def __init__(self, molecule=None, grid=None, truncate=0):
LeastSquaresCharges.__init__(self, molecule=molecule, grid=grid)
self.truncate = truncate
self.hybrids = []
for atom in self.molecule.atoms:
if not atom.frame is None:
self.hybrids.append(atom)
self.num_charges = len(self.molecule.sites_noneq)
import openbabel
from os import path
import sys
sys.path.append( path.dirname( path.dirname( path.abspath(__file__) ) ) )
from charges import LeastSquaresCharges
from Parser import GaussianCube
#from pybel import *
parser = GaussianCube(filename='../../../media/files/chloromethane_b3lyp_augccpvdz_3.75.cub')
data = parser.data.copy()
data['theory'] = 'b3lyp'
data['basis'] = 'augccpvdz'
ls = LeastSquaresCharges(data)
ls.solve()
print ls.solution
mol = openbabel.OBMol()
conv = openbabel.OBConversion()
conv.SetInAndOutFormats("cube", "mol2")
conv.ReadFile(mol, '../../../media/files/chloromethane_b3lyp_augccpvdz_3.75.cub')
#for i, _ in enumerate(data['atoms']):
# a = mol.GetAtom(i+1)
# a.SetPartialCharge(ls.solution[i])
# print a.GetAtomicNum()
# print a.GetPartialCharge()
a = mol.GetAtom(1)
a.GetPartialCharge()
for i, _ in enumerate(data['atoms']):
a = mol.GetAtom(i+1)
a.SetPartialCharge(ls.solution[i])
print a.GetAtomicNum()
print a.GetPartialCharge()
def __init__(self, molecule=None, grid=None):
LeastSquaresCharges.__init__(self, molecule=molecule, grid=grid)
logger.info('Charge constraint using SVD')
def __init__(self, molecule=None, grid=None):
LeastSquaresCharges.__init__(self, molecule=molecule, grid=grid)
logger.info('The total charge leakage will be distributed over all atoms')
def solve(self):
solution = LeastSquaresCharges.solve_normal(self)
self._solution = solution[:-1]
return self._solution
def __init__(self, molecule=None, grid=None):
LeastSquaresCharges.__init__(self, molecule=molecule, grid=grid)
logger.info('Applying total charge constraint using Lagrange multiplier')
self.update()
def __init__(self, molecule=None, grid=None, eliminated=None):
self.eliminated = eliminated
logger.info('Applying total charge constraint by elimination.\nEliminated atom: %s' % eliminated)
LeastSquaresCharges.__init__(self, molecule=molecule, grid=grid)
self.setB()
self.A -= self.B
