def png_atoms_labeled(smiles, fname):
"""Write out png file of molecule with atoms labeled with their index.
Parameters
----------
smiles: str
SMILES
fname: str
absolute path and filename for png
"""
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, smiles)
oedepict.OEPrepareDepiction(mol)
width, height = 300, 200
opts = oedepict.OE2DMolDisplayOptions(width, height,
oedepict.OEScale_AutoScale)
opts.SetAtomPropertyFunctor(oedepict.OEDisplayAtomIdx())
opts.SetAtomPropLabelFont(oedepict.OEFont(oechem.OEDarkGreen))
disp = oedepict.OE2DMolDisplay(mol, opts)
return oedepict.OERenderMolecule(fname, disp)
def show_oemol_struc(oemol,
torsions=False,
atom_indices=[],
width=500,
height=300):
from IPython.display import Image
from openeye import oechem, oedepict
# Highlight element of interest
class NoAtom(oechem.OEUnaryAtomPred):
def __call__(self, atom):
return False
class AtomInTorsion(oechem.OEUnaryAtomPred):
def __call__(self, atom):
return atom.GetIdx() in atom_indices
class NoBond(oechem.OEUnaryBondPred):
def __call__(self, bond):
return False
class BondInTorsion(oechem.OEUnaryBondPred):
def __call__(self, bond):
return (bond.GetBgn().GetIdx()
in atom_indices) and (bond.GetEnd().GetIdx()
in atom_indices)
class CentralBondInTorsion(oechem.OEUnaryBondPred):
def __call__(self, bond):
return (bond.GetBgn().GetIdx()
in atom_indices[1:3]) and (bond.GetEnd().GetIdx()
in atom_indices[1:3])
opts = oedepict.OE2DMolDisplayOptions(width, height,
oedepict.OEScale_AutoScale)
opts.SetAtomPropertyFunctor(oedepict.OEDisplayAtomIdx())
oedepict.OEPrepareDepiction(oemol)
img = oedepict.OEImage(width, height)
display = oedepict.OE2DMolDisplay(oemol, opts)
if torsions:
atoms = oemol.GetAtoms(AtomInTorsion())
bonds = oemol.GetBonds(NoBond())
abset = oechem.OEAtomBondSet(atoms, bonds)
oedepict.OEAddHighlighting(
display,
oechem.OEColor(oechem.OEYellow),
oedepict.OEHighlightStyle_BallAndStick,
abset,
)
oedepict.OERenderMolecule(img, display)
png = oedepict.OEWriteImageToString("png", img)
return Image(png)
def plot_indices(mol2, width=200, height=200):
mol = mol2.CreateCopy()
opts = oedepict.OE2DMolDisplayOptions(width, height, oedepict.OEScale_AutoScale)
opts.SetAtomPropertyFunctor(oedepict.OEDisplayAtomIdx())
oedepict.OEPrepareDepiction(mol)
disp = oedepict.OE2DMolDisplay(mol, opts)
img = oedepict.OEImage(width, height)
oedepict.OERenderMolecule(img, disp)
return img
def genHBIndexGuide(inpmol):
"""
For each mol, generate depiction of molecule with labeled
indices as read in by oechem. Saved as _____
"""
mol = oechem.OEGraphMol(inpmol)
dopt = oedepict.OEPrepareDepictionOptions()
dopt.SetDepictOrientation(oedepict.OEDepictOrientation_Horizontal)
oedepict.OEPrepareDepiction(mol, dopt)
opts = oedepict.OE2DMolDisplayOptions(width, height,
oedepict.OEScale_AutoScale)
opts.SetAtomPropertyFunctor(oedepict.OEDisplayAtomIdx())
oedepict.OERenderMolecule(outfn, mol)
def png_atoms_labeled(smiles,
fname,
map_idx=True,
width=600,
height=400,
label_scale=2.0,
scale_bondwidth=True):
"""Write out png file of molecule with atoms labeled with their map index.
Parameters
----------
smiles: str
SMILES
fname: str
absolute path and filename for png
map_idx: bool
If True, lable atoms with map index instead of atom index. If set to True, input SMILES must have map indices.
"""
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, smiles)
oedepict.OEPrepareDepiction(mol)
opts = oedepict.OE2DMolDisplayOptions(width, height,
oedepict.OEScale_AutoScale)
if map_idx:
# check if molecule has map
if not cmiles.utils.has_atom_map(mol):
raise ValueError(
"Input SMILES must have atom maps to display map indices in image"
)
opts.SetAtomPropertyFunctor(oedepict.OEDisplayAtomMapIdx())
opts.SetAtomPropertyFunctor(oedepict.OEDisplayAtomMapIdx())
if not map_idx:
opts.SetAtomPropertyFunctor(oedepict.OEDisplayAtomIdx())
opts.SetAtomPropertyFunctor(oedepict.OEDisplayAtomMapIdx())
opts.SetAtomPropLabelFont(oedepict.OEFont(oechem.OEDarkGreen))
opts.SetAtomPropLabelFontScale(label_scale)
opts.SetBondWidthScaling(scale_bondwidth)
disp = oedepict.OE2DMolDisplay(mol, opts)
return oedepict.OERenderMolecule(fname, disp)
def _assignDisplayOptions(self):
if self._params["labelAtomCIPStereo"]:
#
self._opts.SetAtomStereoStyle(
oedepict.OEAtomStereoStyle_Display_All)
# self._opts.SetAtomStereoStyle(oedepict.OEAtomStereoStyle_Display_CIPAtomStereo)
if self._params["labelBondCIPStereo"]:
# will include bowties for undefined stereo
# self._opts.SetBondStereoStyle(oedepict.OEBondStereoStyle_Display_All)
self._opts.SetBondStereoStyle(
oedepict.OEBondStereoStyle_Display_CIPBondStereo)
self._opts.SetAtomPropLabelFontScale(0.650)
if self._params["labelAtomIndex"]:
self._opts.SetAtomPropertyFunctor(oedepict.OEDisplayAtomIdx())
self._opts.SetAtomPropLabelFont(oedepict.OEFont(
oechem.OEDarkGreen))
self._opts.SetAtomPropLabelFontScale(0.650)
if self._params["labelBondIndex"]:
self._opts.SetBondPropertyFunctor(oedepict.OEDisplayBondIdx())
self._opts.SetBondPropLabelFont(oedepict.OEFont(oechem.OEDarkBlue))
if self._params["labelAtomName"]:
atomlabel = LabelAtoms()
self._opts.SetAtomPropertyFunctor(atomlabel)
self._opts.SetAtomPropLabelFont(oedepict.OEFont(
oechem.OEDarkGreen))
self._opts.SetAtomPropLabelFontScale(0.650)
if self._params["bondDisplayWidth"] is not None:
pen = oedepict.OEPen(oechem.OEBlack, oechem.OEBlack,
oedepict.OEFill_On,
self._params["bondDisplayWidth"])
self._opts.SetDefaultBondPen(pen)
# remove for the moment. not supported on all platforms
# self._opts.SetBondWidthScaling(False)
#
# 5.0 is minimum size -
self._opts.SetTitleHeight(5.0)
# @ <SNIPPET-OE2DMOLDISPLAY-OPTIONS-ATOM-LABEL-FONT-SCALE> width, height, scale = 300.0, 200.0, oedepict.OEScale_AutoScale opts = oedepict.OE2DMolDisplayOptions(width, height, scale) opts.SetAtomLabelFontScale(1.5) # @ </SNIPPET-OE2DMOLDISPLAY-OPTIONS-ATOM-LABEL-FONT-SCALE> DepictMolecules(opts, smiles, "OE2DMolDisplayOptions_SetAtomLabelFontScale") # @ <SNIPPET-OE2DMOLDISPLAY-OPTIONS-ATOM-PROP-LABEL-FONT> width, height, scale = 300.0, 200.0, oedepict.OEScale_AutoScale opts = oedepict.OE2DMolDisplayOptions(width, height, scale) font = oedepict.OEFont() font.SetStyle(oedepict.OEFontStyle_Bold) font.SetColor(oechem.OEDarkGreen) opts.SetAtomPropLabelFont(font) opts.SetAtomPropertyFunctor(oedepict.OEDisplayAtomIdx()) # @ </SNIPPET-OE2DMOLDISPLAY-OPTIONS-ATOM-PROP-LABEL-FONT> DepictMolecules(opts, smiles, "OE2DMolDisplayOptions_SetAtomPropLabelFont") # @ <SNIPPET-OE2DMOLDISPLAY-OPTIONS-ATOM-PROPERTY-FUNCTOR> width, height, scale = 300.0, 200.0, oedepict.OEScale_AutoScale opts = oedepict.OE2DMolDisplayOptions(width, height, scale) opts.SetAtomPropertyFunctor(oedepict.OEDisplayAtomIdx()) # @ </SNIPPET-OE2DMOLDISPLAY-OPTIONS-ATOM-PROPERTY-FUNCTOR> DepictMolecules(opts, smiles, "OE2DMolDisplayOptions_SetAtomPropertyFunctor") # @ <SNIPPET-OE2DMOLDISPLAY-OPTIONS-ATOM-PROP-LABEL-FONT-SCALE> width, height, scale = 300.0, 200.0, oedepict.OEScale_AutoScale opts = oedepict.OE2DMolDisplayOptions(width, height, scale) opts.SetAtomPropLabelFontScale(1.5) opts.SetAtomPropertyFunctor(oedepict.OEDisplayAtomIdx())
def show_oemol_struc(oemol, torsions=False, atom_indices=[]):
"""
Returns the oedepict image with or without the torsion highlighted
Parameters
----------
oemol: openeye oechem mol object
torsions: boolean, to highlight dihedrals
atom_indices: dihedral atom indices to highlight
Returns
-------
Image: image in png format
"""
from IPython.display import Image
from openeye import oechem, oedepict
width = 400
height = 300
# Highlight element of interest
class NoAtom(oechem.OEUnaryAtomPred):
def __call__(self, atom):
return False
class AtomInTorsion(oechem.OEUnaryAtomPred):
def __call__(self, atom):
return atom.GetIdx() in atom_indices
class NoBond(oechem.OEUnaryBondPred):
def __call__(self, bond):
return False
class BondInTorsion(oechem.OEUnaryBondPred):
def __call__(self, bond):
return (bond.GetBgn().GetIdx() in atom_indices) and (
bond.GetEnd().GetIdx() in atom_indices
)
class CentralBondInTorsion(oechem.OEUnaryBondPred):
def __call__(self, bond):
return (bond.GetBgn().GetIdx() in atom_indices[1:3]) and (
bond.GetEnd().GetIdx() in atom_indices[1:3]
)
opts = oedepict.OE2DMolDisplayOptions(width, height, oedepict.OEScale_AutoScale)
opts.SetAtomPropertyFunctor(oedepict.OEDisplayAtomIdx())
oedepict.OEPrepareDepiction(oemol)
img = oedepict.OEImage(width, height)
display = oedepict.OE2DMolDisplay(oemol, opts)
if torsions:
atoms = oemol.GetAtoms(AtomInTorsion())
bonds = oemol.GetBonds(NoBond())
abset = oechem.OEAtomBondSet(atoms, bonds)
oedepict.OEAddHighlighting(
display,
oechem.OEColor(oechem.OEYellow),
oedepict.OEHighlightStyle_BallAndStick,
abset,
)
oedepict.OERenderMolecule(img, display)
png = oedepict.OEWriteImageToString("png", img)
return Image(png)