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4561 | class SegmentModel(ArbdModel):
def __init__(self, segments=[], local_twist=True, escapable_twist=True,
max_basepairs_per_bead=7,
max_nucleotides_per_bead=4,
origin = None,
dimensions=(5000,5000,5000), temperature=291,
timestep=50e-6, cutoff=50,
decomp_period=10000, pairlistDistance=None,
integrator='Brown',
debye_length = None,
hj_equilibrium_angle = 0,
):
logger.debug('Initializing SegmentModel')
ArbdModel.__init__(self,segments,
origin, dimensions,
temperature=temperature, timestep=timestep,
integrator=integrator, cutoff=cutoff,
decomp_period = decomp_period
)
# self.max_basepairs_per_bead = max_basepairs_per_bead # dsDNA
# self.max_nucleotides_per_bead = max_nucleotides_per_bead # ssDNA
if isinstance(segments,Segment):
segments = [segments]
self.children = self.segments = segments
if (hj_equilibrium_angle > 180) or (hj_equilibrium_angle < -180):
raise ValueError("Holliday junction equilibrium dihedral angle must be in the range from -180 to 180 degrees!")
self.hj_equilibrium_angle = hj_equilibrium_angle
self._generate_bead_callbacks = []
self._bonded_potential = dict() # cache for bonded potentials
self._generate_strands()
self.grid_potentials = []
self._generate_bead_model( max_basepairs_per_bead, max_nucleotides_per_bead, local_twist, escapable_twist)
if debye_length is not None:
nbDnaScheme.debye_length = debye_length
self.debye_length = debye_length
self.add_nonbonded_interaction( nbDnaScheme )
self.useTclForces = False
def set_debye_length(self, value):
if value <= 0:
raise ValueError("The Debye length must be positive")
for s,tA,tB in self.nonbonded_interactions:
try:
s.debye_length = value
except:
...
self.debye_length = value
def get_connections(self,type_=None,exclude=()):
""" Find all connections in model, without double-counting """
added=set()
ret=[]
for s in self.segments:
items = [e for e in s.get_connections_and_locations(type_,exclude=exclude) if e[0] not in added]
added.update([e[0] for e in items])
ret.extend( list(sorted(items,key=lambda x: x[1].address)) )
return ret
def _prepare_location_graph(self):
devlogger.debug('Updating location graphs')
gr = nx.Graph()
## First add all intrahelical connections to graph
for seg in self.segments:
conn_locs = seg.get_connections_and_locations("intrahelical")
## Add intersegment edges
for c,A,B in conn_locs:
gr.add_edge(A, B, weight=0.0) # connected locations are considered immediately adjacent
## Add intrasegment edges
locs = list(sorted( [A for c,A,B in conn_locs], key=lambda l: l.address ))
for l1,l2 in zip(locs[:-1],locs[1:]):
dx = seg.contour_to_nt_pos( l2.address, round_nt=False ) - seg.contour_to_nt_pos( l1.address, round_nt=False )
gr.add_edge(l1, l2, weight = dx)
self._intrahelical_location_graph = gr
## Now add sscrossover locations for SingleStrandedSegments
gr = nx.Graph(gr)
for seg in self.segments:
conn_locs = seg.get_connections_and_locations("intrahelical") + seg.get_connections_and_locations("sscrossover")
for c,A,B in conn_locs:
gr.add_edge(A, B, weight=0.00)
locs = list(sorted( [A for c,A,B in conn_locs], key=lambda l: l.address ))
for l1,l2 in zip(locs[:-1],locs[1:]):
dx = seg.contour_to_nt_pos( l2.address, round_nt=False ) - seg.contour_to_nt_pos( l1.address, round_nt=False )
gr.add_edge(l1, l2, weight = dx)
self._intrahelical_sscrossover_location_graph = gr
def _recursively_get_beads_within_bonds(self,b1,bonds,done=()):
ret = []
done = list(done)
done.append(b1)
if bonds == 0:
return [[]]
for b2 in b1.intrahelical_neighbors:
if b2 in done: continue
for tmp in self._recursively_get_beads_within_bonds(b2, bonds-1, done):
ret.append( [b2]+tmp )
return ret
def _get_intrahelical_beads(self,num=2):
## TODO: add check that this is not called before adding intrahelical_neighbors in _generate_bead_model
assert(num >= 2)
ret = []
for s in self.segments:
for b1 in s.beads:
for bead_list in self._recursively_get_beads_within_bonds(b1, num-1):
assert(len(bead_list) == num-1)
if b1.idx < bead_list[-1].idx: # avoid double-counting
ret.append([b1]+bead_list)
return ret
def _get_intrahelical_angle_beads(self):
return self._get_intrahelical_beads(num=3)
def _get_potential(self, type_, kSpring, d, max_potential = None):
key = (type_, kSpring, d, max_potential)
if key not in self._bonded_potential:
assert( kSpring >= 0 )
if type_ == "bond":
self._bonded_potential[key] = HarmonicBond(kSpring,d, range_=(0,1200), max_potential=max_potential)
elif type_ == "gbond":
self._bonded_potential[key] = HarmonicBond(kSpring,d, range_=(0,1200), max_potential=max_potential, correct_geometry=True, temperature=self.configuration.temperature)
elif type_ == "angle":
self._bonded_potential[key] = HarmonicAngle(kSpring,d, max_potential=max_potential)
# , resolution = 1, maxForce=0.1)
elif type_ == "dihedral":
self._bonded_potential[key] = HarmonicDihedral(kSpring,d, max_potential=max_potential)
else:
raise Exception("Unhandled potential type '%s'" % type_)
return self._bonded_potential[key]
def get_bond_potential(self, kSpring, d, correct_geometry=False):
assert( d > 0.2 )
return self._get_potential("gbond" if correct_geometry else "bond",
kSpring, d)
def get_angle_potential(self, kSpring, d):
return self._get_potential("angle", kSpring, d)
def get_dihedral_potential(self, kSpring, d, max_potential=None):
while d > 180: d-=360
while d < -180: d+=360
return self._get_potential("dihedral", kSpring, d, max_potential)
def _get_wlc_sk_bond_potential(self, d):
## https://aip.scitation.org/doi/full/10.1063/1.4968020
type_='wclsk-bond'
# lp = 2*5 # TODO place these parameters in a logical spot
lp = 15 # https://journals.aps.org/pre/abstract/10.1103/PhysRevE.86.021901
# https://www.pnas.org/content/pnas/109/3/799.full.pdf
lp = 12 # selected semi-empirically to make ssDNA force extension match
key = (type_, d, lp)
assert( d > 0.2 )
if key not in self._bonded_potential:
kT = self.configuration.temperature * 0.0019872065 # kcal/mol
_pot = WLCSKBond( d, lp, kT, range_=(0,1200) )
self._bonded_potential[key] = _pot
return self._bonded_potential[key]
def _get_wlc_sk_angle_potential(self, d):
## https://aip.scitation.org/doi/full/10.1063/1.4968020
type_='wclsk-angle'
## TODO move
lp = 15 # https://journals.aps.org/pre/abstract/10.1103/PhysRevE.86.021901
# https://www.pnas.org/content/pnas/109/3/799.full.pdf
lp = 12 # selected semi-empirically to make ssDNA force extension match
key = (type_, d, lp)
assert( d > 0.2 )
if key not in self._bonded_potential:
kT = self.configuration.temperature * 0.0019872065 # kcal/mol
self._bonded_potential[key] = WLCSKAngle( d, lp, kT )
return self._bonded_potential[key]
def _getParent(self, *beads ):
if len(set([b.parent for b in beads])) == 1:
return beads[0].parent
else:
return self
def _get_twist_spring_constant(self, sep):
""" sep in nt """
twist_persistence_length = 90 # set semi-arbitrarily as there is a large spread in literature
## units "3e-19 erg cm/ 295 k K" "nm" =~ 73
Lp = twist_persistence_length/0.34
return twist_spring_from_lp(sep, Lp, self.configuration.temperature)
def extend(self, other, copy=False, include_strands=True):
if copy == True:
logger.warning("Forcing SegmentModel.extend(...,copy=False,...)")
copy = False
assert( isinstance(other, SegmentModel) )
try:
max_occupancy = max([s.occupancy for s in self.segments if 'occupancy' in s.__dict__])
occupancy0 = 10**np.ceil(np.log10(max_occupancy+1))
except:
pass
if copy:
for s in other.segments:
newseg = deepcopy(s)
try:
newseg.occupancy = occupancy0+s.occupancy
except:
pass
self.segments.append(newseg)
newseg.parent = self
if include_strands:
for s in other.strands:
newstrand = deepcopy(s)
self.strands.append(newstrand)
newstrand.parent = self
else:
for s in other.segments:
try:
s.occupancy = occupancy0+s.occupancy
except:
pass
self.segments.append(s)
s.parent = self
if include_strands:
for s in other.strands:
self.strands.append(s)
s.parent = self
self._clear_beads()
def update(self, segment , copy=False):
assert( isinstance(segment, Segment) )
if copy:
segment = deepcopy(segment)
segment.parent = self
self.segments.append(segment)
self._clear_beads()
""" Mapping between different resolution models """
def clear_atomic(self):
for strand in self.strands:
for s in strand.children:
s.clear_all()
s.oxdna_nt = []
for seg in self.segments:
for d in ('fwd','rev'):
seg.strand_pieces[d] = []
self._generate_strands()
## Clear sequence if needed
for seg in self.segments:
if seg.sequence is not None and len(seg.sequence) != seg.num_nt:
seg.sequence = None
def clear_beads(self):
return self._clear_beads()
def _clear_beads(self):
## TODO: deprecate
for s in self.segments:
try:
s.clear_all()
except:
...
self.clear_all(keep_children=True)
try:
if len(self.strands[0].children[0].children) > 0:
self.clear_atomic()
except:
...
## Check that it worked
assert( len([b for b in self]) == 0 )
locParticles = []
for s in self.segments:
for c,A,B in s.get_connections_and_locations():
for l in (A,B):
if l.particle is not None:
locParticles.append(l.particle)
assert( len(locParticles) == 0 )
assert( len([b for s in self.segments for b in s.beads]) == 0 )
def _update_segment_positions(self, bead_coordinates):
print("WARNING: called deprecated command '_update_segment_positions; use 'update_splines' instead")
return self.update_splines(bead_coordinates)
## Operations on spline coordinates
def translate(self, translation_vector, position_filter=None):
for s in self.segments:
s.translate(translation_vector, position_filter=position_filter)
def rotate(self, rotation_matrix, about=None, position_filter=None):
for s in self.segments:
s.rotate(rotation_matrix, about=about, position_filter=position_filter)
def get_center(self, include_ssdna=False):
if include_ssdna:
segments = self.segments
else:
segments = list(filter(lambda s: isinstance(s,DoubleStrandedSegment),
self.segments))
centers = [s.get_center() for s in segments]
weights = [s.num_nt*2 if isinstance(s,DoubleStrandedSegment) else s.num_nt for s in segments]
# centers,weights = [np.array(a) for a in (centers,weights)]
return np.average( centers, axis=0, weights=weights)
def update_splines(self, bead_coordinates):
""" Set new function for each segments functions
contour_to_position and contour_to_orientation """
for s in self.segments:
# if s.name == "61-1":
# pdb.set_trace()
cabs = s.get_connections_and_locations("intrahelical")
if isinstance(s,SingleStrandedSegment):
cabs = cabs + [[c,A,B] for c,A,B in s.get_connections_and_locations("sscrossover") if A.address == 0 or A.address == 1]
if np.any( [B.particle is None for c,A,B in cabs] ):
print( "WARNING: none type found in connection, skipping" )
cabs = [e for e in cabs if e[2].particle is not None]
def get_beads_and_contour_positions(s):
ret_list = []
def zip_bead_contour(beads,address=None):
if isinstance(address,list):
assert(False)
for b,a in zip(beads,address):
if b is None: continue
try:
ret_list.append((b, b.get_contour_position(s,a)))
except:
...
else:
for b in beads:
if b is None: continue
try:
ret_list.append((b, b.get_contour_position(s,address)))
except:
...
return ret_list
## Add beads from segment s
beads_contours = zip_bead_contour(s.beads)
beads_contours.extend( zip_bead_contour([A.particle for c,A,B in cabs]) )
beads = set([b for b,c in beads_contours])
## Add nearby beads
for c,A,B in cabs:
## TODOTODO test?
filter_fn = lambda x: x is not None and x not in beads
bs = list( filter( filter_fn, B.particle.intrahelical_neighbors ) )
beads_contours.extend( zip_bead_contour( bs, A.address ) )
beads.update(bs)
for i in range(3):
bs = list( filter( filter_fn, [n for b in bs for n in b.intrahelical_neighbors] ) )
beads_contours.extend( zip_bead_contour( bs, A.address ) )
beads.update(bs)
beads_contours = list(set(beads_contours))
beads = list(beads)
## Skip beads that are None (some locations were not assigned a particle to avoid double-counting)
# beads = [b for b in beads if b is not None]
assert( np.any([b is None for b,c in beads_contours]) == False )
# beads = list(filter(lambda x: x[0] is not None, beads))
if isinstance(s, DoubleStrandedSegment):
beads_contours = list(filter(lambda x: x[0].type_.name[0] == "D", beads_contours))
return beads_contours
beads_contours = get_beads_and_contour_positions(s)
contours = [c for b,c in beads_contours]
contour_idx = np.array( np.array(contours)*s.num_nt * 10, dtype=int )
contour_idx,ids1 = np.unique(contour_idx, return_index=True)
beads_contours = [beads_contours[i] for i in ids1]
## TODO: keep closest beads beyond +-1.5 if there are fewer than 2 beads
tmp = []
dist = 1
while len(tmp) < 5 and dist < 3:
tmp = list(filter(lambda bc: np.abs(bc[1]-0.5) < dist, beads_contours))
dist += 0.1
if len(tmp) <= 1:
raise Exception("Failed to fit spline into segment {}".format(s))
beads = [b for b,c in tmp]
contours = [c for b,c in tmp]
ids = [b.idx for b in beads]
if len(beads) <= 1:
pdb.set_trace()
""" Get positions """
positions = bead_coordinates[ids,:].T
tck, u = interpolate.splprep( positions, u=contours, s=0, k=1 )
s.position_spline_params = (tck,u)
""" Get orientation """
def remove_tangential_projection(vector, tangent):
""" Assume tangent is normalized """
v = vector - vector.dot(tangent)*tangent
return v/np.linalg.norm(v)
def get_orientation_vector(bead,tangent):
if 'orientation_bead' in bead.__dict__:
o = bead.orientation_bead
oVec = bead_coordinates[o.idx,:] - bead_coordinates[bead.idx,:]
oVec = remove_tangential_projection(oVec,tangent)
else:
oVec = None
return oVec
def get_previous_idx_if_none(list_):
previous = None
result = []
i = 0
for e in list_:
if e is None:
result.append(previous)
else:
previous = i
i+=1
return result
def get_next_idx_if_none(list_):
tmp = get_previous_idx_if_none(list_[::-1])[::-1]
return [ len(list_)-1-idx if idx is not None else idx for idx in tmp ]
def fill_in_orientation_vectors(contours,orientation_vectors,tangents):
result = []
last_idx = get_previous_idx_if_none( orientation_vectors )
next_idx = get_next_idx_if_none( orientation_vectors )
none_idx = 0
for c,ov,t in zip(contours,orientation_vectors,tangents):
if ov is not None:
result.append(ov)
else:
p = last_idx[none_idx]
n = next_idx[none_idx]
none_idx += 1
if p is None:
if n is None:
## Should be quite rare; give something random if it happens
print("WARNING: unable to interpolate orientation")
o = np.array((1,0,0))
result.append( remove_tangential_projection(o,t) )
else:
o = orientation_vectors[n]
result.append( remove_tangential_projection(o,t) )
else:
if n is None:
o = orientation_vectors[p]
result.append( remove_tangential_projection(o,t) )
else:
cp,cn = [contours[i] for i in (p,n)]
op,on = [orientation_vectors[i] for i in (p,n)]
if (cn-cp) > 1e-6:
o = ((cn-c)*op+(c-cp)*on)/(cn-cp)
else:
o = op+on
result.append( remove_tangential_projection(o,t) )
return result
tangents = s.contour_to_tangent(contours)
orientation_vectors = [get_orientation_vector(b,t) for b,t in zip(beads,tangents)]
if len(beads) > 3 and any([e is not None for e in orientation_vectors] ):
orientation_vectors = fill_in_orientation_vectors(contours, orientation_vectors, tangents)
quats = []
lastq = None
for b,t,oVec in zip(beads,tangents,orientation_vectors):
y = np.cross(t,oVec)
assert( np.abs(np.linalg.norm(y) - 1) < 1e-2 )
q = quaternion_from_matrix( np.array([oVec,y,t]).T)
if lastq is not None:
if q.dot(lastq) < 0:
q = -q
quats.append( q )
lastq = q
# pdb.set_trace()
quats = np.array(quats)
# tck, u = interpolate.splprep( quats.T, u=contours, s=3, k=3 ) ;# cubic spline not as good
tck, u = interpolate.splprep( quats.T, u=contours, s=0, k=1 )
s.quaternion_spline_params = (tck,u)
def update_reader_list_coordinates(self):
new_coords = np.empty(self._reader_list_coordinates.shape)
new_orientations = np.empty(self._reader_list_orientation.shape)
for seg in self.segments:
c = seg.nt_pos_to_contour(np.arange(seg.num_nt))
sl0 = (self._reader_list_hmap == seg._helix_idx)
pos = seg.contour_to_position( c )
orientation = seg.contour_to_orientation( c )
sl1 = (self._reader_list_fwd == True)
order = np.argsort( self._reader_list_hmap_hrank[sl0 & sl1] )
new_coords[sl0 & sl1][order] = pos
new_orientations[sl0 & sl1][order] = orientation
sl1 = (self._reader_list_fwd == False)
order = np.argsort( self._reader_list_hmap_hrank[sl0 & sl1] )
new_coords[sl0 & sl1][order] = pos
new_orientations[sl0 & sl1][order] = np.array([o.dot(rotationAboutAxis((1,0,0),180)) for o in orientation])
self._reader_list_coordinates = new_coords
self._reader_list_orientation = new_orientations
def get_segments_matching(self, pattern):
""" Returns a list of all segments that match the regular expression 'pattern' """
re_pattern = re.compile(pattern)
return [s for s in self.segments if re_pattern.match(s.name) is not None]
def get_crossovers_at_ends(self):
"""
Return a list of all "regular" crossovers where both sides of
the crossover exist at the start or end of a segment
"""
ret_list = []
for s in self.segments:
for c in filter(lambda c: c.type_ == "crossover" or c.type_ == "terminal_crossover", s.connections):
seg1 = c.A.container
seg2 = c.B.container
nt1 = c.A.get_nt_pos()
nt2 = c.B.get_nt_pos()
if (nt1 < 1 and nt2 > seg2.num_nt-2) or (nt2 < 1 and nt1 > seg1.num_nt-2):
if c not in ret_list:
ret_list.append(c)
return ret_list
def convert_crossover_to_intrahelical(self, crossover):
c = crossover
A = c.A if c.B.is_3prime_side_of_connection else c.B
B = c.B if c.B.is_3prime_side_of_connection else c.A
assert( not A.is_3prime_side_of_connection )
assert( B.is_3prime_side_of_connection )
seg1 = A.container
seg2 = B.container
nt1 = A.get_nt_pos()
nt2 = B.get_nt_pos()
# assert( c.A.on_fwd_strand == c.B.on_fwd_strand )
on_fwd_strand_A = A.on_fwd_strand
on_fwd_strand_B = B.on_fwd_strand
# print(nt1, nt2, on_fwd_strand_A, on_fwd_strand_B, c)
if on_fwd_strand_A:
assert( nt1 > seg1.num_nt-2 )
fn = seg1.connect_end3
if on_fwd_strand_B:
assert( nt2 < 1 )
arg = seg2.start5
else:
assert( nt2 > seg2.num_nt-2 )
arg = seg2.end5
else:
assert( nt1 < 1 )
fn = seg1.connect_start3
if on_fwd_strand_B:
assert( nt2 < 1 )
arg = seg2.start5
else:
assert( nt2 > seg2.num_nt-2 )
arg = seg2.end5
c.delete()
fn(arg)
def get_blunt_DNA_ends(self):
return sum([s.get_blunt_DNA_ends for s in self.segments],[])
def convert_crossovers_at_ends_beyond_cutoff_to_intrahelical(self,cutoff):
if cutoff < 0:
raise ValueError("Cutoff should be positive!")
return self.convert_crossovers_to_intrahelical(
position_filter = lambda r1,r2: np.linalg.norm(r2-r1) > cutoff,
terminal_only = True)
def convert_crossovers(self, new_connection_type=None, position_filter=None, terminal_only=False):
conn = self.get_crossovers_at_ends() if terminal_only else [c for c,A,B in self.get_connections('crossover')]+[c for c,A,B in self.get_connections('terminal_crossover')]
for c in conn:
_condition = True
if position_filter is not None:
r1,r2 = [l.container.contour_to_position(l.address)
for l in (c.A,c.B)]
_condition = position_filter(r1,r2)
if _condition:
if new_connection_type is None:
c.delete()
elif new_connection_type == 'intrahelical':
self.convert_crossover_to_intrahelical(c)
else:
raise NotImplementedError('convert_crossovers currently only supports removing crossovers')
def convert_crossovers_to_intrahelical(self, position_filter=None, terminal_only=False):
return self.convert_crossovers('intrahelical', position_filter, terminal_only)
def convert_close_crossovers_to_intrahelical(self,cutoff):
if cutoff < 0:
raise ValueError("Cutoff should be positive!")
for c,A,B in self.get_connections('crossover'):
r1,r2 = [l.container.contour_to_position(l.address)
for l in (c.A,c.B)]
if np.linalg.norm(r2-r1) < cutoff:
self.convert_crossover_to_intrahelical(c)
def _generate_bead_model(self,
max_basepairs_per_bead = None,
max_nucleotides_per_bead = None,
local_twist=False,
escapable_twist=True):
## TODO: deprecate
self.generate_bead_model( max_basepairs_per_bead = max_basepairs_per_bead,
max_nucleotides_per_bead = max_nucleotides_per_bead,
local_twist=local_twist,
escapable_twist=escapable_twist)
def generate_bead_model(self,
max_basepairs_per_bead = 7,
max_nucleotides_per_bead = 4,
local_twist=False,
escapable_twist=True,
sequence_dependent = False,
one_bead_per_monomer = None,
version = None # optionally used to specify a legacy version
):
if sequence_dependent and not local_twist:
raise ValueError("Incompatible options: if sequence_dependent==True, then local_twist must be True")
if sequence_dependent and not one_bead_per_monomer:
raise ValueError("Incompatible options: if sequence_dependent==True, then one_bead_per_monomer must be True")
logger.info(f'Generating bead model with less than {max_basepairs_per_bead} ({max_nucleotides_per_bead}) bp (nt) per bead, with{"" if local_twist else"out"} twist')
self.children = self.segments # is this okay?
self.clear_beads()
if one_bead_per_monomer is None:
one_bead_per_monomer = (max_nucleotides_per_bead == 1) and (max_basepairs_per_bead == 1)
segments = self.segments
for s in segments:
s.local_twist = local_twist
""" Simplify connections """
# d_nt = dict() #
# for s in segments:
# d_nt[s] = 1.5/(s.num_nt-1)
# for s in segments:
# ## replace consecutive crossovers with
# cl = sorted( s.get_connections_and_locations("crossover"), key=lambda x: x[1].address )
# last = None
# for entry in cl:
# c,A,B = entry
# if last is not None and \
# (A.address - last[1].address) < d_nt[s]:
# same_type = c.type_ == last[0].type_
# same_dest_seg = B.container == last[2].container
# if same_type and same_dest_seg:
# if np.abs(B.address - last[2].address) < d_nt[B.container]:
# ## combine
# A.combine = last[1]
# B.combine = last[2]
# ...
# # if last is not None:
# # s.bead_locations.append(last)
# ...
# last = entry
# del d_nt
self._prepare_location_graph() # TODO: automatically regenerate location graph whenever locations or segments are updated
""" Generate beads at intrahelical junctions """
if not one_bead_per_monomer:
## Loop through all connections, generating beads at appropriate locations
devlogger.info( "generate_bead_model: Adding intrahelical beads at junctions" )
for c,A,B in self.get_connections("intrahelical"):
s1,s2 = [l.container for l in (A,B)]
assert( A.particle is None )
assert( B.particle is None )
## TODO: offload the work here to s1
# TODOTODO
a1,a2 = [l.address for l in (A,B)]
for a in (a1,a2):
assert( np.isclose(a,0) or np.isclose(a,1) )
## TODO improve this for combinations of ssDNA and dsDNA (maybe a1/a2 should be calculated differently)
def _get_nearest(seg,address):
b = seg.get_nearest_bead(address)
if b is not None:
assert( b.parent is seg )
""" if above assertion is true, no problem here """
if np.abs(b.get_nt_position(seg) - seg.contour_to_nt_pos(address)) > 0.5:
b = None
return b
""" Search to see whether bead at location is already found """
b = None
if isinstance(s1,DoubleStrandedSegment):
b = _get_nearest(s1,a1)
if b is None and isinstance(s2,DoubleStrandedSegment):
b = _get_nearest(s2,a2)
if b is not None and b.parent not in (s1,s2):
b = None
if b is None:
## need to generate a bead
if isinstance(s2,DoubleStrandedSegment):
b = s2._generate_one_bead(a2,0)
else:
b = s1._generate_one_bead(a1,0)
A.particle = B.particle = b
b.is_intrahelical = True
b.locations.extend([A,B])
if s1 is s2:
b.is_circular_bead = True
# pdb.set_trace()
""" Generate beads at other junctions """
devlogger.info( "generate_bead_model: Adding beads at other junctions" )
for c,A,B in self.get_connections(exclude="intrahelical"):
s1,s2 = [l.container for l in (A,B)]
if A.particle is not None and B.particle is not None:
continue
# assert( A.particle is None )
# assert( B.particle is None )
## TODO: offload the work here to s1/s2 (?)
a1,a2 = [l.address for l in (A,B)]
def maybe_add_bead(location, seg, address, ):
if location.particle is None:
b = seg.get_nearest_bead(address)
try:
distance = seg.contour_to_nt_pos(np.abs(b.contour_position-address))
if seg.resolution is not None:
max_distance = seg.resolution
else:
max_distance = min(max_basepairs_per_bead, max_nucleotides_per_bead)*0.5
if "is_intrahelical" in b.__dict__:
max_distance = 0.5
if distance >= max_distance:
raise Exception("except")
## combine beads
b.update_position( 0.5*(b.contour_position + address) ) # avg position
except:
b = seg._generate_one_bead(address,0)
location.particle = b
b.locations.append(location)
maybe_add_bead(A,s1,a1)
maybe_add_bead(B,s2,a2)
""" Some tests """
for c,A,B in self.get_connections("intrahelical"):
for l in (A,B):
if l.particle is None: continue
assert( l.particle.parent is not None )
""" Generate beads in between """
devlogger.info( "generate_bead_model: Adding intrahelical beads between connections" )
for s in segments:
s._generate_beads( self, max_basepairs_per_bead, max_nucleotides_per_bead, version=version )
else:
""" Generate beads in each segment """
for s in segments:
s._generate_beads( self, max_basepairs_per_bead, max_nucleotides_per_bead, one_bead_per_monomer, version=version )
""" Associate beads with junctions """
# for c,A,B in self.get_connections("intrahelical"):
for c,A,B in self.get_connections():
for l in (A,B):
seg = l.container
a = l.address
b = seg.get_nearest_bead(a)
l.particle = b
b.locations.append(l)
"""
b.is_intrahelical = True
b.locations.extend([A,B])
if s1 is s2:
b.is_circular_bead = True
"""
# """ Combine beads at junctions as needed """
# for c,A,B in self.get_connections():
# ...
# ## Debug
# all_beads = [b for s in segments for b in s.beads]
# positions = np.array([b.position for b in all_beads])
# dists = positions[:,np.newaxis,:] - positions[np.newaxis,:,:]
# ids = np.where( np.sum(dists**2,axis=-1) + 0.02**2*np.eye(len(dists)) < 0.02**2 )
# print( ids )
# pdb.set_trace()
""" Add intrahelical neighbors at connections """
devlogger.info( "generate_bead_model: Adding intrahelical neighbors at connections" )
special_seps = dict()
for c,A,B in self.get_connections("intrahelical"):
b1,b2 = [l.particle for l in (A,B)]
if b1 is b2:
## already handled by Segment._generate_beads, unless A,B are on same segment
if A.container == B.container:
sorted_sites = sorted([(abs(L.address-b1.contour_position),L)
for L in (A,B)], key=lambda x: x[0])
close_site, far_site = [s[1] for s in sorted_sites]
b3 = far_site.container.get_nearest_bead(far_site.address)
b1.intrahelical_neighbors.append(b3)
b3.intrahelical_neighbors.append(b1)
if far_site.address > 0.5:
sep = b1.contour_position + (1-b3.contour_position)
else:
sep = b3.contour_position + (1-b1.contour_position)
sep = A.container.num_nt * sep
special_seps[(b1,b3)] = special_seps[(b3,b1)] = sep
else:
for b in (b1,b2): assert( b is not None )
b1.make_intrahelical_neighbor(b2)
def _combine_zero_sep_beads():
skip_keys = []
for b1,b2 in [k for k,v in special_seps.items() if v == 0]:
if (b1,b2) in skip_keys: continue
del special_seps[(b1,b2)]
del special_seps[(b2,b1)]
skip_keys.append((b2,b1))
for b in b2.intrahelical_neighbors:
if b is b1: continue
if b is not b1 and b.parent is b2.parent:
sep = np.abs(b2.contour_position - b.contour_position) * b.parent.num_nt
special_seps[(b,b1)] = sep
special_seps[(b1,b)] = sep
b1.combine(b2)
for k in list(special_seps.keys()):
if b2 in k:
if b2 == k[0]:
newkey = (b1,k[1])
else:
newkey = (k[0],b2)
special_seps[newkey] = special_seps[k]
del special_seps[k]
devlogger.debug( "generate_bead_model: Combining select beads connections" )
_combine_zero_sep_beads()
""" Reassign bead types """
devlogger.info( "generate_bead_model: Assigning bead types" )
beadtype_s = dict()
beadtype_count = dict(D=0,O=0,S=0)
def _assign_bead_type(bead, num_nt, decimals):
num_nt0 = bead.num_nt
bead.num_nt = np.around( np.float32(num_nt), decimals=decimals )
char = bead.type_.name[0].upper()
key = (char, bead.num_nt)
if key in beadtype_s:
bead.type_ = beadtype_s[key]
else:
t0 = bead.type_
newname = f'{char}{beadtype_count[char]:03d}'
kwargs = {k:v for k,v in bead.type_.__dict__.items() if k not in ParticleType.excludedAttributes}
t = ParticleType( name=newname, **kwargs )
t.__dict__["nts"] = bead.num_nt*2 if char in ("D","O") else bead.num_nt
t.mass = t.nts * 150
t.diffusivity = 120 if t.nts == 0 else min( 50 / np.sqrt(t.nts/5), 120)
beadtype_count[char] += 1
#print( "{} --> {} ({})".format(num_nt0, bead.num_nt, t.name) )
bead.type_ = t
beadtype_s[key]=t
beadtype_s[key] = bead.type_ = t
# (cluster_size[c-1])
import scipy.cluster.hierarchy as hcluster
beads = [b for s in segments for b in s if b.type_.name[0].upper() in ("D","O")]
data = np.array([b.num_nt for b in beads])[:,np.newaxis]
order = int(2-np.log10(2*max_basepairs_per_bead)//1)
try:
clusters = hcluster.fclusterdata(data, float(max_basepairs_per_bead)/500, criterion="distance")
cluster_size = [np.mean(data[clusters == i]) for i in np.unique(clusters)]
except:
clusters = np.arange(len(data))+1
cluster_size = data.flatten()
for b,c in zip(beads,clusters):
_assign_bead_type(b, cluster_size[c-1], decimals=order)
beads = [b for s in segments for b in s if b.type_.name[0].upper() in ("S")]
data = np.array([b.num_nt for b in beads])[:,np.newaxis]
order = int(2-np.log10(max_nucleotides_per_bead)//1)
try:
clusters = hcluster.fclusterdata(data, float(max_nucleotides_per_bead)/500, criterion="distance")
cluster_size = [np.mean(data[clusters == i]) for i in np.unique(clusters)]
except:
clusters = np.arange(len(data))+1
cluster_size = data.flatten()
for b,c in zip(beads,clusters):
_assign_bead_type(b, cluster_size[c-1], decimals=order)
self._beadtype_s = beadtype_s
self._apply_grid_potentials_to_beads(beadtype_s)
# for bead in [b for s in segments for b in s]:
# num_nt0 = bead.num_nt
# # bead.num_nt = np.around( np.float32(num_nt), decimals=decimals )
# key = (bead.type_.name[0].upper(), bead.num_nt)
# if key in beadtype_s:
# bead.type_ = beadtype_s[key]
# else:
# t = deepcopy(bead.type_)
# t.__dict__["nts"] = bead.num_nt*2 if t.name[0].upper() in ("D","O") else bead.num_nt
# # t.name = t.name + "%03d" % (t.nts*10**decimals)
# t.name = t.name + "%.16f" % (t.nts)
# print( "{} --> {} ({})".format(num_nt0, bead.num_nt, t.name) )
# beadtype_s[key] = bead.type_ = t
""" Update bead indices """
devlogger.info( "generate_bead_model: Update bead indices" )
self._countParticleTypes() # probably not needed here
self._updateParticleOrder()
def k_dsdna_bond(d):
conversion = 0.014393265 # units "pN/AA" kcal_mol/AA^2
elastic_modulus_times_area = 1000 # pN http://markolab.bmbcb.northwestern.edu/marko/Cocco.CRP.02.pdf
return conversion*elastic_modulus_times_area/d
def k_ssdna_bond(d):
# conversion = 0.014393265 # units "pN/AA" kcal_mol/AA^2
# ## TODO: get better numbers our ssDNA model
# elastic_modulus_times_area = 800 # pN http://markolab.bmbcb.northwestern.edu/marko/Cocco.CRP.02.pdf
return conversion*elastic_modulus_times_area/d
def k_dsdna_angle(sep, Lp=None):
Lp_eff = get_effective_dsDNA_Lp(sep, Lp)
Lp_eff = Lp_eff/0.34 # convert from nm to bp
return angle_spring_from_lp(sep,Lp_eff)
def k_xover_angle(sep, Lp=50):
Lp = Lp/0.34 # convert from nm to bp
return 0.25 * angle_spring_from_lp(sep,Lp)
""" Add intrahelical bond potentials """
dists = dict() # intrahelical distances built for later use
intra_beads = self._get_intrahelical_beads()
devlogger.info(f"generate_bead_model: Adding {len(intra_beads)} intrahelical bond potentials")
for b1,b2 in intra_beads:
# assert( not np.isclose( np.linalg.norm(b1.get_collapsed_position() - b2.get_collapsed_position()), 0 ) )
if np.linalg.norm(b1.get_collapsed_position() - b2.get_collapsed_position()) < 0.1:
devlogger.warning("some beads are very close")
parent = self._getParent(b1,b2)
if (b1,b2) in special_seps:
sep = special_seps[(b1,b2)]
else:
seg = b2.parent
c0 = b2.contour_position
sep = np.abs(b1.get_nt_position(seg,c0)-b2.get_nt_position(seg))
is_dsdna = b1.type_.name[0] == "D" and b2.type_.name[0] == "D"
if is_dsdna:
d = 3.4*sep
else:
# d = 6.5*sep # https://journals.aps.org/pre/abstract/10.1103/PhysRevE.86.021901
d = 6.4*sep # https://journals.aps.org/pre/abstract/10.1103/PhysRevE.86.021901
if b1.type_.name[0] != b2.type_.name[0]:
""" Add a small extra distance to junction """
d += 3
if b1 not in dists:
dists[b1] = dict()
if b2 not in dists:
dists[b2] = dict()
# dists[b1].append([b2,sep])
# dists[b2].append([b1,sep])
dists[b1][b2] = sep
dists[b2][b1] = sep
if b1 is b2: continue
# dists[[b1,b2]] = dists[[b2,b1]] = sep
if is_dsdna:
k = k_dsdna_bond(d)
bond = self.get_bond_potential(k,d,correct_geometry=True)
else:
bond = self._get_wlc_sk_bond_potential(d)
parent.add_bond( b1, b2, bond, exclude=True )
# for s in self.segments:
# sepsum = 0
# beadsum = 0
# for b1 in s.beads:
# beadsum += b1.num_nt
# for bead_list in self._recursively_get_beads_within_bonds(b1, 1):
# assert(len(bead_list) == 1)
# if b1.idx < bead_list[-1].idx: # avoid double-counting
# for b2 in bead_list:
# if b2.parent == b1.parent:
# sepsum += dists[b1][b2]
# sepsum += sep
# print("Helix {}: bps {}, beads {}, separation {}".format(s.name, s.num_nt, beadsum, sepsum))
""" Add intrahelical angle potentials """
def get_effective_dsDNA_Lp(sep, Lp0=50):
""" The persistence length of our model was found to be a
little off (probably due to NB interactions). This
attempts to compensate """
## For 1 bp, Lp=559, for 25 Lp = 524
beads_per_bp = sep/2
# return 0.93457944*Lp0 ;# factor1
return 0.97*Lp0 ;# factor2
# factor = bead_per_bp * (0.954-0.8944
# return Lp0 * bead_per_bp
_beads = self._get_intrahelical_angle_beads()
devlogger.info( f"generate_bead_model: Adding {len(_beads)} intrahelical angle potentials")
for b1,b2,b3 in _beads:
parent = self._getParent(b1,b2,b3)
seg = b2.parent
c0 = b2.contour_position
sep = dists[b2][b1] + dists[b2][b3]
if b1.type_.name[0] == "D" and b2.type_.name[0] == "D" and b3.type_.name[0] == "D":
k = k_dsdna_angle(sep, seg.persistence_length)
if local_twist:
k_dihed = 0.25*k
k *= 0.75 # reduce because orientation beads impose similar springs
dihed = self.get_dihedral_potential(k_dihed,180)
parent.add_dihedral(b1,b2,b2.orientation_bead,b3, dihed)
angle = self.get_angle_potential(k,180)
elif b1.type_.name[0] == "S" and b2.type_.name[0] == "S" and b3.type_.name[0] == "S":
# angle = self._get_wlc_sk_angle_potential(sep*6.5) # TODO move 6.5 somewhere sensible
angle = self._get_wlc_sk_angle_potential(sep*6.4) # TODO move 6.4 somewhere sensible
else:
## Considered as a sscrossover below
continue
parent.add_angle( b1, b2, b3, angle )
""" Add intrahelical exclusions """
beads = dists.keys()
def _recursively_get_beads_within(b1,d,done=()):
ret = []
self
intra_beads
if b1 not in dists:
print("Skipping exclusions for",b1)
return ret
for b2,sep in dists[b1].items():
if b2 in done: continue
if sep < d:
ret.append( b2 )
done.append( b2 )
tmp = _recursively_get_beads_within(b2, d-sep, done)
if len(tmp) > 0: ret.extend(tmp)
return ret
exclusions = set()
for b1 in beads:
""" In addition to bond exclusiosn, only add exclusions
within like-type segments (i.e. dsDNA or ssDNA, not
junctions between the two) """
t = type(b1.parent)
if t is DoubleStrandedSegment:
cutoff = 20
elif t is SingleStrandedSegment:
cutoff = 5
else:
raise ValueError("Unexpected polymer segment type")
for b in _recursively_get_beads_within(b1, cutoff, done=[b1]):
if isinstance(b.parent,t):
exclusions.add((b1,b))
else:
break
# exclusions.update( tmp )
## Add exclusions very near crossovers
for c,A,B in sum([self.get_connections(term) for term in ("crossover","terminal_crossover")],[]):
b1,b2 = [loc.particle for loc in (A,B)]
near_b1 = _recursively_get_beads_within(b1, 3, done=[])
near_b2 = _recursively_get_beads_within(b2, 3, done=[])
for bi in near_b1:
for bj in near_b2:
exclusions.add((bi,bj))
devlogger.info(f"generate_bead_model: Adding {len(exclusions)} exclusions")
for b1,b2 in exclusions:
parent = self._getParent(b1,b2)
parent.add_exclusion( b1, b2 )
""" Twist potentials """
if local_twist:
devlogger.info( "generate_bead_model: Adding twist potentials")
for b1 in beads:
if "orientation_bead" not in b1.__dict__: continue
for b2,sep in dists[b1].items():
if "orientation_bead" not in b2.__dict__: continue
if b2.idx < b1.idx: continue # Don't double-count
p1,p2 = [b.parent for b in (b1,b2)]
o1,o2 = [b.orientation_bead for b in (b1,b2)]
parent = self._getParent( b1, b2 )
_Lp = (p1.persistence_length + p2.persistence_length) * 0.5
""" Add heuristic 90 degree potential to keep orientation bead orthogonal """
k = 0.25*k_dsdna_angle(sep, _Lp)
pot = self.get_angle_potential(k,90)
parent.add_angle(o1,b1,b2, pot)
parent.add_angle(b1,b2,o2, pot)
## TODO: improve this
twist_per_nt = 0.5 * (p1.twist_per_nt + p2.twist_per_nt)
angle = sep*twist_per_nt
if angle > 360 or angle < -360:
print("WARNING: twist angle out of normal range... proceeding anyway")
# raise Exception("The twist between beads is too large")
k = self._get_twist_spring_constant(sep)
if escapable_twist:
pot = self.get_dihedral_potential(k,angle,max_potential=1)
else:
pot = self.get_dihedral_potential(k,angle)
parent.add_dihedral(o1,b1,b2,o2, pot)
def count_crossovers(beads):
count = 0
for b in beads:
for l in b.locations:
if l.connection is not None:
if l.connection.type_ in ("crossover","terminal_crossover"):
count += 1
return count
def add_local_crossover_strand_orientation_potential(b1,b2, b1_on_fwd_strand):
""" Adds a dihedral angle potential so bead b2 at opposite
end of crossover stays on correct side of helix of b1 """
u1 = b1.get_intrahelical_above(all_types=False)
d1 = b1.get_intrahelical_below(all_types=False)
sign = 1 if b1_on_fwd_strand else -1
# if b1.parent.name == "8-1" or b2.parent.name == "8-1":
# print()
# print(b1.parent.name, b2.parent.name, b1_on_fwd_strand)
# import pdb
# pdb.set_trace()
a,b,c = b2,b1,d1
if c is None or c is a:
c = u1
sign *= -1
if c is None or c is a: return
try:
d = b1.orientation_bead
except:
return
k = k_xover_angle(sep=1) # TODO
pot = self.get_dihedral_potential(k, sign*120)
self.add_dihedral( a,b,c,d, pot )
def add_local_tee_orientation_potential(b1,b2, b1_on_fwd_strand, b2_on_fwd_strand):
""" b1 is the end of a helix, b2 is in the middle This
adds a dihedral angle potential so helix of b1 is oriented
properly relative to strand on b2 """
u1,u2 = [b.get_intrahelical_above(all_types=False) for b in (b1,b2)]
d1,d2 = [b.get_intrahelical_below(all_types=False) for b in (b1,b2)]
angle = 150
if not b2_on_fwd_strand: angle -= 180
a,b,c = u2,b2,b1
if a is None:
a = d2
angle -= 180
try:
d = b1.orientation_bead
except:
d = None
angle -= 120
while angle > 180:
angle -= 360
while angle < -180:
angle += 360
k = k_xover_angle(sep=1) # TODO
if a is not None and d is not None:
pot = self.get_dihedral_potential(k,angle)
self.add_dihedral( a,b,c,d, pot )
## Add 180 degree angle potential
a,b,c = b2,b1,u1
if c is None: c = d1
if c is not None:
pot = self.get_angle_potential(0.5*k,180)
self.add_angle( a,b,c, pot )
def add_parallel_crossover_potential(b1,b2):
## Get beads above and below
u1,u2 = [b.get_intrahelical_above(all_types=False) for b in (b1,b2)]
d1,d2 = [b.get_intrahelical_below(all_types=False) for b in (b1,b2)]
dotProduct = b1.parent.contour_to_tangent(b1.contour_position).dot(
b2.parent.contour_to_tangent(b2.contour_position) )
if dotProduct < 0:
tmp = d2
d2 = u2
u2 = tmp
a = None
if u1 is not None and u2 is not None:
t0 = self.hj_equilibrium_angle
a,b,c,d = (u1,b1,b2,u2)
elif d1 is not None and d2 is not None:
t0 = self.hj_equilibrium_angle
a,b,c,d = (d1,b1,b2,d2 )
elif d1 is not None and u2 is not None:
t0 = self.hj_equilibrium_angle-180
a,b,c,d = (d1,b1,b2,u2)
elif u1 is not None and d2 is not None:
t0 = self.hj_equilibrium_angle-180
a,b,c,d = (u1,b1,b2,d2)
if t0 > 180:
t0 = t0-360
elif t0 < -180:
t0 = t0+360
## TODO?: Check length-dependence of this potential
if a is not None:
k_intrinsic = 0.00086
k = [1/k for k in (4*k_xover_angle( dists[b][a] ),
k_intrinsic,
4*k_xover_angle( dists[c][d] ))]
k = sum(k)**-1
k = k * count_crossovers((b1,b2))/4
pot = self.get_dihedral_potential(k,t0)
self.add_dihedral( a,b,c,d, pot )
...
""" Functions for adding crossover potentials """
def add_ss_crossover_potentials(connection,A,B, add_bond=True):
b1,b2 = [loc.particle for loc in (A,B)]
if (b1,b2,A.on_fwd_strand,B.on_fwd_strand) in processed_crossovers:
return
processed_crossovers.add((b1,b2,A.on_fwd_strand,B.on_fwd_strand))
processed_crossovers.add((b2,b1,B.on_fwd_strand,A.on_fwd_strand))
if b1 is b2:
""" Catch attempts to add "crossover potentials" at
intrahelical junctions between ds and ssDNA """
if A.container is not b1.parent:
b1 = A.container.get_nearest_bead(A.address)
if B.container is not b2.parent:
b2 = B.container.get_nearest_bead(B.address)
if b1 is b2:
return
if b1 is None or b2 is None:
return
## TODO: improve parameters
if add_bond:
pot = self.get_bond_potential(4,12)
self.add_bond(b1,b2, pot)
## Add potentials to provide a sensible orientation
## TODO refine potentials against all-atom simulation data
if local_twist:
add_local_crossover_strand_orientation_potential(b1,b2, A.on_fwd_strand)
add_local_crossover_strand_orientation_potential(b2,b1, B.on_fwd_strand)
def add_crossover_potentials(connection,A,B):
## TODO: use a better description here
b1,b2 = [loc.particle for loc in (A,B)]
if (b1,b2,A.on_fwd_strand,B.on_fwd_strand) in processed_crossovers:
return
processed_crossovers.add((b1,b2,A.on_fwd_strand,B.on_fwd_strand))
processed_crossovers.add((b2,b1,B.on_fwd_strand,A.on_fwd_strand))
if b1 is b2:
""" Catch attempts to add "crossover potentials" at
intrahelical junctions between ds and ssDNA """
return
""" Add parallel helices potential, possibly """
## Add potential to provide a particular orinetation
nt1,nt2 = [l.get_nt_pos() for l in (A,B)]
is_end1, is_end2 = [nt in (0,l.container.num_nt-1) for nt,l in zip((nt1,nt2),(A,B))]
is_T_junction = (is_end1 and not is_end2) or (is_end2 and not is_end1)
if (not is_end1) and (not is_end2):
## TODO?: Only apply this potential if not local_twist
add_parallel_crossover_potential(b1,b2)
# dotProduct = b1.parent.contour_to_tangent(b1.contour_position).dot(
# b2.parent.contour_to_tangent(b2.contour_position) )
if local_twist:
if is_T_junction:
""" Special case: one helix extends away from another in T-shaped junction """
""" Add bond potential """
k = 1.0 * count_crossovers((b1,b2))
pot = self.get_bond_potential(k,12.5)
self.add_bond(b1,b2, pot)
if is_end1:
b1_forward = A.on_fwd_strand if nt1 == 0 else not A.on_fwd_strand
add_local_tee_orientation_potential(b1,b2, b1_forward, B.on_fwd_strand)
else:
add_local_crossover_strand_orientation_potential(b1,b2, A.on_fwd_strand)
if is_end2:
b2_forward = B.on_fwd_strand if nt2 == 0 else not B.on_fwd_strand
add_local_tee_orientation_potential(b2,b1, b2_forward, A.on_fwd_strand)
else:
add_local_crossover_strand_orientation_potential(b2,b1, B.on_fwd_strand)
else:
""" Add bond potential """
k = 1.0 * count_crossovers((b1,b2))
pot = self.get_bond_potential(k,18.5)
self.add_bond(b1,b2, pot)
""" Normal case: add orientation potential """
add_local_crossover_strand_orientation_potential(b1,b2, A.on_fwd_strand)
add_local_crossover_strand_orientation_potential(b2,b1, B.on_fwd_strand)
else:
""" Add bond potential """
k = 1.0 * count_crossovers((b1,b2))
pot = self.get_bond_potential(k,18.5)
self.add_bond(b1,b2, pot)
""" Add connection potentials """
devlogger.info( "generate_bead_model: Adding connection potentials")
processed_crossovers = set()
# pdb.set_trace()
for c,A,B in self.get_connections("sscrossover"):
p1,p2 = [loc.container for loc in (A,B)]
assert(any([isinstance(p,SingleStrandedSegment) for p in (p1,p2)]))
add_ss_crossover_potentials(c,A,B)
for c,A,B in self.get_connections("intrahelical"):
ps = [loc.container for loc in (A,B)]
if any([isinstance(p,SingleStrandedSegment) for p in ps]) and \
any([isinstance(p,DoubleStrandedSegment) for p in ps]):
add_ss_crossover_potentials(c,A,B, add_bond=False)
for c,A,B in sum([self.get_connections(term) for term in ("crossover","terminal_crossover")],[]):
p1,p2 = [loc.container for loc in (A,B)]
if any([isinstance(p,SingleStrandedSegment) for p in (p1,p2)]):
add_ss_crossover_potentials(c,A,B)
else:
add_crossover_potentials(c,A,B)
## todotodo check that this works
for crossovers in self.get_consecutive_crossovers():
if local_twist: break
## filter crossovers
for i in range(len(crossovers)-2):
c1,A1,B1,dir1 = crossovers[i]
c2,A2,B2,dir2 = crossovers[i+1]
s1,s2 = [l.container for l in (A1,A2)]
sep = A1.particle.get_nt_position(s1,near_address=A1.address) - A2.particle.get_nt_position(s2,near_address=A2.address)
sep = np.abs(sep)
assert(sep >= 0)
n1,n2,n3,n4 = (B1.particle, A1.particle, A2.particle, B2.particle)
"""
<cos(q)> = exp(-s/Lp) = integrate( cos[x] exp(-A x^2), {x, 0, pi} ) / integrate( exp(-A x^2), {x, 0, pi} )
"""
## From http://www.annualreviews.org/doi/pdf/10.1146/annurev.bb.17.060188.001405
## units "3e-19 erg cm/ 295 k K" "nm" =~ 73
Lp = s1.twist_persistence_length/0.34 # set semi-arbitrarily as there is a large spread in literature
def get_spring(sep):
kT = self.configuration.temperature * 0.0019872065 # kcal/mol
fitFun = lambda x: np.real(erf( (4*np.pi*x + 1j)/(2*np.sqrt(x)) )) * np.exp(-1/(4*x)) / erf(2*np.sqrt(x)*np.pi) - np.exp(-sep/Lp)
k = opt.leastsq( fitFun, x0=np.exp(-sep/Lp) )
return k[0][0] * 2*kT*0.00030461742
k = get_spring( max(sep,1) )
k = (1/k + 2/k_xover_angle(sep=1))**-1
t0 = sep*s1.twist_per_nt # TODO weighted avg between s1 and s2
# pdb.set_trace()
if A1.on_fwd_strand: t0 -= 120
if dir1 != dir2:
A2_on_fwd = not A2.on_fwd_strand
else:
A2_on_fwd = A2.on_fwd_strand
if A2_on_fwd: t0 += 120
# t0 = (t0 % 360
# if n2.idx == 0:
# print( n1.idx,n2.idx,n3.idx,n4.idx,k,t0,sep )
if sep == 0:
# pot = self.get_angle_potential(k,t0)
# self.add_angle( n1,n2,n4, pot )
pass
elif len(set((n1,n2,n3,n4))) != 4:
print("WARNING: skipping crossover dihedral angle potential because beads are too close")
else:
pot = self.get_dihedral_potential(k,t0)
self.add_dihedral( n1,n2,n3,n4, pot )
for seg in self.segments:
for callback in seg._generate_bead_callbacks:
callback(seg)
for callback in self._generate_bead_callbacks:
callback(self)
# ## remove duplicate potentials; ## TODO ensure that they aren't added twice in the first place?
# self.remove_duplicate_terms()
def walk_through_helices(segment, direction=1, processed_segments=None):
"""
First and last segment should be same for circular helices
"""
assert( direction in (1,-1) )
if processed_segments == None:
processed_segments = set()
def segment_is_new_helix(s):
return isinstance(s,DoubleStrandedSegment) and s not in processed_segments
new_s = None
s = segment
## iterate intrahelically connected dsDNA segments
while segment_is_new_helix(s):
conn_locs = s.get_contour_sorted_connections_and_locations("intrahelical")[::direction]
processed_segments.add(new_s)
new_s = None
new_dir = None
for i in range(len(conn_locs)):
c,A,B = conn_locs[i]
## TODO: handle change of direction
# TODOTODO
address = 1*(direction==-1)
if A.address == address and segment_is_new_helix(B.container):
new_s = B.container
assert(B.address in (0,1))
new_dir = 2*(B.address == 0) - 1
break
yield s,direction
s = new_s # will break if None
direction = new_dir
# if new_s is None:
# break
# else:
# s = new_s
# yield s
## return s
def get_consecutive_crossovers(self):
## TODOTODO TEST
crossovers = []
processed_segments = set()
for s1 in self.segments:
if not isinstance(s1,DoubleStrandedSegment):
continue
if s1 in processed_segments: continue
s0,d0 = list(SegmentModel.walk_through_helices(s1,direction=-1))[-1]
# s,direction = get_start_of_helices()
tmp = []
for s,d in SegmentModel.walk_through_helices(s0,-d0):
if s == s0 and len(tmp) > 0:
## end of circular helix, only add first crossover
cl_list = s.get_contour_sorted_connections_and_locations("crossover")
if len(cl_list) > 0:
tmp.append( cl_list[::d][0] + [d] )
else:
tmp.extend( [cl + [d] for cl in s.get_contour_sorted_connections_and_locations("crossover")[::d]] )
processed_segments.add(s)
crossovers.append(tmp)
return crossovers
def set_sequence(self, sequence, force=True, fill_sequence='random'):
if force:
self.strands[0].set_sequence(sequence)
else:
try:
self.strands[0].set_sequence(sequence)
except:
...
for s in self.segments:
s.assign_unset_sequence(fill_sequence)
def _set_cadnano2_sequence(self, cadnano_sequence_csv_file, sequence_fill='T'):
try:
self.segments[0]._cadnano_helix
except:
raise Exception("Cannot set sequence of a non-cadnano model using a cadnano sequence file")
starts = dict()
for strand in self.strands[1:]:
if strand.is_circular: continue
s = strand.strand_segments[0]
hid = s.segment._cadnano_helix
idx = s.segment._cadnano_bp_to_zidx[int(s.start)]
starts["{:d}[{:d}]".format(hid,idx)] = strand
base_set = tuple('ATCG')
with open(cadnano_sequence_csv_file) as fh:
reader = csv.reader(fh)
for values in reader:
if values[0] == "Start": continue
start,end,seq = values[:3]
strand = starts[start]
if sequence_fill in base_set:
seq = [sequence_fill if s == '?' else s for s in seq]
else:
seq = [random.choice(base_set) if s == '?' else s for s in seq]
if len([s for s in seq if s not in base_set]) > 0:
print(seq)
strand.set_sequence(seq)
def _generate_strands(self):
## clear strands
try:
for s in self.strands:
try:
self.children.remove(s)
except:
pass
except:
pass
try:
for seg in self.segments:
try:
for d in ('fwd','rev'):
seg.strand_pieces[d] = []
except:
pass
except:
pass
self.strands = strands = []
""" Ensure unconnected ends have 5prime Location objects """
for seg in self.segments:
## TODO move into Segment calls
five_prime_locs = sum([seg.get_locations(s) for s in ("5prime","crossover","terminal_crossover")],[])
three_prime_locs = sum([seg.get_locations(s) for s in ("3prime","crossover","terminal_crossover")],[])
def is_start_5prime(l):
is_end = l.get_nt_pos() < 1 and l.on_fwd_strand
return is_end and (l.connection is None or l.is_3prime_side_of_connection is not False)
def is_end_5prime(l):
is_end = l.get_nt_pos() > seg.num_nt-2 and not l.on_fwd_strand
return is_end and (l.connection is None or l.is_3prime_side_of_connection is not False)
def is_start_3prime(l):
is_start = l.get_nt_pos() < 1 and not l.on_fwd_strand
return is_start and (l.connection is None or l.is_3prime_side_of_connection is not True)
def is_end_3prime(l):
is_start = l.get_nt_pos() > seg.num_nt-2 and l.on_fwd_strand
return is_start and (l.connection is None or l.is_3prime_side_of_connection is not True)
if seg.start5.connection is None:
if len(list(filter( is_start_5prime, five_prime_locs ))) == 0:
seg.add_5prime(0) # TODO ensure this is the same place
if 'end5' in seg.__dict__ and seg.end5.connection is None:
if len(list(filter( is_end_5prime, five_prime_locs ))) == 0:
seg.add_5prime(seg.num_nt-1,on_fwd_strand=False)
if 'start3' in seg.__dict__ and seg.start3.connection is None:
if len(list(filter( is_start_3prime, three_prime_locs ))) == 0:
seg.add_3prime(0,on_fwd_strand=False)
if seg.end3.connection is None:
if len(list(filter( is_end_3prime, three_prime_locs ))) == 0:
seg.add_3prime(seg.num_nt-1)
# print( [(l,l.get_connected_location()) for l in seg.locations] )
# addresses = np.array([l.address for l in seg.get_locations("5prime")])
# if not np.any( addresses == 0 ):
# ## check if end is connected
# for c,l,B in self.get_connections_and_locations():
# if c[0]
""" Build strands from connectivity of helices """
def _recursively_build_strand(strand, segment, pos, is_fwd, mycounter=0, move_at_least=0.5):
seg = segment
history = []
while True:
mycounter+=1
if mycounter > 10000:
raise Exception("Too many iterations")
#if seg.name == "22-1" and pos > 140:
# if seg.name == "22-2":
# import pdb
# pdb.set_trace()
# if _DEBUG_TRACE and seg.name == "69-0" and is_fwd == False:
# import pdb
# pdb.set_trace()
end_pos, next_seg, next_pos, next_dir, move_at_least = seg.get_strand_segment(pos, is_fwd, move_at_least)
history.append((seg,pos,end_pos,is_fwd))
try:
strand.add_dna(seg, pos, end_pos, is_fwd)
except CircularDnaError:
## Circular DNA was found
break
except:
print("Unexpected error:", sys.exc_info()[0])
# import pdb
# pdb.set_trace()
# seg.get_strand_segment(pos, is_fwd, move_at_least)
# strand.add_dna(seg, pos, end_pos, is_fwd)
raise
if next_seg is None:
break
else:
seg,pos,is_fwd = (next_seg, next_pos, next_dir)
strand.history = list(history)
return history
strand_counter = 0
history = []
for seg in self.segments:
locs = filter(lambda l: l.connection is None, seg.get_5prime_locations())
if locs is None: continue
# for pos, is_fwd in locs:
for l in locs:
if _DEBUG_TRACE:
print("Tracing 5prime",l)
if l.connection is not None:
print(" Skipping connected 5prime",l)
continue
# TODOTODO
pos = seg.contour_to_nt_pos(l.address, round_nt=True)
is_fwd = l.on_fwd_strand
s = Strand(segname="S{:03d}".format(len(strands)))
strand_history = _recursively_build_strand(s, seg, pos, is_fwd)
history.append((l,strand_history))
# print("{} {}".format(seg.name,s.num_nt))
strands.append(s)
## Trace circular DNA
def strands_cover_segment(segment, is_fwd=True):
direction = 'fwd' if is_fwd else 'rev'
nt = 0
for sp in segment.strand_pieces[direction]:
nt += sp.num_nt
return nt == segment.num_nt
def find_nt_not_in_strand(segment, is_fwd=True):
fwd_str = 'fwd' if is_fwd else 'rev'
def check(val):
assert(val >= 0 and val < segment.num_nt)
# print("find_nt_not_in_strand({},{}) returning {}".format(
# segment, is_fwd, val))
return val
if is_fwd:
last = -1
for sp in segment.strand_pieces[fwd_str]:
if sp.start-last > 1:
return check(last+1)
last = sp.end
return check(last+1)
else:
last = segment.num_nt
for sp in reversed(segment.strand_pieces[fwd_str]):
if last-sp.start > 1:
return check(last-1)
last = sp.end
return check(last-1)
def add_strand_if_needed(seg,is_fwd):
history = []
while not strands_cover_segment(seg, is_fwd):
pos = nt = find_nt_not_in_strand(seg, is_fwd)
if _DEBUG_TRACE:
print("Tracing circular strand", pos, is_fwd)
s = Strand(segname="S{:03d}".format(len(strands)),
is_circular = True)
history = _recursively_build_strand(s, seg, pos, is_fwd)
strands.append(s)
return history
for seg in self.segments:
add_strand_if_needed(seg,True)
if isinstance(seg, DoubleStrandedSegment):
add_strand_if_needed(seg,False)
self.strands = sorted(strands, key=lambda s:s.num_nt)[::-1]
def check_strands():
dsdna = filter(lambda s: isinstance(s,DoubleStrandedSegment), self.segments)
for s in dsdna:
nt_fwd = nt_rev = 0
for sp in s.strand_pieces['fwd']:
nt_fwd += sp.num_nt
for sp in s.strand_pieces['rev']:
nt_rev += sp.num_nt
assert( nt_fwd == s.num_nt and nt_rev == s.num_nt )
# print("{}: {},{} (fwd,rev)".format(s.name, nt_fwd/s.num_nt,nt_rev/s.num_nt))
check_strands()
## relabel segname
counter = 0
for s in self.strands:
if s.segname is None:
s.segname = "D%03d" % counter
counter += 1
def _assign_basepairs(self):
## Assign basepairs
for seg in self.segments:
if isinstance(seg, DoubleStrandedSegment):
strands1 = seg.strand_pieces['fwd'] # already sorted
strands2 = seg.strand_pieces['rev']
nts1 = [nt for s in strands1 for nt in s.children]
nts2 = [nt for s in strands2 for nt in s.children[::-1]]
assert(len(nts1) == len(nts2))
for nt1,nt2 in zip(nts1,nts2):
## TODO weakref
nt1.basepair = nt2
nt2.basepair = nt1
def write_atomic_bp_restraints(self, output_name, spring_constant=1.0):
## TODO: ensure atomic model was generated already
## TODO: allow ENM to be created without first building atomic model
with open("%s.exb" % output_name,'w') as fh:
for seg in self.segments:
## Continue unless dsDNA
if not isinstance(seg,DoubleStrandedSegment): continue
for strand_piece in seg.strand_pieces['fwd']:
assert( strand_piece.is_fwd )
for nt1 in strand_piece.children:
nt2 = nt1.basepair
if nt1.resname == 'ADE':
names = (('N1','N3'),('N6','O4'))
elif nt1.resname == 'GUA':
names = (('N2','O2'),('N1','N3'),('O6','N4'))
elif nt1.resname == 'CYT':
names = (('O2','N2'),('N3','N1'),('N4','O6'))
elif nt1.resname == 'THY':
names = (('N3','N1'),('O4','N6'))
else:
raise Exception("Unrecognized nucleotide!")
for n1, n2 in names:
i = nt1._get_atomic_index(name=n1)
j = nt2._get_atomic_index(name=n2)
fh.write("bond %d %d %f %.2f\n" % (i,j,spring_constant,2.8))
def write_atomic_ENM(self, output_name, lattice_type=None, interhelical_bonds=True):
## TODO: ensure atomic model was generated already
if lattice_type is None:
try:
lattice_type = self.lattice_type
except:
lattice_type = "square"
else:
try:
if lattice_type != self.lattice_type:
print("WARNING: printing ENM with a lattice type ({}) that differs from model's lattice type ({})".format(lattice_type,self.lattice_type))
except:
pass
if lattice_type == "square":
enmTemplate = enmTemplateSQ
elif lattice_type == "honeycomb":
enmTemplate = enmTemplateHC
else:
raise Exception("Lattice type '%s' not supported" % self.latticeType)
## TODO: allow ENM to be created without first building atomic model
noStackPrime = 0
noBasepair = 0
with open("%s.exb" % output_name,'w') as fh:
# natoms=0
pairtypes = ('pair','stack','cross','paircross')
bonds = {k:[] for k in pairtypes}
for seg in self.segments:
## Continue unless dsDNA
if not isinstance(seg,DoubleStrandedSegment): continue
for strand_piece in seg.strand_pieces['fwd'] + seg.strand_pieces['rev']:
for nt1 in strand_piece.children:
other = []
nt2 = nt1.basepair
if strand_piece.is_fwd:
other.append((nt2,'pair'))
nt2 = nt2.get_intrahelical_above()
if nt2 is not None and strand_piece.is_fwd:
## TODO: check if this already exists
other.append((nt2,'paircross'))
nt2 = nt1.get_intrahelical_above()
if nt2 is not None:
other.append((nt2,'stack'))
try:
nt2 = nt2.basepair
except:
assert( isinstance(nt2.parent.segment, SingleStrandedSegment) )
nt2 = None
if nt2 is not None and strand_piece.is_fwd:
other.append((nt2,'cross'))
for nt2,pairtype in other:
"""
if np.linalg.norm(nt2.position-nt1.position) > 7:
import pdb
pdb.set_trace()
"""
key = ','.join((pairtype,nt1.sequence[0],nt2.sequence[0]))
for n1, n2, d in enmTemplate[key]:
d = float(d)
k = 0.1
if lattice_type == 'honeycomb':
correctionKey = ','.join((key,n1,n2))
assert(correctionKey in enmCorrectionsHC)
dk,dr = enmCorrectionsHC[correctionKey]
k = float(dk)
d += float(dr)
i = nt1._get_atomic_index(name=n1)
j = nt2._get_atomic_index(name=n2)
bonds[pairtype].append((i,j,k,d))
# print("NO STACKS found for:", noStackPrime)
# print("NO BASEPAIRS found for:", noBasepair)
for k,bondlist in bonds.items():
if len(bondlist) != len(set(bondlist)):
devlogger.warning("Duplicate ENM bonds for pair type {}".format(k))
fh.write("# {}\n".format(k.upper()))
for b in set(bondlist):
fh.write("bond %d %d %f %.2f\n" % b)
## Loop dsDNA regions
push_bonds = []
processed_segs = set()
## TODO possibly merge some of this code with SegmentModel.get_consecutive_crossovers()
for segI in self.segments: # TODOTODO: generalize through some abstract intrahelical interface that effectively joins "segments", for now interhelical bonds that cross intrahelically-connected segments are ignored
if not isinstance(segI,DoubleStrandedSegment): continue
## Loop over dsDNA regions connected by crossovers
conn_locs = segI.get_contour_sorted_connections_and_locations("crossover")
other_segs = list(set([B.container for c,A,B in conn_locs]))
for segJ in other_segs:
if (segI,segJ) in processed_segs:
continue
processed_segs.add((segI,segJ))
processed_segs.add((segJ,segI))
## TODO perhaps handle ends that are not between crossovers
## Loop over ordered pairs of crossovers between the two
cls = filter(lambda x: x[-1].container == segJ, conn_locs)
cls = sorted( cls, key=lambda x: x[1].get_nt_pos() )
for cl1,cl2 in zip(cls[:-1],cls[1:]):
c1,A1,B1 = cl1
c2,A2,B2 = cl2
ntsI1,ntsI2 = [segI.contour_to_nt_pos(A.address) for A in (A1,A2)]
ntsJ1,ntsJ2 = [segJ.contour_to_nt_pos(B.address) for B in (B1,B2)]
ntsI = ntsI2-ntsI1+1
ntsJ = ntsJ2-ntsJ1+1
# assert( np.isclose( ntsI, int(round(ntsI)) ) )
# assert( np.isclose( ntsJ, int(round(ntsJ)) ) )
ntsI,ntsJ = [int(round(i)) for i in (ntsI,ntsJ)]
## Find if dsDNA "segments" are pointing in same direction
## could move this block out of the loop
tangentA = segI.contour_to_tangent(A1.address)
tangentB = segJ.contour_to_tangent(B1.address)
dot1 = tangentA.dot(tangentB)
tangentA = segI.contour_to_tangent(A2.address)
tangentB = segJ.contour_to_tangent(B2.address)
dot2 = tangentA.dot(tangentB)
if dot1 > 0.5 and dot2 > 0.5:
...
elif dot1 < -0.5 and dot2 < -0.5:
## TODO, reverse
...
# print("Warning: {} and {} are on antiparallel helices (not yet implemented)... skipping".format(A1,B1))
continue
else:
# print("Warning: {} and {} are on helices that do not point in similar direction... skipping".format(A1,B1))
continue
## Go through each nucleotide between the two
for ijmin in range(min(ntsI,ntsJ)):
i=j=ijmin
if ntsI < ntsJ:
j = int(round(float(ntsJ*i)/ntsI))
elif ntsJ < ntsI:
i = int(round(float(ntsI*j)/ntsJ))
ntI_idx = int(round(ntsI1+i))
ntJ_idx = int(round(ntsJ1+j))
## Skip nucleotides that are too close to crossovers
if i < 11 or j < 11: continue
if ntsI2-ntI_idx < 11 or ntsJ2-ntJ_idx < 11: continue
## Find phosphates at ntI/ntJ
for direction in [True,False]:
try:
i = segI._get_atomic_nucleotide(ntI_idx, direction)._get_atomic_index(name="P")
j = segJ._get_atomic_nucleotide(ntJ_idx, direction)._get_atomic_index(name="P")
push_bonds.append((i,j))
except:
# print("WARNING: could not find 'P' atom in {}:{} or {}:{}".format( segI, ntI_idx, segJ, ntJ_idx ))
...
if len(push_bonds) != len(set(push_bonds)):
devlogger.warning("Duplicate enrgmd push bonds")
push_bonds = list(set( push_bonds ))
# print("PUSH BONDS:", len(push_bonds))
if interhelical_bonds:
if not self.useTclForces:
with open("%s.exb" % output_name, 'a') as fh:
fh.write("# PUSHBONDS\n")
for i,j in push_bonds:
fh.write("bond %d %d %f %.2f\n" % (i,j,1.0,31))
else:
flat_push_bonds = list(sum(push_bonds))
atomList = list(set( flat_push_bonds ))
with open("%s.forces.tcl" % output_name,'w') as fh:
fh.write("set atomList {%s}\n\n" %
" ".join([str(x-1) for x in atomList]) )
fh.write("set bonds {%s}\n" %
" ".join([str(x-1) for x in flat_push_bonds]) )
fh.write("""
foreach atom $atomList {
addatom $atom
}
proc calcforces {} {
global atomList bonds
loadcoords rv
foreach i $atomList {
set force($i) {0 0 0}
}
foreach {i j} $bonds {
set rvec [vecsub $rv($j) $rv($i)]
# lassign $rvec x y z
# set r [expr {sqrt($x*$x+$y*$y+$z*$z)}]
set r [getbond $rv($j) $rv($i)]
set f [expr {2*($r-31.0)/$r}]
vecadd $force($i) [vecscale $f $rvec]
vecadd $force($j) [vecscale [expr {-1.0*$f}] $rvec]
}
foreach i $atomList {
addforce $i $force($i)
}
}
""")
def get_bounding_box( self, num_points=3 ):
positions = np.zeros( (len(self.segments)*num_points, 3) )
i = 0
for s in self.segments:
for c in np.linspace(0,1,num_points):
positions[i] = (s.contour_to_position(c))
i += 1
min_ = np.array([np.min(positions[:,i]) for i in range(3)])
max_ = np.array([np.max(positions[:,i]) for i in range(3)])
return min_,max_
def get_bounding_box_center( self, num_points=3 ):
min_,max_ = self.get_bounding_box(num_points)
return 0.5*(max_+min_)
def dimensions_from_structure( self, padding_factor=1.5, isotropic=False ):
min_,max_ = self.get_bounding_box()
dx,dy,dz = (max_-min_+30)*padding_factor
if isotropic:
dx = dy = dz = max((dx,dy,dz))
return np.array([dx,dy,dz])
def add_grid_potential(self, grid_file, scale=1, per_nucleotide=True, filter_fn=None):
grid_file = Path(grid_file)
if not grid_file.is_file():
raise ValueError("Grid file {} does not exist".format(grid_file))
if not grid_file.is_absolute():
grid_file = Path.cwd() / grid_file
self.grid_potentials.append((grid_file,scale,per_nucleotide, filter_fn))
try:
self._apply_grid_potentials_to_beads(self._beadtype_s)
except:
pass
def _apply_grid_potentials_to_beads(self, bead_type_dict ):
for grid_file, scale, per_nucleotide, filter_fn in self.grid_potentials:
def add_grid_to_type(particle_type):
s = scale*particle_type.nts if per_nucleotide else scale
try:
particle_type.grid = list(particle_type.grid) + [(grid_file, s)]
except:
particle_type.grid = [(grid_file, s)]
particle_type.grid = tuple(particle_type.grid)
if filter_fn is None:
for key,particle_type in bead_type_dict.items():
add_grid_to_type(particle_type)
else:
grid_types = dict()
for b in filter(filter_fn, sum([seg.beads for seg in self.segments],[])):
t = b.type_
# if t.name[0] == "O": continue # there are cases where an advanced user may want to apply grid to O beads
if t not in grid_types:
new_type = ParticleType(name=t.name+'G',charge=t.charge, parent=t)
add_grid_to_type(new_type)
grid_types[t] = new_type
b.type_ = grid_types[t]
def _generate_atomic_model(self, scale=1):
## TODO: deprecate
self.generate_atomic_model(scale=scale)
def generate_atomic_model(self, scale=1):
self.clear_beads()
try:
for seg in self.segments:
seg.sequence[0]
except:
logger.warning('Sequence unset for some part of the model: randomzing')
for seg in self.segments:
seg.randomize_unset_sequence()
self.children = self.strands # TODO: is this going to be okay? probably
first_atomic_index = 0
for s in self.strands:
first_atomic_index = s.generate_atomic_model(scale,first_atomic_index)
self._assign_basepairs()
def write_namd_configuration( self, output_name, minimization_steps=4800, num_steps = 1e6,
output_directory = 'output',
update_dimensions=True, extrabonds=True ):
num_steps = int(num_steps//12)*12
minimization_steps = int(minimization_steps//24)*24
if num_steps < 12:
raise ValueError("Must run with at least 12 steps")
if minimization_steps < 24:
raise ValueError("Must run with at least 24 minimization steps")
format_data = self.__dict__.copy() # get parameters from System object
if 'temperature' not in format_data:
format_data['temperature'] = 295
format_data['extrabonds'] = """extraBonds on
extraBondsFile $prefix.exb
""" if extrabonds else ""
if self.useTclForces:
format_data['margin'] = ""
format_data['tcl_forces'] = """tclForces on
tclForcesScript $prefix.forces.tcl
"""
else:
format_data['margin'] = """margin 30
"""
format_data['tcl_forces'] = ""
if update_dimensions:
format_data['dimensions'] = self.dimensions_from_structure()
for k,v in zip('XYZ', format_data['dimensions']):
format_data['origin'+k] = -v*0.5
format_data['cell'+k] = v
format_data['prefix'] = output_name
format_data['minimization_steps'] = int(minimization_steps//2)
format_data['num_steps'] = num_steps
format_data['output_directory'] = output_directory
filename = '{}.namd'.format(output_name)
with open(filename,'w') as fh:
fh.write("""
set prefix {prefix}
set nLast 0; # increment when continueing a simulation
set n [expr $nLast+1]
set out {output_directory}/$prefix-$n
set temperature {temperature}
structure $prefix.psf
coordinates $prefix.pdb
outputName $out
XSTfile $out.xst
DCDfile $out.dcd
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters charmm36.nbfix/par_all36_na.prm
parameters charmm36.nbfix/par_water_ions_na.prm
wrapAll off
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
switching on
switchdist 8
cutoff 10
pairlistdist 12
{margin}
# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 3
stepspercycle 12
# PME (for full-system periodic electrostatics)
PME no
PMEGridSpacing 1.2
# Constant Temperature Control
langevin on ;# do langevin dynamics
# langevinDamping 1 ;# damping coefficient (gamma); used in original study
langevinDamping 0.1 ;# less friction for faster relaxation
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# output
useGroupPressure yes
xstFreq 4800
outputEnergies 4800
dcdfreq 4800
restartfreq 48000
#############################################################
## EXTRA FORCES ##
#############################################################
# ENM and intrahelical extrabonds
{extrabonds}
{tcl_forces}
#############################################################
## RUN ##
#############################################################
# Continuing a job from the restart files
cellBasisVector1 {cellX} 0 0
cellBasisVector2 0 {cellY} 0
cellBasisVector3 0 0 {cellZ}
if {{$nLast == 0}} {{
temperature 300
fixedAtoms on
fixedAtomsForces on
fixedAtomsFile $prefix.fixed.pdb
fixedAtomsCol B
minimize {minimization_steps:d}
fixedAtoms off
minimize {minimization_steps:d}
}} else {{
bincoordinates {output_directory}/$prefix-$nLast.restart.coor
binvelocities {output_directory}/$prefix-$nLast.restart.vel
}}
run {num_steps:d}
""".format(**format_data))
def atomic_simulate(self, output_name, output_directory='output', dry_run = False, namd2=None, log_file=None, num_procs=None, gpu=None, minimization_steps=4800, num_steps=1e6, write_pqr=False, copy_ff_from=get_arbdmodel_resource_path("charmm36.nbfix") ):
import shutil
if self.cacheUpToDate == False:
self._countParticleTypes()
self._updateParticleOrder()
if output_directory == '': output_directory='.'
self.write_pdb( output_name + ".pdb" )
self.write_pdb( output_name + ".fixed.pdb", beta_from_fixed=True )
if write_pqr: self.write_pqr( output_name + ".pqr" )
self.write_psf( output_name + ".psf" )
self.write_namd_configuration( output_name, output_directory = output_directory, minimization_steps=minimization_steps, num_steps=num_steps )
if copy_ff_from is not None and copy_ff_from != '':
try:
shutil.copytree( copy_ff_from, Path(copy_ff_from).stem )
except FileExistsError:
pass
# os.sync()
if not dry_run:
if namd2 is None:
for path in os.environ["PATH"].split(os.pathsep):
path = path.strip('"')
fname = os.path.join(path, "namd2")
if os.path.isfile(fname) and os.access(fname, os.X_OK):
namd2 = fname
break
if namd2 is None: raise Exception("NAMD2 was not found")
if not os.path.exists(namd2):
raise Exception("NAMD2 was not found")
if not os.path.isfile(namd2):
raise Exception("NAMD2 was not found")
if not os.access(namd2, os.X_OK):
raise Exception("NAMD2 is not executable")
if not os.path.exists(output_directory):
os.makedirs(output_directory)
elif not os.path.isdir(output_directory):
raise Exception("output_directory '%s' is not a directory!" % output_directory)
if num_procs is None:
import multiprocessing
num_procs = max(1,multiprocessing.cpu_count()-1)
cmd = [namd2, '+p{}'.format(num_procs), "%s.namd" % output_name]
cmd = tuple(str(x) for x in cmd)
print("Running NAMD2 with: %s" % " ".join(cmd))
if log_file is None or (hasattr(log_file,'write') and callable(log_file.write)):
fd = sys.stdout if log_file is None else log_file
process = subprocess.Popen(cmd, stdout=subprocess.PIPE, universal_newlines=True)
for line in process.stdout:
fd.write(line)
fd.flush()
else:
with open(log_file,'w') as fd:
process = subprocess.Popen(cmd, stdout=log_file, universal_newlines=True)
process.communicate()
""" OxDNA """
## https://dna.physics.ox.ac.uk/index.php/Documentation#Input_file
def generate_oxdna_model(self, scale=1):
self.clear_beads()
self.children = self.strands
for s in self.strands:
s.generate_oxdna_model()
def _write_oxdna_configuration(self, filename, gpu=0):
_angstroms_to_oxdna = 0.11739845 ## units "AA" "8.518e-10 m"
with open(filename,'w') as fh:
fh.write("""t = {temperature}
b = {dimX} {dimY} {dimZ}
E = 0 0 0
""".format(temperature=self.configuration.temperature,
dimX = self.dimensions[0]*_angstroms_to_oxdna,
dimY = self.dimensions[1]*_angstroms_to_oxdna,
dimZ = self.dimensions[2]*_angstroms_to_oxdna))
base_vec = np.array((1,0,0)) # TODO
norm_vec = np.array((0,0,1)) # TODO
## Traverse 3'-to-5'
for nt in [nt for s in self.strands for nt in s.oxdna_nt[::-1]]:
data = dict()
# o = nt.collapsedOrientation()
o = nt.orientation
for k,v in zip('x y z'.split(),nt.get_collapsed_position()):
data[k] = v * _angstroms_to_oxdna
for k,v in zip('x y z'.split(),o.dot(base_vec)):
data['b'+k] = v
for k,v in zip('x y z'.split(),o.dot(norm_vec)):
data['n'+k] = v
fh.write("{x} {y} {z} {bx} {by} {bz} {nx} {ny} {nz} 0 0 0 0 0 0\n".format(**data)
)
def _write_oxdna_topology(self,filename):
strands = [s for s in self.strands if s.num_nt > 0]
with open(filename,'w') as fh:
fh.write("{num_nts} {num_strands}\n".format(
num_nts = sum([s.num_nt for s in strands]),
num_strands = len(self.strands)))
idx = 0
sidx = 1
for strand in strands:
prev = idx+strand.num_nt-1 if strand.is_circular else -1
last = idx if strand.is_circular else -1
## Traverse 3'-to-5'
sequence = [seq for s in strand.strand_segments
for seq in s.get_sequence()][::-1]
for seq in sequence[:-1]:
## strand seq 3' 5'
fh.write("{} {} {} {}\n".format(sidx, seq, prev, idx+1))
prev = idx
idx += 1
seq = sequence[-1]
fh.write("{} {} {} {}\n".format(sidx, seq, prev, last))
idx += 1
sidx += 1
def _write_oxdna_input(self, filename,
topology,
conf_file,
trajectory_file,
last_conf_file,
log_file,
num_steps = 1e6,
interaction_type = 'DNA2',
salt_concentration = None,
print_conf_interval = None,
print_energy_every = None,
timestep = 0.003,
sim_type = "MD",
backend = None,
backend_precision = None,
seed = None,
newtonian_steps = 103,
diff_coeff = 2.50,
thermostat = "john",
list_type = "cells",
ensemble = "nvt",
delta_translation = 0.22,
delta_rotation = 0.22,
verlet_skin = 0.5,
max_backbone_force = 100,
external_forces_file = None,
seq_dep_file = None,
gpu = 0
):
if seed is None:
import random
seed = random.randint(1,99999)
temperature = self.configuration.temperature
num_steps = int(num_steps)
newtonian_steps = int(newtonian_steps)
if print_conf_interval is None:
# print_conf_interval = min(num_steps//100)
print_conf_interval = 10000
print_conf_interval = int(print_conf_interval)
if print_energy_every is None:
print_energy_every = print_conf_interval
print_energy_every = int(print_energy_every)
if max_backbone_force is not None:
max_backbone_force = 'max_backbone_force = {}'.format(max_backbone_force)
if interaction_type in ('DNA2',):
if salt_concentration is None:
try:
## units "80 epsilon0 295 k K / (2 (AA)**2 e**2/particle)" mM
salt_concentration = 9331.3126/self.debye_length**2
except:
salt_concentration = 0.5
salt_concentration = 'salt_concentration = {}'.format(salt_concentration)
else:
salt_concentration = ''
if backend is None:
backend = 'CUDA' if sim_type == 'MD' else 'CPU'
if backend_precision is None:
backend_precision = 'mixed' if backend == 'CUDA' else 'double'
if sim_type == 'VMMC':
ensemble = 'ensemble = {}'.format(ensemble)
delta_translation = 'delta_translation = {}'.format(delta_translation)
delta_rotation = 'delta_rotation = {}'.format(delta_rotation)
else:
ensemble = ''
delta_translation = ''
delta_rotation = ''
if external_forces_file is None:
external_forces = "external_forces = 0"
else:
external_forces = "external_forces = 1\nexternal_forces_file = {}".format(external_forces_file)
if seq_dep_file is None:
sequence_dependence = ""
else:
if seq_dep_file == "oxDNA2":
seq_dep_file = get_resource_path("oxDNA2_sequence_dependent_parameters.txt")
elif seq_dep_file == "oxDNA1":
seq_dep_file = get_resource_path("oxDNA1_sequence_dependent_parameters.txt")
sequence_dependence = "use_average_seq = 1\nseq_dep_file = {}".format(seq_dep_file)
with open(filename,'w') as fh:
fh.write("""##############################
#### PROGRAM PARAMETERS ####
##############################
interaction_type = {interaction_type}
{salt_concentration}
sim_type = {sim_type}
backend = {backend}
CUDA_device = {gpu}
backend_precision = {backend_precision}
#debug = 1
seed = {seed}
##############################
#### SIM PARAMETERS ####
##############################
steps = {num_steps:d}
newtonian_steps = {newtonian_steps:d}
diff_coeff = {diff_coeff}
thermostat = {thermostat}
list_type = {list_type}
{ensemble}
{delta_translation}
{delta_rotation}
T = {temperature:f} K
dt = {timestep}
verlet_skin = {verlet_skin}
{max_backbone_force}
{external_forces}
{sequence_dependence}
##############################
#### INPUT / OUTPUT ####
##############################
box_type = orthogonal
topology = {topology}
conf_file = {conf_file}
lastconf_file = {last_conf_file}
trajectory_file = {trajectory_file}
refresh_vel = 1
log_file = {log_file}
no_stdout_energy = 1
restart_step_counter = 1
energy_file = {log_file}.energy.dat
print_conf_interval = {print_conf_interval}
print_energy_every = {print_energy_every}
time_scale = linear
""".format( **locals() ))
def simulate_oxdna(self, output_name, directory='.', output_directory='output', topology=None, configuration=None, oxDNA=None, gpu=0, **oxdna_args):
if output_directory == '': output_directory='.'
d_orig = os.getcwd()
if not os.path.exists(directory):
os.makedirs(directory)
os.chdir(directory)
try:
if oxDNA is None:
for path in os.environ["PATH"].split(os.pathsep):
path = path.strip('"')
fname = os.path.join(path, "oxDNA")
if os.path.isfile(fname) and os.access(fname, os.X_OK):
oxDNA = fname
break
if oxDNA is None: raise Exception("oxDNA was not found")
if not os.path.exists(oxDNA):
raise Exception("oxDNA was not found")
if not os.path.isfile(oxDNA):
raise Exception("oxDNA was not found")
if not os.access(oxDNA, os.X_OK):
raise Exception("oxDNA is not executable")
if not os.path.exists(output_directory):
os.makedirs(output_directory)
elif not os.path.isdir(output_directory):
raise Exception("output_directory '%s' is not a directory!" % output_directory)
if configuration is None:
configuration = "{}.conf".format(output_name)
self._write_oxdna_configuration(configuration)
# elif not Path(configuration).exists():
# raise Exception("Unable to find oxDNA configuration file '{}'.".format(configuration))
if topology is None:
topology = "{}-topology.dat".format(output_name)
self._write_oxdna_topology(topology)
elif not Path(topology).exists():
raise Exception("Unable to find oxDNA topology file '{}'.".format(topology))
last_conf_file = "{}/{}.last.conf".format(output_directory,output_name)
input_file = "{}-input".format(output_name)
self._write_oxdna_input(input_file,
topology = topology,
conf_file = configuration,
trajectory_file = "{}/{}.dat".format(output_directory,output_name),
last_conf_file = last_conf_file,
log_file="{}/{}.log".format(output_directory,output_name),
gpu = gpu,
**oxdna_args)
# os.sync()
## TODO: call oxdna
cmd = [oxDNA, input_file]
cmd = tuple(str(x) for x in cmd)
print("Running oxDNA with: %s" % " ".join(cmd))
process = subprocess.Popen(cmd, stdout=subprocess.PIPE, universal_newlines=True)
for line in process.stdout:
sys.stdout.write(line)
sys.stdout.flush()
return topology,last_conf_file
finally:
os.chdir(d_orig)
""" Visualization """
def vmd_tube_tcl(self, file_name="drawTubes.tcl"):
with open(file_name, 'w') as tclFile:
tclFile.write("## beginning TCL script \n")
def draw_tube(segment,radius_value=10, color="cyan", resolution=5):
tclFile.write("## Tube being drawn... \n")
contours = np.linspace(0,1, max(2,1+segment.num_nt//resolution) )
rs = [segment.contour_to_position(c) for c in contours]
radius_value = str(radius_value)
tclFile.write("graphics top color {} \n".format(str(color)))
for i in range(len(rs)-2):
r0 = rs[i]
r1 = rs[i+1]
filled = "yes" if i in (0,len(rs)-2) else "no"
tclFile.write("graphics top cylinder {{ {} {} {} }} {{ {} {} {} }} radius {} resolution 30 filled {} \n".format(r0[0], r0[1], r0[2], r1[0], r1[1], r1[2], str(radius_value), filled))
tclFile.write("graphics top sphere {{ {} {} {} }} radius {} resolution 30\n".format(r1[0], r1[1], r1[2], str(radius_value)))
r0 = rs[-2]
r0 = rs[-1]
tclFile.write("graphics top cylinder {{ {} {} {} }} {{ {} {} {} }} radius {} resolution 30 filled yes \n".format(r0[0], r0[1], r0[2], r1[0], r1[1], r1[2], str(radius_value)))
## material
tclFile.write("graphics top materials on \n")
tclFile.write("graphics top material AOEdgy \n")
## iterate through the model segments
for s in self.segments:
if isinstance(s,DoubleStrandedSegment):
tclFile.write("## dsDNA! \n")
draw_tube(s,10,"cyan")
elif isinstance(s,SingleStrandedSegment):
tclFile.write("## ssDNA! \n")
draw_tube(s,3,"orange",resolution=1.5)
else:
raise Exception ("your model includes beads that are neither ssDNA nor dsDNA")
## tclFile complete
tclFile.close()
def vmd_cylinder_tcl(self, file_name="drawCylinders.tcl"):
#raise NotImplementedError
with open(file_name, 'w') as tclFile:
tclFile.write("## beginning TCL script \n")
def draw_cylinder(segment,radius_value=10,color="cyan"):
tclFile.write("## cylinder being drawn... \n")
r0 = segment.contour_to_position(0)
r1 = segment.contour_to_position(1)
radius_value = str(radius_value)
color = str(color)
tclFile.write("graphics top color {} \n".format(color))
tclFile.write("graphics top cylinder {{ {} {} {} }} {{ {} {} {} }} radius {} resolution 30 filled yes \n".format(r0[0], r0[1], r0[2], r1[0], r1[1], r1[2], radius_value))
## material
tclFile.write("graphics top materials on \n")
tclFile.write("graphics top material AOEdgy \n")
## iterate through the model segments
for s in self.segments:
if isinstance(s,DoubleStrandedSegment):
tclFile.write("## dsDNA! \n")
draw_cylinder(s,10,"cyan")
elif isinstance(s,SingleStrandedSegment):
tclFile.write("## ssDNA! \n")
draw_cylinder(s,3,"orange")
else:
raise Exception ("your model includes beads that are neither ssDNA nor dsDNA")
## tclFile complete
tclFile.close()
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