def read(self, string):
doc = minidom.parseString(string)
elements = doc.getElementsByTagName("atom")
atomlist = []
for atom in elements:
sym = atom.getAttribute("elementType")
atno = sym2no[sym]
x = float(atom.getAttribute("x3"))
y = float(atom.getAttribute("y3"))
z = float(atom.getAttribute("z3"))
atomlist.append((atno, (x, y, z)))
data = Data()
data.build_molecule(atomlist=atomlist)
return data
def read(self, string):
doc = minidom.parseString(string)
elements = doc.getElementsByTagName("atom")
atomlist=[]
for atom in elements:
sym = atom.getAttribute("elementType")
atno = sym2no[sym]
x = float(atom.getAttribute("x3"))
y = float(atom.getAttribute("y3"))
z = float(atom.getAttribute("z3"))
atomlist.append((atno,(x,y,z)))
data = Data()
data.build_molecule(atomlist = atomlist)
return data
def read(self,string):
"""
Arguments:
- string: String to parse
Return:
- data: Data object, with a molecule and a molecules
attribute.
"""
from PyQuante.Element import sym2no
from PyQuante.Molecule import Molecule
geometries = []
igeo = 1
lines = string.splitlines()
while 1:
try:
line = lines.pop(0)
except IndexError:
break
if not line: break
nat = int(line.split()[0])
title = lines.pop(0)
atoms = []
for i in xrange(nat):
line = lines.pop(0)
words = line.split()
atno = sym2no[words[0]]
x,y,z = map(float,words[1:])
atoms.append((atno,(x,y,z)))
atoms = Molecule("XYZ geometry #%d" % igeo,atoms)
igeo += 1
geometries.append(atoms)
data = Data()
data.molecule = geometries[0] # First geometry
data.molecules = geometries
return data
def read(self, string):
"""
Arguments:
- string: String to parse
Return:
- data: Data object, with a molecule and a molecules
attribute.
"""
from PyQuante.Element import sym2no
from PyQuante.Molecule import Molecule
geometries = []
igeo = 1
lines = string.splitlines()
while 1:
try:
line = lines.pop(0)
except IndexError:
break
if not line: break
nat = int(line.split()[0])
title = lines.pop(0)
atoms = []
for i in xrange(nat):
line = lines.pop(0)
words = line.split()
atno = sym2no[words[0]]
x, y, z = map(float, words[1:])
atoms.append((atno, (x, y, z)))
atoms = Molecule("XYZ geometry #%d" % igeo, atoms)
igeo += 1
geometries.append(atoms)
data = Data()
data.molecule = geometries[0] # First geometry
data.molecules = geometries
return data
def dump(self, filename, format=None):
from PyQuante.IO.Data import Data
data = Data()
data.molecule = self
hand = FileHandler()
hand.write(filename, data, format)
def as_string(self, format="xyz"):
from PyQuante.IO.Data import Data
data = Data()
data.molecule = self
hand = StringHandler()
return hand.write(data, format)
def dump(self,filename, format=None):
from PyQuante.IO.Data import Data
data = Data()
data.molecule = self
hand = FileHandler()
hand.write(filename,data,format)
def as_string(self,format="xyz"):
from PyQuante.IO.Data import Data
data = Data()
data.molecule = self
hand = StringHandler()
return hand.write(data, format)
def testWriteString(self):
sh = SH()
data = Data(molecule=PYQ)
sh.write(data, format="cml")
