def homologousonePointcrossover(eaObj, inParent):
similarpoints = [] # Creating a list to store points with similar angles found
randParent = Pose()
# Searching for similar angles
while (len(similarpoints) == 0):
randParent.assign(randomParent(eaObj, inParent))
for i in range(1, inParent.pose.size()):
if((inParent.pose.phi(i) == randParent.phi(i)) and
(inParent.pose.psi(i) == randParent.psi(i)) and
(inParent.pose.omega(i) == randParent.omega(i))):
similarpoints.append(i)
child = Pose()
child.assign(inParent.pose)
# Now we select a random point from the list of points that had similar angles as our crossOverPoint
crossOverPoint = random.choice(similarpoints)
# We should switch the values from the parents
for residue in range(1, crossOverPoint):
Pose.replace_residue(
child, residue, Pose.residue(randParent, residue), True)
inParent.pose.assign(child)
def get_NGL_selection_from_AtomID(pose: pyrosetta.Pose,
atom_id: pyrosetta.AtomID):
pose_resi = atom_id.rsd()
residue = pose.residue(pose_resi)
atom_name = residue.atom_name(atom_id.atomno()).strip()
pdb_resi, chain = pose.pdb_info().pose2pdb(pose_resi).strip().split()
return f'[{residue.name3().strip()}]{pdb_resi}:{chain}.{atom_name}'
def make_mutant(self,
pose: pyrosetta.Pose,
mutation: str,
chain='A') -> pyrosetta.Pose:
"""
Make a point mutant (``A23D``).
:param pose: pose
:param mutation:
:param chain:
:return:
"""
mutant = pose.clone()
pose2pdb = pose.pdb_info().pdb2pose
rex = re.match('(\w)(\d+)(\w)', mutation)
r = pose2pdb(res=int(rex.group(2)), chain=chain)
rn = pose.residue(r).name1()
assert rn == rex.group(
1
), f'residue {r}(pose)/{rex.group(2)}(pdb) is a {rn}, not a {rex.group()}'
MutateResidue = pyrosetta.rosetta.protocols.simple_moves.MutateResidue
MutateResidue(target=r,
new_res=self._name3[rex.group(3)]).apply(mutant)
self.relax_around_mover(mutant,
int(rex.group(2)),
chain,
distance=12,
cycles=15)
return mutant
def movement(self, original: pyrosetta.Pose, resi: int, chain: str, distance: int,
trials: int = 50, temperature: int = 1.0, replicate_number: int = 10):
"""
This method adapted from a notebook of mine, but not from an official source, is not well written.
It should be a filter and score combo.
It returns the largest bb_rmsd of the pdb residue resi following backrub.
"""
# this code is experimental
n = self.get_neighbour_vector(pose=original, resi=resi, chain=chain, distance=distance,
own_chain_only=False)
# resi
if chain is None: # pose numbering.
target_res = resi
else:
target_res = original.pdb_info().pdb2pose(chain=chain, res=resi)
# prep
rv = pyrosetta.rosetta.core.select.residue_selector.ResidueVector(n)
backrub = pyrosetta.rosetta.protocols.backrub.BackrubMover()
backrub.set_pivot_residues(rv)
# https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/GenericMonteCarloMover
monégasque = pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover(maxtrials=trials,
max_accepted_trials=trials,
# gen.max_accepted_trials() = 0
task_scaling=5,
# gen.task_scaling()
mover=backrub,
temperature=temperature,
sample_type='low',
drift=True)
monégasque.set_scorefxn(self.scorefxn)
# monégasque.add_filter(filters , False , 0.005 , 'low' , True )
# define the first 4 atoms (N C CA O)
am = pyrosetta.rosetta.utility.vector1_unsigned_long(4)
for i in range(1, 5):
am[i] = i
# find most deviant
best_r = 0
for i in range(replicate_number):
variant = original.clone()
monégasque.apply(variant)
if monégasque.accept_counter() > 0:
variant = monégasque.last_accepted_pose() # pretty sure redundant
# bb_rmsd is all residues: pyrosetta.rosetta.core.scoring.bb_rmsd(pose, ori)
r = pyrosetta.rosetta.core.scoring.residue_rmsd_nosuper(variant.residue(target_res),
original.residue(target_res), am)
if r > best_r:
best_r = r
return best_r
def add_cst(self, pose: pyrosetta.Pose,
res_i: int, atm_i: str, res_j: int, atm_j: str,
distance: float = 2.4,
sigma: float = 0.1) \
-> pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraint:
AtomID = pyrosetta.rosetta.core.id.AtomID
id_i = AtomID(pose.residue(res_i).atom_index(atm_i), res_i)
id_j = AtomID(pose.residue(res_j).atom_index(atm_j), res_j)
ijfunc = pyrosetta.rosetta.core.scoring.constraints.BoundFunc(
0.0, distance, sigma, 'cst1')
cst_ij = pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraint(
id_i, id_j, ijfunc)
pose.add_constraint(cst_ij)
return cst_ij
def add_bfactor_from_score(pose: pyrosetta.Pose):
"""
Adds the bfactors from total_score.
Snippet for testing in Jupyter
>>> import nglview as nv
>>> view = nv.show_rosetta(pose)
>>> # view = nv.show_file('test.cif')
>>> view.clear_representations()
>>> view.add_tube(radiusType="bfactor", color="bfactor", radiusScale=0.10, colorScale="RdYlBu")
>>> view
``replace_res_remap_bfactors`` may have been a cleaner strategy. This was quicker to write.
If this fails, it may be because the pose was not scored first.
"""
if pose.pdb_info().obsolete():
raise ValueError(
'Pose pdb_info is flagged as obsolete (change `pose.pdb_info().obsolete(False)`)'
)
# scores
energies = pose.energies()
def get_res_score(res):
total_score = pyrosetta.rosetta.core.scoring.ScoreType.total_score
# if pose.residue(res).is_polymer()
try:
return energies.residue_total_energies(res)[total_score]
except:
return float('nan')
# the array goes from zero (nan) to n_residues
total_scores = np.array(
[float('nan')] +
[get_res_score(res) for res in range(1,
pose.total_residue() + 1)])
mask = np.isnan(total_scores)
total_scores -= np.nanmin(total_scores)
total_scores *= 100 / np.nanmax(total_scores)
total_scores = np.nan_to_num(total_scores, nan=100)
total_scores[mask] = 0.
# add to pose
pdb_info = pose.pdb_info()
for res in range(pose.total_residue()):
for i in range(pose.residue(res + 1).natoms()):
pdb_info.bfactor(res + 1, i + 1, total_scores[res + 1])
def pose2pandas(pose: pyrosetta.Pose,
scorefxn: pyrosetta.ScoreFunction) -> pd.DataFrame:
"""
Return a pandas dataframe from the scores of the pose
:param pose:
:return:
"""
pose.energies().clear_energies()
scorefxn(pose)
scores = pd.DataFrame(pose.energies().residue_total_energies_array())
pi = pose.pdb_info()
scores['residue'] = scores.index.to_series() \
.apply(lambda r: pose.residue( r +1) \
.name1() + pi.pose2pdb( r +1)
)
return scores
def __init__(self, mutation_name: str, chain: str, pose: pyrosetta.Pose):
self.mutation = self.parse_mutation(mutation_name)
rex = re.match('(\w)(\d+)(\w)', self.mutation)
self.pdb_resi = int(rex.group(2))
self.chain = chain
self.from_resn1 = rex.group(1)
self.from_resn3 = self._name3[rex.group(1)]
self.to_resn1 = rex.group(3)
self.to_resn3 = self._name3[rex.group(3)]
pose2pdb = pose.pdb_info().pdb2pose
self.pose_resi = pose2pdb(res=self.pdb_resi, chain=self.chain)
if self.pose_resi != 0:
self.pose_residue = pose.residue(self.pose_resi)
self.pose_resn1 = self.pose_residue.name1()
self.pose_resn3 = self.pose_residue.name3()
else:
self.pose_residue = None
self.pose_resn1 = None
self.pose_resn3 = None
def input_silent_score_seq(filename):
hbond_list = {}
torsion_list = {}
score_list = {}
seq_list = {}
# sfd=SilentFileData()
sfd = SilentFileData(SilentFileOptions())
sfd.read_file(filename)
p = Pose()
sf_tags = sfd.tags()
for tag in sf_tags:
silent_struct = sfd.get_structure(tag)
silent_struct.fill_pose(p)
en = silent_struct.energies()[1]
score_list[tag] = en.value()
seq_list[tag] = [p.residue(i).name() for i in range(1, p.size() + 1)]
torsion_list[tag] = get_torsions(p)
hbond_list[tag] = find_hbonds(p)
return torsion_list, hbond_list, score_list, seq_list
def twoPointcrossover(eaObj, inParent):
randParent = Pose()
randParent.assign(randomParent(eaObj, inParent))
crossOverPoint1 = randint(1, inParent.pose.size())
crossOverPoint2 = randint(1, inParent.pose.size())
# the first crossover point should be smaller than the second one.
while(crossOverPoint1 >= crossOverPoint2):
crossOverPoint1 = randint(1, inParent.pose.size())
crossOverPoint2 = randint(1, inParent.pose.size())
# The crossover'd child
child = Pose()
child.assign(inParent.pose)
# We switch the values between the two crossover points with values from the random parent
for residue in range(crossOverPoint1, crossOverPoint2):
Pose.replace_residue(
child, residue, Pose.residue(randParent, residue), True)
inParent.pose.assign(child)
def onePointcrossover(eaObj, inParent):
# Get random parent from population, ensure that we didn't get the same one.
randParent = Pose()
randParent.assign(randomParent(eaObj, inParent))
# Pick a random point in the sequence of the strand of amino acids to crossover
crossOverPoint = randint(1, inParent.pose.size())
# Create a new pose to be crossover'd by the two parents
child = Pose()
child.assign(inParent.pose)
"""
We iterate through the size of the crossover point (since we already have one of the parents copied)
one by one until the offspring has reached it's crossoverpoint and we should have a fully newborn
offspring by the end of the loop.
"""
for residue in range(1, crossOverPoint):
Pose.replace_residue(
child, residue, Pose.residue(randParent, residue), True)
inParent.pose.assign(child)
def pose_from_sequence( seq , res_type = 'fa_standard' , name = '' , chain_id = 'A' ):
"""
Returns a pose generated from amino acid single letters in <seq> using
the <res_type> ResidueType, the new pose's PDBInfo is named <name>
and all residues have chain ID <chain_id>
example:
pose=pose_from_sequence('LIGAND')
See also:
Pose
make_pose_from_sequence
pose_from_file
pose_from_rcsb
"""
pose=Pose()
make_pose_from_sequence(pose,seq,res_type)
#pdb_info = rosetta.core.pose.PDBInfo(pose.total_residue()) # actual, for other code
pdb_info = PDBInfo(pose.total_residue()) # create a PDBInfo object
for i in range(0,pose.total_residue()):
if pose.residue(i+1).is_protein():
# set to a more reasonable default
pose.set_phi(i+1,-150)
pose.set_psi(i+1,150)
pose.set_omega(i+1,180)
# set PDBInfo info for chain and number
#pdb_info.chain(i+1,chain_id)
#pdb_info.number(i+1,i+1)
#### you can alternatively use the deprecated method set_extended_torsions
#### which requires a Pose and a Loop object...so make a large loop
#set_extended_torsions( pose , Loop ( 1 , pose.total_residue() ) )
# set the PDBInfo
pose.pdb_info(pdb_info)
# default name to first 3 letters
if not name:
name = seq[:4]
pose.pdb_info().name(name)
# print pose
return pose
ATOM 8 HA SER A 1 4.525 0.411 -1.793 1.00 0.00 H
ATOM 9 1HB SER A 1 4.783 1.209 -4.524 1.00 0.00 H
ATOM 10 2HB SER A 1 5.814 1.615 -3.161 1.00 0.00 H
ATOM 11 HG SER A 1 6.258 -0.895 -3.881 1.00 0.00 H
HETATM 12 CV A__ A 2 3.512 -1.512 -7.034 1.00 0.00 X
HETATM 13 NZ A__ A 2 4.049 -1.531 -5.683 1.00 0.00 N
HETATM 14 1HZ A__ A 2 4.411 -0.616 -5.451 1.00 0.00 H
HETATM 15 2HZ A__ A 2 3.316 -1.777 -5.031 1.00 0.00 H
HETATM 16 3HZ A__ A 2 4.794 -2.211 -5.622 1.00 0.00 H
TER
CONECT 12 13
CONECT 13 12 14 15 16
CONECT 14 13
CONECT 15 13
CONECT 16 13
"""
pose = Pose()
pose_from_pdbstring(pose, contents)
sc_donor = {
1: [pick_ray(pose.residue(1), "HG", "OG")],
2: [
pick_ray(pose.residue(2), "1HZ", "NZ"),
pick_ray(pose.residue(2), "2HZ", "NZ"),
pick_ray(pose.residue(2), "3HZ", "NZ")
]
}
sc_acceptor = {1: [pick_ray(pose.residue(1), "OG", "CB")]}
TER
CONECT 1 2
CONECT 2 1 3 4
CONECT 3 2
CONECT 4 2
CONECT 5 6
CONECT 6 5 7 8
CONECT 7 6
CONECT 8 6 9 10
CONECT 9 8
CONECT 10 8
"""
pose = Pose()
pose_from_pdbstring(pose, contents)
sc_donor = {
2: [
pick_ray(pose.residue(2), "1HD2", "ND2"),
pick_ray(pose.residue(2), "2HD2", "ND2")
]
}
sc_acceptor = {
1: [
pick_ray(pose.residue(1), "OE1", "CD"),
pick_ray(pose.residue(1), "OE2", "CD")
],
2: [pick_ray(pose.residue(2), "OD1", "CG")]
}
def calc_binding_energy(pose, scorefxn, center, cutoff=8.0):
# create a copy of the pose for manipulation
test_pose = Pose()
test_pose.assign(pose)
# setup packer options
# the sidechain conformations of residues "near the interface", defined as
# within <cutoff> Angstroms of an interface residue, may change and
# must be repacked, if all residues are repacked, aberrant sidechain
# conformations near the interface, but independent of complex
# interactions, will be repacked for the mutant and wild-type structures
# preventing them from adding noise to the score difference
# this method of setting up a PackerTask is different from packer_task.py
tf = standard_task_factory() # create a TaskFactory
tf.push_back(core.pack.task.operation.RestrictToRepacking()
) # restrict it to repacking
# this object contains repacking options, instead of turning the residues
# "On" or "Off" directly, this will create an object for these options
# and assign it to the TaskFactory
prevent_repacking = core.pack.task.operation.PreventRepacking()
# the "center" (nbr_atom) of the mutant residue, for distance calculation
center = test_pose.residue(center).nbr_atom_xyz()
for i in range(1, test_pose.total_residue() + 1):
# the .distance_squared method is (a little) lighter than .norm
# if the residue is further than <cutoff> Angstroms away, do not repack
if center.distance_squared(
test_pose.residue(i).nbr_atom_xyz()) > cutoff**2:
prevent_repacking.include_residue(i)
# apply these settings to the TaskFactory
tf.push_back(prevent_repacking)
# setup a PackRotamersMover
packer = protocols.minimization_packing.PackRotamersMover(scorefxn)
packer.task_factory(tf)
#### create a Mover for performing translation
#### RigidBodyTransMover is SUPPOSED to translate docking partners of a
#### pose based on an axis and magnitude
#### test it using the PyMOLMover, it does not perform a simple translation
#### I also observed a "Hbond Tripped" error when packing after applying
#### the Mover, it appears to store inf and NaN values into hbonds
#transmover = RigidBodyTransMover()
# calc_interaction_energy separates the chains by 500.0 Angstroms,
# so does this Mover
# if using this Mover, the step_size MUST be a float
# if this setting is left to default, it will move the proteins
# VERY far apart
#transmover.step_size( 5.0 )
# repack the test_pose
packer.apply(test_pose)
# score this structure
before = scorefxn(test_pose)
# separate the docking partners
#### since RigidBodyTransMover DOES NOT WORK, it is not used
#transmover.apply(test_pose)
# here are two methods for applying a translation onto a pose structure
# both require an xyzVector
xyz = rosetta.numeric.xyzVector_double_t() # a Vector for coordinates
xyz.x = 500.0 # arbitrary separation magnitude, in the x direction
xyz.y = 0.0 #...I didn't have this and it defaulted to 1e251...?
xyz.z = 0.0 #...btw thats like 1e225 light years,
# over 5e245 yrs at Warp Factor 9.999 (thanks M. Pacella)
#### here is a hacky method for translating the downstream partner of a
# pose protein-protein complex (must by two-body!)
chain2starts = len(pose.chain_sequence(1)) + 1
for r in range(chain2starts, test_pose.total_residue() + 1):
for a in range(1, test_pose.residue(r).natoms() + 1):
test_pose.residue(r).set_xyz(a, test_pose.residue(r).xyz(a) + xyz)
# here is an elegant way to do it, it assumes that jump number 1
# defines the docking partners "connectivity"
# the pose.jump method returns a jump object CREATED from the pose jump
# data, the pose itself does not own a Jump object, thus you can use
# Jump methods, such as pose.jump(1).set_translation, however the object
# has not been properly constructed for manipulation, thus performing
# a change does not cause any problems, but is not permanently applied
#translate = test_pose.jump( 1 ) # copy this information explicitly
# adjust its translation via vector addition
#translate.set_translation( translate.get_translation() + xyz )
#test_pose.set_jump( 1 , translate )
# as explained above, this call will NOT work
#test_pose.jump(1).set_translation( test_pose.get_translation() + xyz )
# repack the test_pose after separation
packer.apply(test_pose)
# return the change in score
return before - scorefxn(test_pose)
ATOM 30 O ALA A 3 8.260 5.868 1.023 1.00 0.00 O
ATOM 31 OXT ALA A 3 8.596 5.737 -1.023 1.00 0.00 O
ATOM 32 CB ALA A 3 8.190 3.050 -1.199 1.00 0.00 C
ATOM 33 H ALA A 3 5.710 4.705 -0.000 1.00 0.00 H
ATOM 34 HA ALA A 3 7.999 3.333 0.913 1.00 0.00 H
ATOM 35 1HB ALA A 3 9.280 3.059 -1.185 1.00 0.00 H
ATOM 36 2HB ALA A 3 7.835 2.021 -1.154 1.00 0.00 H
ATOM 37 3HB ALA A 3 7.835 3.516 -2.117 1.00 0.00 H
TER
"""
pose = Pose()
pose_from_pdbstring(pose, contents)
n_rays = {
1: pick_ray(pose.residue(1), "1H", "N"),
3: pick_ray(pose.residue(3), "H", "N")
}
c_rays = {
1: pick_ray(pose.residue(1), "O", "C"),
2: pick_ray(pose.residue(2), "O", "C"),
3: pick_ray(pose.residue(3), "O", "C")
}
sc_donor = {}
sc_acceptor = {}
cat_pi = []
CONECT 1 2
CONECT 2 1 3 4 5
CONECT 3 2
CONECT 4 2
CONECT 5 2
CONECT 6 7
CONECT 7 6 8 9
CONECT 8 7
CONECT 9 7 10 11
CONECT 10 9
CONECT 11 9
"""
pose = Pose()
pose_from_pdbstring(pose, contents)
sc_donor = {
1: [
pick_ray(pose.residue(1), "1HZ", "NZ"),
pick_ray(pose.residue(1), "2HZ", "NZ"),
pick_ray(pose.residue(1), "3HZ", "NZ")
],
2: [
pick_ray(pose.residue(2), "1HD2", "ND2"),
pick_ray(pose.residue(2), "2HD2", "ND2")
]
}
sc_acceptor = {2: [pick_ray(pose.residue(2), "OD1", "CG")]}
HETATM 9 3HZ A__ A 2 5.292 -0.607 -4.650 1.00 0.00 H
TER
CONECT 1 2
CONECT 2 1 3 4
CONECT 3 2
CONECT 4 2
CONECT 5 6
CONECT 6 5 7 8 9
CONECT 7 6
CONECT 8 6
CONECT 9 6
"""
pose = Pose()
pose_from_pdbstring(pose, contents)
sc_donor = {
2: [
pick_ray(pose.residue(2), "1HZ", "NZ"),
pick_ray(pose.residue(2), "2HZ", "NZ"),
pick_ray(pose.residue(2), "3HZ", "NZ")
]
}
sc_acceptor = {
1: [
pick_ray(pose.residue(1), "OE1", "CD"),
pick_ray(pose.residue(1), "OE2", "CD")
]
}
CONECT 9 8 10 11
CONECT 10 9 13 14
CONECT 11 9 15 16
CONECT 12 8
CONECT 13 10
CONECT 14 10
CONECT 15 11
CONECT 16 11
"""
pose = Pose()
pose_from_pdbstring(pose, contents)
sc_donor = {
1: [
pick_ray(pose.residue(1), "1HD2", "ND2"),
pick_ray(pose.residue(1), "2HD2", "ND2")
],
2: [
pick_ray(pose.residue(2), "HE", "NE"),
pick_ray(pose.residue(2), "1HH1", "NH1"),
pick_ray(pose.residue(2), "2HH1", "NH1"),
pick_ray(pose.residue(2), "1HH2", "NH2"),
pick_ray(pose.residue(2), "2HH2", "NH2")
]
}
sc_acceptor = {
1: [
pick_ray(pose.residue(1), "OD1", "CG")
]
ATOM 5 N SER A 2 7.756 -0.439 -5.359 1.00 0.00 N
ATOM 6 CA SER A 2 7.794 -1.267 -4.159 1.00 0.00 C
ATOM 7 C SER A 2 7.667 -0.419 -2.900 1.00 0.00 C
ATOM 8 O SER A 2 8.086 0.738 -2.875 1.00 0.00 O
ATOM 9 CB SER A 2 9.083 -2.064 -4.116 1.00 0.00 C
ATOM 10 OG SER A 2 9.881 -1.788 -5.234 1.00 0.00 O
ATOM 11 H SER A 2 8.106 0.507 -5.315 1.00 0.00 H
ATOM 12 HA SER A 2 6.952 -1.961 -4.191 1.00 0.00 H
ATOM 13 1HB SER A 2 9.630 -1.821 -3.206 1.00 0.00 H
ATOM 14 2HB SER A 2 8.852 -3.128 -4.084 1.00 0.00 H
ATOM 15 HG SER A 2 9.394 -1.147 -5.756 1.00 0.00 H
TER
CONECT 1 2
CONECT 2 1 3 4
CONECT 3 2
CONECT 4 2
"""
pose = Pose()
pose_from_pdbstring(pose, contents)
sc_donor = {2: [pick_ray(pose.residue(2), "HG", "OG")]}
sc_acceptor = {
1: [
pick_ray(pose.residue(1), "OE1", "CD"),
pick_ray(pose.residue(1), "OE2", "CD")
],
2: [pick_ray(pose.residue(2), "OG", "CB")]
}
ATOM 33 O ALA A 3 8.260 5.868 1.023 1.00 0.00 O
ATOM 34 OXT ALA A 3 8.596 5.737 -1.023 1.00 0.00 O
ATOM 35 CB ALA A 3 8.190 3.050 -1.199 1.00 0.00 C
ATOM 36 H ALA A 3 5.710 4.705 -0.000 1.00 0.00 H
ATOM 37 HA ALA A 3 7.999 3.333 0.913 1.00 0.00 H
ATOM 38 1HB ALA A 3 9.280 3.059 -1.185 1.00 0.00 H
ATOM 39 2HB ALA A 3 7.835 2.021 -1.154 1.00 0.00 H
ATOM 40 3HB ALA A 3 7.835 3.516 -2.117 1.00 0.00 H
TER
"""
pose = Pose()
pose_from_pdbstring(pose, contents)
n_rays = {
1: pick_ray(pose.residue(1), "1H", "N"),
2: pick_ray(pose.residue(2), "H", "N"),
3: pick_ray(pose.residue(3), "H", "N")
}
c_rays = {
1: pick_ray(pose.residue(1), "O", "C"),
2: pick_ray(pose.residue(2), "O", "C"),
3: pick_ray(pose.residue(3), "O", "C")
}
sc_donor = {
2: [
pick_ray(pose.residue(2), "HE2", "NE2")
]
}
ATOM 28 O ALA A 3 8.260 5.868 1.023 1.00 0.00 O
ATOM 29 OXT ALA A 3 8.596 5.737 -1.023 1.00 0.00 O
ATOM 30 CB ALA A 3 8.190 3.050 -1.199 1.00 0.00 C
ATOM 31 H ALA A 3 5.710 4.705 -0.000 1.00 0.00 H
ATOM 32 HA ALA A 3 7.999 3.333 0.913 1.00 0.00 H
ATOM 33 1HB ALA A 3 9.280 3.059 -1.185 1.00 0.00 H
ATOM 34 2HB ALA A 3 7.835 2.021 -1.154 1.00 0.00 H
ATOM 35 3HB ALA A 3 7.835 3.516 -2.117 1.00 0.00 H
TER
"""
pose = Pose()
pose_from_pdbstring(pose, contents)
n_rays = {
1: pick_ray(pose.residue(1), "1H", "N"),
2: pick_ray(pose.residue(2), "H", "N"),
3: pick_ray(pose.residue(3), "H", "N")
}
c_rays = {
1: pick_ray(pose.residue(1), "O", "C"),
2: pick_ray(pose.residue(2), "O", "C"),
3: pick_ray(pose.residue(3), "O", "C")
}
sc_donor = { }
sc_acceptor = {
2: [
pick_ray(pose.residue(2), "OD1", "CG"),
ATOM 37 O ALA A 3 8.260 5.868 1.023 1.00 0.00 O
ATOM 38 OXT ALA A 3 8.596 5.737 -1.023 1.00 0.00 O
ATOM 39 CB ALA A 3 8.190 3.050 -1.199 1.00 0.00 C
ATOM 40 H ALA A 3 5.710 4.705 -0.000 1.00 0.00 H
ATOM 41 HA ALA A 3 7.999 3.333 0.913 1.00 0.00 H
ATOM 42 1HB ALA A 3 9.280 3.059 -1.185 1.00 0.00 H
ATOM 43 2HB ALA A 3 7.835 2.021 -1.154 1.00 0.00 H
ATOM 44 3HB ALA A 3 7.835 3.516 -2.117 1.00 0.00 H
TER
"""
pose = Pose()
pose_from_pdbstring(pose, contents)
n_rays = {
1: pick_ray(pose.residue(1), "1H", "N"),
2: pick_ray(pose.residue(2), "H", "N"),
3: pick_ray(pose.residue(3), "H", "N")
}
c_rays = {
1: pick_ray(pose.residue(1), "O", "C"),
2: pick_ray(pose.residue(2), "O", "C"),
3: pick_ray(pose.residue(3), "O", "C")
}
sc_donor = {2: [pick_ray(pose.residue(2), "HH", "OH")]}
sc_acceptor = {2: [pick_ray(pose.residue(2), "OH", "CZ")]}
cat_pi = [(pick_ray(pose.residue(2), "CE1",
dump_pdb(pose, "T110_Basic._.pdb")
print('accessing pose attributes')
print(pose)
# TODO: remove extra blank lines at end
print('there are ', pose.total_residue(), 'residues in this pose object')
print('phi of residue 5 is ', pose.phi(5))
print('psi of residue 5 is ', pose.psi(5))
print('set phi of residue 5 to -60')
pose.set_phi(1, -60)
print('set psi of residue 5 to -50')
pose.set_psi(1, -50)
print('accessing residue 5 from pose')
res5 = pose.residue(5)
print(res5)
print('accessing atoms from residue 5')
at5N = res5.atom('N')
at5CA = res5.atom("CA")
at5C = res5.atom("C")
print(at5N)
# TODO: above should print atom type key not magic number
# 2/23/9: hm, not sure this is possible b/c atom does not know which AtomTypeSet to use!
print('xyz of at5N:', at5N.xyz().x, at5N.xyz().y, at5N.xyz().z)
print('norm of xyz at5N:', at5N.xyz().norm)
print(res5.atoms()) # <-- Still missing
ATOM 20 2HB SER A 2 3.626 -3.951 -6.042 1.00 0.00 H
ATOM 21 HG SER A 2 3.450 -3.695 -3.412 1.00 0.00 H
TER
CONECT 1 2
CONECT 2 1 3 6
CONECT 3 2 4 5
CONECT 4 3 7 8
CONECT 5 3 9 10
CONECT 6 2
CONECT 7 4
CONECT 8 4
CONECT 9 5
CONECT 10 5
"""
pose = Pose()
pose_from_pdbstring(pose, contents)
sc_donor = {
1: [
pick_ray(pose.residue(1), "HE", "NE"),
pick_ray(pose.residue(1), "1HH1", "NH1"),
pick_ray(pose.residue(1), "2HH1", "NH1"),
pick_ray(pose.residue(1), "1HH2", "NH2"),
pick_ray(pose.residue(1), "2HH2", "NH2")
],
2: [pick_ray(pose.residue(2), "HG", "OG")]
}
sc_acceptor = {2: [pick_ray(pose.residue(2), "OG", "CB")]}
CONECT 7 4
CONECT 8 4
CONECT 9 5
CONECT 10 5
CONECT 11 12
CONECT 12 11 13 14
CONECT 13 12
CONECT 14 12 15 16
CONECT 15 14
CONECT 16 14
"""
pose = Pose()
pose_from_pdbstring(pose, contents)
sc_donor = {
1: [
pick_ray(pose.residue(1), "HE", "NE"),
pick_ray(pose.residue(1), "1HH1", "NH1"),
pick_ray(pose.residue(1), "2HH1", "NH1"),
pick_ray(pose.residue(1), "1HH2", "NH2"),
pick_ray(pose.residue(1), "2HH2", "NH2")
],
2: [
pick_ray(pose.residue(2), "1HD2", "ND2"),
pick_ray(pose.residue(2), "2HD2", "ND2")
]
}
sc_acceptor = {2: [pick_ray(pose.residue(2), "OD1", "CG")]}
ATOM 12 OG SER A 2 4.273 -0.309 -4.595 1.00 0.00 O
ATOM 13 H SER A 2 1.939 -0.680 -2.908 1.00 0.00 H
ATOM 14 HA SER A 2 3.320 1.908 -2.627 1.00 0.00 H
ATOM 15 1HB SER A 2 3.330 1.306 -5.420 1.00 0.00 H
ATOM 16 2HB SER A 2 4.691 1.679 -4.374 1.00 0.00 H
ATOM 17 HG SER A 2 3.848 -0.782 -3.875 1.00 0.00 H
TER
CONECT 1 2
CONECT 2 1 3 4
CONECT 3 2
CONECT 4 2 5 6
CONECT 5 4
CONECT 6 4
"""
pose = Pose()
pose_from_pdbstring(pose, contents)
sc_donor = {
1: [
pick_ray(pose.residue(1), "1HD2", "ND2"),
pick_ray(pose.residue(1), "2HD2", "ND2")
],
2: [pick_ray(pose.residue(2), "HG", "OG")]
}
sc_acceptor = {
1: [pick_ray(pose.residue(1), "OD1", "CG")],
2: [pick_ray(pose.residue(2), "OG", "CB")]
}
ATOM 40 O ALA A 3 8.260 5.868 1.023 1.00 0.00 O
ATOM 41 OXT ALA A 3 8.596 5.737 -1.023 1.00 0.00 O
ATOM 42 CB ALA A 3 8.190 3.050 -1.199 1.00 0.00 C
ATOM 43 H ALA A 3 5.710 4.705 -0.000 1.00 0.00 H
ATOM 44 HA ALA A 3 7.999 3.333 0.913 1.00 0.00 H
ATOM 45 1HB ALA A 3 9.280 3.059 -1.185 1.00 0.00 H
ATOM 46 2HB ALA A 3 7.835 2.021 -1.154 1.00 0.00 H
ATOM 47 3HB ALA A 3 7.835 3.516 -2.117 1.00 0.00 H
TER
"""
pose = Pose()
pose_from_pdbstring(pose, contents)
n_rays = {
1: pick_ray(pose.residue(1), "1H", "N"),
2: pick_ray(pose.residue(2), "H", "N"),
3: pick_ray(pose.residue(3), "H", "N")
}
c_rays = {
1: pick_ray(pose.residue(1), "O", "C"),
2: pick_ray(pose.residue(2), "O", "C"),
3: pick_ray(pose.residue(3), "O", "C")
}
sc_donor = {
2: [
pick_ray(pose.residue(2), "HE", "NE"),
pick_ray(pose.residue(2), "1HH1", "NH1"),
pick_ray(pose.residue(2), "2HH1", "NH1"),
def test_apply_pose(self):
new_pose = Pose()
new_pose.assign(self.pose)
self.small_mv(new_pose)
assert new_pose.residue(6).xyz(4) != self.pose.residue(6).xyz(4)
CONECT 6 5 7 10
CONECT 7 6 8 9
CONECT 8 7 11 12
CONECT 9 7 13 14
CONECT 10 6
CONECT 11 8
CONECT 12 8
CONECT 13 9
CONECT 14 9
"""
pose = Pose()
pose_from_pdbstring(pose, contents)
sc_donor = {
2: [
pick_ray(pose.residue(2), "HE", "NE"),
pick_ray(pose.residue(2), "1HH1", "NH1"),
pick_ray(pose.residue(2), "2HH1", "NH1"),
pick_ray(pose.residue(2), "1HH2", "NH2"),
pick_ray(pose.residue(2), "2HH2", "NH2")
]
}
sc_acceptor = {
1: [
pick_ray(pose.residue(1), "OE1", "CD"),
pick_ray(pose.residue(1), "OE2", "CD")
]
}
