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Dev-long_traj #2

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db24167
Misspelled command.
lvotapka Apr 19, 2022
f8d603a
Fixed early loop termination error and added anchor selection
ilkerdvc Apr 25, 2022
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22 changes: 16 additions & 6 deletions seekrtools/long_trajectory/long_trajectory.py
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Original file line number Diff line number Diff line change
Expand Up @@ -82,7 +82,7 @@ def anchor_mmvt_output_slicer_dicer(model, anchor):
for output_file_name in output_file_list:
with open(output_file_name) as f:
for line in f.readlines():
if line.startswith("#") or line.startwith("CHECKPOINT"):
if line.startswith("#") or line.startswith("CHECKPOINT"):
continue
line_split = line.strip().split(",")
dest_milestone_alias = int(line_split[0])
Expand Down Expand Up @@ -143,8 +143,10 @@ def make_fragment_list(model):



def make_long_trajectory(model, all_anchors_fragment_list, starting_anchor_index):
ITER = 1000
def make_long_trajectory(model, all_anchors_fragment_list, starting_anchor_index, ITER = 200000):




current_anchor_index = starting_anchor_index

Expand All @@ -155,6 +157,7 @@ def make_long_trajectory(model, all_anchors_fragment_list, starting_anchor_index

long_traj = current_fragment.traj[:]


for i in range(ITER):
current_anchor = model.anchors[current_anchor_index]
dest_milestone_index = current_fragment.dest_milestone
Expand All @@ -164,13 +167,20 @@ def make_long_trajectory(model, all_anchors_fragment_list, starting_anchor_index
break

next_anchor_index = dest_milestone.neighbor_anchor_index
next_anchor_fragment_dict = all_anchors_fragment_list[next_anchor_index]
try:
next_anchor_fragment_dict = all_anchors_fragment_list[next_anchor_index]
except IndexError:
print("Trajectory terminated before final iteration at : " + str(i))
break
next_anchor_fragment_list = next_anchor_fragment_dict[dest_milestone.index]
if len(next_anchor_fragment_list) == 0:
print("Max Iteration number reached : " + str(i))
break
next_fragment = random.choice(next_anchor_fragment_list)
long_traj += next_fragment.traj
current_anchor_index = next_anchor_index
current_fragment = next_fragment

return long_traj


Expand All @@ -184,4 +194,4 @@ def make_long_trajectory(model, all_anchors_fragment_list, starting_anchor_index

long_traj = make_long_trajectory(model, all_anchors_fragment_list, bound_anchor)

long_traj.save("muller_test.dcd")
long_traj.save("muller_test.dcd")