def CalculateHydrophobicMoment3(
sequence,
angle=100. / 180. * math.pi,
hydrophobicity_dict=hydrophobicity_dict_eisenberg):
if type(sequence) == type(seq.SequenceHandle()):
sequence = sequence.GetGaplessString()
elif type(sequence) != type(str()):
sequence = entity_alg.CreateSequenceFromView(
sequence, 'temp').GetGaplessString()
v = geom.Rotate(geom.Vec2(1.0, 0.0), -angle)
moment = geom.Vec2()
for r in sequence:
v = geom.Rotate(v, angle)
moment += hydrophobicity_dict[r] * v
vm = moment / geom.Length(moment)
m_max = moment
for i in range(-3, 4):
v = geom.Rotate(geom.Vec2(1.0, 0.0), -angle)
moment = geom.Vec2()
for r in sequence:
v = geom.Rotate(v, angle)
v2 = v - 0.2 * i * vm
v2 = geom.Dot(v2, vm) / geom.Length(v2) * vm
moment += hydrophobicity_dict[r] * v2
if geom.Length(moment) > geom.Length(m_max): m_max = moment
return geom.Length(m_max)
def CalculateCharge(sequence):
if type(sequence) == type(seq.SequenceHandle()):
sequence = sequence.GetGaplessString()
elif type(sequence) != type(str()):
sequence = entity_alg.CreateSequenceFromView(
sequence, 'temp').GetGaplessString()
c = 0
for s in sequence:
c += residue_charge_dict[s]
return c
def CalculateHydrophobicity(sequence,
hydrophobicity_dict=hydrophobicity_dict_eisenberg):
if type(sequence) == type(seq.SequenceHandle()):
sequence = sequence.GetGaplessString()
elif type(sequence) != type(str()):
sequence = entity_alg.CreateSequenceFromView(
sequence, 'temp').GetGaplessString()
hydrophobicity = 0.0
for r in sequence:
hydrophobicity += hydrophobicity_dict[r]
return hydrophobicity
def CalculateHydrophobicMoment(
sequence,
angle=100. / 180. * math.pi,
hydrophobicity_dict=hydrophobicity_dict_eisenberg):
if type(sequence) == type(seq.SequenceHandle()):
sequence = sequence.GetGaplessString()
elif type(sequence) != type(str()):
sequence = entity_alg.CreateSequenceFromView(
sequence, 'temp').GetGaplessString()
v = geom.Rotate(geom.Vec2(1.0, 0.0), -angle)
moment = geom.Vec2()
for r in sequence:
v = geom.Rotate(v, angle)
moment += hydrophobicity_dict[r] * v
return geom.Length(moment)
def CalculateChargeWithSlidingWindow(sequence, w=11):
if type(sequence) == type(seq.SequenceHandle()):
sequence = sequence.GetGaplessString()
elif type(sequence) != type(str()):
sequence = entity_alg.CreateSequenceFromView(
sequence, 'temp').GetGaplessString()
charge_list = []
before = int(w / 2.)
after = w - before
n = len(sequence)
for i in range(n):
b = max(0, i - before)
e = min(n, i + after)
l = float(e - b)
charge_list.append(CalculateCharge(sequence[b:e]) / l)
return charge_list
def CalculateHydrophobicityWithSlidingWindow(
sequence, w=11, hydrophobicity_dict=hydrophobicity_dict_eisenberg):
if type(sequence) == type(seq.SequenceHandle()):
sequence = sequence.GetGaplessString()
elif type(sequence) != type(str()):
sequence = entity_alg.CreateSequenceFromView(
sequence, 'temp').GetGaplessString()
hydrophobicity_list = []
before = int(w / 2.)
after = w - before
n = len(sequence)
for i in range(n):
b = max(0, i - before)
e = min(n, i + after)
l = float(e - b)
hydrophobicity_list.append(
CalculateHydrophobicity(sequence[b:e],
hydrophobicity_dict_eisenberg) / l)
return hydrophobicity_list