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v2 = hydrogenPosition - donorPosition
v1norm = np.linalg.norm(v1)
v2norm = np.linalg.norm(v2)
dot = np.dot(v1, v2)
angle = np.degrees(np.arccos(dot / (v1norm * v2norm)))
if angle >= hbondcutangle:
dist = distarray[idx1, conv_hatom]
new_hbond = HydrogenBond(convindex2, convindex1, global_hatom, dist, angle,
hbondcutoff,
hbondcutangle)
hydrogenBonds.append(new_hbond)
# print str(convindex1) + " " + str(convindex2)
# print "hbond found: %d,%d,%d"%(convindex2,global_hatom,convindex1)
# print angle
# finalize
newAtomContact = AtomContact(int(frame), float(distance), float(weight), int(convindex1),
int(convindex2),
hydrogenBonds)
currentFrameContacts.append(newAtomContact)
contactResults.append(currentFrameContacts)
stop = time.time()
# show trajectory information and selection information
print("trajectory with %d frames loaded" % len(u.trajectory))
print("Selection 1: ", len(sel1.positions), ", Selection2: ", len(sel2.positions))
print("analyzeTime: ", stop-start)
return contactResults