def draw_frag_pdf(frag_dict, scaffold=None, pdf_filename='fragments.pdf'):
from openeye import oechem, oedepict
import re
itf = oechem.OEInterface()
PageByPage = True
suppress_h = True
rows = 7
cols = 5
ropts = oedepict.OEReportOptions(rows, cols)
ropts.SetHeaderHeight(25)
ropts.SetFooterHeight(25)
ropts.SetCellGap(2)
ropts.SetPageMargins(10)
report = oedepict.OEReport(ropts)
cellwidth, cellheight = report.GetCellWidth(), report.GetCellHeight()
opts = oedepict.OE2DMolDisplayOptions(cellwidth, cellheight,
oedepict.OEScale_Default * 0.5)
opts.SetAromaticStyle(oedepict.OEAromaticStyle_Circle)
pen = oedepict.OEPen(oechem.OEBlack, oechem.OEBlack, oedepict.OEFill_On,
1.0)
opts.SetDefaultBondPen(pen)
oedepict.OESetup2DMolDisplayOptions(opts, itf)
if scaffold:
oemol = oechem.OEGraphMol()
scaffold_smi = re.sub(r"\(\[R([1-9])+]\)", r"([*])", scaffold.smiles)
oechem.OESmilesToMol(oemol, scaffold_smi)
cell = report.NewCell()
mol = oechem.OEMol(oemol)
mol.SetTitle(f'{scaffold.smiles}')
oedepict.OEPrepareDepiction(mol, False, suppress_h)
disp = oedepict.OE2DMolDisplay(mol, opts)
oedepict.OERenderMolecule(cell, disp)
headerpen = oedepict.OEPen(oechem.OEWhite, oechem.OELightGrey,
oedepict.OEFill_Off, 1.0)
oedepict.OEDrawBorder(cell, headerpen)
for rx, smis in frag_dict.items():
for idx, smi in enumerate(smis):
if smi != None:
# Create oemol
oemol = oechem.OEGraphMol()
oechem.OESmilesToMol(oemol, smi)
# Render molecule
cell = report.NewCell()
mol = oechem.OEMol(oemol)
mol.SetTitle(f'R{rx} #{idx+1}')
oedepict.OEPrepareDepiction(mol, False, suppress_h)
disp = oedepict.OE2DMolDisplay(mol, opts)
oedepict.OERenderMolecule(cell, disp)
oedepict.OEWriteReport(pdf_filename, report)
def prepare(self):
"""[summary]
# OESuppressHydrogens(self.__oeMol, retainPolar=False,retainStereo=True,retainIsotope=True)
oechem.OESuppressHydrogens(self.__oeMol)
"""
self.__setupImage()
for idx, cell in enumerate(self.__grid.GetCells()):
ccId, oeMol, title = self._molTitleList[idx]
logger.debug("Preparing %s %r", ccId, title)
#
if self._params["suppressHydrogens"]:
# mol = oeMol.getGraphMolSuppressH()
# OESuppressHydrogens(self.__oeMol, retainPolar=False,retainStereo=True,retainIsotope=True)
mol = oechem.OESuppressHydrogens(oechem.OEGraphMol(oeMol))
else:
mol = oeMol
#
if self.__useTitle and title:
mol.SetTitle(title)
self._opts.SetTitleHeight(5.0)
else:
mol.SetTitle("")
#
#
oedepict.OEPrepareDepiction(mol)
self._opts.SetDimensions(cell.GetWidth(), cell.GetHeight(),
oedepict.OEScale_AutoScale)
self._assignDisplayOptions()
disp = oedepict.OE2DMolDisplay(mol, self._opts)
oedepict.OERenderMolecule(cell, disp)
if self._params["cellBorders"]:
oedepict.OEDrawBorder(cell,
oedepict.OEPen(oedepict.OEBlackPen))
def png_wiberg_labels(mol, fname, width=600, height=400):
"""
Generate png figure of molecule. Bonds are labeled with Wiberg bond order
Parameters
----------
mol: OpenEye OEMol
fname: str
filename for png
width: int
height: int
Returns
-------
bool:
"""
oedepict.OEPrepareDepiction(mol)
opts = oedepict.OE2DMolDisplayOptions(width, height,
oedepict.OEScale_AutoScale)
# opts.SetAtomPropertyFunctor(oedepict.OEDisplayAtomIdx())
# opts.SetAtomPropLabelFont(oedepict.OEFont(oechem.OEDarkGreen))
bondlabel = LabelBondOrder()
opts.SetBondPropertyFunctor(bondlabel)
disp = oedepict.OE2DMolDisplay(mol, opts)
return oedepict.OERenderMolecule(fname, disp)
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 main(argv=[__name__]):
# import configuration file
itf = oechem.OEInterface()
oechem.OEConfigure(itf, InterfaceData)
# add configuration for image size and display options
oedepict.OEConfigureImageOptions(itf)
oedepict.OEConfigure2DMolDisplayOptions(itf)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
ifname = itf.GetString("-in")
ofname = itf.GetString("-out")
ifs = oechem.oemolistream(ifname)
mol = oechem.OEGraphMol()
oechem.OEReadMolecule(ifs, mol)
oedepict.OEPrepareDepiction(mol)
width, height = oedepict.OEGetImageWidth(itf), oedepict.OEGetImageHeight(itf)
opts = oedepict.OE2DMolDisplayOptions(width, height, oedepict.OEScale_AutoScale)
# set up display options from command line parameters
oedepict.OESetup2DMolDisplayOptions(opts, itf)
disp = oedepict.OE2DMolDisplay(mol, opts)
oedepict.OERenderMolecule(ofname, disp)
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
oedepict.OEConfigureReportOptions(itf)
oedepict.OEConfigurePrepareDepictionOptions(itf)
oedepict.OEConfigure2DMolDisplayOptions(itf)
if not oechem.OEParseCommandLine(itf, argv):
return 1
iname = itf.GetString("-in")
ifs = oechem.oemolistream()
ifs.SetConfTest(oechem.OEAbsoluteConfTest()) # VTL
if not ifs.open(iname):
oechem.OEThrow.Fatal("Cannot open input file!")
oname = itf.GetString("-out")
ext = oechem.OEGetFileExtension(oname)
if ext != "pdf":
oechem.OEThrow.Fatal("Output must be PDF format.")
ofs = oechem.oeofstream()
if not ofs.open(oname):
oechem.OEThrow.Fatal("Cannot open output file!")
if itf.HasString("-ringdict"):
rdfname = itf.GetString("-ringdict")
if not oechem.OEInit2DRingDictionary(rdfname):
oechem.OEThrow.Warning("Cannot use user-defined ring dictionary!")
ropts = oedepict.OEReportOptions()
oedepict.OESetupReportOptions(ropts, itf)
ropts.SetFooterHeight(25.0)
report = oedepict.OEReport(ropts)
popts = oedepict.OEPrepareDepictionOptions()
oedepict.OESetupPrepareDepictionOptions(popts, itf)
dopts = oedepict.OE2DMolDisplayOptions()
oedepict.OESetup2DMolDisplayOptions(dopts, itf)
dopts.SetDimensions(report.GetCellWidth(), report.GetCellHeight(),
oedepict.OEScale_AutoScale)
for mol in ifs.GetOEMols(): # VTL ignore confs; dont use GetOEGraphMols
print(mol.GetTitle()) # VTL
cell = report.NewCell()
oedepict.OEPrepareDepiction(mol, popts)
disp = oedepict.OE2DMolDisplay(mol, dopts)
oedepict.OERenderMolecule(cell, disp)
font = oedepict.OEFont(oedepict.OEFontFamily_Default,
oedepict.OEFontStyle_Bold, 12,
oedepict.OEAlignment_Center, oechem.OEBlack)
for pagenum, footer in enumerate(report.GetFooters()):
text = "Page %d of %d" % (pagenum + 1, report.NumPages())
oedepict.OEDrawTextToCenter(footer, text, font)
oedepict.OEWriteReport(ofs, ext, report)
return 0
def Draw2DSurfacePartialCharge(image, mol):
oedepict.OEPrepareDepiction(mol)
oechem.OEMMFFAtomTypes(mol)
oechem.OEMMFF94PartialCharges(mol)
opts = oedepict.OE2DMolDisplayOptions(image.GetWidth(), image.GetHeight(),
oedepict.OEScale_AutoScale)
opts.SetTitleLocation(oedepict.OETitleLocation_Hidden)
opts.SetScale(oegrapheme.OEGetMoleculeSurfaceScale(mol, opts))
coloranion = oechem.OEColorStop(-1.0, oechem.OEColor(oechem.OEDarkRed))
colorcation = oechem.OEColorStop(+1.0, oechem.OEColor(oechem.OEDarkBlue))
colorg = oechem.OELinearColorGradient(coloranion, colorcation)
colorg.AddStop(oechem.OEColorStop(0.0, oechem.OEColor(oechem.OEWhite)))
arcfxn = AtomPartialChargeArcFxn(colorg)
for atom in mol.GetAtoms():
oegrapheme.OESetSurfaceArcFxn(mol, atom, arcfxn)
disp = oedepict.OE2DMolDisplay(mol, opts)
oegrapheme.OEDraw2DSurface(disp)
oedepict.OERenderMolecule(image, disp)
def smiles_to_png(smiles, file_path, image_size=200):
"""Creates a png image of the 2D representation of
a given smiles pattern.
Parameters
----------
smiles: str
The smiles pattern to generate the png of.
file_path: str
The path of the output png file.
image_size: int
The size in pixels of the square image.
"""
from openeye import oedepict
from openforcefield.topology import Molecule
if os.path.isfile(file_path):
return
off_molecule = Molecule.from_smiles(smiles)
oe_molecule = off_molecule.to_openeye()
# oe_molecule.SetTitle(off_molecule.to_smiles())
oedepict.OEPrepareDepiction(oe_molecule)
options = oedepict.OE2DMolDisplayOptions(image_size, image_size, oedepict.OEScale_AutoScale)
display = oedepict.OE2DMolDisplay(oe_molecule, options)
oedepict.OERenderMolecule(file_path, display)
def main(argv=[__name__]):
itf = oechem.OEInterface()
oechem.OEConfigure(itf, InterfaceData)
oedepict.OEConfigureImageWidth(itf, 400.0)
oedepict.OEConfigureImageHeight(itf, 400.0)
oedepict.OEConfigureImageGridParams(itf)
oedepict.OEConfigurePrepareDepictionOptions(itf)
oedepict.OEConfigure2DMolDisplayOptions(itf)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
oname = itf.GetString("-out")
ext = oechem.OEGetFileExtension(oname)
if not oedepict.OEIsRegisteredImageFile(ext):
oechem.OEThrow.Fatal("Unknown image type!")
ofs = oechem.oeofstream()
if not ofs.open(oname):
oechem.OEThrow.Fatal("Cannot open output file!")
width, height = oedepict.OEGetImageWidth(itf), oedepict.OEGetImageHeight(
itf)
image = oedepict.OEImage(width, height)
rows = oedepict.OEGetImageGridNumRows(itf)
cols = oedepict.OEGetImageGridNumColumns(itf)
grid = oedepict.OEImageGrid(image, rows, cols)
popts = oedepict.OEPrepareDepictionOptions()
oedepict.OESetupPrepareDepictionOptions(popts, itf)
dopts = oedepict.OE2DMolDisplayOptions()
oedepict.OESetup2DMolDisplayOptions(dopts, itf)
dopts.SetDimensions(grid.GetCellWidth(), grid.GetCellHeight(),
oedepict.OEScale_AutoScale)
celliter = grid.GetCells()
for iname in itf.GetStringList("-in"):
ifs = oechem.oemolistream()
if not ifs.open(iname):
oechem.OEThrow.Warning("Cannot open %s input file!" % iname)
continue
for mol in ifs.GetOEGraphMols():
if not celliter.IsValid():
break
oedepict.OEPrepareDepiction(mol, popts)
disp = oedepict.OE2DMolDisplay(mol, dopts)
oedepict.OERenderMolecule(celliter.Target(), disp)
celliter.Next()
oedepict.OEWriteImage(ofs, ext, image)
return 0
def smiles_to_image_grid_mod(
smiles: set,
output_path: str,
cols: int = 8,
cell_width: int = 200,
cell_height: int = 200,
):
from openeye import oechem, oedepict
itf = oechem.OEInterface()
PageByPage = True
suppress_h = True
rows = math.ceil(len(smiles) / cols)
image = oedepict.OEImage(cell_width * cols, cell_height * rows)
grid = oedepict.OEImageGrid(image, rows, cols)
opts = oedepict.OE2DMolDisplayOptions(
grid.GetCellWidth(), grid.GetCellHeight(), oedepict.OEScale_AutoScale
)
opts.SetAromaticStyle(oedepict.OEAromaticStyle_Circle)
opts.SetTitleLocation(oedepict.OETitleLocation_Bottom)
for i, (smi, cell) in enumerate(zip(smiles, grid.GetCells())):
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, smi)
center_bond = []
for atom in mol.GetAtoms():
if atom.GetMapIdx() >0:
center_bond.append(atom.GetIdx())
# print(smi, center_bond)
assert len(center_bond) == 2
oedepict.OEPrepareDepiction(mol, False, suppress_h)
disp = oedepict.OE2DMolDisplay(mol, opts)
# Highlight element of interest
class NoAtom(oechem.OEUnaryAtomPred):
def __call__(self, atom):
return False
class NoBond(oechem.OEUnaryBondPred):
def __call__(self, bond):
return False
class CentralBondInTorsion(oechem.OEUnaryBondPred):
def __call__(self, bond):
return (bond.GetBgn().GetIdx() in center_bond) and (bond.GetEnd().GetIdx() in center_bond)
atoms = mol.GetAtoms(NoAtom())
bonds = mol.GetBonds(CentralBondInTorsion())
abset = oechem.OEAtomBondSet(atoms, bonds)
oedepict.OEAddHighlighting(disp, oechem.OEColor(oechem.OEMandarin), oedepict.OEHighlightStyle_BallAndStick, abset)
oedepict.OERenderMolecule(cell, disp)
oedepict.OEWriteImage(output_path, image)
def generate_ligands_figure(molecules, figsize=None, filename='ligands.png'):
""" Plot an image with all of the ligands passed in
Parameters
----------
molecules : list
list of openeye.oemol objects
figsize : list or tuple
list or tuple of len() == 2 of the horizontal and vertical lengths of image
filename : string
name of file to save the image
Returns
-------
"""
from openeye import oechem, oedepict
to_draw = []
for lig in molecules:
oedepict.OEPrepareDepiction(lig)
to_draw.append(oechem.OEGraphMol(lig))
dim = int(np.ceil(len(to_draw)**0.5))
if figsize is None:
x_len = 1000 * dim
y_len = 500 * dim
image = oedepict.OEImage(x_len, y_len)
else:
assert (len(figsize) == 2
), "figsize arguement should be a tuple or list of length 2"
image = oedepict.OEImage(figsize[0], figsize[1])
rows, cols = dim, dim
grid = oedepict.OEImageGrid(image, rows, cols)
opts = oedepict.OE2DMolDisplayOptions(grid.GetCellWidth(),
grid.GetCellHeight(),
oedepict.OEScale_AutoScale)
minscale = float("inf")
for mol in to_draw:
minscale = min(minscale, oedepict.OEGetMoleculeScale(mol, opts))
# print(mol.GetTitle())
opts.SetScale(minscale)
for idx, cell in enumerate(grid.GetCells()):
mol = to_draw[idx]
disp = oedepict.OE2DMolDisplay(mol, opts)
oedepict.OERenderMolecule(cell, disp)
oedepict.OEWriteImage(filename, image)
return
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 DrawMolecule(image, mol, width, height, offset):
frame = oedepict.OEImageFrame(image, width, height, offset)
oedepict.OEDrawBorder(frame, oedepict.OELightGreyPen)
opts = oedepict.OE2DMolDisplayOptions(width, height,
oedepict.OEScale_AutoScale)
disp = oedepict.OE2DMolDisplay(mol, opts)
clearbackground = True
oedepict.OERenderMolecule(frame, disp, not clearbackground)
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 depict(mol, width=500, height=200):
from IPython.display import Image
dopt = oedepict.OEPrepareDepictionOptions()
dopt.SetDepictOrientation(oedepict.OEDepictOrientation_Horizontal)
oedepict.OEPrepareDepiction(mol, dopt)
opts = oedepict.OE2DMolDisplayOptions(width, height,
oedepict.OEScale_AutoScale)
disp = oedepict.OE2DMolDisplay(mol, opts)
ofs = oechem.oeosstream()
oedepict.OERenderMolecule(ofs, 'png', disp)
ofs.flush()
return Image(data="".join(ofs.str()))
def render_molecule(
smiles: str,
path: str,
width: int = 320,
height: int = 240,
file_format: str = "svg",
clearbackground: bool = False,
force_regenerate: bool = False,
) -> None:
"""
Render the molecule (from SMILES) to an image
Parameters
----------
smiles : str
The SMILES string
filename : str
Output filename, with image format (pdf, png, jpg) detected from filename
width : int, optional, default=320
Default image width
height : int, optional, default=240
Default image height
clearbackground : bool, optional, default=False
For PNG, whether background should be clear
"""
# Import the openeye toolkit
from openeye import oechem, oedepict
output_name = get_image_filename(smiles)
output_path = os.path.join(path, os.extsep.join([output_name,
file_format]))
if not force_regenerate and os.path.exists(output_path):
logging.info("Skipping already-rendered molecule: %s", smiles)
return
# Generate OpenEye OEMol object from SMILES
# see https://docs.eyesopen.com/toolkits/python/oechemtk/molctordtor.html?highlight=smiles#construction-from-smiles
mol = oechem.OEGraphMol()
if not oechem.OESmilesToMol(mol, smiles):
raise ValueError(
f"Failed to convert SMILES string to molecule: {smiles}")
# Configure options (lots more are available)
# see https://docs.eyesopen.com/toolkits/python/depicttk/OEDepictClasses/OE2DMolDisplayOptions.html
opts = oedepict.OE2DMolDisplayOptions()
opts.SetWidth(width)
opts.SetHeight(height)
# Render image
oedepict.OEPrepareDepiction(mol)
disp = oedepict.OE2DMolDisplay(mol, opts)
oedepict.OERenderMolecule(output_path, disp, clearbackground)
def mol2svg(self, mol, svg_file):
oechem.OEAssignImplicitHydrogens(mol)
oechem.OEAddExplicitHydrogens(mol)
oedepict.OEPrepareDepiction(mol)
width = 1000
height = 1000
opts = oedepict.OE2DMolDisplayOptions(width, height,
oedepict.OEScale_AutoScale)
pens = opts.GetDefaultBondPen()
pens.SetLineWidth(10)
disp = oedepict.OE2DMolDisplay(mol, opts)
oedepict.OERenderMolecule(svg_file, disp)
def oedepict_pdf(all_probe_mols, subdir):
"""
Generate a PDF report of all molecules together, color-coded
by parameter ID and labeled with parameter ID and SMILES tag.
Parameters
----------
all_probe_mols:
key is string of a parameter id to be probed;
value is a list of oegraphmols with this parameter id
subdir : string
Name of subdirectory in which to save results.pdf file
"""
multi = oedepict.OEMultiPageImageFile(oedepict.OEPageOrientation_Landscape,
oedepict.OEPageSize_US_Letter)
image = multi.NewPage()
opts = oedepict.OE2DMolDisplayOptions()
rows, cols = 4, 4
grid = oedepict.OEImageGrid(image, rows, cols)
grid.SetCellGap(20)
grid.SetMargins(20)
citer = grid.GetCells()
colors = list(oechem.OEGetContrastColors())
for i, (param, mol_list) in enumerate(all_probe_mols.items()):
pen = oedepict.OEPen(oechem.OEWhite, colors[i], oedepict.OEFill_Off, 4.0)
for mol in mol_list:
# go to next page
if not citer.IsValid():
image = multi.NewPage()
grid = oedepict.OEImageGrid(image, rows, cols)
grid.SetCellGap(20)
grid.SetMargins(20)
citer = grid.GetCells()
cell = citer.Target()
mol.SetTitle(f"{param} {oechem.OEGetSDData(mol, 'SMILES QCArchive')}")
oedepict.OEPrepareDepiction(mol)
opts.SetDimensions(cell.GetWidth(), cell.GetHeight(), oedepict.OEScale_AutoScale)
disp = oedepict.OE2DMolDisplay(mol, opts)
oedepict.OERenderMolecule(cell, disp)
oedepict.OEDrawBorder(cell, pen)
citer.Next()
oedepict.OEWriteMultiPageImage(f"{subdir}/results.pdf", multi)
def align2d(file1, file2):
atomexpr = oechem.OEExprOpts_AtomicNumber | oechem.OEExprOpts_RingMember
bondexpr = oechem.OEExprOpts_RingMember
ifs1 = oechem.oemolistream(file1)
ifs2 = oechem.oemolistream(file2)
ifs1.SetConfTest(oechem.OEAbsCanonicalConfTest())
ifs2.SetConfTest(oechem.OEAbsCanonicalConfTest())
popts, dopts, report = prep_pdf_writer()
for mol1, mol2 in zip(ifs1.GetOEMols(), ifs2.GetOEMols()):
oechem.OESuppressHydrogens(mol1)
oechem.OESuppressHydrogens(mol2)
oechem.OEGenerate2DCoordinates(mol2)
ss = oechem.OESubSearch(mol2, atomexpr, bondexpr)
oechem.OEPrepareSearch(mol1, ss)
alignres = oedepict.OEPrepareAlignedDepiction(mol1, ss)
if not alignres.IsValid():
oechem.OEThrow.Error(
"Substructure is not found in input molecule!")
cell1 = report.NewCell()
cell2 = report.NewCell()
oedepict.OEPrepareDepiction(mol1, popts)
oedepict.OEPrepareDepiction(mol2, popts)
disp1 = oedepict.OE2DMolDisplay(mol1, dopts)
disp2 = oedepict.OE2DMolDisplay(mol2, dopts)
oedepict.OERenderMolecule(cell1, disp1)
oedepict.OERenderMolecule(cell2, disp2)
ofs = oechem.oeofstream()
if not ofs.open('output.pdf'):
oechem.OEThrow.Fatal("Cannot open output file!")
oedepict.OEWriteReport(ofs, "pdf", report)
def highlight_atoms_in_mol(mol2, dihedralAtomIndices, width=200, height=200):
mol = mol2.CreateCopy()
opts = oedepict.OE2DMolDisplayOptions(width, height, oedepict.OEScale_AutoScale)
oedepict.OEPrepareDepiction(mol)
disp = oedepict.OE2DMolDisplay(mol, opts)
img = oedepict.OEImage(width, height)
hstyle = oedepict.OEHighlightByBallAndStick(oechem.OEBlueTint)
for atom_idx in dihedralAtomIndices:
oedepict.OEAddHighlighting(disp, hstyle, oechem.OEHasAtomIdx(atom_idx))
oedepict.OERenderMolecule(img, disp)
return img
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
oedepict.OEConfigureImageOptions(itf)
oedepict.OEConfigurePrepareDepictionOptions(itf)
oedepict.OEConfigure2DMolDisplayOptions(itf)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
iname = itf.GetString("-in")
oname = itf.GetString("-out")
ext = oechem.OEGetFileExtension(oname)
if not oedepict.OEIsRegisteredImageFile(ext):
oechem.OEThrow.Fatal("Unknown image type!")
ifs = oechem.oemolistream()
if not ifs.open(iname):
oechem.OEThrow.Fatal("Cannot open input file!")
ofs = oechem.oeofstream()
if not ofs.open(oname):
oechem.OEThrow.Fatal("Cannot open output file!")
mol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ifs, mol):
oechem.OEThrow.Fatal("Cannot read input file!")
if itf.HasString("-ringdict"):
rdfname = itf.GetString("-ringdict")
if not oechem.OEInit2DRingDictionary(rdfname):
oechem.OEThrow.Warning("Cannot use user-defined ring dictionary!")
popts = oedepict.OEPrepareDepictionOptions()
oedepict.OESetupPrepareDepictionOptions(popts, itf)
oedepict.OEPrepareDepiction(mol, popts)
width, height = oedepict.OEGetImageWidth(itf), oedepict.OEGetImageHeight(
itf)
dopts = oedepict.OE2DMolDisplayOptions(width, height,
oedepict.OEScale_AutoScale)
oedepict.OESetup2DMolDisplayOptions(dopts, itf)
disp = oedepict.OE2DMolDisplay(mol, dopts)
oedepict.OERenderMolecule(ofs, ext, disp)
return 0
def DepictMolecules(opts, smiles, basefilename, drawborder=False):
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, smiles)
oedepict.OEPrepareDepiction(mol)
disp = oedepict.OE2DMolDisplay(mol, opts)
image = oedepict.OEImage(disp.GetWidth(), disp.GetHeight())
oedepict.OERenderMolecule(image, disp)
if drawborder:
oedepict.OEDrawBorder(image, oedepict.OELightGreyPen)
oedepict.OEWriteImage(basefilename + ".png", image)
oedepict.OEWriteImage(basefilename + ".pdf", image)
def Draw2DSurface(image, mol):
oedepict.OEPrepareDepiction(mol)
opts = oedepict.OE2DMolDisplayOptions(image.GetWidth(), image.GetHeight(),
oedepict.OEScale_AutoScale)
opts.SetTitleLocation(oedepict.OETitleLocation_Hidden)
opts.SetScale(oegrapheme.OEGetMoleculeSurfaceScale(mol, opts))
arcfxn = AtomColorArcFxn()
for atom in mol.GetAtoms():
oegrapheme.OESetSurfaceArcFxn(mol, atom, arcfxn)
disp = oedepict.OE2DMolDisplay(mol, opts)
oegrapheme.OEDraw2DSurface(disp)
oedepict.OERenderMolecule(image, disp)
def depictMatch(mol, match, width=500, height=200):
from IPython.display import Image
dopt = oedepict.OEPrepareDepictionOptions()
dopt.SetDepictOrientation(oedepict.OEDepictOrientation_Horizontal)
dopt.SetSuppressHydrogens(True)
oedepict.OEPrepareDepiction(mol, dopt)
opts = oedepict.OE2DMolDisplayOptions(width, height,
oedepict.OEScale_AutoScale)
disp = oedepict.OE2DMolDisplay(mol, opts)
hstyle = oedepict.OEHighlightStyle_Color
hcolor = oechem.OEColor(oechem.OELightBlue)
oedepict.OEAddHighlighting(disp, hcolor, hstyle, match)
ofs = oechem.oeosstream()
oedepict.OERenderMolecule(ofs, 'png', disp)
ofs.flush()
return Image(data="".join(ofs.str()))
def DepictMoleculesWithHighlight(smiles, ss, highlight, basefilename):
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, smiles)
oedepict.OEPrepareDepiction(mol)
opts = oedepict.OE2DMolDisplayOptions(220, 160, oedepict.OEScale_AutoScale)
disp = oedepict.OE2DMolDisplay(mol, opts)
unique = True
for match in ss.Match(mol, unique):
oedepict.OEAddHighlighting(disp, highlight, match)
image = oedepict.OEImage(disp.GetWidth(), disp.GetHeight())
oedepict.OERenderMolecule(image, disp)
oedepict.OEWriteImage(basefilename + ".png", image)
oedepict.OEWriteImage(basefilename + ".pdf", image)
def DepictMoleculesWithHighlight(smiles, ss, highlight, basefilename):
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, smiles)
oedepict.OEPrepareDepiction(mol)
opts = oedepict.OE2DMolDisplayOptions(250, 160, oedepict.OEScale_AutoScale)
opts.SetTitleLocation(oedepict.OETitleLocation_Hidden)
disp = oedepict.OE2DMolDisplay(mol, opts)
unique = True
oedepict.OEAddHighlightOverlay(disp, highlight, ss.Match(mol, unique))
image = oedepict.OEImage(disp.GetWidth(), disp.GetHeight())
oedepict.OERenderMolecule(image, disp)
oedepict.OEWriteImage(basefilename + ".png", image)
oedepict.OEWriteImage(basefilename + ".pdf", image)
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
oedepict.OEConfigureImageOptions(itf)
oedepict.OEConfigure2DMolDisplayOptions(itf)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
iname = itf.GetString("-in")
oname = itf.GetString("-out")
ext = oechem.OEGetFileExtension(oname)
if not oedepict.OEIsRegisteredImageFile(ext):
oechem.OEThrow.Fatal("Unknown image type!")
ifs = oechem.oemolistream()
if not ifs.open(iname):
oechem.OEThrow.Fatal("Cannot open input file!")
if ifs.GetFormat() != oechem.OEFormat_MDL:
oechem.OEThrow.Fatal("Input file is not an MDL query file")
ofs = oechem.oeofstream()
if not ofs.open(oname):
oechem.OEThrow.Fatal("Cannot open output file!")
mol = oechem.OEGraphMol()
if not oechem.OEReadMDLQueryFile(ifs, mol):
oechem.OEThrow.Fatal("Cannot read mdl query input file!")
clearcoords, suppressH = False, False
oedepict.OEPrepareDepiction(mol, clearcoords, suppressH)
width, height = oedepict.OEGetImageWidth(itf), oedepict.OEGetImageHeight(
itf)
opts = oedepict.OE2DMolDisplayOptions(width, height,
oedepict.OEScale_AutoScale)
oedepict.OESetup2DMolDisplayOptions(opts, itf)
disp = oedepict.OE2DMolDisplay(mol, opts)
oedepict.OERenderMolecule(ofs, ext, disp)
return 0
def prepare(self):
self.__setupImage()
rows = self._params["gridRows"]
cols = self._params["gridCols"]
grid = oedepict.OEImageGrid(self.__image, rows, cols)
citer = grid.GetCells()
for ccId, oeMol, title in self._molTitleList:
logger.debug("Preparing %s %r", ccId, title)
if not citer.IsValid():
# go to next page
self.__image = self.__multi.NewPage()
grid = oedepict.OEImageGrid(self.__image, rows, cols)
grid.SetCellGap(self._params["cellGap"])
grid.SetMargins(self._params["cellMargin"])
citer = grid.GetCells()
cell = citer.Target()
#
if self._params["suppressHydrogens"]:
# mol = oeMol.getGraphMolSuppressH()
# OESuppressHydrogens(self.__oeMol, retainPolar=False,retainStereo=True,retainIsotope=True)
mol = oechem.OESuppressHydrogens(oechem.OEGraphMol(oeMol))
else:
mol = oeMol
if self.__useTitle and title:
mol.SetTitle(title)
self._opts.SetTitleHeight(5.0)
else:
mol.SetTitle("")
#
#
oedepict.OEPrepareDepiction(mol)
self._opts.SetDimensions(cell.GetWidth(), cell.GetHeight(),
oedepict.OEScale_AutoScale)
self._assignDisplayOptions()
disp = oedepict.OE2DMolDisplay(mol, self._opts)
oedepict.OERenderMolecule(cell, disp)
oedepict.OEDrawBorder(cell, oedepict.OEPen(oedepict.OEBlackPen))
citer.Next()
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 Draw2DSurfaces(image, mol):
oedepict.OEPrepareDepiction(mol)
opts = oedepict.OE2DMolDisplayOptions(image.GetWidth(), image.GetHeight(),
oedepict.OEScale_AutoScale)
opts.SetTitleLocation(oedepict.OETitleLocation_Hidden)
opts.SetScale(oegrapheme.OEGetMoleculeSurfaceScale(mol, opts, 1.50))
disp = oedepict.OE2DMolDisplay(mol, opts)
Draw2DSurface(disp, oechem.OEHasAtomicNum(oechem.OEElemNo_C), 1.00,
oechem.OEBlack)
Draw2DSurface(disp, oechem.OEHasAtomicNum(oechem.OEElemNo_N), 1.25,
oechem.OEDarkBlue)
Draw2DSurface(disp, oechem.OEHasAtomicNum(oechem.OEElemNo_O), 1.50,
oechem.OEDarkRed)
oedepict.OERenderMolecule(image, disp)
