackboneMover
self.angle_max = get_ramp_angle_max( current_angle_max = self.angle_max,
target_angle_max = self.angle_min,
current_step = trial_num,
total_steps = self.trials )
#########################################
#### RAMP WITH SCORE FUNCTION UPDATE ####
#########################################
if self.ramp_sf:
# if this is the first move, adjust the fa_atr and fa_rep terms by the corresponding factors
if trial_num == 1:
# store the original fa_atr and fa_rep
FA_ATR_ORIG = self.sf.get_weight( fa_atr )
FA_REP_ORIG = self.sf.get_weight( fa_rep )
# adjust the fa_atr weight by the passed fa_atr_ramp_factor
FA_ATR_NEW = FA_ATR_ORIG * self.fa_atr_ramp_factor
self.sf.set_weight( fa_atr, FA_ATR_NEW )
# adjust the fa_rep weight by the passed fa_rep_ramp_factor
FA_REP_NEW = FA_REP_ORIG * self.fa_rep_ramp_factor
self.sf.set_weight( fa_rep, FA_REP_NEW )
# else, adjust the score weight
else:
# ramp up or down the appropriate scoring terms
self.sf.set_weight( fa_atr, get_ramp_score_weight( current_weight = self.sf.get_weight( fa_atr ),
target_weight = FA_ATR_ORIG,
current_step = trial_num,
total_steps = self.trials ) )
self.sf.set_weight( fa_rep, get_ramp_score_weight( current_weight = self.sf.get_weight( fa_rep ),
target_weight = FA_REP_ORIG,
current_step = trial_num,
total_steps = self.trials ) )
# DEBUG
#print "\n".join( [ "%s %s" %( str( score_type ), str( self.sf.get_weight( score_type ) ) ) for score_type in self.sf.get_nonzero_weighted_scoretypes() ] )
# give ramped sf back to MC and MinMover
# this is because PyRosetta apparently doesn't do the whole pointer thing with the sf
self.mc.score_function( self.sf )
self.mc.reset_scorefxn( working_pose, self.sf )
self.min_mover.score_function( self.sf )
##########################
#### MAKE SUGAR MOVES ####
##########################
# make as many moves per trial as desired
# SugarSmallMover
if self.make_small_moves:
working_pose.assign( SugarSmallMover( self.mm, self.moves_per_trial, self.angle_max, working_pose,
move_all_torsions = self.move_all_torsions ) )
# SugarShearMover
elif self.make_shear_moves:
pass
# relay score information
if self.verbose:
print "score after sugar moves:", self.watch_sf( working_pose )
##############
#### PACK ####
##############
# pack the sugars and surrounding residues, if desired
if self.pack_after_x_rounds > 0:
if trial_num % self.pack_after_x_rounds == 0:
self.pack_rotamers_mover.apply( working_pose )
if self.verbose:
print "score after local pack:", self.watch_sf( working_pose )
###################
#### MINIMIZE #####
###################
# minimize the backbone of the sugars, if desired
if self.minimize_each_round:
self.min_mover.apply( working_pose )
if self.verbose:
print "score after min:", self.watch_sf( working_pose )
###############################
#### ACCEPT OR REJECT MOVE ####
###############################
# accept or reject the total move using the MonteCarlo object
if self.mc.boltzmann( working_pose ):
# up the counters and send to pymol
num_mc_accepts += 1
try:
# switching between a name for pymol and for the decoy
# just for clarity
if self.pmm_name is not None:
working_pose.pdb_info().name( self.pmm_name )
self.pmm.apply( working_pose )
working_pose.pdb_info().name( self.decoy_name )
else:
self.pmm.apply( working_pose )
# if pymol doesn't work for whatever reason, pass
except:
pass
num_mc_checks += 1
# print out the MC acceptance rate every 3 trials and on the last trial
mc_acceptance = round( ( float( num_mc_accepts ) / float( num_mc_checks ) * 100 ), 2 )
if self.verbose:
if trial_num % 3 == 0 or trial_num == self.trials:
print "Moves made so far:", num_mc_checks,
print " Moves accepted:", num_mc_accepts,
print " Acceptance rate:", mc_acceptance
# add any relevant data to the class object
self.mc_acceptance = mc_acceptance
return working_pose
from pyrosetta import init, get_fa_scorefxn, standard_packer_task, standard_task_factory
from pyrosetta.rosetta import core, protocols
init(
extra_options="-constant_seed"
) # WARNING: option '-constant_seed' is for testing only! MAKE SURE TO REMOVE IT IN PRODUCTION RUNS!!!!!
import os
os.chdir('.test.output')
print('Packing and Design ----------------------------------------------')
print('mover: PackRotamersMover')
pose = core.import_pose.pose_from_file("../test/data/test_in.pdb")
scorefxn = get_fa_scorefxn() # create_score_function('standard')
#task_pack = core.pack.task.TaskFactory.create_packer_task(pose)
task_pack = standard_packer_task(pose)
task_pack.restrict_to_repacking()
task_pack.nonconst_residue_task(5).prevent_repacking()
print(task_pack)
pack = protocols.minimization_packing.PackRotamersMover(scorefxn, task_pack)
pack.apply(pose)
rotamer_trials = protocols.minimization_packing.RotamerTrialsMover(
scorefxn, task_pack)
rotamer_trials.apply(pose)
#TODO add task interface commands like:
#prevent_repacking(1,total_residue) or (res) or (True [=all])
#allow_repacking() # same argument options/overload
# ... needs discussion with Mini community...task is 'commutative'