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):
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, "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):
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, "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 generateZigZag(self): unitVectLength = self._bondLength * math.sqrt(2.-2.*math.cos(2.*math.pi/3.)) by = math.sqrt(self._bondLength * self._bondLength - unitVectLength*unitVectLength/4) bondsArray = list() Cx = self._m * unitVectLength + math.cos(math.pi/3.) * self._n * unitVectLength Cy = math.sin(math.pi/3.) * self._n * unitVectLength Cangle = math.atan2(Cy, Cx) xMin = -self._length * math.cos(Cangle) xMax = Cx zMax = self._length + Cx xsteps = int((xMax - xMin) / unitVectLength) + 1 zsteps = int(zMax / unitVectLength) + 1 # determine gap widths # generate coordinates z = 0. for zi in range(zsteps): row1 = list() if zi % 2 == 0: x = xMin else: x = xMin + unitVectLength / 2. for xi in range(xsteps): row1.append([x,0.,z]) x += unitVectLength row2 = list() if zi % 2 == 0: x = xMin + unitVectLength / 2. else: x = xMin z += by for xi in range(xsteps): row2.append([x,0.,z]) x += unitVectLength bondsArray.append([row1,row2]) z += self._bondLength n = 1 # first two rows for row in range(len(bondsArray)): coords = bondsArray[row][0] rowLength = xsteps for coord in coords: atr = AtomAttributes(self.ai, coord, 0., []) self.add_node(n, attrs=[atr]) if row > 0: self.add_bond([n,n-rowLength]) n += 1 coords = bondsArray[row][1] rowLength = xsteps atr = AtomAttributes(self.ai, coords[0], 0., []) self.add_node(n, attrs=[atr]) self.add_bond([n,n-rowLength]) if row % 2 == 0: self.add_bond([n,n-rowLength+1]) n += 1 for coord in coords[1:-1]: atr = AtomAttributes(self.ai, coord, []) self.add_node(n, attrs=[atr]) self.add_bond([n,n-rowLength]) if row % 2 == 0: self.add_bond([n,n-rowLength+1]) else: self.add_bond([n,n-rowLength-1]) n += 1 atr = AtomAttributes(self.ai, coords[-1], 0., []) self.add_node(n, attrs=[atr]) self.add_bond([n,n-rowLength]) if row % 2 == 1: self.add_bond([n,n-rowLength-1]) n += 1
class Element(Molecule):
_FORCE_FIELD_PARAMETERS = { # reference
"H": [-0.03, 1.3582],
"B": [-.0100, 2.085], # (1)
"HE": [-.0100, 2.495], # (1)
"KR": [-.0100, 3.599], # (1)
"RN": [-.0100, 4.009], # (1)
"SE": [-.0430, 3.510], # (1)
"AT": [-.3200, 3.884], # (1)
"BR": [-.3200, 3.884], # (1)
"XE": [-.0100, 3.849], # (1)
"I": [-.8000, 3.635], # (1)
"AL": [-.2500, 4.740], # (1)
"AS": [-.0600, 3.564], # (1)
"BA": [-.1600, 3.385], # (1)
"BE": [-.0030, 1.960], # (1)
"CA": [-.0600, 3.107], # (1)
"CS": [-.0045, 5.183], # (1)
"CU": [-.0600, 2.459], # (1)
"FE": [-.0200, 2.610], # (1)
"GE": [-.0450, 3.029], # (1)
"K": [-.0100, 4.187], # (1)
"LI": [-.0070, 2.202], # (1)
"MG": [-.0450, 2.564], # (1)
"MN": [-.7000, 2.851], # (1)
"NI": [-.0500, 1.782], # (1)
"PD": [-.0100, 2.388], # (1)
"PT": [-.0100, 2.370], # (1)
"RB": [-.0065, 4.741], # (1)
"RH": [-.0250, 2.797], # (1)
"RU": [-.0250, 2.940], # (1)
"SI": [-.3100, 4.455], # (1)
"SN": [-.0450, 3.385], # (1)
"SR": [-.1719, 3.523], # (1)
"YB": [-.0600, 3.127], # (1)
"ZN": [-.2500, 1.942], # (1)
"ZR": [-.0100, 3.617], # (1)
"C": [-0.032, 2.0],
"N": [-0.18, 1.79],
"O": [-0.12, 1.7],
"F": [-.1000, 2.029], # (1)
"NA": [-0.1153, 2.275],
"P": [-0.585, 2.15],
"S": [-0.565, 2.05],
"CL": [-0.3002, 1.735],
"AR": [-.01, 3.35],
"AU": [-0.53537, 3.2]
}
_ATTRIBUTES = {
"H":
AtomAttributes(
AtomInfo("H", "H", "H", 0.417, 1.00794, 0.0, 1.0, ' ', "H", "ELT",
"A", 1), [0., 0., 0.]),
"O":
AtomAttributes(
AtomInfo("O", "O", "O", -0.834, 15.9994, 0.0, 1.0, ' ', "O", "ELT",
"A", 1), [0., 0., 0.]),
"C":
AtomAttributes(
AtomInfo("C", "C", "C", 0.147156, 12.0107, 1.0, 1.0, ' ', "C",
"ELT", "A", 1), [0., 0., 0.]),
"F":
AtomAttributes(
AtomInfo("F", "F", "F", -1, 18.9984032, 1.0, 1.0, ' ', "F", "ELT",
"A", 1), [0., 0., 0.]),
"N":
AtomAttributes(
AtomInfo("N", "N", "N", -0.341313, 14.0067, 1.0, 1.0, ' ', "N",
"ELT", "A", 1), [0., 0., 0.]),
"NA":
AtomAttributes(
AtomInfo("NA", "NA", "NA", 1.0, 22.98977, 1.0, 1.0, ' ', "NA",
"ELT", "A", 1), [0., 0., 0.]),
"P":
AtomAttributes(
AtomInfo("P", "P", "P", 0.39354, 30.9738, 1.0, 1.0, ' ', "P",
"ELT", "A", 1), [0., 0., 0.]),
"S":
AtomAttributes(
AtomInfo("S", "S", "S", 0.0, 32.065, 1.0, 1.0, ' ', "S", "ELT",
"A", 1), [0., 0., 0.]),
"CL":
AtomAttributes(
AtomInfo("CL", "CL", "CL", -0.14, 35.453, 0.0, 1.0, ' ', "CL",
"ELT", "A", 1), [0., 0., 0.]),
"AR":
AtomAttributes(
AtomInfo("AR", "AR", "AR", 0.0, 39.9500, 0.0, 1.0, ' ', "O", "ELT",
"A", 1), [0., 0., 0.]),
"AU":
AtomAttributes(
AtomInfo("AU", "AU", "AU", 0.0, 96.96657, 0.0, 1.0, ' ', "AU",
"ELT", "A", 1), [0., 0., 0.])
}
_ENAME_TO_SYMBOL = {
"Argon": "AR",
"Carbon": "C",
"Chlorine": "CL",
"Hydrogen": "H",
"Fluorine": "F",
"Gold": "AU",
"Nitrogen": "N",
"Oxygen": "O",
"Phosphorous": "P",
"Sodium": "NA",
"Sulfur": "S"
}
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)
#self.copyChargesToForceField()
@staticmethod
def nameToSymbol(ename):
return Element._ENAME_TO_SYMBOL[ename]
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, "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 __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()