Scoring of structures

This examples illustrates how to use IMP.bff.AVNetworkRestraint for scoring structures in a trajectory.

import json
import tqdm
import pylab as plt

import RMF
import IMP
import IMP.rmf
import IMP.atom
import IMP.bff

Load an RMF file and create a hierarchy

print("Creating IMP Model")
m = IMP.Model()
rmf_fn = IMP.bff.get_example_path("structure/T4L/t4l_docking.rmf3")

print("Loading RMF")
frame_index = 0
f = RMF.open_rmf_file_read_only(rmf_fn)
hier = IMP.rmf.create_hierarchies(f, m)[frame_index]
IMP.rmf.load_frame(f, RMF.FrameID(frame_index))

Creating IMP Model
Loading RMF

Load fps.json file and create restraint for scoring

print("Creating FRET restraint")
fps_json_path = IMP.bff.get_example_path("structure/T4L/fret.fps.json")
with open(fps_json_path) as fp:
    fps_json = json.load(fp)
score_set_c1 = "chi2_C1_33p"
fret_restraint = IMP.bff.AVNetworkRestraint(
    hier, fps_json_path,
    score_set=score_set_c1
)
v = fret_restraint.unprotected_evaluate(None)

Creating FRET restraint

Score each frame in the RMF file and plot score

print("Scoring frames")
scores = list()
for frame in tqdm.tqdm(f.get_root_frames()):
    IMP.rmf.load_frame(f, frame)
    v = fret_restraint.unprotected_evaluate(None)
    scores.append(v)

Scoring frames

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Plot score for each frame

plt.plot(scores, "o-")
plt.xlabel("Frame")
plt.ylabel("Score")
plt.show()