def __init__(self):
mix = Mixture()
mix.loadWFM(WOLFFIA_WFY_DIR + "/PABApentane.wfm")
print(mix.molecules())
Molecule.__init__(self,
"PABA-Pentane",
molecule=mix.getMolecule("PABA-Pentane_1"))
self.changeResidues("PAB")
def __init__(self, m, n, q):
diamondMix = Mixture()
diamondMix.loadWFM(WOLFFIA_WFY_DIR + "/diamond.wfm")
diamondCell = diamondMix.getMolecule('Diamond_1')
sal = Element("NA")
sal.moveBy([-1, -1, -1]) # put it out of the way
#'Crece' el diamante
tempMixture = Mixture()
for dm in range(m):
for dn in range(n):
for dq in range(q):
newCell = diamondCell.copy()
newCell.moveby([dm * 5.43, dn * 5.43, dq * 5.43])
tempMixture.add(newCell)
tempMixture.add(sal)
G = tempMixture.copy()
H = tempMixture.copy()
Coord = []
overlapAtoms = []
atomNeighbors = []
toEliminate = []
#Hace que las moleculas se conecten al atomo de Na y hace de la mezcla una molecula
for p, mol in enumerate(G):
molecule = G.getMolecule(mol)
for idx, atom1 in enumerate(molecule):
if molecule.getAttributes(
atom1).getInfo().getElement() == "NA":
molSal = mol
numMolecule = p
atomSal = molecule.atom(idx)
for p, mol in enumerate(G):
molecule = G.getMolecule(mol)
if p != numMolecule:
molC = mol
atomC = molecule.atom(1)
H.addBond([molSal, atomSal], [molC, atomC])
#Pone las coordenadas de la mezcla en una lista
for p, mol in enumerate(H):
molecule = H.getMolecule(mol)
for atom in molecule:
coordinates = molecule.getAttributes(atom).getCoord()
Coord.append(coordinates)
#Te da los atomos que estan en la misma posicion
for a, coord1 in enumerate(Coord):
#print a,coord1
for x, coord2 in enumerate(Coord):
if a < x and math.fabs(
coord1[0] - coord2[0]) < TOLERANCE and math.fabs(
coord1[1] - coord2[1]) < TOLERANCE and math.fabs(
coord1[2] - coord2[2]) < TOLERANCE:
overlapAtoms.append(a)
overlapAtoms.append(x)
toEliminate.append(x)
#Te dice los vecinos de los atomos
for mol in H:
molecule = H.getMolecule(mol)
for i in range(len(overlapAtoms) / 2):
vecinos = molecule.neighbors(overlapAtoms[2 * i + 1] + 1)
#atomNeighbors.append(overlapAtoms[2*i+1]+1)
atomNeighbors.append(vecinos)
G = H.copy()
for p, mol in enumerate(G):
molecule = G.getMolecule(mol)
for i, j in enumerate(atomNeighbors):
#print i, len(j), j[0]
mol1 = mol
atom1 = molecule.atom(overlapAtoms[2 * i])
#print atom1, "atomo 1", i
if len(j) == 1:
atom2 = molecule.atom(j[0] - 1)
#print j[0]
#print atom2, atom1
H.addBond([mol1, atom1], [mol1, atom2])
elif len(j) == 2:
atom2A = molecule.atom(j[0] - 1)
atom2B = molecule.atom(j[1] - 1)
H.addBond([mol1, atom1], [mol1, atom2A])
H.addBond([mol1, atom1], [mol1, atom2B])
#toEliminate.sort()
G = H.copy()
#print "a Eliminarse", toEliminate
toEliminate = sorted(set(toEliminate))
#Busca el indice del atomo Na
for p, mol in enumerate(G):
molecule = G.getMolecule(mol)
for idx, atom1 in enumerate(molecule):
if molecule.getAttributes(
atom1).getInfo().getElement() == "NA":
idxNa = idx + 1
#Elimina los atomos 'repetidos' y el atomo de Na
for p, mol in enumerate(G):
molecule = G.getMolecule(mol)
for i in reversed(toEliminate):
#print i+1
molecule.removeAtom(i + 1)
molecule.removeAtom(idxNa)
Molecule.__init__(self, "Diamond", next(G.moleculeGenerator()))
# Fix atom types
for atom in self:
N = len(self.neighbors(atom))
if N == 4:
self.getAtomAttributes(atom).getInfo().setType("C")
if N == 1:
self.getAtomAttributes(atom).getInfo().setType("C2")
if N == 2:
self.getAtomAttributes(atom).getInfo().setType("C3")
self.getForceField().setBond(('C', 'C'), 222., NonBond._EPSILON)
self.getForceField().setBond(('C', 'C'), 1.512, NonBond._SIGMA)
