diff --git a/segmentmodel.py b/segmentmodel.py
index 85faa80da3f0700e52b2b5fbcfb697bb369c6b54..3b57a50a30b788a7db6b4283ea5fa82562c6c555 100644
--- a/segmentmodel.py
+++ b/segmentmodel.py
@@ -20,16 +20,16 @@ TODO:
+ fix handling of crossovers for atomic representation
+ map to atomic representation
+ add nicks
- - transform ssDNA nucleotides
+ + transform ssDNA nucleotides
- shrink ssDNA
- - shrink dsDNA backbone
+ + shrink dsDNA backbone
+ make orientation continuous
- - sequence
+ + sequence
- handle circular dna
+ ensure crossover bead potentials aren't applied twice
+ remove performance bottlenecks
- test for large systems
- - assign sequence
+ + assign sequence
- ENM
- rework Location class
- remove recursive calls
@@ -236,193 +236,16 @@ class SegmentParticle(PointParticle):
self.intrahelical_neighbors.append(b)
b.intrahelical_neighbors.append(self)
-
- # def get_nt_position(self,seg):
- # if seg == self.parent:
- # return seg.contour_to_nt_pos(self.contour_position)
- # else:
- # cl = [e for e in self.parent.get_connections_and_locations() if e[2].container is seg]
-
- # dc = [(self.contour_position - A.address)**2 for c,A,B in cl]
-
- # if len(dc) == 0:
- # import pdb
- # pdb.set_trace()
-
- # i = np.argmin(dc)
- # c,A,B = cl[i]
- # ## TODO: generalize, removing np.abs and conditional
- # delta_nt = np.abs( A.container.contour_to_nt_pos(self.contour_position - A.address) )
- # B_nt_pos = seg.contour_to_nt_pos(B.address)
- # if B.address < 0.5:
- # return B_nt_pos-delta_nt
- # else:
- # return B_nt_pos+delta_nt
-
- def get_nt_position_old(self, seg, nearest_position_on_seg=None):
- if seg == self.parent:
- return seg.contour_to_nt_pos(self.contour_position)
- else:
-
- def get_nt_pos(contour1, seg1, seg2):
- cl = [e for e in seg1.get_connections_and_locations("intrahelical") if e[2].container is seg2]
- dc = [(contour1 - A.address)**2 for c,A,B in cl]
- if len(dc) == 0: return None,None
-
- i = np.argmin(dc)
- c,A,B = cl[i]
-
- ## TODO: generalize, removing np.abs and conditional
- # delta_nt = np.abs( seg1.contour_to_nt_pos(contour1 - A.address) )
- delta_nt = seg1.contour_to_nt_pos(contour1) - seg1.contour_to_nt_pos(A.address)
- B_nt_pos = seg2.contour_to_nt_pos(B.address)
- dirA = 2*(A.address > 0.5)-1
- dirB = 2*(B.address < 0.5)-1
- direction = dirA*dirB
- if c.type_ in ("intrahelical",):
- pass
- elif c.type_ in ("crossover","terminal-crossover"):
- direction *= -1
- else:
- raise Exception("Unhandled connection type {}".format(c.type_))
- distance = np.abs(delta_nt)+np.abs(B_nt_pos)
- return B_nt_pos + direction*delta_nt, distance
-
- pos,dist = get_nt_pos(self.contour_position, self.parent, seg)
- if pos is None:
- ## Particle is not directly connected
- visited_segs = set(seg)
- positions = []
- for l in self.locations:
- if l.container == self.parent: continue
- if l.connection.type_ != "intrahelical": continue
- pos0,dist = get_nt_pos(self.contour_position, self.parent, l.container)
- assert(pos0 is not None)
- pos0 = l.container.nt_pos_to_contour(pos0)
- pos,dist = get_nt_pos( pos0, l.container, seg )
- if pos is not None:
- positions.append( pos )
- assert( len(positions) > 0 )
- if len(positions) > 1:
- import pdb
- pdb.set_trace()
- pos = positions[0]
- return pos
-
def get_nt_position(self, seg):
""" Returns the "address" of the nucleotide relative to seg in
nucleotides, taking the shortest (intrahelical) contour length route to seg
"""
-
if seg == self.parent:
return seg.contour_to_nt_pos(self.contour_position)
else:
pos = self.get_contour_position(seg)
return seg.contour_to_nt_pos(pos)
-
- # def get_nt_pos(contour1, seg1, seg2):
- # cl = [e for e in seg1.get_connections_and_locations("intrahelical") if e[2].container is seg2]
- # dc = [(contour1 - A.address)**2 for c,A,B in cl]
- # if len(dc) == 0: return None,None
-
- # i = np.argmin(dc)
- # c,A,B = cl[i]
-
- # ## TODO: generalize, removing np.abs and conditional
- # # delta_nt = np.abs( seg1.contour_to_nt_pos(contour1 - A.address) )
- # delta_nt = seg1.contour_to_nt_pos(contour1) - seg1.contour_to_nt_pos(A.address)
- # B_nt_pos = seg2.contour_to_nt_pos(B.address)
- # dirA = 2*(A.address > 0.5)-1
- # dirB = 2*(B.address < 0.5)-1
- # direction = dirA*dirB
- # distance = np.abs(delta_nt)+np.abs(B_nt_pos)
- # return B_nt_pos + direction*delta_nt, distance
- # pos,dist = get_nt_pos(self.contour_position, self.parent, seg)
-
- cutoff = 30*3
- target_seg = seg
-
- ## depth-first search
- ## TODO cache distances to nearby locations?
- def descend_search_tree(seg, contour_in_seg, distance=0, visited_segs=[]):
- nonlocal cutoff
-
- if seg == target_seg:
- # pdb.set_trace()
- ## Found a segment in our target
- sign = (contour_in_seg == 1) - (contour_in_seg == 0)
- assert( sign in (1,-1) )
- if distance < cutoff: # TODO: check if this does anything
- cutoff = distance
- return [[distance, contour_in_seg+sign*seg.nt_pos_to_contour(distance)]]
- if distance > cutoff:
- return None
-
- ret_list = []
- ## Find intrahelical locations in seg that we might pass through
- for c,A,B in seg.get_connections_and_locations("intrahelical"):
- if B.container in visited_segs: continue
- dx = seg.contour_to_nt_pos( np.abs(A.address-contour_in_seg),
- round_nt=False)
- results = descend_search_tree( B.container, B.address,
- distance+dx, visited_segs + [seg] )
- if results is not None:
- ret_list.extend( results )
- return ret_list
-
- results = descend_search_tree(self.parent, self.contour_position)
- if results is None or len(results) == 0:
- raise Exception("Could not find location in segment") # TODO better error
- return sorted(results,key=lambda x:x[0])[0][1]
-
- # def descend_search_tree(seg, target_seg, distance, from_contour):
- # if distance > cutoff:
- # return None
- # ret_list = []
-
- # ## Find intrahelical locations in seg that we might pass through
- # for c,A,B in seg.get_connections_and_locations("intrahelical"):
- # if np.isclose(A.address, from_contour): continue
- # if B.container == target_seg:
- # ## Found a segment in our target
- # ...
- # else:
- # ret_list.append( [B.container, seg.num_nts] ]
-
-
- # curr_seg = seg
- # dist = 0
- # for c,A,B in curr_seg.get_connections_and_locations("intrahelical"):
- # while
-
- # cl = [e for e in seg1.get_connections_and_locations("intrahelical") if e[2].container is seg2]
-
-
-
- # if dist is not None and dist < closest_distance:
- # closest_distance
- # if pos is None:
- # ## Particle is not directly connected
- # visited_segs = set(seg)
- # positions = []
- # for l in self.locations:
- # if l.container == self.parent: continue
- # if l.connection.type_ != "intrahelical": continue
- # pos0,dist = get_nt_pos(self.contour_position, self.parent, l.container)
- # assert(pos0 is not None)
- # pos0 = l.container.nt_pos_to_contour(pos0)
- # pos,dist = get_nt_pos( pos0, l.container, seg )
- # if pos is not None:
- # positions.append( pos )
- # assert( len(positions) > 0 )
- # if len(positions) > 1:
- # import pdb
- # pdb.set_trace()
- # pos = positions[0]
- # return pos
-
-
def get_contour_position(self,seg):
if seg == self.parent:
return self.contour_position