#state.addMolecule(newPABA)
oh[0].merge(newPABA, [(oxygen, 114)])
#neutralize total charge
ch = oh[0].atom_attributes(oxygen).getInfo().getCharge()
if atype == "O2":
oh[0].atom_attributes(oxygen).getInfo().setCharge(ch -
(-0.208801))
else:
oh[0].atom_attributes(oxygen).getInfo().setCharge(ch -
(-0.208801))
print "Force field ", oh[0].getForceField()._BONDS
oh[0].getForceField().setBond(('C15', 'O6'), 1.42, 1)
oh[0].getForceField().setBond(('C15', 'O6'), 428, 0)
oh[0].getForceField().setBond(('C15', 'O2'), 1.42, 1)
oh[0].getForceField().setBond(('C15', 'O2'), 428, 0)
oh[0].getForceField().setAngle(('C15', 'O2', 'C2'), 131.929, 0)
oh[0].getForceField().setAngle(('C15', 'O2', 'C2'), 78., 1)
oh[0].getForceField().setAngle(('C15', 'O6', 'C6'), 131.929, 0)
oh[0].getForceField().setAngle(('C15', 'O6', 'C6'), 104., 1)
oh[0].getForceField().setAngle(('C14', 'C15', 'O6'), 113.391, 0)
oh[0].getForceField().setAngle(('C14', 'C15', 'O6'), 40., 1)
oh[0].getForceField().setAngle(('C14', 'C15', 'O2'), 113.391, 0)
oh[0].getForceField().setAngle(('C14', 'C15', 'O2'), 40., 1)
mixture.save(FileName)
def __init2__(self,n,m,q):
super(Diamond,self).__init__(ident="Diamond")
allCells = Mixture()
allCells.loadWFM(WOLFFIA_WFY_DIR + "/diamond.wfm")
#print allCells.moleculeNames()
#print allCells.nodes()
cell = allCells.getMolecule(allCells.nodes()[0])
for x in range(n):
for y in range(m):
line = Molecule()
for z in range(q):
newCell = cell.copy()
newCell.moveBy([x*self._CELL_WIDTH_,y*self._CELL_WIDTH_,z*self._CELL_WIDTH_])
addAndJoin(line, newCell)
print "Diamond __init__",x,y
addAndJoin(self, line)
#print allCells.enclosingBox()
'''
#==========================================================================
#==========================================================================
if __name__ == '__main__':
d = Diamond(3, 3, 3)
print(d.edges())
d.writePDB("/home/jse/Desktop/Diamantito.pdb")
m = Mixture()
m.add(d)
m.save("/home/jse/Desktop/Diamantito.wfm")