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 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 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 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 CreateGrid(image):
rows, cols = 3, 3
grid = oedepict.OEImageGrid(image, rows, cols)
grid.SetCellGap(5)
grid.SetMargins(0)
for cell in grid.GetCells():
oedepict.OEDrawBorder(cell, oedepict.OERedPen)
return grid
def __setupImage(self):
"""Internal method to configure a single page image."""
#
self.__image = oedepict.OEImage(self._params["imageSizeX"],
self._params["imageSizeY"])
self.__grid = oedepict.OEImageGrid(self.__image,
self._params["gridRows"],
self._params["gridCols"])
self.__grid.SetCellGap(self._params["cellGap"])
self.__grid.SetMargins(self._params["cellMargin"])
self._opts = oedepict.OE2DMolDisplayOptions(
self.__grid.GetCellWidth(), self.__grid.GetCellHeight(),
oedepict.OEScale_AutoScale)
#
logger.debug("Num columns %d", self.__grid.NumCols())
logger.debug("Num rows %d", self.__grid.NumRows())
if len(sys.argv) != 3:
oechem.OEThrow.Usage("%s <rxnfile> <imagefile>" % sys.argv[0])
ifs = oechem.oemolistream(sys.argv[1])
mol = oechem.OEGraphMol()
if not oechem.OEReadRxnFile(ifs, mol):
oechem.OEThrow.Fatal("%s error reading reaction file" % sys.argv[0])
oedepict.OEPrepareDepiction(mol)
image = oedepict.OEImage(900, 100)
rows, cols = 1, 3
grid = oedepict.OEImageGrid(image, rows, cols)
opts = oedepict.OE2DMolDisplayOptions(grid.GetCellWidth(),
grid.GetCellHeight(),
oedepict.OEScale_AutoScale)
cell = grid.GetCell(1, 1)
mol.SetTitle("Reaction display")
opts.SetAtomVisibilityFunctor(
oechem.OEIsTrueAtom()) # explicitly set the default
disp = oedepict.OE2DMolDisplay(mol, opts)
rxnscale = disp.GetScale()
oedepict.OERenderMolecule(cell, disp)
cell = grid.GetCell(1, 2)
mol.SetTitle("Reactant display")
def gen_pdf(
tid_clusters_list: list,
output_path: str,
cols: int = 8,
cell_width: int = 200,
cell_height: int = 200,
):
from openeye import oechem, oedepict
from openforcefield.topology import Molecule
itf = oechem.OEInterface()
PageByPage = True
suppress_h = True
n = sum([len(clusters) for tid, clusters in tid_clusters_list.items()])
rows = math.ceil(n / 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)
count = 0
for tid, clusters in tid_clusters_list.items():
for cluster in clusters:
torsions = cluster['torsions']
label = cluster['cluster_label']
torsions = cluster['torsions']
for torsion in torsions:
cell = grid.GetCell(count // cols + 1, count % cols + 1)
smi = torsion['mol_index']
atom_indices = torsion['indices']
# mol = oechem.OEGraphMol()
# oechem.OESmilesToMol(mol, smi)
off_mol = Molecule.from_smiles(smi,
allow_undefined_stereo=True)
off_mol = off_mol.canonical_order_atoms()
mol = Molecule.to_openeye(off_mol)
title = '{} ({})'.format(tid, set(torsion['covered_tids']))
mol.SetTitle(title)
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 AtomInTorsion(oechem.OEUnaryAtomPred):
def __call__(self, atom):
return atom.GetIdx() in atom_indices
class NoBond(oechem.OEUnaryBondPred):
def __call__(self, bond):
return False
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])
atoms = mol.GetAtoms(AtomInTorsion())
bonds = mol.GetBonds(NoBond())
abset = oechem.OEAtomBondSet(atoms, bonds)
oedepict.OEAddHighlighting(
disp, oechem.OEColor(oechem.OEYellow),
oedepict.OEHighlightStyle_BallAndStick, abset)
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)
count += 1
oedepict.OEWriteImage(output_path, image)
def gen_pdf(
cluster_dic: list,
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
n = sum([len(dic['torsions']) for dic in cluster_dic])
rows = math.ceil(n / 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, (dic, cell) in enumerate(zip(cluster_dic, grid.GetCells())):
count = 0
for i, dic in enumerate(cluster_dic):
if 'cluster_label' in dic:
label = dic['cluster_label']
torsions = dic['torsions']
for torsion in torsions:
cell = grid.GetCell(count // cols + 1, count % cols + 1)
smi = torsion['mol_index']
atom_indices = torsion['indices']
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, smi)
title = 'label:{} {}'.format(label, torsion['covered_tids'])
mol.SetTitle(title)
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 AtomInTorsion(oechem.OEUnaryAtomPred):
def __call__(self, atom):
return atom.GetIdx() in atom_indices
class NoBond(oechem.OEUnaryBondPred):
def __call__(self, bond):
return False
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])
atoms = mol.GetAtoms(AtomInTorsion())
bonds = mol.GetBonds(NoBond())
abset = oechem.OEAtomBondSet(atoms, bonds)
oedepict.OEAddHighlighting(
disp, oechem.OEColor(oechem.OEYellow),
oedepict.OEHighlightStyle_BallAndStick, abset)
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)
count += 1
elif 'mol_index' in dic:
cell = grid.GetCell(count // cols + 1, count % cols + 1)
smi = dic['mol_index']
atom_indices = dic['indices']
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, smi)
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 AtomInTorsion(oechem.OEUnaryAtomPred):
def __call__(self, atom):
return atom.GetIdx() in atom_indices
class NoBond(oechem.OEUnaryBondPred):
def __call__(self, bond):
return False
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])
atoms = mol.GetAtoms(AtomInTorsion())
bonds = mol.GetBonds(NoBond())
abset = oechem.OEAtomBondSet(atoms, bonds)
oedepict.OEAddHighlighting(disp, oechem.OEColor(oechem.OEYellow),
oedepict.OEHighlightStyle_BallAndStick,
abset)
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)
count += 1
else:
for cluster in cluster_dic[dic]:
label = cluster['cluster_label']
torsions = cluster['torsions']
for torsion in torsions:
cell = grid.GetCell(count // cols + 1, count % cols + 1)
smi = torsion['mol_index']
atom_indices = torsion['indices']
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, smi)
title = 'tid: {}, label:{}'.format(dic, label)
mol.SetTitle(title)
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 AtomInTorsion(oechem.OEUnaryAtomPred):
def __call__(self, atom):
return atom.GetIdx() in atom_indices
class NoBond(oechem.OEUnaryBondPred):
def __call__(self, bond):
return False
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])
atoms = mol.GetAtoms(AtomInTorsion())
bonds = mol.GetBonds(NoBond())
abset = oechem.OEAtomBondSet(atoms, bonds)
oedepict.OEAddHighlighting(
disp, oechem.OEColor(oechem.OEYellow),
oedepict.OEHighlightStyle_BallAndStick, abset)
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)
count += 1
oedepict.OEWriteImage(output_path, image)