def filereader():
obmol = ob.OBMol()
notatend = obconversion.ReadFile(obmol, filename)
while notatend:
yield Molecule(obmol)
obmol = ob.OBMol()
notatend = obconversion.Read(obmol)
def readstring(format, string):
"""Read in a molecule from a string.
Required parameters:
format - see the informats variable for a list of available
input formats
string
Example:
>>> input = "C1=CC=CS1"
>>> mymol = readstring("smi", input)
>>> len(mymol.atoms)
5
"""
obmol = ob.OBMol()
obconversion = ob.OBConversion()
formatok = obconversion.SetInFormat(format)
if not formatok:
raise ValueError("%s is not a recognised OpenBabel format" % format)
success = obconversion.ReadString(obmol, string)
if not success:
raise IOError("Failed to convert '%s' to format '%s'" %
(string, format))
return Molecule(obmol)
def readfile(format, filename):
"""Iterate over the molecules in a file.
Required parameters:
format - see the informats variable for a list of available
input formats
filename
You can access the first molecule in a file using the next() method
of the iterator:
mol = readfile("smi", "myfile.smi").next()
You can make a list of the molecules in a file using:
mols = list(readfile("smi", "myfile.smi"))
You can iterate over the molecules in a file as shown in the
following code snippet:
>>> atomtotal = 0
>>> for mol in readfile("sdf", "head.sdf"):
... atomtotal += len(mol.atoms)
...
>>> print atomtotal
43
"""
obconversion = ob.OBConversion()
formatok = obconversion.SetInFormat(format)
if not formatok:
raise ValueError("%s is not a recognised OpenBabel format" % format)
if not os.path.isfile(filename):
raise IOError("No such file: '%s'" % filename)
obmol = ob.OBMol()
notatend = obconversion.ReadFile(obmol, filename)
while notatend:
yield Molecule(obmol)
obmol = ob.OBMol()
notatend = obconversion.Read(obmol)
def readstring(format, string, opt=None):
"""Read in a molecule from a string.
Required parameters:
format - see the informats variable for a list of available
input formats
string
Optional parameters:
opt - a dictionary of format-specific options
For format options with no parameters, specify the
value as None.
Example:
>>> input = "C1=CC=CS1"
>>> mymol = readstring("smi", input)
>>> len(mymol.atoms)
5
"""
if opt is None:
opt = {}
obmol = ob.OBMol()
obconversion = ob.OBConversion()
formatok = obconversion.SetInFormat(format)
if not formatok:
raise ValueError("%s is not a recognised Open Babel format" % format)
for k, v in opt.items():
if v is None:
obconversion.AddOption(k, obconversion.INOPTIONS)
else:
obconversion.AddOption(k, obconversion.INOPTIONS, str(v))
success = obconversion.ReadString(obmol, string)
if not success:
raise IOError("Failed to convert '%s' to format '%s'" %
(string, format))
return Molecule(obmol)
def draw(self, show=True, filename=None, update=False, usecoords=False):
"""Create a 2D depiction of the molecule.
Optional parameters:
show -- display on screen (default is True)
filename -- write to file (default is None)
update -- update the coordinates of the atoms to those
determined by the structure diagram generator
(default is False)
usecoords -- don't calculate 2D coordinates, just use
the current coordinates (default is False)
Tkinter and Python Imaging Library are required for image display.
"""
obconversion = ob.OBConversion()
formatok = obconversion.SetOutFormat("_png2")
if not formatok:
raise ImportError("PNG depiction support not found. You should "
"compile Open Babel with support for Cairo. See "
"installation instructions for more "
"information.")
# Need to copy to avoid removing hydrogens from self
workingmol = Molecule(ob.OBMol(self.OBMol))
workingmol.removeh()
if not usecoords:
_operations['gen2D'].Do(workingmol.OBMol)
if update:
if workingmol.OBMol.NumAtoms() != self.OBMol.NumAtoms():
raise RuntimeError("It is not possible to update the original "
"molecule with the calculated coordinates, "
"as the original molecule contains "
"explicit hydrogens for which no "
"coordinates have been calculated.")
else:
for i in range(workingmol.OBMol.NumAtoms()):
self.OBMol.GetAtom(i + 1).SetVector(
workingmol.OBMol.GetAtom(i + 1).GetVector())
if filename:
filedes = None
else:
if sys.platform[:3] == "cli" and show:
raise RuntimeError("It is only possible to show the molecule "
"if you provide a filename. The reason for "
"this is that I kept having problems "
"when using temporary files.")
filedes, filename = tempfile.mkstemp()
workingmol.write("_png2", filename=filename, overwrite=True)
if show:
if sys.platform[:4] == "java":
image = javax.imageio.ImageIO.read(java.io.File(filename))
frame = javax.swing.JFrame(visible=1)
frame.getContentPane().add(
javax.swing.JLabel(javax.swing.ImageIcon(image)))
frame.setSize(300, 300)
frame.setDefaultCloseOperation(
javax.swing.WindowConstants.DISPOSE_ON_CLOSE)
frame.show()
elif sys.platform[:3] == "cli":
form = _MyForm()
form.setup(filename, self.title)
Application.Run(form)
else:
if not tk:
raise ImportError("Tkinter or Python Imaging Library not "
"found, but is required for image "
"display. See installation instructions "
"for more information.")
root = tk.Tk()
root.title((hasattr(self, "title") and self.title)
or self.__str__().rstrip())
frame = tk.Frame(root, colormap="new",
visual='truecolor').pack()
image = PIL.open(filename)
imagedata = piltk.PhotoImage(image)
tk.Label(frame, image=imagedata).pack()
tk.Button(root, text="Close",
command=root.destroy).pack(fill=tk.X)
root.mainloop()
if filedes:
os.close(filedes)
os.remove(filename)
def clone(self):
return Molecule(ob.OBMol(self.OBMol))