def angleangle(types, frc):
coeffs,missing = [],[]
for t in types:
# jj'_______k'
# /\
# / \ E = K*(theta-theta0)*(theta'-theta0')
# i/ \k,i'
# ijkl kjil ijlk
aa1,aa2,aa3 = sortaa(t[:]),sortaa([t[3],t[1],t[0],t[2]]),sortaa([t[0],t[1],t[3],t[2]])
m1,m2,m3 = frc.get_param(aa1,'aa'),frc.get_param(aa2,'aa'),frc.get_param(aa3,'aa')
# Gives the three types of angles possible in a torsion term.
# a1=ijk a2=ijl a3=kjl
a1,a2,a3 = sort(t[0:3]), sort([t[0],t[1],t[3]]), sort([t[2],t[1],t[3]])
t1,t2,t3 = frc.get_param(a1,'a'),frc.get_param(a2,'a'),frc.get_param(a3,'a')
if any([p==None for p in [t1,t2,t3,m1,m2,m3]]):
if m1==None and not ['aa',aa1] in missing: missing += [['aa',aa1]]
if m2==None and not ['aa',aa2] in missing: missing += [['aa',aa2]]
if m3==None and not ['aa',aa3] in missing: missing += [['aa',aa3]]
if t1 == None: missing += [[ 'a', a1]]
if t2 == None: missing += [[ 'a', a2]]
if t3 == None: missing += [[ 'a', a3]]
c = 6*[0.0]
else:
c = m1 + m2 + m3 + [t1[0],t2[0],t3[0]]
coeffs.append(tuple(c))
return coeffs,missing
def bondbond(types, frc):
coeffs,missing = [],[]
for t in types:
b1,b2 = frc.get_param(sort(t[0:2]),'b'),frc.get_param(sort(t[1:3]),'b')
bb = frc.get_param(t, 'bb')
try:
c = bb + [b1[0], b2[0]]
except:
missing += [['bb',t]]
c = 3*[0.0]
coeffs.append(tuple(c))
return coeffs,missing
def bondbond13(types, frc):
coeffs,missing = [],[]
for t in types:
b1,b3 = frc.get_param(sort(t[0:2]),'b'), frc.get_param(sort(t[2:4]),'b')
bb13 = frc.get_param(t, 'bb13')
if b1==None or b3==None or bb13==None:
missing += [['bb13', t]]
c = 3*[0.0]
else:
c = bb13 + [b1[0], b3[0]]
coeffs.append(tuple(c))
return coeffs,missing
def bondbond(types, frc):
coeffs, missing = [], []
for t in types:
b1, b2 = frc.get_param(sort(t[0:2]),
'b'), frc.get_param(sort(t[1:3]), 'b')
bb = frc.get_param(t, 'bb')
try:
c = bb + [b1[0], b2[0]]
except:
missing += [['bb', t]]
c = 3 * [0.0]
coeffs.append(tuple(c))
return coeffs, missing
def bondbond13(types, frc):
coeffs, missing = [], []
for t in types:
b1, b3 = frc.get_param(sort(t[0:2]),
'b'), frc.get_param(sort(t[2:4]), 'b')
bb13 = frc.get_param(t, 'bb13')
if b1 == None or b3 == None or bb13 == None:
missing += [['bb13', t]]
c = 3 * [0.0]
else:
c = bb13 + [b1[0], b3[0]]
coeffs.append(tuple(c))
return coeffs, missing
def angleangletorsion(types, frc):
coeffs, missing = [], []
for t in types:
a1, a2 = sort(t[0:3]), sort(t[1:4])
t1, t2 = frc.get_param(a1, 'a'), frc.get_param(a2, 'a')
aat = frc.get_param(t, 'aat')
if t1 == None or t2 == None or aat == None:
missing += [['aat', t]]
c = 3 * [0.0]
else:
c = aat + [t1[0], t2[0]]
coeffs.append(tuple(c))
return coeffs, missing
def bondangle(types, frc):
coeffs,missing = [],[]
for t in types:
b1,b2 = frc.get_param(sort(t[0:2]),'b'),frc.get_param(sort(t[1:3]),'b')
ba = frc.get_param(t, 'ba')
try:
if len(ba) == 1: ba += ba
c = ba + [b1[0], b2[0]]
except:
c = 4*[0.0]
missing += [['ba', t]]
coeffs.append(tuple(c))
return coeffs,missing
def angletorsion(types, frc):
coeffs,missing = [],[]
for t in types:
a1,a2 = frc.get_param(sort(t[0:3]),'a'),frc.get_param(sort(t[1:4]),'a')
at = frc.get_param(t, 'at')
if a1==None or a2==None or at==None:
missing += [['at', t]]
c = 8*[0.0]
else:
if len(at) == 3: at += at
c = at + [a1[0], a2[0]]
coeffs.append(tuple(c))
return coeffs,missing
def endbondtorsion(types, frc):
coeffs,missing = [],[]
for t in types:
b1,b3 = frc.get_param(sort(t[0:2]),'b'), frc.get_param(sort(t[2:4]),'b')
ebt = frc.get_param(t, 'ebt')
if b1==None or b3==None or ebt==None:
missing += [['ebt', t]]
c = 8*[0.0]
else:
if len(ebt) == 3: ebt += ebt
c = ebt + [b1[0], b3[0]]
coeffs.append(tuple(c))
return coeffs,missing
def angleangletorsion(types, frc):
coeffs,missing = [],[]
for t in types:
a1,a2=sort(t[0:3]),sort(t[1:4])
t1,t2 = frc.get_param(a1,'a'),frc.get_param(a2,'a')
aat = frc.get_param(t, 'aat')
if t1==None or t2==None or aat==None:
missing += [['aat', t]]
c = 3*[0.0]
else:
c = aat + [t1[0], t2[0]]
coeffs.append(tuple(c))
return coeffs,missing
def bondangle(types, frc):
coeffs, missing = [], []
for t in types:
b1, b2 = frc.get_param(sort(t[0:2]),
'b'), frc.get_param(sort(t[1:3]), 'b')
ba = frc.get_param(t, 'ba')
try:
if len(ba) == 1: ba += ba
c = ba + [b1[0], b2[0]]
except:
c = 4 * [0.0]
missing += [['ba', t]]
coeffs.append(tuple(c))
return coeffs, missing
def angletorsion(types, frc):
coeffs, missing = [], []
for t in types:
a1, a2 = frc.get_param(sort(t[0:3]),
'a'), frc.get_param(sort(t[1:4]), 'a')
at = frc.get_param(t, 'at')
if a1 == None or a2 == None or at == None:
missing += [['at', t]]
c = 8 * [0.0]
else:
if len(at) == 3: at += at
c = at + [a1[0], a2[0]]
coeffs.append(tuple(c))
return coeffs, missing
def endbondtorsion(types, frc):
coeffs, missing = [], []
for t in types:
b1, b3 = frc.get_param(sort(t[0:2]),
'b'), frc.get_param(sort(t[2:4]), 'b')
ebt = frc.get_param(t, 'ebt')
if b1 == None or b3 == None or ebt == None:
missing += [['ebt', t]]
c = 8 * [0.0]
else:
if len(ebt) == 3: ebt += ebt
c = ebt + [b1[0], b3[0]]
coeffs.append(tuple(c))
return coeffs, missing
def midbondtorsion(types, frc):
coeffs, missing = [], []
for t in types:
mb = frc.get_param(sort(t[1:3]), 'b')
mbt = frc.get_param(t, 'mbt')
if mb == None or mbt == None:
missing += [['mbt', t]]
c = 4 * [0.0]
else:
c = mbt + [mb[0]]
coeffs.append(tuple(c))
return coeffs, missing
def midbondtorsion(types, frc):
coeffs,missing = [],[]
for t in types:
mb = frc.get_param(sort(t[1:3]),'b')
mbt = frc.get_param(t, 'mbt')
if mb==None or mbt==None:
missing += [['mbt', t]]
c = 4*[0.0]
else:
c = mbt + [mb[0]]
coeffs.append(tuple(c))
return coeffs,missing
def angleangle(types, frc):
coeffs, missing = [], []
for t in types:
# jj'_______k'
# /\
# / \ E = K*(theta-theta0)*(theta'-theta0')
# i/ \k,i'
# ijkl kjil ijlk
aa1, aa2, aa3 = sortaa(t[:]), sortaa([t[3], t[1], t[0], t[2]]), sortaa(
[t[0], t[1], t[3], t[2]])
m1, m2, m3 = frc.get_param(aa1, 'aa'), frc.get_param(
aa2, 'aa'), frc.get_param(aa3, 'aa')
# Gives the three types of angles possible in a torsion term.
# a1=ijk a2=ijl a3=kjl
a1, a2, a3 = sort(t[0:3]), sort([t[0], t[1],
t[3]]), sort([t[2], t[1], t[3]])
t1, t2, t3 = frc.get_param(a1, 'a'), frc.get_param(a2,
'a'), frc.get_param(
a3, 'a')
if any([p == None for p in [t1, t2, t3, m1, m2, m3]]):
if m1 == None and not ['aa', aa1] in missing:
missing += [['aa', aa1]]
if m2 == None and not ['aa', aa2] in missing:
missing += [['aa', aa2]]
if m3 == None and not ['aa', aa3] in missing:
missing += [['aa', aa3]]
if t1 == None: missing += [['a', a1]]
if t2 == None: missing += [['a', a2]]
if t3 == None: missing += [['a', a3]]
c = 6 * [0.0]
else:
c = m1 + m2 + m3 + [t1[0], t2[0], t3[0]]
coeffs.append(tuple(c))
return coeffs, missing