def DrawFigures(pen, basefilename):
image = oedepict.OEImage(80, 80)
DrawFigure(image, pen)
oedepict.OEWriteImage(basefilename + ".png", image)
oedepict.OEWriteImage(basefilename + ".pdf", image)
def DrawHelloWorlds(font, basefilename):
image = oedepict.OEImage(200, 60)
DrawHelloWorld(image, font)
oedepict.OEWriteImage(basefilename + ".png", image)
oedepict.OEWriteImage(basefilename + ".pdf", image)
def DepictColorGradient(colorg, opts, basefilename):
width, height = 400, 100
image = oedepict.OEImage(width, height)
oegrapheme.OEDrawColorGradient(image, colorg, opts)
oedepict.OEWriteImage(basefilename + ".png", image)
oedepict.OEWriteImage(basefilename + ".pdf", image)
def DepictPeptide(opts, smiles, basefilename):
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, smiles)
oedepict.OEPrepareDepiction(mol)
image = oedepict.OEImage(400, 200)
oegrapheme.OEDrawPeptide(image, mol, opts)
oedepict.OEWriteImage(basefilename + ".svg", image)
oedepict.OEWriteImage(basefilename + ".pdf", image)
oedepict.OEWriteImage(basefilename + ".png", image)
def DrawQuadraticBezier():
# @ <SNIPPET-DRAW-QUADRATIC-BEZIER>
image = oedepict.OEImage(100, 100)
b = oedepict.OE2DPoint(20, 70)
e = oedepict.OE2DPoint(80, 70)
c = b + oedepict.OE2DPoint(30, -80)
pen = oedepict.OEPen(oechem.OELightGreen, oechem.OEBlack,
oedepict.OEFill_On, 2.0)
image.DrawQuadraticBezier(b, c, e, pen)
# @ </SNIPPET-DRAW-QUADRATIC-BEZIER>
oedepict.OEWriteImage("DrawQuadraticBezier.png", image)
oedepict.OEWriteImage("DrawQuadraticBezier.pdf", image)
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 DrawCubicBezier():
# @ <SNIPPET-CUBIC-BEZIER>
image = oedepict.OEImage(100, 100)
b = oedepict.OE2DPoint(20, 70)
e = oedepict.OE2DPoint(60, 70)
c1 = b + oedepict.OE2DPoint(50, -60)
c2 = e + oedepict.OE2DPoint(50, -60)
pen = oedepict.OEPen(oechem.OELightGreen, oechem.OEBlack,
oedepict.OEFill_On, 2.0)
image.DrawCubicBezier(b, c1, c2, e, pen)
# @ </SNIPPET-CUBIC-BEZIER>
oedepict.OEWriteImage("DrawCubicBezier.png", image)
oedepict.OEWriteImage("DrawCubicBezier.pdf", image)
def write(self, imagePath):
try:
dirPath, _ = os.path.split(imagePath)
if not os.access(dirPath, os.W_OK):
os.makedirs(dirPath, mode=0o755)
except Exception:
pass
oedepict.OEWriteImage(imagePath, self.__image)
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 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 DrawPolygon():
# @ <SNIPPET-DRAW-POLYGON>
image = oedepict.OEImage(100, 100)
polygon = []
polygon.append(oedepict.OE2DPoint(20, 20))
polygon.append(oedepict.OE2DPoint(40, 40))
polygon.append(oedepict.OE2DPoint(60, 20))
polygon.append(oedepict.OE2DPoint(80, 40))
polygon.append(oedepict.OE2DPoint(80, 80))
polygon.append(oedepict.OE2DPoint(20, 80))
pen = oedepict.OEPen(oechem.OELightGreen, oechem.OEBlack,
oedepict.OEFill_On, 2.0)
image.DrawPolygon(polygon, pen)
# @ </SNIPPET-DRAW-POLYGON>
oedepict.OEWriteImage("DrawPolygon.png", image)
oedepict.OEWriteImage("DrawPolygon.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 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 WriteTable(tableoptions, basefilename):
image = oedepict.OEImage(300, 200)
table = oedepict.OEImageTable(image, tableoptions)
for idx, cell in enumerate(table.GetHeaderCells()):
table.DrawText(cell, "(header %d)" % (idx + 1))
for idx, cell in enumerate(table.GetStubColumnCells()):
table.DrawText(cell, "(stub %d)" % (idx + 1))
onlybody = True
for row in range(1, table.NumRows(onlybody) + 1):
for col in range(1, table.NumColumns(onlybody) + 1):
cell = table.GetBodyCell(row, col)
table.DrawText(cell, "(body %d, %d)" % (row, col))
oedepict.OEDrawBorder(image, oedepict.OELightGreyPen)
oedepict.OEWriteImage(basefilename + ".png", image)
oedepict.OEWriteImage(basefilename + ".pdf", image)
def DrawPath():
# @ <SNIPPET-DRAW-PATH>
image = oedepict.OEImage(100, 100)
path = oedepict.OE2DPath(oedepict.OE2DPoint(20, 80))
path.AddLineSegment(oedepict.OE2DPoint(80, 80))
path.AddLineSegment(oedepict.OE2DPoint(80, 40))
path.AddCurveSegment(oedepict.OE2DPoint(80,
10), oedepict.OE2DPoint(20, 10),
oedepict.OE2DPoint(20, 40))
pen = oedepict.OEPen(oechem.OELightGreen, oechem.OEBlack,
oedepict.OEFill_On, 2.0)
image.DrawPath(path, pen)
# @ </SNIPPET-DRAW-PATH>
oedepict.OEWriteImage("DrawPath.png", image)
oedepict.OEWriteImage("DrawPath.pdf", image)
# @ <SNIPPET-GET-PATH-POINTS>
for p in path.GetPoints():
pos = p.GetPoint()
print(" %.1f %.1f %d" % (pos.GetX(), pos.GetY(), p.GetPointType()))
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")
opts.SetAtomVisibilityFunctor(
OEAtomVisibilityShowRxnRole(oechem.OERxnRole_Reactant))
opts.SetScale(rxnscale)
disp = oedepict.OE2DMolDisplay(mol, opts)
oedepict.OERenderMolecule(cell, disp)
cell = grid.GetCell(1, 3)
mol.SetTitle("Product display")
opts.SetAtomVisibilityFunctor(
OEAtomVisibilityShowRxnRole(oechem.OERxnRole_Product))
opts.SetScale(rxnscale)
disp = oedepict.OE2DMolDisplay(mol, opts)
oedepict.OERenderMolecule(cell, disp)
# @ </SNIPPET-ATOM-VISIBILITY>
oedepict.OEWriteImage(sys.argv[2], image)
def main(argv=[__name__]):
"""
itf = oechem.OEInterface()
oechem.OEConfigure(itf, InterfaceData)
if not oechem.OEParseCommandLine(itf, argv):
return 1
oname = itf.GetString("-out")
iname = itf.GetString("-in")
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!")
## INPUT PARAMETERS
#########################################################
#########################################################
mm = 'tyk2/og_pdbs'
qml = 'tyk2/forward_snapshots'
phase = 'solvent'
which_ligand = 'old'
dir_name = iname
ligand_pdbs_mm = glob.glob(f"{mm}/{dir_name}/{which_ligand}*{phase}.pdb")
print(len(ligand_pdbs_mm))
ligand_pdbs_qml = glob.glob(f"{qml}/{dir_name}/{which_ligand}*{phase}.pdb")
print(len(ligand_pdbs_qml))
#d = np.load('full_data_dict.npy', allow_pickle=True)
from_ligand, to_ligand = iname.replace('from', '').replace('to', '').replace('lig', '')
print(from_ligand)
print(to_ligand)
#key1 = (1, 8)
#key2 = ('solvent', which_ligand)
#########################################################
#########################################################
#d = d.flatten()[0]
#work = d[key1][key2]
#print(work)
for i, (mm_pdb_path, ani_pdb_path) in enumerate(zip(ligand_pdbs_mm, ligand_pdbs_qml)):
print(mm_pdb_path, ani_pdb_path)
if i == 0:
MM_mol = createOEMolFromSDF(mm_pdb_path, 0)
ANI_mol = createOEMolFromSDF(ani_pdb_path, 0)
else:
# there absolutely must be a better/faster way of doing this because this is ugly and slow
MM_mol.NewConf(createOEMolFromSDF(mm_pdb_path, 0))
ANI_mol.NewConf(createOEMolFromSDF(ani_pdb_path, 0))
"""
ofs = oechem.oeofstream()
oname = f"tor_out"
ext = oechem.OEGetFileExtension(oname)
mm_pdb_path = f"og_lig0_solvent.pdb"
ani_pdb_path = f"forward_lig0.solvent.pdb"
MM_mol = createOEMolFromSDF(mm_pdb_path, 0)
ANI_mol = createOEMolFromSDF(ani_pdb_path, 0)
mol = MM_mol
mol2 = ANI_mol
for m in [mol, mol2]:
oechem.OESuppressHydrogens(m)
oechem.OECanonicalOrderAtoms(m)
oechem.OECanonicalOrderBonds(m)
m.Sweep()
refmol = None
stag = "dihedral_histogram"
itag = oechem.OEGetTag(stag)
nrbins = 20
print(mol.NumConfs())
print(mol2.NumConfs())
get_dihedrals(mol, itag)
set_dihedral_histograms(mol, itag, nrbins)
get_dihedrals(mol2, itag)
#set_weighted_dihedral_histograms(mol2, itag, work, nrbins)
set_dihedral_histograms(mol2, itag, nrbins)
width, height = 800, 400
image = oedepict.OEImage(width, height)
moffset = oedepict.OE2DPoint(0, 0)
mframe = oedepict.OEImageFrame(image, width * 0.70, height, moffset)
doffset = oedepict.OE2DPoint(mframe.GetWidth(), height * 0.30)
dframe = oedepict.OEImageFrame(image, width * 0.30, height * 0.5, doffset)
flexibility = True
colorg = get_color_gradient(nrbins, flexibility)
opts = oedepict.OE2DMolDisplayOptions(mframe.GetWidth(),
mframe.GetHeight(),
oedepict.OEScale_AutoScale)
depict_dihedrals(mframe, dframe, mol, mol2, refmol, opts, itag, nrbins,
colorg)
if flexibility:
lopts = oedepict.OELegendLayoutOptions(
oedepict.OELegendLayoutStyle_HorizontalTopLeft,
oedepict.OELegendColorStyle_LightBlue,
oedepict.OELegendInteractiveStyle_Hover)
lopts.SetButtonWidthScale(1.2)
lopts.SetButtonHeightScale(1.2)
lopts.SetMargin(oedepict.OEMargin_Right, 40.0)
lopts.SetMargin(oedepict.OEMargin_Bottom, 80.0)
legend = oedepict.OELegendLayout(image, "Legend", lopts)
legend_area = legend.GetLegendArea()
draw_color_gradient(legend_area, colorg)
oedepict.OEDrawLegendLayout(legend)
iconscale = 0.5
oedepict.OEAddInteractiveIcon(image, oedepict.OEIconLocation_TopRight,
iconscale)
oedepict.OEDrawCurvedBorder(image, oedepict.OELightGreyPen, 10.0)
oedepict.OEWriteImage(ofs, ext, image)
return 0
mol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ifs, mol):
oechem.OEThrow.Fatal("Unable to read molecule in %s" % filename)
return mol
if len(sys.argv) != 3:
oechem.OEThrow.Usage("%s <receptor> <ligand>" % sys.argv[0])
receptor = ImportMolecule(sys.argv[1])
ligand = ImportMolecule(sys.argv[2])
asite = oechem.OEInteractionHintContainer(receptor, ligand)
oechem.OEPerceiveInteractionHints(asite)
oegrapheme.OEPrepareActiveSiteDepiction(asite)
# @ <SNIPPET-OERENDERACTIVESITE-IMAGE-ADISP>
# initializing asite oechem.OEInteractionHintContainer(receptor, ligand) object
image = oedepict.OEImage(800.0, 600.0)
opts = oegrapheme.OE2DActiveSiteDisplayOptions(image.GetWidth(), image.GetHeight())
opts.SetRenderInteractiveLegend(True)
adisp = oegrapheme.OE2DActiveSiteDisplay(asite, opts)
oegrapheme.OERenderActiveSite(image, adisp)
oedepict.OEWriteImage("OERenderActiveSite-image-adisp.svg", image)
# @ </SNIPPET-OERENDERACTIVESITE-IMAGE-ADISP>
oedepict.OEWriteImage("OERenderActiveSite-image-adisp.pdf", image)
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)
image = oedepict.OEImage(500, 300)
rows, cols = 1, 2
grid = oedepict.OEImageGrid(image, rows, cols)
overlaps = oegraphsim.OEGetFPOverlap(refmol, fitmol,
oegraphsim.OEGetFPType(oegraphsim.OEFPType_Tree))
oedepict.OEPrepareMultiAlignedDepiction(fitmol, refmol, overlaps)
opts = oedepict.OE2DMolDisplayOptions(grid.GetCellWidth(), grid.GetCellHeight(),
oedepict.OEScale_AutoScale)
opts.SetTitleLocation(oedepict.OETitleLocation_Hidden)
refscale = oedepict.OEGetMoleculeScale(refmol, opts)
fitscale = oedepict.OEGetMoleculeScale(fitmol, opts)
opts.SetScale(min(refscale, fitscale))
refdisp = oedepict.OE2DMolDisplay(refmol, opts)
fitdisp = oedepict.OE2DMolDisplay(fitmol, opts)
refcell = grid.GetCell(1, 1)
oedepict.OERenderMolecule(refcell, refdisp)
fitcell = grid.GetCell(1, 2)
oedepict.OERenderMolecule(fitcell, fitdisp)
oedepict.OEWriteImage("FPAlign.png", image)
# @ </SNIPPET-FINGERPRINT-ALIGN>
oedepict.OEWriteImage("FPAlign.pdf", image)
# Customer is hereby permitted to use, copy, and modify the Sample Code,
# subject to these terms. OpenEye claims no rights to Customer's
# modifications. Modification of Sample Code is at Customer's sole and
# exclusive risk. Sample Code may require Customer to have a then
# current license or subscription to the applicable OpenEye offering.
# THE SAMPLE CODE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED. OPENEYE DISCLAIMS ALL WARRANTIES, INCLUDING, BUT
# NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
# PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall OpenEye be
# liable for any damages or liability in connection with the Sample Code
# or its use.
from openeye import oechem
from openeye import oedepict
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol,
"c1cc(N)cc(S(=O)(=O)O)c1 3-aminobenzenesulfonic acid")
oedepict.OEPrepareDepiction(mol)
# @ <SNIPPET-OEDEPICTMOLECULE-IMAGE-DISP>
oedepict.OEPrepareDepiction(mol)
image = oedepict.OEImage(200.0, 200.0)
opts = oedepict.OE2DMolDisplayOptions(image.GetWidth(), image.GetHeight(),
oedepict.OEScale_AutoScale)
disp = oedepict.OE2DMolDisplay(mol, opts)
oedepict.OERenderMolecule(image, disp)
# @ </SNIPPET-OEDEPICTMOLECULE-IMAGE-DISP>
oedepict.OEWriteImage("OERenderMolecule-image-disp.png", image)
oedepict.OEWriteImage("OERenderMolecule-image-disp.pdf", image)
from openeye import oegrapheme
from openeye import oeshape
###############################################################
# USED TO GENERATE CODE SNIPPETS FOR THE GRAPHEME DOCUMENTATION
###############################################################
if len(sys.argv) != 2:
oechem.OEThrow.Usage("%s <mol file>" % sys.argv[0])
ifs = oechem.oemolistream(sys.argv[1])
refmol = oechem.OEGraphMol()
oechem.OEReadMolecule(ifs, refmol)
# @ <SNIPPET-RENDER-SHAPE-QUERY>
opts = oegrapheme.OEShapeQueryDisplayOptions()
opts.SetTitleLocation(oedepict.OETitleLocation_Hidden)
arcpen = oedepict.OEPen(oechem.OEWhite, oechem.OELightGrey, oedepict.OEFill_On,
2.0)
opts.SetSurfaceArcFxn(oegrapheme.OEDefaultArcFxn(arcpen))
cff = oeshape.OEColorForceField()
cff.Init(oeshape.OEColorFFType_ImplicitMillsDean)
disp = oegrapheme.OEShapeQueryDisplay(refmol, cff, opts)
image = oedepict.OEImage(420.0, 280.0)
oegrapheme.OERenderShapeQuery(image, disp)
# @ </SNIPPET-RENDER-SHAPE-QUERY>
oedepict.OEWriteImage("RenderShapeQuery.png", image)
oedepict.OEWriteImage("RenderShapeQuery.pdf", image)
# SaaS offerings (each a "Customer").
# Customer is hereby permitted to use, copy, and modify the Sample Code,
# subject to these terms. OpenEye claims no rights to Customer's
# modifications. Modification of Sample Code is at Customer's sole and
# exclusive risk. Sample Code may require Customer to have a then
# current license or subscription to the applicable OpenEye offering.
# THE SAMPLE CODE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED. OPENEYE DISCLAIMS ALL WARRANTIES, INCLUDING, BUT
# NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
# PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall OpenEye be
# liable for any damages or liability in connection with the Sample Code
# or its use.
from openeye import oedepict
# @ <SNIPPET-DRAW-LINE>
width, height = 100, 100
# Create image
image = oedepict.OEImage(width, height)
# Draw line with default pen
bgn = oedepict.OE2DPoint(10.0, 10.0)
end = oedepict.OE2DPoint(90.0, 90.0)
image.DrawLine(bgn, end, oedepict.OEBlackPen)
# Write image to SVG file
oedepict.OEWriteImage("DrawLine.svg", image)
# @ </SNIPPET-DRAW-LINE>
oedepict.OEWriteImage("DrawLine.png", image)
oedepict.OEWriteImage("DrawLine.pdf", image)
# @ <SNIPPET-IMAGE-FRAME>
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)
image = oedepict.OEImage(400, 400)
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, "C1CC(O)CNC1")
oedepict.OEPrepareDepiction(mol)
DrawMolecule(image, mol, 60, 60, oedepict.OE2DPoint(50.0, 40.0))
DrawMolecule(image, mol, 180, 180, oedepict.OE2DPoint(180.0, 120.0))
DrawMolecule(image, mol, 80, 80, oedepict.OE2DPoint(300.0, 20.0))
DrawMolecule(image, mol, 50, 50, oedepict.OE2DPoint(150.0, 320.0))
DrawMolecule(image, mol, 20, 20, oedepict.OE2DPoint(360.0, 360.0))
oedepict.OEWriteImage("ImageFrame.png", image)
# @ </SNIPPET-IMAGE-FRAME>
oedepict.OEWriteImage("ImageFrame.pdf", image)
oedepict.OEFill_Off, 2.0,
oedepict.OEStipple_ShortDash)
arcfxnA = oegrapheme.OEDefaultArcFxn(penA)
for arc in oegrapheme.OEGet2DSurfaceArcs(
disp, oegrapheme.OESurfaceArcScale_Minimum):
arcfxnA(layer, arc)
penB = oedepict.OEPen(oechem.OEGrey, oechem.OEGrey, oedepict.OEFill_Off,
2.0)
arcfxnB = oegrapheme.OEDefaultArcFxn(penB)
for arc in oegrapheme.OEGet2DSurfaceArcs(disp, radiusScales):
arcfxnB(layer, arc)
oedepict.OERenderMolecule(image, disp)
# @ </SNIPPET-DRAW-2D-SURFACE-VARIOUS-RADII>
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, "c1cc(sc1CCl)Br")
oedepict.OEPrepareDepiction(mol)
imagewidth, imageheight = 300.0, 240.0
image = oedepict.OEImage(imagewidth, imageheight)
DrawSurfaces(image, mol)
oedepict.OEWriteImage("Draw2DSurfaceVariousRadii.png", image)
oedepict.OEWriteImage("Draw2DSurfaceVariousRadii.pdf", image)
#
# TERMS FOR USE OF SAMPLE CODE The software below ("Sample Code") is
# provided to current licensees or subscribers of OpenEye products or
# SaaS offerings (each a "Customer").
# Customer is hereby permitted to use, copy, and modify the Sample Code,
# subject to these terms. OpenEye claims no rights to Customer's
# modifications. Modification of Sample Code is at Customer's sole and
# exclusive risk. Sample Code may require Customer to have a then
# current license or subscription to the applicable OpenEye offering.
# THE SAMPLE CODE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED. OPENEYE DISCLAIMS ALL WARRANTIES, INCLUDING, BUT
# NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
# PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall OpenEye be
# liable for any damages or liability in connection with the Sample Code
# or its use.
from openeye import oechem
from openeye import oedepict
from openeye import oegrapheme
# @ <SNIPPET-DRAW-COLOR-GRADIENT>
colorg = oechem.OELinearColorGradient(oechem.OEColorStop(0.0, oechem.OEYellow))
colorg.AddStop(oechem.OEColorStop(+1.0, oechem.OEOrange))
colorg.AddStop(oechem.OEColorStop(-1.0, oechem.OEGreen))
image = oedepict.OEImage(400, 100)
oegrapheme.OEDrawColorGradient(image, colorg)
oedepict.OEWriteImage("DrawColorGradient.png", image)
# @ </SNIPPET-DRAW-COLOR-GRADIENT>
oedepict.OEWriteImage("DrawColorGradient.pdf", image)
def main(argv=[__name__]):
itf = oechem.OEInterface()
oechem.OEConfigure(itf, InterfaceData)
oedepict.OEConfigureImageWidth(itf, 900.0)
oedepict.OEConfigureImageHeight(itf, 600.0)
oedepict.OEConfigure2DMolDisplayOptions(
itf, oedepict.OE2DMolDisplaySetup_AromaticStyle)
oechem.OEConfigureSplitMolComplexOptions(
itf, oechem.OESplitMolComplexSetup_LigName)
if not oechem.OEParseCommandLine(itf, argv):
return 1
iname = itf.GetString("-complex")
oname = itf.GetString("-out")
ifs = oechem.oemolistream()
if not ifs.open(iname):
oechem.OEThrow.Fatal("Cannot open input file!")
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!")
complexmol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ifs, complexmol):
oechem.OEThrow.Fatal("Unable to read molecule from %s" % iname)
if not oechem.OEHasResidues(complexmol):
oechem.OEPerceiveResidues(complexmol, oechem.OEPreserveResInfo_All)
# Separate ligand and protein
sopts = oechem.OESplitMolComplexOptions()
oechem.OESetupSplitMolComplexOptions(sopts, itf)
ligand = oechem.OEGraphMol()
protein = oechem.OEGraphMol()
water = oechem.OEGraphMol()
other = oechem.OEGraphMol()
pfilter = sopts.GetProteinFilter()
wfilter = sopts.GetWaterFilter()
sopts.SetProteinFilter(oechem.OEOrRoleSet(pfilter, wfilter))
sopts.SetWaterFilter(
oechem.OEMolComplexFilterFactory(
oechem.OEMolComplexFilterCategory_Nothing))
oechem.OESplitMolComplex(ligand, protein, water, other, complexmol, sopts)
if ligand.NumAtoms() == 0:
oechem.OEThrow.Fatal("Cannot separate complex!")
# Perceive interactions
asite = oechem.OEInteractionHintContainer(protein, ligand)
if not asite.IsValid():
oechem.OEThrow.Fatal("Cannot initialize active site!")
asite.SetTitle(ligand.GetTitle())
oechem.OEPerceiveInteractionHints(asite)
oegrapheme.OEPrepareActiveSiteDepiction(asite)
# Depict active site with interactions
width, height = oedepict.OEGetImageWidth(itf), oedepict.OEGetImageHeight(
itf)
image = oedepict.OEImage(width, height)
cframe = oedepict.OEImageFrame(image, width * 0.80, height,
oedepict.OE2DPoint(0.0, 0.0))
lframe = oedepict.OEImageFrame(image, width * 0.20, height,
oedepict.OE2DPoint(width * 0.80, 0.0))
opts = oegrapheme.OE2DActiveSiteDisplayOptions(cframe.GetWidth(),
cframe.GetHeight())
oedepict.OESetup2DMolDisplayOptions(opts, itf)
adisp = oegrapheme.OE2DActiveSiteDisplay(asite, opts)
oegrapheme.OERenderActiveSite(cframe, adisp)
lopts = oegrapheme.OE2DActiveSiteLegendDisplayOptions(10, 1)
oegrapheme.OEDrawActiveSiteLegend(lframe, adisp, lopts)
oedepict.OEWriteImage(oname, image)
return 0
opts.SetTitleLocation(oedepict.OETitleLocation_Hidden)
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, smiles[r])
oedepict.OEPrepareDepiction(mol)
disp = oedepict.OE2DMolDisplay(mol, opts)
oedepict.OERenderMolecule(cell, disp)
# depicting data in table
cell = maintable.GetBodyCell(r + 1, 2)
table = oedepict.OEImageTable(cell, datatableopts)
table.DrawText(table.GetHeaderCell(1, False), "Property")
table.DrawText(table.GetHeaderCell(1), "Value")
table.DrawText(table.GetStubColumnCell(1), "Name")
table.DrawText(table.GetBodyCell(1, 1), mol.GetTitle())
table.DrawText(table.GetStubColumnCell(2), "SMILES")
table.DrawText(table.GetBodyCell(2, 1), oechem.OEMolToSmiles(mol))
table.DrawText(table.GetStubColumnCell(3), "MV")
table.DrawText(table.GetBodyCell(3, 1),
"%.3f" % oechem.OECalculateMolecularWeight(mol))
oedepict.OEWriteImage("ImageTable.png", image)
# @ </SNIPPET-IMAGE-TABLE>
oedepict.OEWriteImage("ImageTable.pdf", image)
# liable for any damages or liability in connection with the Sample Code
# or its use.
from openeye import oechem
from openeye import oedepict
imagewidth, imageheight = 350, 250
image = oedepict.OEImage(imagewidth, imageheight)
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, "c1cccnc1O")
oedepict.OEPrepareDepiction(mol)
oedepict.OERenderMolecule(image, mol)
# @ <SNIPPET-LEGEND-LAYOUT>
opts = oedepict.OELegendLayoutOptions(
oedepict.OELegendLayoutStyle_VerticalTopRight,
oedepict.OELegendColorStyle_LightGreen,
oedepict.OELegendInteractiveStyle_Toggle)
opts.SetButtonWidthScale(1.5)
opts.SetButtonHeightScale(1.5)
legend = oedepict.OELegendLayout(image, "Legend", opts)
legend_area = legend.GetLegendArea()
oedepict.OEAddWatermark(legend_area, "This is the legend area")
oedepict.OEAddInteractiveIcon(image, oedepict.OEIconLocation_BottomRight, 0.75)
oedepict.OEDrawLegendLayout(legend)
oedepict.OEWriteImage("LegendLayout.svg", image)
# @ </SNIPPET-LEGEND-LAYOUT>