def filter_junction(self, pose, junction_res, src_pose_N_info,
src_pose_C_info, src_pose_N_jct_res,
src_pose_C_jct_res):
"""TODO: Summary
Args:
pose (TYPE): Description
junction_res (TYPE): Description
src_pose_N_info (TYPE): Description
src_pose_C_info (TYPE): Description
src_pose_N_jct_res (TYPE): Description
src_pose_C_jct_res (TYPE): Description
Returns:
TYPE: Description
"""
nc, nc_no_helix, n_helix_contacted, n_helix_contacted_before, n_helix_contacted_after, begin_res, end_res = count_contacts_accross_junction(
pose, junction_res)
jct_pose = Pose()
for res_id in range(begin_res, end_res):
jct_pose.append_residue_by_bond(pose.residue(res_id))
# mode=pyrosetta.rosetta.core.chemical.type_set_mode_from_string("centroid")
# centroid_jct_pose=jct_pose.clone()
# pyrosetta.rosetta.core.util.switch_to_residue_type_set(centroid_jct_pose,mode )
score0 = self.scorefxn(jct_pose)
# AV.test_pair_alignment(,resN,resC)
test, result = self.AV.test_pair_alignment(
src_pose_N_info, src_pose_C_info, src_pose_N_jct_res,
src_pose_C_jct_res)
# Assign grades
if test is None:
super_grade = 'F'
elif result < self.superimpose_rmsd:
super_grade = 'A'
else:
super_grade = 'B'
if nc < self.num_contact_threshold - 7:
nc_grade = 'F'
elif nc < self.num_contact_threshold:
nc_grade = 'B'
else:
nc_grade = 'A'
if nc_no_helix < self.num_contact_no_helix_threshold:
nc_no_helix_grade = 'B'
else:
nc_no_helix_grade = 'A'
if n_helix_contacted < self.n_helix_contacted_threshold:
helix_contact_grade = 'B'
else:
helix_contact_grade = 'A'
grade = super_grade + nc_grade + nc_no_helix_grade + helix_contact_grade
return grade
def generate_canonical_rotamer_residues_phipsi(residue_name3, target_phi_psi):
raise NotImlementedError
canonical_residue = generate_canonical_residue(residue_name3)
test_sequence = "AAX[%s]AA" % residue_name3
target_phi, target_psi = target_phi_psi
sf = get_score_function()
tryrot = TryRotamers(resnum=3,
scorefxn=sf,
explosion=0,
jump_num=0,
clash_check=True,
solo_res=False,
include_current=False)
test_pose = Pose()
make_pose_from_sequence(test_pose, test_sequence, "fa_standard")
for i in range(1, test_pose.size() + 1):
test_pose.set_psi(i, target_psi)
test_pose.set_phi(i, target_phi)
test_pose.set_omega(i, 180)
tryrot.setup_rotamer_set(test_pose)
rotamer_set = tryrot.rotamer_set()
# print('rotamer_set.num_rotamers()',
# residue_name3, target_phi_psi, rotamer_set.num_rotamers())
rotamers = [
rotamer_set.rotamer(i).clone()
for i in range(1,
rotamer_set.num_rotamers() + 1)
]
for r in rotamers:
r.orient_onto_residue(canonical_residue)
r.seqpos(1)
return rotamers
def mutate_residue(pose, mutant_position, mutant_aa, pack_radius,
pack_scorefxn):
if pose.is_fullatom() == False:
IOError('mutate_residue only works with fullatom poses')
test_pose = Pose()
test_pose.assign(pose)
# Create a packer task (standard)
task = TaskFactory.create_packer_task(test_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 = 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 = 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 == 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
center = pose.residue(mutant_position).nbr_atom_xyz()
for i in range(1, pose.total_residue() + 1):
dist = center.distance_squared(test_pose.residue(i).nbr_atom_xyz())
# only pack the mutating residue and any within the pack_radius
print(i, pack_radius, dist, pow(float(pack_radius), 2))
print('##################################################')
if i != mutant_position and dist > pow(float(pack_radius), 2):
task.nonconst_residue_task(i).prevent_repacking()
# apply the mutation and pack nearby residues
packer = PackRotamersMover(pack_scorefxn, task)
packer.apply(test_pose)
return test_pose
def generate_canonical_residue(residue_name3):
work_pose = Pose()
make_pose_from_sequence(work_pose,
"X[%s]" % residue_name3,
"fa_standard",
auto_termini=False)
work_residue = rosetta.core.conformation.Residue(work_pose.residue(1))
ca_loc = work_residue.xyz("CA")
for a in range(work_residue.natoms()):
work_residue.set_xyz(a + 1, work_residue.xyz(a + 1) - ca_loc)
return work_residue
def poses_from_silent(silent_filename):
"""Returns an Iterator object which is composed of Pose objects from a silent file.
@atom-moyer
"""
sfd = rosetta.core.io.silent.SilentFileData(
rosetta.core.io.silent.SilentFileOptions())
sfd.read_file(silent_filename)
for tag in sfd.tags():
ss = sfd.get_structure(tag)
pose = Pose()
ss.fill_pose(pose)
pose.pdb_info().name(tag)
yield pose
def run_mcmc(pose):
#
old_score = score(pose)
old_pose = Pose()
old_pose.assign(pose)
# sample;
sample(pose)
new_score = score(pose)
# accept?
P = math.exp(-1 * (new_score - old_score) / 1.5)
print(P)
if P > 1:
return pose
else:
p = random.uniform(0, 1.0)
if p < P:
return pose
else:
return old_pose
# 举例使用FastDesign快速设计一些序列和结构:
from pyrosetta import pose_from_pdb, init, create_score_function
from pyrosetta.rosetta.protocols.denovo_design.movers import FastDesign
from pyrosetta.rosetta.core.pack.task import TaskFactory
from pyrosetta.rosetta.core.pose import Pose
from pyrosetta.io import poses_to_silent
# init
init('')
# load pose
starting_pose = pose_from_pdb('./data/EHEE_rd4_0976.pdb')
ref2015 = create_score_function('ref2015')
design_tf = TaskFactory()
# setup FastDesign
fastdesign = FastDesign(ref2015, 1)
fastdesign.set_default_movemap() #使用默认的Movemap()
fastdesign.set_task_factory(design_tf)
# design for 10 times:
for i in range(10):
design_pose = Pose()
design_pose.assign(starting_pose) # assign pose
fastdesign.apply(design_pose) ## apply design
# output to silent file;
poses_to_silent(design_pose, './data/design_result.silent')
import pyrosetta
from pyrosetta.rosetta.core.pose import Pose
from pyrosetta.rosetta.core.conformation import Residue
from pyrosetta.rosetta.core.kinematics import FoldTree
from pyrosetta.rosetta.core.select.residue_selector import ResidueIndexSelector
pyrosetta.init(
extra_options="-constant_seed -out:mute all"
) # WARNING: option '-constant_seed' is for testing only! MAKE SURE TO REMOVE IT IN PRODUCTION RUNS!!!!!
import os
os.chdir('.test.output')
pose1 = pyrosetta.pose_from_sequence('ACDEFGHI')
# Test __len__
assert (len(Pose().residues) == 0)
assert (len(pose1.residues) == 8)
assert (len(pose1) == 8) # Deprecated
# Test __iter__
for residue in Pose().residues:
pass
for residue in pose1.residues:
pass
for residue in pose1: # Deprecated
pass
# Test __getitem__
# assert(pose1.residues[0] == ValueError)
def pose_from_sequence(seq, res_type="fa_standard", auto_termini=True):
"""
Returns a pose generated from a single-letter sequence of amino acid
residues in <seq> using the <res_type> ResidueType and creates N- and C-
termini if <auto_termini> is set to True.
Unlike make_pose_from_sequence(), this method generates a default PDBInfo
and sets all torsion angles to 180 degrees.
Example:
pose = pose_from_sequence("THANKSEVAN")
See also:
Pose
make_pose_from_sequence()
pose_from_file()
pose_from_rcsb()
"""
pose = Pose()
make_pose_from_sequence(pose, seq, res_type, auto_termini)
#print 'Setting phi, psi, omega...'
for i in range(0, pose.total_residue()):
res = pose.residue(i + 1)
if not res.is_protein() or res.is_peptoid() or res.is_carbohydrate():
continue
pose.set_phi(i + 1, 180)
pose.set_psi(i + 1, 180)
pose.set_omega(i + 1, 180)
#print 'Attaching PDBInfo...'
# Empty PDBInfo (rosetta.core.pose.PDBInfo()) is not correct here;
# we have to reserve space for atoms....
pose.pdb_info(rosetta.core.pose.PDBInfo(pose))
pose.pdb_info().name(seq[:8])
# print pose
return pose