''' Created on 2011-1-23 @author: madlee ''' from kuai.unit import default_units from math import pi as PI SPEED_OF_LIGHT = default_units.parse(299792458, 'm/s')
def setup_model(mols, partable, par):
if isinstance(mols, Molecule):
mols = [(mols, 1)]
elif len(mols) == 2 and isinstance(mols[0], Molecule):
mols = [mols]
result = Model()
result.parameters = par
result.mols = mols
result.charges = []
result.masses = []
result.coords = []
result.atomtype = []
result.group_id = []
masses_table = partable["atom/mass"]
type2id = partable["atom/type"]
amu, _, _ = default_units.parse(1, "amu")
angerstron, _, _ = default_units.parse(1, "A")
next_group_id = 0
for m, n in mols:
charges = []
masses = []
coords = []
atomtype = []
group_id = []
for a in m.atoms:
if hasattr(a, "partial_charge"):
charges.append(a.partial_charge)
else:
charges.append(0.0)
if a.type in masses_table:
masses.append(par[masses_table[a.type]])
else:
masses.append(a.weight * amu)
if hasattr(a, "group_id"):
group_id.append(a.group_id)
assert a.type in type2id
atomtype.append(type2id[a.type])
coords.append(a.coord.x * angerstron)
coords.append(a.coord.y * angerstron)
coords.append(a.coord.z * angerstron)
result.masses += masses * n
result.coords += coords * n
result.charges += charges * n
result.atomtype += atomtype * n
group_id_map = {}
for i in group_id:
group_id_map[i] = 0
gid_in_m = [i for i in group_id_map.iterkeys()]
gid_in_m.sort()
for i in range(len(gid_in_m)):
group_id_map[gid_in_m[i]] = i
for i in range(len(group_id)):
group_id[i] = group_id_map[group_id[i]]
for i in range(n):
result.group_id += [gid + next_group_id for gid in group_id]
next_group_id += len(gid_in_m)
if len(result.charges) != len(result.masses):
del result.charges
if len(result.group_id) != len(result.masses):
del result.group_id
return result
def read_ppf(file):
line = file.next().rstrip()
if line != '#DFF:PPF':
raise RuntimeError("The input file is not a valid PPF file.")
line = file.next().rstrip()
if not line.startswith('#PROTOCOL'):
raise RuntimeError("The input file is not a valid PPF file.")
tokens = line.split('=')
if len(tokens) != 2:
raise RuntimeError("The input file is not a valid PPF file.")
type = tokens[1].strip()
COULOMB_CONST, _, _ = default_units.parse(8.987551787e9, 'N m2 / C2')
index = {}
parameters = [0.0, COULOMB_CONST]
index['forcefield']={'type':type}
for line in file:
tokens = parse_line(line)
if tokens:
if tokens[0] == 'E0':
# Useless term
pass
elif tokens[0] == 'ATYPE':
if 'atom/mass' not in index:
index['atom/mass'] = {}
key2par = index['atom/mass']
key = ' '.join(tokens[1])
tokens = tokens[2]
assert len(tokens) == 2
par = tokens[1]
par, _, _ = default_units.parse(par, 'amu')
key2par[key] = len(parameters)
parameters.append(par)
elif tokens[0] == 'N12_6':
if 'nonbond/lj12_6' not in index:
index['nonbond/lj12_6'] = {}
key2par = index['nonbond/lj12_6']
key = ' '.join(tokens[1])
tokens = tokens[2]
assert len(tokens) == 2
key2par[key] = len(parameters)
par, _, _ = default_units.parse(tokens[0], 'A')
parameters.append(par)
par, _, _ = default_units.parse(tokens[1], 'kcal/mol')
parameters.append(par)
elif tokens[0] == 'ATC':
if 'atom/charge' not in index:
index['atom/charge'] = {}
key2par = index['atom/charge']
key = ' '.join(tokens[1])
tokens = tokens[2]
assert len(tokens) == 1
key2par[key] = len(parameters)
par, _, _ = default_units.parse(tokens[0], 'e')
parameters.append(par)
elif tokens[0] == 'BINC':
if 'bond/binc' not in index:
index['bond/binc'] = {}
key2par = index['bond/binc']
key = tokens[1]
assert len(key) == 2
if key[0] > key[1]:
key[0], key[1] = key[1], key[0]
reverse=True
else:
reverse=False
key = ' '.join(key)
tokens = tokens[2]
assert len(tokens) == 1
key2par[key] = len(parameters)
par, _, _ = default_units.parse(tokens[0], 'e')
if reverse:
parameters.append(-par)
else:
parameters.append(par)
elif tokens[0] == 'BHARM':
if 'bond/harmonic' not in index:
index['bond/harmonic'] = {}
key2par = index['bond/harmonic']
key = tokens[1]
assert len(key) == 2
if key[0] > key[1]:
key[0], key[1] = key[1], key[0]
reverse=True
else:
reverse=False
key = ' '.join(key)
tokens = tokens[2]
assert len(tokens) == 2
key2par[key] = len(parameters)
par, _, _ = default_units.parse(tokens[0], 'A')
parameters.append(par)
par, _, _ = default_units.parse(tokens[1], 'kcal/mol/A2')
parameters.append(par)
elif tokens[0] == 'AHARM':
if 'angle/harmonic' not in index:
index['angle/harmonic'] = {}
key2par = index['angle/harmonic']
key = tokens[1]
assert len(key) == 3
if key[0] > key[2]:
key[0], key[2] = key[2], key[0]
reverse=True
else:
reverse=False
key = ' '.join([i.strip() for i in key])
tokens = tokens[2]
assert len(tokens) == 2
key2par[key] = len(parameters)
par, _, _ = default_units.parse(tokens[0], 'deg')
parameters.append(par)
par, _, _ = default_units.parse(tokens[1], 'kcal/mol/rad2')
parameters.append(par)
elif tokens[0] == 'TCOSP':
if 'torsion/cos_poly5' not in index:
index['torsion/cos_poly5'] = {}
key2par = index['torsion/cos_poly5']
key = tokens[1]
assert len(key) == 4
if key[1] > key[2] or key[1] == key[2] and key[0] > key[3]:
key[0], key[3] = key[3], key[0]
key[1], key[2] = key[2], key[1]
reverse=True
else:
reverse=False
key = ' '.join([i.strip() for i in key])
tokens = tokens[2]
assert len(tokens) % 3 == 0
key2par[key] = len(parameters)
v = [0] * 5
k = [0] * 6
for i in range(0, len(tokens), 3):
n = int(tokens[i+2]+.1)
kI = tokens[i+1]
phi = tokens[i+0]
if phi > 150:
assert abs(phi-180) < 1
kI = -kI
else:
assert abs(phi) < 1
if n % 2 == 0:
kI = -kI
assert v[n] == 0
v[n] = 2 * kI
k[0]=v[2]+(v[1]+v[3])/2
k[1]=0.5*(3*v[3]-v[1])
k[2]=-v[2]+4*v[4]
k[3]=-2*v[3]
k[4]=-4*v[4]
k[5]=0
for i in range(0, len(k)):
k[i], _, _ = default_units.parse(k[i], 'kcal/mol')
parameters += k
elif tokens[0] == 'IBCOS':
if 'improper_torsion/cos_poly5' not in index:
index['improper_torsion/cos_poly5'] = {}
key2par = index['improper_torsion/cos_poly5']
key = tokens[1]
assert len(key) == 4
key = ' '.join(key)
tokens = tokens[2]
assert len(tokens) % 3 == 0
key2par[key] = len(parameters)
v = [0] * 6
k = [0] * 6
for i in range(0, len(tokens), 3):
n = int(tokens[i+2]+.1)
kI = tokens[i+1]
phi = tokens[i+0]
if phi > 150:
assert abs(phi-180) < 1
kI = -kI
else:
assert abs(phi) < 1
if n % 2 == 0:
kI = -kI
assert v[n] == 0
v[n] = 2 * kI
k[0]=v[2]+(v[1]+v[3])/2
k[1]=0.5*(3*v[3]-v[1])
k[2]=-v[2]+4*v[4]
k[3]=-2*v[3]
k[4]=-4*v[4]
k[5]=0
for i in range(0, len(k)):
k[i], _, _ = default_units.parse(k[i], 'kcal/mol')
parameters += k
else:
raise RuntimeError("The function %s is not supported yet." % tokens[0])
if type == 'AMBER':
index['forcefield']['scale14/vdw'] = 0.5
index['forcefield']['scale14/columnb'] = 1 / 1.2
atomtype, newindex = combine(index['nonbond/lj12_6'], parameters, combine_arithmatic)
newindex[':columnb-constant:'] = 1
index['pair-nonbond/lj12_6'] = newindex
index['atom/type'] = atomtype
index['pair-14/lj12_6'] = scale_vdw(newindex, parameters, 0.5, 1)
columnb14 = parameters[newindex[':columnb-constant:']] / 1.2
index['pair-14/lj12_6'][':columnb-constant:'] = len(parameters)
parameters.append(columnb14)
else:
raise RuntimeError("The force field type %s is not supported yet." % type)
return index, parameters
