def showvirtualAtoms(filename):
sm = get_sm(filename)
cg = sm.bg
clash_energy = fbe.StemVirtualResClashEnergy()
clash_energy.eval_energy(sm)
forJson = {"virtual_atoms": []}
virtualAtoms = ftug.virtual_atoms(sm.bg, sidechain=True)
for residuePos in virtualAtoms.keys():
stem = cg.get_node_from_residue_num(residuePos)
if stem[0] != "s": continue #Only virtual res for stems!
residue = virtualAtoms[residuePos]
for aname in residue.keys():
isClashing = False
if stem in clash_energy.bad_bulges:
for clashing in clash_energy.bad_atoms[stem]:
if np.allclose(residue[aname], clashing):
isClashing = True
break
atomInfo = {
"atomname": aname,
"center": residue[aname].tolist(),
"is_clashing": isClashing,
"loop": stem
}
forJson["virtual_atoms"].append(atomInfo)
return jsonify(forJson)
def setUp(self):
self.cg = ftmc.CoarseGrainRNA.from_bg_file(
'test/fess/data/1GID_A-structure1.coord')
self.cg_copy = ftmc.CoarseGrainRNA.from_bg_file(
'test/fess/data/1GID_A-structure1.coord')
self.sm = fbm.SpatialModel(self.cg)
self.cg2 = ftmc.CoarseGrainRNA.from_bg_file(
'test/fess/data/1GID_A-clash.coord')
self.sm2 = fbm.SpatialModel(self.cg2)
real_stats_fn = 'fess/stats/all_nr3.36.stats'
self.stat_source = stat_container.StatStorage(real_stats_fn)
self.sm.constraint_energy = fbe.StemVirtualResClashEnergy()
self.sm2.constraint_energy = fbe.StemVirtualResClashEnergy()
e1 = fbe.RoughJunctionClosureEnergy()
e2 = fbe.RoughJunctionClosureEnergy()
for e, sm in [(e1, self.sm), (e2, self.sm2)]:
for ml in sm.bg.defines:
if ml[0] == "m":
sm.junction_constraint_energy[ml] = e
self.builder = fbb.Builder(self.stat_source)
def setUp(self):
self.cg = ftmc.CoarseGrainRNA.from_bg_file(
'test/fess/data/1GID_A-structure1.coord')
self.cg2 = ftmc.CoarseGrainRNA.from_bg_file(
'test/fess/data/1GID_A-structure2.coord')
self.cg_clash = ftmc.CoarseGrainRNA.from_bg_file(
'test/fess/data/1GID_A-clash.coord')
self.cg.add_all_virtual_residues()
self.cg2.add_all_virtual_residues()
self.cg_clash.add_all_virtual_residues()
#self.sm = fbm.SpatialModel(cg)
#self.sm.load_sampled_elems()
#self.sm2 = fbm.SpatialModel(cg2)
#self.sm2.load_sampled_elems()
#self.sm_clash= fbm.SpatialModel(cg_clash)
#self.sm_clash.load_sampled_elems()
self.energy = fbe.StemVirtualResClashEnergy()
def getStructureJson(sm):
clash_energy = fbe.StemVirtualResClashEnergy()
try:
clash_energy.eval_energy(sm)
except KeyError:
sm.bg.add_all_virtual_residues()
clash_energy.eval_energy(sm)
forJson = {"loops": [], "bad_bulges": [], "status": "OK"}
for element in sm.bg.coords:
forJson["loops"].append(cylinderToThree(sm.bg.coords[element],
element))
if clash_energy.bad_bulges:
forJson["bad_bulges"] = list(set(clash_energy.bad_bulges))
forJson["dotbracket"] = sm.bg.to_dotbracket_string()
forJson["sequence"] = sm.bg.seq
return jsonify(forJson)
def structureStats(filename):
sm = get_sm(filename)
cg = sm.bg
clash_energy = fbe.StemVirtualResClashEnergy()
clash_energy.eval_energy(sm)
numclashes = sum(
len(clash_energy.bad_atoms[x]) for x in clash_energy.bad_atoms)
junction_energy = fbe.RoughJunctionClosureEnergy()
j = junction_energy.eval_energy(sm)
print("J Energy is ", j)
return render_template("structureinfo.html",
cg=cg,
numclashes=numclashes,
clashbulges=", ".join(
sorted(set(clash_energy.bad_bulges),
key=lambda x: int(x[1:]))),
bad_junctions=", ".join(
sorted(set(junction_energy.bad_bulges),
key=lambda x: int(x[1:]))))