def opls_options(molecule, parameter_file='oplsaa.prm'):
elements, atom_types, bond_types, angle_types, dihedral_types = files.read_opls_parameters(parameter_file)
elements_by_structure_indices = dict( [ (t.index2, elements_by_atomic_number[t.element] ) for t in atom_types ] )
elements_by_structure_indices[0] = 'X'
def add_to_list(dic,key,value):
if key in dic:
dic[key].append(value)
else:
dic[key] = [value]
dihedral_types_by_element={}
for d in dihedral_types:
structure_indices = d.index2s
elements = [ elements_by_structure_indices[i] for i in structure_indices]
add_to_list(dihedral_types_by_element, tuple(elements), d)
add_to_list(dihedral_types_by_element, tuple(reversed(elements)), d)
atoms, bonds, angles, dihedrals = files.read_cml(molecule, parameter_file=None)
for a in atoms:
a.index2_options = []
for d in dihedrals:
elements = tuple([ a.element for a in d.atoms ])
options = dihedral_types_by_element[elements]
options_by_i = [ [],[],[],[] ]
if elements in dihedral_types_by_element:
print elements
for a in d.atoms:
a.index2_options.append( set() )
for t in dihedral_types_by_element[elements]:
#print '\t', t.index2s
for i in range(4):
d.atoms[i].index2_options[-1].add( t.index2s[i] )
else:
print 'Error: dihedral', elements, 'does not exist in OPLS file', parameter_file
for a in atoms:
print a.element
for option in a.index2_options:
print '\t', option
options = a.index2_options[0]
for i in xrange(1,len(a.index2_options)):
options = options.intersection( a.index2_options[i] )
print '\t\t', options
def opt_opls(molecule, parameter_file='oplsaa.prm', taboo_time=100): elements, atom_types, bond_types, angle_types, dihedral_types = files.read_opls_parameters(parameter_file) atoms, bonds, angles, dihedrals = files.read_cml(molecule, parameter_file=None) bond_types_by_index2 = dict( [ (tuple(t.index2s),t) for t in bond_types ] + [ (tuple(reversed(t.index2s)),t) for t in bond_types ] ) angle_types_by_index2 = dict( [ (tuple(t.index2s),t) for t in angle_types ] + [ (tuple(reversed(t.index2s)),t) for t in angle_types ] ) dihedral_types_by_index2 = dict( [ (tuple(t.index2s),t) for t in dihedral_types ] + [ (tuple(reversed(t.index2s)),t) for t in dihedral_types ] ) charges_by_index = dict( [ (t.index,t.charge) for t in atom_types ] ) for a in atoms: a.possible_types = set() for t in atom_types: if elements_by_atomic_number[t.element] == a.element and t.bond_count==len(a.bonded): a.possible_types.add(t.index2) a.possible_types = list(a.possible_types) #a.possible_types.append(0) def count_conflicts(types): for i,a in enumerate(atoms): a.index2 = types[i] conflicts = 0 for b in bonds: index2s = (b.atoms[0].index2, b.atoms[1].index2) if not index2s in bond_types_by_index2: conflicts += 1 for a in angles: index2s = (a.atoms[0].index2, a.atoms[1].index2, a.atoms[2].index2) if not index2s in angle_types_by_index2: conflicts += 1 for d in dihedrals: index2s_0 = (d.atoms[0].index2, d.atoms[1].index2, d.atoms[2].index2, d.atoms[3].index2) index2s_1 = (0, d.atoms[1].index2, d.atoms[2].index2, d.atoms[3].index2) index2s_2 = (d.atoms[0].index2, d.atoms[1].index2, d.atoms[2].index2, 0) in0 = index2s_0 in dihedral_types_by_index2 in1 = index2s_1 in dihedral_types_by_index2 in2 = index2s_2 in dihedral_types_by_index2 if not in0 and not in1 and not in2: conflicts += 1 return conflicts import random types = [random.choice(a.possible_types) for a in atoms] taboo = [0 for a in atoms] best = count_conflicts(types) step = 0 for step in range(100000): i = random.randint( 0, len(types)-1 ) for guess in types: if taboo[i]>0: i = random.randint( 0, len(types)-1 ) else: break old_type = types[i] types[i] = random.choice(atoms[i].possible_types) conflicts = count_conflicts(types) if conflicts <= best: best = conflicts taboo[i] = taboo_time else: types[i] = old_type taboo = [t-1 if t>0 else 0 for t in taboo] if step % 10000 == 0: print best, conflicts, types step += 1 def types_from_index2(x): return [t for t in atom_types if t.index2==x and t.index<=440] for i,tt in enumerate( [ types_from_index2(x) for x in types] ): #print i, atoms[i].element atoms[i].index_options = [t.index for t in tt] #for t in tt: # print '\t', t.index, t.notes def net_charge(types): charge = 0.0 for t in types: charge += charges_by_index[t] return charge types = [random.choice(a.index_options) for a in atoms] taboo = [0 for a in atoms] best = net_charge(types) for step in range(100000): i = random.randint( 0, len(types)-1 ) for guess in types: if taboo[i]>0: i = random.randint( 0, len(types)-1 ) else: break old_type = types[i] types[i] = random.choice(atoms[i].index_options) charge = net_charge(types) if abs(charge) <= abs(best): best = charge taboo[i] = taboo_time else: types[i] = old_type taboo = [t-1 if t>0 else 0 for t in taboo] if step % 10000 == 0: print best, charge, types step += 1 for t in types: for t2 in atom_types: if t2.index==t: print t2.element, t2.notes