def bkchem_mol_to_oasa_mol(mol):
m = oasa.molecule()
for a in mol.atoms:
m.add_vertex(bkchem_atom_to_oasa_atom(a))
for b in mol.bonds:
b2 = bkchem_bond_to_oasa_bond(b)
aa1, aa2 = b.atoms
v1 = m.vertices[mol.atoms.index(aa1)]
v2 = m.vertices[mol.atoms.index(aa2)]
b2.vertices = (v1, v2)
m.add_edge(v1, v2, b2)
return m
def bkchem_mol_to_oasa_mol( mol):
m = oasa.molecule()
for a in mol.atoms:
m.add_vertex( bkchem_atom_to_oasa_atom( a))
for b in mol.bonds:
b2 = bkchem_bond_to_oasa_bond( b)
aa1, aa2 = b.atoms
v1 = m.vertices[ mol.atoms.index( aa1)]
v2 = m.vertices[ mol.atoms.index( aa2)]
b2.vertices = (v1, v2)
m.add_edge( v1, v2, b2)
return m
def _read_summary_formula(self, text):
mols = []
for line in text.splitlines():
sum_dict = oasa.periodic_table.formula_dict(line)
mol = oasa.molecule()
for (symbol,count) in sum_dict.iteritems():
for i in range(count):
a = oasa.atom(symbol)
a.valency = 0
mol.add_vertex(a)
mols.append(mol)
return mols
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)
OASA is used for 2D coordinate generation and depiction. Tkinter and
Python Imaging Library are required for image display.
"""
etab = ob.OBElementTable()
if not oasa:
errormessage = ("OASA not found, but is required for 2D structure "
"generation and depiction. OASA is part of BKChem. "
"See installation instructions for more "
"information.")
raise ImportError(errormessage)
mol = oasa.molecule()
for atom in self.atoms:
v = mol.create_vertex()
v.symbol = etab.GetSymbol(atom.atomicnum)
v.charge = atom.formalcharge
if usecoords:
v.x, v.y, v.z = atom.coords[0] * 30., atom.coords[1] * 30., 0.0
mol.add_vertex(v)
for bond in ob.OBMolBondIter(self.OBMol):
e = mol.create_edge()
e.order = bond.GetBO()
if bond.IsHash():
e.type = "h"
elif bond.IsWedge():
e.type = "w"
mol.add_edge(bond.GetBeginAtomIdx() - 1,
bond.GetEndAtomIdx() - 1,
e)
# I'm sure there's a more elegant way to do the following, but here goes...
# let's set the stereochemistry around double bonds
self.write("can") # Perceive UP/DOWNness
for bond in ob.OBMolBondIter(self.OBMol):
ends = bond.GetBeginAtomIdx(), bond.GetEndAtomIdx()
if bond.GetBO() == 2:
stereobonds = [[b for b in ob.OBAtomBondIter(self.OBMol.GetAtom(x)) if b.GetIdx() != bond.GetIdx() and (b.IsUp() or b.IsDown())]
for x in ends]
if stereobonds[0] and stereobonds[1]: # Needs to be defined at either end
if stereobonds[0][0].IsUp() == stereobonds[1][0].IsUp():
# Either both up or both down
stereo = oasa.stereochemistry.cis_trans_stereochemistry.SAME_SIDE
else:
stereo = oasa.stereochemistry.cis_trans_stereochemistry.OPPOSITE_SIDE
atomids = [(b[0].GetBeginAtomIdx(), b[0].GetEndAtomIdx()) for b in stereobonds]
extremes = []
for id, end in zip(ends, atomids):
if end[0] == id:
extremes.append(end[1])
else:
extremes.append(end[0])
center = mol.get_edge_between(mol.atoms[ends[0] - 1], mol.atoms[ends[1] - 1])
st = oasa.stereochemistry.cis_trans_stereochemistry(
center = center, value = stereo,
references = (mol.atoms[extremes[0] - 1], mol.atoms[ends[0] - 1],
mol.atoms[ends[1] - 1], mol.atoms[extremes[1] - 1]))
mol.add_stereochemistry(st)
mol.remove_unimportant_hydrogens()
if not usecoords:
oasa.coords_generator.calculate_coords(mol, bond_length=30)
if update:
newcoords = [(v.x / 30., v.y / 30., 0.0) for v in mol.vertices]
for atom, newcoord in zip(ob.OBMolAtomIter(self.OBMol), newcoords):
atom.SetVector(*newcoord)
if filename or show:
maxx = max([v.x for v in mol.vertices])
minx = min([v.x for v in mol.vertices])
maxy = max([v.y for v in mol.vertices])
miny = min([v.y for v in mol.vertices])
maxcoord = max(maxx - minx, maxy - miny)
fontsize = 16
bondwidth = 6
linewidth = 2
if maxcoord > 270: # 300 - margin * 2
for v in mol.vertices:
v.x *= 270. / maxcoord
v.y *= 270. / maxcoord
fontsize *= math.sqrt(270. / maxcoord)
bondwidth *= math.sqrt(270. / maxcoord)
linewidth *= math.sqrt(270. / maxcoord)
if filename:
filedes = None
else:
filedes, filename = tempfile.mkstemp()
canvas = oasa.cairo_out.cairo_out()
canvas.show_hydrogens_on_hetero = True
canvas.font_size = fontsize
canvas.bond_width = bondwidth
canvas.line_width = linewidth
canvas.mol_to_cairo(mol, filename)
if show:
if not tk:
errormessage = ("Tkinter or Python Imaging "
"Library not found, but is required for image "
"display. See installation instructions for "
"more information.")
raise ImportError(errormessage)
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)
label = tk.Label(frame, image=imagedata).pack()
quitbutton = tk.Button(root, text="Close", command=root.destroy).pack(fill=tk.X)
root.mainloop()
if filedes:
os.close(filedes)
os.remove(filename)
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)
OASA is used for depiction. Tkinter and Python
Imaging Library are required for image display.
"""
writetofile = filename is not None
if not usecoords:
# Do the SDG
sdg = cdk.layout.StructureDiagramGenerator()
sdg.setMolecule(self.Molecule)
sdg.generateExperimentalCoordinates()
newmol = Molecule(sdg.getMolecule())
if update:
for atom, newatom in zip(self.atoms, newmol.atoms):
coords = newatom.Atom.getPoint2d()
atom.Atom.setPoint3d(javax.vecmath.Point3d(coords.x, coords.y, 0.0))
else:
newmol = self
if writetofile or show:
if writetofile:
filedes = None
else:
filedes, filename = tempfile.mkstemp()
# Create OASA molecule
if not oasa:
errormessage = (
"OASA not found, but is required for 2D structure "
"depiction. OASA is part of BKChem. "
"See installation instructions for more "
"information."
)
raise ImportError, errormessage
mol = oasa.molecule()
atomnos = []
for newatom in newmol.atoms:
if not usecoords:
coords = newatom.Atom.getPoint2d()
else:
coords = newatom.Atom.getPoint3d()
if not coords:
coords = newatom.Atom.getPoint2d()
v = mol.create_vertex()
v.charge = newatom.formalcharge
v.symbol = _isofact.getElement(newatom.atomicnum).getSymbol()
mol.add_vertex(v)
v.x, v.y, v.z = coords.x * 30.0, coords.y * 30.0, 0.0
for i in range(self.Molecule.getBondCount()):
bond = self.Molecule.getBond(i)
bo = _revbondtypes[bond.getOrder()]
atoms = [self.Molecule.getAtomNumber(x) for x in bond.atoms().iterator()]
e = mol.create_edge()
e.order = bo
if bond.getStereo() == cdk.CDKConstants.STEREO_BOND_DOWN:
e.type = "h"
elif bond.getStereo() == cdk.CDKConstants.STEREO_BOND_UP:
e.type = "w"
mol.add_edge(atoms[0], atoms[1], e)
mol.remove_unimportant_hydrogens()
maxx = max([v.x for v in mol.vertices])
minx = min([v.x for v in mol.vertices])
maxy = max([v.y for v in mol.vertices])
miny = min([v.y for v in mol.vertices])
maxcoord = max(maxx - minx, maxy - miny)
for v in mol.vertices:
if str(v.x) == "-1.#IND":
v.x = minx
if str(v.y) == "-1.#IND":
v.y = miny
fontsize = 16
bondwidth = 6
linewidth = 2
if maxcoord > 270: # 300 - margin * 2
for v in mol.vertices:
v.x *= 270.0 / maxcoord
v.y *= 270.0 / maxcoord
fontsize *= math.sqrt(270.0 / maxcoord)
bondwidth *= math.sqrt(270.0 / maxcoord)
linewidth *= math.sqrt(270.0 / maxcoord)
canvas = oasa.cairo_out.cairo_out()
canvas.show_hydrogens_on_hetero = True
canvas.font_size = fontsize
canvas.bond_width = bondwidth
canvas.line_width = linewidth
canvas.mol_to_cairo(mol, filename)
if show:
if not tk:
errormessage = (
"Tkinter or Python Imaging "
"Library not found, but is required for image "
"display. See installation instructions for "
"more information."
)
raise ImportError, errormessage
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)
label = tk.Label(frame, image=imagedata).pack()
quitbutton = tk.Button(root, text="Close", command=root.destroy).pack(fill=tk.X)
root.mainloop()
if filedes:
os.close(filedes)
os.remove(filename)
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)
OASA is used for depiction. Tkinter and Python
Imaging Library are required for image display.
"""
writetofile = filename is not None
if not usecoords:
# Do the SDG
sdg = cdk.layout.StructureDiagramGenerator()
sdg.setMolecule(self.Molecule)
sdg.generateExperimentalCoordinates()
newmol = Molecule(sdg.getMolecule())
if update:
for atom, newatom in zip(self.atoms, newmol.atoms):
coords = newatom.Atom.getPoint2d()
atom.Atom.setPoint3d(javax.vecmath.Point3d(
coords.x, coords.y, 0.0))
else:
newmol = self
if writetofile or show:
if writetofile:
filedes = None
else:
filedes, filename = tempfile.mkstemp()
# Create OASA molecule
if not oasa:
errormessage = ("OASA not found, but is required for 2D structure "
"depiction. OASA is part of BKChem. "
"See installation instructions for more "
"information.")
raise ImportError, errormessage
mol = oasa.molecule()
atomnos = []
for newatom in newmol.atoms:
if not usecoords:
coords = newatom.Atom.getPoint2d()
else:
coords = newatom.Atom.getPoint3d()
if not coords:
coords = newatom.Atom.getPoint2d()
v = mol.create_vertex()
v.charge = newatom.formalcharge
v.symbol = _isofact.getElement(newatom.atomicnum).getSymbol()
mol.add_vertex(v)
v.x, v.y, v.z = coords.x * 30., coords.y * 30., 0.0
for i in range(self.Molecule.getBondCount()):
bond = self.Molecule.getBond(i)
bo = _revbondtypes[bond.getOrder()]
atoms = [self.Molecule.getAtomNumber(x) for x in bond.atoms().iterator()]
e = mol.create_edge()
e.order = bo
if bond.getStereo() == cdk.CDKConstants.STEREO_BOND_DOWN:
e.type = "h"
elif bond.getStereo() == cdk.CDKConstants.STEREO_BOND_UP:
e.type = "w"
mol.add_edge(atoms[0], atoms[1], e)
mol.remove_unimportant_hydrogens()
maxx = max([v.x for v in mol.vertices])
minx = min([v.x for v in mol.vertices])
maxy = max([v.y for v in mol.vertices])
miny = min([v.y for v in mol.vertices])
maxcoord = max(maxx - minx, maxy - miny)
for v in mol.vertices:
if str(v.x) == "-1.#IND":
v.x = minx
if str(v.y) == "-1.#IND":
v.y = miny
fontsize = 16
bondwidth = 6
linewidth = 2
if maxcoord > 270: # 300 - margin * 2
for v in mol.vertices:
v.x *= 270. / maxcoord
v.y *= 270. / maxcoord
fontsize *= math.sqrt(270. / maxcoord)
bondwidth *= math.sqrt(270. / maxcoord)
linewidth *= math.sqrt(270. / maxcoord)
canvas = oasa.cairo_out.cairo_out()
canvas.show_hydrogens_on_hetero = True
canvas.font_size = fontsize
canvas.bond_width = bondwidth
canvas.line_width = linewidth
canvas.mol_to_cairo(mol, filename)
if show:
if not tk:
errormessage = ("Tkinter or Python Imaging "
"Library not found, but is required for image "
"display. See installation instructions for "
"more information.")
raise ImportError, errormessage
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)
label = tk.Label(frame, image=imagedata).pack()
quitbutton = tk.Button(root, text="Close", command=root.destroy).pack(fill=tk.X)
root.mainloop()
if filedes:
os.close(filedes)
os.remove(filename)
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
This sets the atom coordinates to those
determined by the structure diagram generator
(default is ``False``)
**usecoords** -- use the current coordinates
This causes the current coordinates to be used
instead of calculating new 2D coordinates
(default is ``False``)
OASA is used for 2D coordinate generation and depiction. Tkinter and
Python Imaging Library are required for image display.
"""
etab = ob.OBElementTable()
if not oasa:
errormessage = (
"OASA not found, but is required for 2D structure "
"generation and depiction. OASA is part of BKChem. "
"See installation instructions for more "
"information.")
raise ImportError(errormessage)
mol = oasa.molecule()
for atom in self.atoms:
v = mol.create_vertex()
v.symbol = etab.GetSymbol(atom.atomicnum)
v.charge = atom.formalcharge
if usecoords:
v.x, v.y, v.z = atom.coords[0] * 30., atom.coords[1] * 30., 0.0
mol.add_vertex(v)
for bond in ob.OBMolBondIter(self.OBMol):
e = mol.create_edge()
e.order = bond.GetBO()
if bond.IsHash():
e.type = "h"
elif bond.IsWedge():
e.type = "w"
mol.add_edge(bond.GetBeginAtomIdx() - 1,
bond.GetEndAtomIdx() - 1, e)
# I'm sure there's a more elegant way to do the following, but here goes...
# let's set the stereochemistry around double bonds
self.write("can") # Perceive UP/DOWNness
for bond in ob.OBMolBondIter(self.OBMol):
ends = bond.GetBeginAtomIdx(), bond.GetEndAtomIdx()
if bond.GetBO() == 2:
stereobonds = [[
b for b in ob.OBAtomBondIter(self.OBMol.GetAtom(x))
if b.GetIdx() != bond.GetIdx() and (b.IsUp() or b.IsDown())
] for x in ends]
if stereobonds[0] and stereobonds[
1]: # Needs to be defined at either end
if stereobonds[0][0].IsUp() == stereobonds[1][0].IsUp():
# Either both up or both down
stereo = oasa.stereochemistry.cis_trans_stereochemistry.SAME_SIDE
else:
stereo = oasa.stereochemistry.cis_trans_stereochemistry.OPPOSITE_SIDE
atomids = [(b[0].GetBeginAtomIdx(), b[0].GetEndAtomIdx())
for b in stereobonds]
extremes = []
for id, end in zip(ends, atomids):
if end[0] == id:
extremes.append(end[1])
else:
extremes.append(end[0])
center = mol.get_edge_between(mol.atoms[ends[0] - 1],
mol.atoms[ends[1] - 1])
st = oasa.stereochemistry.cis_trans_stereochemistry(
center=center,
value=stereo,
references=(mol.atoms[extremes[0] - 1],
mol.atoms[ends[0] - 1],
mol.atoms[ends[1] - 1],
mol.atoms[extremes[1] - 1]))
mol.add_stereochemistry(st)
mol.remove_unimportant_hydrogens()
if not usecoords:
oasa.coords_generator.calculate_coords(mol, bond_length=30)
if update:
newcoords = [(v.x / 30., v.y / 30., 0.0) for v in mol.vertices]
for atom, newcoord in zip(ob.OBMolAtomIter(self.OBMol),
newcoords):
atom.SetVector(*newcoord)
if filename or show:
maxx = max([v.x for v in mol.vertices])
minx = min([v.x for v in mol.vertices])
maxy = max([v.y for v in mol.vertices])
miny = min([v.y for v in mol.vertices])
maxcoord = max(maxx - minx, maxy - miny)
fontsize = 16
bondwidth = 6
linewidth = 2
if maxcoord > 270: # 300 - margin * 2
for v in mol.vertices:
v.x *= 270. / maxcoord
v.y *= 270. / maxcoord
fontsize *= math.sqrt(270. / maxcoord)
bondwidth *= math.sqrt(270. / maxcoord)
linewidth *= math.sqrt(270. / maxcoord)
if filename:
filedes = None
else:
filedes, filename = tempfile.mkstemp()
canvas = oasa.cairo_out.cairo_out()
canvas.show_hydrogens_on_hetero = True
canvas.font_size = fontsize
canvas.bond_width = bondwidth
canvas.line_width = linewidth
canvas.mol_to_cairo(mol, filename)
if show:
if not tk:
errormessage = (
"Tkinter or Python Imaging "
"Library not found, but is required for image "
"display. See installation instructions for "
"more information.")
raise ImportError(errormessage)
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)
label = tk.Label(frame, image=imagedata).pack()
quitbutton = tk.Button(root,
text="Close",
command=root.destroy).pack(fill=tk.X)
root.mainloop()
if filedes:
os.close(filedes)
os.remove(filename)