def __init__(self):
Molecule.__init__(self, "WATER")
# print NANOCAD_PDB_DIR + "/Solvents/WATER.pdb" , NANOCAD_PDB_DIR + "/Solvents/WATER.psf"
#self.load(NANOCAD_PDB_DIR + "/Solvents/WATER.pdb" , NANOCAD_PDB_DIR + "/Solvents/WATER.psf")
# build water molecule
atr = AtomAttributes(WATER.otObj,
[4.01300001, 0.83099997, -9.08300018])
#print "----------------------->", str(atr)
self.add_atom(atr, [])
atr = AtomAttributes(WATER.htObj,
[4.94099998, 0.84399998, -8.83699989])
#print "----------------------->", str(atr)
self.add_atom(atr, [1])
atr = AtomAttributes(WATER.htObj, [3.75, -0.068, -9.29300022])
#print "----------------------->", str(atr)
self.add_atom(atr, [1])
if WATER._FORCE_FIELD == None:
print("WATER generating FF")
WATER._FORCE_FIELD = ForceField(
self, NANOCAD_FORCE_FIELDS + "/WATER.prm")
#print "WATER1", WATER._FORCE_FIELD._BONDS
self.setForceField(WATER._FORCE_FIELD)
#print "WATER2", self.getForceField()._BONDS
self.copyChargesToForceField()
def __init__(self):
Molecule.__init__(self, "H2O2")
# print NANOCAD_PDB_DIR + "/Solvents/WATER.pdb" , NANOCAD_PDB_DIR + "/Solvents/WATER.psf"
#self.load(NANOCAD_PDB_DIR + "/Solvents/WATER.pdb" , NANOCAD_PDB_DIR + "/Solvents/WATER.psf")
# build water H2O2
atr = AtomAttributes("OT1", "O", "OT", [ -0.077, 0.000, 0.730 ], 0.834, 15.9994, 0.0, 1.0, ' ', "OT ", "XXX", "A", 1)
#print "----------------------->", str(atr)
self.add_node(1, attrs=[atr])
atr = AtomAttributes("OT2", "O", "OT", [ 0.077, 0.000, -0.730], 0.834, 15.9994, 0.0, 1.0, ' ', "OT ", "XXX", "A", 1)
#print "----------------------->", str(atr)
self.add_node(2, attrs=[atr])
atr = AtomAttributes("HT1", "H", "HT", [ -1.077, 0.000, 1.730], 0.417, 1.00794, 0.0, 1.0, ' ', "HT ", "XXX", "A", 1)
#print "----------------------->", str(atr)
self.add_node(3, attrs=[atr])
atr = AtomAttributes("HT2", "H", "HT", [ 1.077, 0.000, -1.730], 0.417, 1.00794, 0.0, 1.0, ' ', "HT ", "XXX", "A", 1)
#print "----------------------->", str(atr)
self.add_node(4, attrs=[atr])
self.addBond(1, 2)
self.addBond(1, 3)
self.addBond(2, 4)
#self.add_angle(3,1,2)
#self.add_angle(1,2,4)
#self.add_dihedral(1,2,3,4)
self.setForceField(_FORCE_FIELD )
self.copyChargesToForceField()
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):
Molecule.__init__(self, "SDSplusNA")
#print NANOCAD_PDB_DIR + "/Solvents/THF.pdb" , NANOCAD_PDB_DIR + "/Solvents/THF.psf"
self.load(NANOCAD_PDB_DIR + "/Surfactant/SDSplusNA.pdb",
NANOCAD_PDB_DIR + "/Surfactant/SDSplusNA.psf")
self.setForceField(_FORCE_FIELD)
def __init__(self):
Molecule.__init__(self, "Argon")
atr = AtomAttributes("AR", "AR", "AR", [0.0, 0.0, 0.0], 0.0, 39.9500,
0.0, 1.0, ' ', "OT ", "WAT", "A", 1)
#print "----------------------->", str(atr)
self.add_node(1, attrs=[atr])
self.setForceField(self._FORCE_FIELD)
self.copyChargesToForceField()
def __init__(self):
Molecule.__init__(self, "AcetoneAllH")
#print NANOCAD_PDB_DIR + "/Solvents/Acetone-All-H.pdb" , NANOCAD_PDB_DIR + "/Solvents/Acetone-All-H.psf"
self.load(NANOCAD_PDB_DIR + "/Solvents/AcetoneAllH.pdb",
NANOCAD_PDB_DIR + "/Solvents/AcetoneAllH.psf")
if AcetoneAllH._FORCE_FIELD == None:
AcetoneAllH._FORCE_FIELD = ForceField(
self, NANOCAD_FORCE_FIELDS + "/AcetoneAllH.prm")
self.setForceField(AcetoneAllH._FORCE_FIELD)
self.copyChargesToForceField()
def __init__(self, chain, molname=None):
print("Polymer")
if type(self) == Polymer:
raise Molecule.MoleculeError(
"Polymer is an abstract class. Should not be directly instantiated."
)
if molname == None:
molname = str(chain)
Molecule.__init__(self, molname)
if hasattr(self, 'MONOMERS_PDBS'): self.chainOldStyle(chain)
else: self.chainMolStyle(chain)
def __init__(self):
Molecule.__init__(self, "Na")
atr = AtomAttributes(Na.ai, [0.0, 0.0, 0.0])
self.add_atom(atr, [])
#print NANOCAD_PDB_DIR + "/Solvents/THF.pdb" , NANOCAD_PDB_DIR + "/Solvents/THF.psf"
self.load(NANOCAD_PDB_DIR + "/Ions/Na.pdb",
NANOCAD_PDB_DIR + "/Ions/Na.psf")
if Na._FORCE_FIELD == None:
Na._FORCE_FIELD = ForceField(self)
Na._FORCE_FIELD.setNonBond("Na", -0.1153, NonBond._EPSILON)
Na._FORCE_FIELD.setNonBond("Na", 2.275, NonBond._SIGMA)
Na._FORCE_FIELD.setNonBond("Na", 1., NonBond._CHARGE)
self.setForceField(Na._FORCE_FIELD)
self.copyChargesToForceField()
def __init__(self):
Molecule.__init__(self, "CLF4")
atr = AtomAttributes(CLF4.ai1, [0., 0., 0.])
self.add_atom(atr, [])
atr = AtomAttributes(CLF4.ai2, [0.58099997, -1.07599998, -1.27499998])
self.add_atom(atr, [1])
atr = AtomAttributes(CLF4.ai3, [1.29900002, 0.29100001, 1.16199994])
self.add_atom(atr, [1])
atr = AtomAttributes(CLF4.ai4, [-0.509, 1.53499997, -0.71100003])
self.add_atom(atr, [1])
if CLF4._FORCE_FIELD == None:
CLF4._FORCE_FIELD = ForceField(self,
NANOCAD_FORCE_FIELDS + "/CLF4.prm")
self.setForceField(CLF4._FORCE_FIELD)
self.copyChargesToForceField()
def __init__(self,n,m,length, element="C", bondLength=1.421, mass=12.011):
Molecule.__init__(self, element + "_hP4(" + str(n) + "," + str(n) + ")")
self.coords = []
self._n = n
self._m = m
self._length = length
self._mass = mass
self._bondLength = bondLength
self._element = element
self._ribbonWidth = 0.
self.ai = AtomInfo("C", self._element, "C", 0., self._mass, 'HP4')
self.generateZigZag()
self.rotateSheet()
#self.removeLoneAtoms()
self.recalculateDimensions()
def __init__(self, symbol):
try:
symbol = symbol.upper()
nbParameters = Element._FORCE_FIELD_PARAMETERS[symbol]
except:
import logging
logger = logging.getLogger(self.__class__.__name__)
logger.error("Invalid element symbol \"" + str(symbol) + "\"")
print("Invalid element symbol \"" + str(symbol) + "\"")
return
Molecule.__init__(self, symbol)
self.add_node(1, attrs=[copy.deepcopy(Element._ATTRIBUTES[symbol])])
ff = ForceField(self)
ff.setNonBond(symbol, nbParameters[NonBond._EPSILON], NonBond._EPSILON)
ff.setNonBond(symbol, nbParameters[NonBond._SIGMA] / 2.,
NonBond._SIGMA) # VDw DISTANCE DIVIDED BY 2!!!!!
self.setForceField(ff)
def __init__(self):
Molecule.__init__(self, "DMF")
#print NANOCAD_PDB_DIR + "/Solvents/DMF.pdb" , NANOCAD_PDB_DIR + "/Solvents/DMF.psf"
#self.load(NANOCAD_PDB_DIR + "/Solvents/DMF.pdb" , NANOCAD_PDB_DIR + "/Solvents/DMF.psf")
atr = AtomAttributes(DMF.ai1, [0.045, -0.12800001, 0.038])
self.add_atom(atr, [])
atr = AtomAttributes(DMF.ai2, [-0.38, 1.09099996, -0.31900001])
self.add_atom(atr, [1])
atr = AtomAttributes(DMF.ai3, [0.45500001, 2.171, -0.19499999])
self.add_atom(atr, [2])
atr = AtomAttributes(DMF.ai4, [1.38699996, -0.30599999, 0.55500001])
self.add_atom(atr, [1])
atr = AtomAttributes(DMF.ai5, [-0.838, -1.26999998, -0.094])
self.add_atom(atr, [1])
atr = AtomAttributes(DMF.ai6, [-1.38, 1.22399998, -0.70499998])
self.add_atom(atr, [2])
atr = AtomAttributes(DMF.ai7, [1.37600005, -0.192, 1.63900006])
self.add_atom(atr, [4])
atr = AtomAttributes(DMF.ai8, [2.04699993, 0.442, 0.117])
self.add_atom(atr, [4])
atr = AtomAttributes(DMF.ai9, [1.74600005, -1.30299997, 0.29800001])
self.add_atom(atr, [4])
atr = AtomAttributes(DMF.ai10, [-1.12800002, -1.38699996, -1.13800001])
self.add_atom(atr, [5])
atr = AtomAttributes(DMF.ai11, [-1.72899997, -1.11199999, 0.51499999])
self.add_atom(atr, [5])
atr = AtomAttributes(DMF.ai12, [-0.322, -2.16899991, 0.243])
self.add_atom(atr, [5])
if DMF._FORCE_FIELD == None:
DMF._FORCE_FIELD = ForceField(self,
NANOCAD_FORCE_FIELDS + "/DMF.prm")
self.setForceField(DMF._FORCE_FIELD)
self.copyChargesToForceField()
def chainOldStyle(self, chain):
print("chainOldStyle")
if len(chain) == 1:
self.load(self.ONE_MONOMER_PDB[chain[0]])
return
for dn in range(len(chain)):
# print "Polymer(",NANOCAD_PDB_DIR+self.MONOMERS_PDBS[chain[dn]],")"
monomer = Molecule(chain[dn])
monomer.load(NANOCAD_PDB_DIR + self.MONOMERS_PDBS[chain[dn]],
NANOCAD_PDB_DIR + self.MONOMERS_PSFS[chain[dn]])
monomer.rotateRad(0.0, dn * self.ANGLE, 0.0)
monomer.moveby([0.0, self.DISPL * dn, 0.0])
if self.order() == 0:
self.merge(monomer, [])
elif hasattr(self, 'START_ATOM'):
self.merge(monomer, [[
self.order() - self.NUM_ATOMS_BACKBONE_MONOMER +
self.END_ATOM, self.START_ATOM
]])
else:
self.merge(monomer, [[self.order(), 1]])
def __init__(self, parent, molecule=None):
'''
Constructor
'''
super(CHARMMParameterFinderDialog, self).__init__(parent, modal=1)
self.ui = Ui_CHARMMParameterFinderDialog()
self.ui.setupUi(self)
self.parent = parent
self.forceField = None
self.pairing = None
self.thread = None
self.molecule = Molecule(molecule.molname(), molecule)
self.originalMolecule = molecule
self.ui.timeLeftClock.setValue(self.ui.timeLimitSlider.value())
self.timer = QtCore.QTimer()
self.connect(self.timer, QtCore.SIGNAL('timeout()'), self.on_timer)
self.ui.acceptButton.setEnabled(False)
self.ui.reportTextEdit.setReadOnly(True)
self.ui.startButton.setEnabled(False)
def __init__(self):
Molecule.__init__(self, "THF")
#print NANOCAD_PDB_DIR + "/Solvents/THF.pdb" , NANOCAD_PDB_DIR + "/Solvents/THF.psf"
#self.load(NANOCAD_PDB_DIR + "/Solvents/THF.pdb" , NANOCAD_PDB_DIR + "/Solvents/THF.psf")
atr = AtomAttributes(THF.atr1, [0.180, 0.300, -2.690])
self.add_atom(atr, [])
atr = AtomAttributes(THF.atr2, [1.084, 0.909, -2.675])
self.add_atom(atr, [1])
atr = AtomAttributes(THF.atr3, [-0.637, 0.671, -3.309])
self.add_atom(atr, [1])
atr = AtomAttributes(THF.atr4, [-0.350, 0.030, -1.310])
self.add_atom(atr, [1])
atr = AtomAttributes(THF.atr5, [-1.282, -0.535, -1.328])
self.add_atom(atr, [4])
atr = AtomAttributes(THF.atr6, [-0.371, 0.969, -0.757])
self.add_atom(atr, [4])
atr = AtomAttributes(THF.atr7, [0.820, -0.800, -0.800])
self.add_atom(atr, [4])
atr = AtomAttributes(THF.atr8, [0.539, -1.361, 0.091])
self.add_atom(atr, [7])
atr = AtomAttributes(THF.atr9, [1.667, -0.126, -0.669])
self.add_atom(atr, [7])
atr = AtomAttributes(THF.atr10, [1.110, -1.690, -1.900])
self.add_atom(atr, [7])
atr = AtomAttributes(THF.atr11, [0.460, -1.140, -3.080])
self.add_atom(atr, [1, 10])
atr = AtomAttributes(THF.atr12, [-0.501, -1.639, -3.207])
self.add_atom(atr, [11])
atr = AtomAttributes(THF.atr13, [1.120, -1.188, -3.946])
self.add_atom(atr, [11])
'''
self.addBond(1,2)
self.addBond(1,3)
self.addBond(1,4)
self.addBond(1,11)
self.addBond(4,5)
self.addBond(4,6)
self.addBond(4,7)
self.addBond(7,8)
self.addBond(7,9)
self.addBond(7,10)
self.addBond(10,11)
self.addBond(11,12)
self.addBond(11,13)
'''
#self.add_angle()
#self.add_angle()
#self.add_angle()
#self.add_angle()
#self.add_dihedrals ()
#self.add_dihedrals ()
if THF._FORCE_FIELD == None:
THF._FORCE_FIELD = ForceField(self,
NANOCAD_FORCE_FIELDS + "/THF.prm")
self.setForceField(THF._FORCE_FIELD)
self.copyChargesToForceField()
def __init__(self): Molecule.__init__(self, "Xylene") #print NANOCAD_PDB_DIR + "/Solvents/THF.pdb" , NANOCAD_PDB_DIR + "/Solvents/THF.psf" self.load(NANOCAD_PDB_DIR + "/Solvents/Xylene.pdb" , NANOCAD_PDB_DIR + "/Solvents/Xylene.psf")
def __init__(self,
n,
m,
length,
element="C",
bondLength=1.421,
mass=12.011):
self.coords = []
self._n = n
self._m = m
self._length = length
self._mass = mass
self._bondLength = bondLength
self._element = element
self.EPSILON = bondLength / 2.
sheet = Hexagonal2D(n, m, length, element, bondLength, mass)
unitVectLength = self._bondLength * math.sqrt(
2. - 2. * math.cos(2. * math.pi / 3.))
#tubePerimeter = unitVectLength * math.sqrt(n*n+m*m)
tubePerimeter = sheet.getWidth() + self._bondLength
#print tubePerimeter
radius = tubePerimeter / 2. / math.pi
xToAngleFactor = 2. * math.pi / tubePerimeter
atoms = sheet.atoms()
for atom in atoms:
attr = sheet.getAtomAttributes(atom)
coords = attr.getCoord()
angle = coords[0] * xToAngleFactor
attr.setCoord([
radius * math.cos(angle), radius * math.sin(angle), coords[2]
])
sheet.setAtomAttributes(atom, attr)
# close tube
incomplete = []
#print "degree:",
for atom in atoms:
#print sheet.degree(atom),
if sheet.degree(atom) < 3:
incomplete.append(atom)
for atom1 in incomplete:
for atom2 in incomplete:
if atom1 != atom2 and not sheet.has_edge(
atom1, atom2) and sheet.distance(
atom1, atom2) < bondLength + self.EPSILON:
sheet.addBond(atom1, atom2)
#print "sheet.addBond(",atom1,", ",atom2
# remove redundant atoms and bonds
#for i in range(len(atoms)):
# for j in range(i+1,len(atoms)):
# if sheet.distance(atoms[i], atoms[j]) < self.EPSILON:
# print "caca",sheet.distance(atoms[i], atoms[j])
# sheet.removeAtom(atoms[i])
# break
molname = element + "_Tube(" + str(m) + "," + str(n) + ")"
Molecule.__init__(self, molname, sheet)
if Tube._FORCE_FIELD == None:
Tube._FORCE_FIELD = ForceField(self,
NANOCAD_FORCE_FIELDS + "/CNT.prm")
self.setForceField(Tube._FORCE_FIELD)
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)
def _processFirstFrame(self):
"""
Gets the first pybel Molecule and puts its Wolffia equivalent Mixture in self.currentMolecule.
Returns the first frame.
Raises whichever exception that pybel throws (probably StopIteration).
"""
mol = next(self.molIterator)
chemicalGraphMixed = ChemicalGraph()
etable = openbabel.OBElementTable()
n = 0
for atom in mol.atoms:
atomType = atom.OBAtom.GetResidue().GetAtomID(atom.OBAtom)
symbol = etable.GetSymbol(atom.atomicnum)
coords = list(atom.coords)
name = etable.GetName(atom.atomicnum)
residue = atom.OBAtom.GetResidue().GetName()
psfType = atom.OBAtom.GetResidue().GetAtomID(atom.OBAtom).strip()
#print "_processFirstFrame: '" + psfType + "'"
charge = atom.partialcharge
mass = atom.atomicmass
if self.psf != None:
psfType = self.psf.getType(n)
charge = self.psf.getCharge(n)
mass = self.psf.getMass(n)
print("CoordinateFile _processFirstFrame charge ", charge)
ai = AtomInfo(atomType, symbol, psfType, charge, mass, 1, 1, 1, name, residue)
atr = AtomAttributes(ai, coords, [])
chemicalGraphMixed.add_node(n + 1, attrs=[atr])
n += 1
# add edges
print('_processFirstFrame add edges')
if self.psf != None:
for b in self.psf.bonds:
try: # avoids adding an edge twice
chemicalGraphMixed.add_edge(b)
except AdditionError:
pass
if len(mol.atoms) != len(self.psf.atoms):
raise MixtureError("Amount of atoms in " + self.fileName + " and psf File files are different (" + str(len(self.atoms)) + " vs " + str(len(self.psf.atoms)) + ").")
else:
for bond in openbabel.OBMolBondIter(mol.OBMol):
chemicalGraphMixed.add_edge([bond.GetBeginAtom().GetIdx(), bond.GetEndAtom().GetIdx()])
molecules = list(chemicalGraphMixed.connectedComponents())
self.currentMolecule = Mixture()
#print '_processFirstFrame Añadir'+ str(list(molecules)) + ' moléculas a mezcla: ',
if len(molecules) == 1:
self.currentMolecule.add(Molecule(self.mixtureName, molecule=molecules[0]))
else:
n = 0
for m in molecules:
self.currentMolecule.add(
Molecule(self.mixtureName + "(" + str(n) + ")", molecule=m),
checkForInconsistentNames=False)
n += 1
return self.currentMolecule
def __init__(self):
Molecule.__init__(self, "SDS")
#print NANOCAD_PDB_DIR + "/Solvents/THF.pdb" , NANOCAD_PDB_DIR + "/Solvents/THF.psf"
self.load(NANOCAD_PDB_DIR + "/Surfactant/SDS.pdb",
NANOCAD_PDB_DIR + "/Surfactant/SDS.psf")
