def draw_reference_dihedral(image, group, itag, center, radius):
"""
Draws dihedral angle of the reference molecule.
:type image: oedepict.OEImageBase
:type group: oechem.OEGroupBase
:type itag: int
:type center: oedepict.OE2DPoint
:type radius: float
"""
if not group.HasData(itag):
return
angle = group.GetData(itag)
v = oedepict.OE2DPoint(0.0, -1.0)
bgn = oedepict.OELengthenVector(oedepict.OERotateVector(v, angle),
radius / 6.0)
end = oedepict.OELengthenVector(oedepict.OERotateVector(v, angle),
radius / 3.0)
redpen = oedepict.OEPen(oechem.OERed, oechem.OERed, oedepict.OEFill_Off,
2.0)
image.DrawLine(center + bgn, center + end, redpen)
fontsize = int(math.floor(radius * 0.12))
font = oedepict.OEFont(oedepict.OEFontFamily_Default,
oedepict.OEFontStyle_Bold, fontsize,
oedepict.OEAlignment_Center, oechem.OERed)
dim = radius / 2.5
textframe = oedepict.OEImageFrame(
image, dim, dim, center - oedepict.OE2DPoint(dim / 2.0, dim / 2.0))
oedepict.OEDrawTextToCenter(textframe, "{:.1f}".format(angle), font)
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__]):
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 draw_dihedral_circle(image, center, radius, nrbins, nrconfs):
"""
Draws the base radial histogram.
:type image: oedepict.OEImageBase
:type center: oedepict.OE2DPoint
:type radius: float
:type nrbins: int
:type nrconfs: int
"""
grey = oechem.OEColor(210, 210, 210)
pen = oedepict.OEPen(grey, grey, oedepict.OEFill_On, 1.0)
image.DrawCircle(center, radius, pen)
linegrey = oechem.OEColor(220, 220, 220)
linepen = oedepict.OEPen(linegrey, linegrey, oedepict.OEFill_On, 1.0)
angleinc = 360.0 / float(nrbins)
v = oedepict.OE2DPoint(0.0, -1.0)
for i in range(0, nrbins):
end = oedepict.OELengthenVector(
oedepict.OERotateVector(v, i * angleinc), radius)
image.DrawLine(center, center + end, linepen)
fontsize = int(math.floor(radius * 0.1))
font = oedepict.OEFont(oedepict.OEFontFamily_Default,
oedepict.OEFontStyle_Bold, fontsize,
oedepict.OEAlignment_Center, oechem.OEBlack)
for i in range(0, 4):
angle = i * 90.0
end = oedepict.OELengthenVector(oedepict.OERotateVector(v, angle),
radius * 1.20)
text = '{:.1f}'.format(angle)
dim = radius / 2.5
textframe = oedepict.OEImageFrame(
image, dim, dim,
center + end - oedepict.OE2DPoint(dim / 2.0, dim / 2.0))
oedepict.OEDrawTextToCenter(textframe, text, font)
minradius = radius / 3.0
whitepen = oedepict.OEPen(oechem.OEWhite, oechem.OEWhite,
oedepict.OEFill_On, 1.0,
oedepict.OEStipple_NoLine)
image.DrawCircle(center, minradius, whitepen)
font.SetSize(int(fontsize * 1.5))
top = oedepict.OE2DPoint(image.GetWidth() / 2.0, -10.0)
image.DrawText(top, 'torsion histogram', font)
top = oedepict.OE2DPoint(image.GetWidth() / 2.0, -30.0)
image.DrawText(top, 'MM: blue; ANI: red', font)
bottom = oedepict.OE2DPoint(image.GetWidth() / 2.0,
image.GetHeight() + 26.0)
image.DrawText(bottom, 'number of conformations: {}'.format(nrconfs), font)
def DepictMoleculesWithData(report, mollist, iname, tags, opts):
from openeye import oechem
from openeye import oedepict
for mol in mollist:
# render molecule
cell = report.NewCell()
oedepict.OEPrepareDepiction(mol)
disp = oedepict.OE2DMolDisplay(mol, opts)
oedepict.OERenderMolecule(cell, disp)
oedepict.OEDrawCurvedBorder(cell, oedepict.OELightGreyPen, 10.0)
# render corresponding data
cell = report.NewCell()
RenderData(cell, mol, tags)
# add input filnename to headers
headerfont = oedepict.OEFont(
oedepict.OEFontFamily_Default,
oedepict.OEFontStyle_Default,
12,
oedepict.OEAlignment_Center,
oechem.OEBlack,
)
headerpos = oedepict.OE2DPoint(report.GetHeaderWidth() / 2.0,
report.GetHeaderHeight() / 2.0)
for header in report.GetHeaders():
header.DrawText(headerpos, iname, headerfont)
# add page number to footers
footerfont = oedepict.OEFont(
oedepict.OEFontFamily_Default,
oedepict.OEFontStyle_Default,
12,
oedepict.OEAlignment_Center,
oechem.OEBlack,
)
footerpos = oedepict.OE2DPoint(report.GetFooterWidth() / 2.0,
report.GetFooterHeight() / 2.0)
for pageidx, footer in enumerate(report.GetFooters()):
footer.DrawText(footerpos, "- %d -" % (pageidx + 1), footerfont)
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)
def HighlightCell(cell, idx):
font = oedepict.OEFont(oedepict.OEFontFamily_Default,
oedepict.OEFontStyle_Default, 10,
oedepict.OEAlignment_Center, oechem.OEBlack)
color = oechem.OEColor(oechem.OELightGrey)
borderpen = oedepict.OEPen(color, color, oedepict.OEFill_On, 1.0)
oedepict.OEDrawBorder(cell, borderpen)
p = oedepict.OE2DPoint(cell.GetWidth() / 2.0,
cell.GetHeight() / 2.0 + font.GetSize() / 2.0)
cell.DrawText(p, "(%d)" % idx, font)
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 draw_dihedral_histogram(image, histogram, histogram_ref, center, radius,
nrbins, nrconfs):
"""
Draws the radial histogram of a torsional angle.
:type image: oedepict.OEImageBase
:type histogram: list(int)
:type center: oedepict.OE2DPoint
:type radius: float
:type nrbins: int
:type nrconfs: int
:type nrbins: int
"""
minradius = radius / 3.0
maxvalue = max(max(histogram), max(histogram_ref))
radiusinc = (radius - minradius) / maxvalue
angleinc = 360.0 / float(nrbins)
valuepen = oedepict.OEPen(oechem.OERoyalBlue, oechem.OERoyalBlue,
oedepict.OEFill_On, 2.0)
maxvalue = 0
maxvalueidx = 0
for i in range(0, len(histogram)):
value = histogram[i]
if value == 0:
continue
if value > maxvalue:
maxvalue = value
maxvalueidx = i
arcradius = value * radiusinc + minradius
if arcradius < 1.0:
continue
bgnangle = i * angleinc
endangle = (i + 1) * angleinc
image.DrawPie(center, bgnangle, endangle, arcradius, valuepen)
valuepen = oedepict.OEPen(oechem.OERed, oechem.OERed, oedepict.OEFill_Off,
2.0)
for i in range(0, len(histogram_ref)):
value = histogram_ref[i]
if value == 0:
continue
if value > maxvalue:
maxvalue = value
maxvalueidx = i
arcradius = value * radiusinc + minradius
if arcradius < 1.0:
continue
bgnangle = i * angleinc
endangle = (i + 1) * angleinc
image.DrawPie(center, bgnangle, endangle, arcradius, valuepen)
percent = maxvalue / (nrconfs / 100.0)
whitepen = oedepict.OEPen(oechem.OEWhite, oechem.OEWhite,
oedepict.OEFill_On, 0.2,
oedepict.OEStipple_NoLine)
image.DrawCircle(center, minradius, whitepen)
fontsize = int(math.floor(radius * 0.1))
font = oedepict.OEFont(oedepict.OEFontFamily_Default,
oedepict.OEFontStyle_Bold, fontsize,
oedepict.OEAlignment_Center, oechem.OEWhite)
angle = maxvalueidx * angleinc
if angle >= 180.0:
angle += angleinc * 0.3
else:
angle += angleinc * 0.7
textangle = get_text_angle(angle)
v = oedepict.OE2DPoint(0.0, -1.0)
pos = oedepict.OELengthenVector(oedepict.OERotateVector(v, angle),
radius * 0.80)
font.SetRotationAngle(textangle)
image.DrawText(center + pos, "{:.1f}%".format(percent * 100), font)
opts.SetAtomColor(oechem.OEElemNo_N, oechem.OEColor(0, 0,
80)) # very dark blue
# @ </SNIPPET-OE2DMOLDISPLAY-OPTIONS-ATOM-COLOR>
DepictMolecules(opts, smiles, "OE2DMolDisplayOptions_SetAtomColor")
# @ <SNIPPET-OE2DMOLDISPLAY-OPTIONS-ATOM-COLOR-STYLE>
width, height, scale = 300.0, 200.0, oedepict.OEScale_AutoScale
opts = oedepict.OE2DMolDisplayOptions(width, height, scale)
opts.SetAtomColorStyle(oedepict.OEAtomColorStyle_BlackMonochrome)
# @ </SNIPPET-OE2DMOLDISPLAY-OPTIONS-ATOM-COLOR-STYLE>
DepictMolecules(opts, smiles, "OE2DMolDisplayOptions_SetAtomColorStyle")
# @ <SNIPPET-OE2DMOLDISPLAY-OPTIONS-ATOM-LABEL-FONT>
width, height, scale = 300.0, 200.0, oedepict.OEScale_AutoScale
opts = oedepict.OE2DMolDisplayOptions(width, height, scale)
font = oedepict.OEFont()
font.SetFamily(oedepict.OEFontFamily_Courier)
font.SetStyle(oedepict.OEFontStyle_Bold)
opts.SetAtomLabelFont(font)
# @ </SNIPPET-OE2DMOLDISPLAY-OPTIONS-ATOM-LABEL-FONT>
DepictMolecules(opts, smiles, "OE2DMolDisplayOptions_SetAtomLabelFont")
# @ <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
def visualize_phenyls(smiles, fname, rows, cols, bond_idx, wbos, colors):
"""
Visualize molecules with highlighted bond and labeled with WBO
Parameters
----------
smiles : list of SMILES to visualize. Torsion atoms should have map indices (1, 2, 3, 4)
fname : str
filename
rows : int
cols : int
bond_idx : tuple of atom maps of bond to highlight. Since all torsions are mapped with (1, 2, 3, 4), the same tuple
is used for all SMILES.
wbos : list of floats
colors : list of hex values for colors
"""
itf = oechem.OEInterface()
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_AutoScale)
oedepict.OESetup2DMolDisplayOptions(opts, itf)
# align to first molecule
ref_mol = oechem.OEGraphMol()
oechem.OESmilesToMol(ref_mol, smiles[0])
oedepict.OEPrepareDepiction(ref_mol)
mols = []
minscale = float("inf")
for s in smiles:
mol = oechem.OEMol()
oechem.OESmilesToMol(mol, s)
mols.append(mol)
oedepict.OEPrepareDepiction(mol, False, True)
minscale = min(minscale, oedepict.OEGetMoleculeScale(mol, opts))
opts.SetScale(minscale)
print(minscale)
opts.SetScale(minscale)
for i, mol in enumerate(mols):
cell = report.NewCell()
#mol = oechem.OEMol()
#oechem.OESmilesToMol(mol, s)
#oedepict.OEPrepareDepiction(mol, False, True)
bond = get_bond(mol, bond_idx)
atom_bond_set = oechem.OEAtomBondSet()
atom_bond_set.AddAtoms([bond.GetBgn(), bond.GetEnd()])
atom_bond_set.AddBond(bond)
hstyle = oedepict.OEHighlightStyle_BallAndStick
hcolor = oechem.OEColor(colors[i])
overlaps = oegraphsim.OEGetFPOverlap(
ref_mol, mol, oegraphsim.OEGetFPType(oegraphsim.OEFPType_Tree))
oedepict.OEPrepareMultiAlignedDepiction(mol, ref_mol, overlaps)
disp = oedepict.OE2DMolDisplay(mol, opts)
oedepict.OEAddHighlighting(disp, hcolor, hstyle, atom_bond_set)
font = oedepict.OEFont(oedepict.OEFontFamily_Default,
oedepict.OEFontStyle_Default, 24,
oedepict.OEAlignment_Default, oechem.OEBlack)
bond_label = oedepict.OEHighlightLabel("{:.2f}".format(wbos[i]),
hcolor)
bond_label.SetFontScale(4.0)
bond_label.SetFont(font)
oedepict.OEAddLabel(disp, bond_label, atom_bond_set)
oedepict.OERenderMolecule(cell, disp)
#oedepict.OEDrawCurvedBorder(cell, oedepict.OELightGreyPen, 10.0)
return (oedepict.OEWriteReport(fname, report))
# 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
# @ <SNIPPET-BOND-PROP-INDEX>
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, "c1cc(N)cc(S(=O)(=O)O)c1")
oedepict.OEPrepareDepiction(mol)
width, height = 300, 200
opts = oedepict.OE2DMolDisplayOptions(width, height,
oedepict.OEScale_AutoScale)
opts.SetBondPropertyFunctor(oedepict.OEDisplayBondIdx())
opts.SetBondPropLabelFont(oedepict.OEFont(oechem.OEDarkBlue))
disp = oedepict.OE2DMolDisplay(mol, opts)
oedepict.OERenderMolecule("BondPropIndex.png", disp)
# @ </SNIPPET-BOND-PROP-INDEX>
oedepict.OERenderMolecule("BondPropIndex.pdf", disp)
def visualize_mols(smiles,
fname,
rows,
cols,
bond_idx,
wbos,
colors,
align_to=0,
circle=None):
"""
Visualize molecules with highlighted bond and labeled with WBO
Parameters
----------
smiles : list of SMILES to visualize.
bond atoms should have map indices
fname : str
filename
rows : int
cols : int
bond_idx : tuple of atom maps of bond to highlight.
wbos : list of floats
colors : list of hex values for colors
align_to: int, optional, default 0
index for which molecule to align to. If zero, will align to first molecules in SMILES list
"""
itf = oechem.OEInterface()
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_AutoScale)
oedepict.OESetup2DMolDisplayOptions(opts, itf)
# align to chosen molecule
ref_mol = oechem.OEGraphMol()
oechem.OESmilesToMol(ref_mol, smiles[align_to])
oedepict.OEPrepareDepiction(ref_mol)
mols = []
minscale = float("inf")
for s in smiles:
mol = oechem.OEMol()
oechem.OESmilesToMol(mol, s)
mols.append(mol)
oedepict.OEPrepareDepiction(mol, False, True)
minscale = min(minscale, oedepict.OEGetMoleculeScale(mol, opts))
opts.SetScale(minscale)
for i, mol in enumerate(mols):
cell = report.NewCell()
oedepict.OEPrepareDepiction(mol, False, True)
bond = get_bond(mol, bond_idx)
atom_bond_set = oechem.OEAtomBondSet()
atom_bond_set.AddAtoms([bond.GetBgn(), bond.GetEnd()])
atom_bond_set.AddBond(bond)
hstyle = oedepict.OEHighlightStyle_BallAndStick
if i == 3:
hcolor = oechem.OERed
else:
hcolor = oechem.OEColor(*colors[i])
overlaps = oegraphsim.OEGetFPOverlap(
ref_mol, mol, oegraphsim.OEGetFPType(oegraphsim.OEFPType_Tree))
oedepict.OEPrepareMultiAlignedDepiction(mol, ref_mol, overlaps)
#opts.SetBondPropLabelFontScale(4.0)
disp = oedepict.OE2DMolDisplay(mol, opts)
oedepict.OEAddHighlighting(disp, hcolor, hstyle, atom_bond_set)
font = oedepict.OEFont(oedepict.OEFontFamily_Default,
oedepict.OEFontStyle_Default, 24,
oedepict.OEAlignment_Default, oechem.OEBlack)
bond_label = oedepict.OEHighlightLabel("{:.2f}".format(wbos[i]),
hcolor)
bond_label.SetFontScale(4.0)
bond_label.SetFont(font)
# generate circle
atom_bond_set_circle = oechem.OEAtomBondSet()
if circle is not None:
color = oechem.OEColor(*colors[i])
highlight = oedepict.OEHighlightByCogwheel(color)
highlight.SetBallRadiusScale(5.0)
for m in circle:
print(m)
if m == 1:
continue
atom = mol.GetAtom(oechem.OEHasMapIdx(m))
print(atom)
atom_bond_set_circle.AddAtom(atom)
for bond_tuple in itertools.combinations(circle, 2):
bond_test = get_bond(mol, bond_tuple)
if bond_test:
atom_bond_set_circle.AddBond(bond_test)
#highlight.SetColor(color)
oedepict.OEAddHighlighting(disp, highlight, atom_bond_set_circle)
oedepict.OEAddLabel(disp, bond_label, atom_bond_set)
oedepict.OERenderMolecule(cell, disp)
# oedepict.OEDrawCurvedBorder(cell, oedepict.OELightGreyPen, 10.0)
return (oedepict.OEWriteReport(fname, report))
from openeye import oechem
from openeye import oedepict
# @ <SNIPPET-DEPICT-MOL-WITH-HYPERLINK>
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, "OC(=O)c1ccccc1")
oedepict.OEPrepareDepiction(mol)
width, height = 150.0, 150.0
image = oedepict.OEImage(width, height)
opts = oedepict.OE2DMolDisplayOptions(width, height,
oedepict.OEScale_AutoScale)
opts.SetTitleLocation(oedepict.OETitleLocation_Bottom)
# associate font with URI
font = oedepict.OEFont(oedepict.OEFontFamily_Default,
oedepict.OEFontStyle_Default, 10,
oedepict.OEAlignment_Center, oechem.OEBlue)
font.SetHyperlink("http://www.eyesopen.com/oedepict-tk")
opts.SetTitleFont(font)
mol.SetTitle("Generated by OEDepict")
disp = oedepict.OE2DMolDisplay(mol, opts)
oedepict.OERenderMolecule(image, disp)
oedepict.OEWriteImage("DepictMolWithHyperlink.pdf", image)
oedepict.OEWriteImage("DepictMolWithHyperlink.svg", image)
# @ </SNIPPET-DEPICT-MOL-WITH-HYPERLINK>
pen = oedepict.OEPen(oechem.OEBlack, oechem.OEDarkBlue, oedepict.OEFill_Off, 2.0)
tableopts.SetCellBorderPen(pen)
# @ </SNIPPET-OEIMAGETABLEOPTIONS-SETCELLBORDERPEN>
WriteTable(tableopts, "OEImageTableOptions_SetCellBorderPen")
# @ <SNIPPET-OEIMAGETABLEOPTIONS-SETCELLCOLOR>
tableopts = oedepict.OEImageTableOptions(4, 4, oedepict.OEImageTableStyle_MediumBlue)
evenrow = True
tableopts.SetCellColor(oechem.OELightGrey, not evenrow)
# @ </SNIPPET-OEIMAGETABLEOPTIONS-SETCELLCOLOR>
WriteTable(tableopts, "OEImageTableOptions_SetCellColor")
# @ <SNIPPET-OEIMAGETABLEOPTIONS-SETCELLFONT>
tableopts = oedepict.OEImageTableOptions(4, 4, oedepict.OEImageTableStyle_MediumBlue)
font = oedepict.OEFont(oedepict.OEFontFamily_Default,
oedepict.OEFontStyle_Italic | oedepict.OEFontStyle_Bold,
8, oedepict.OEAlignment_Left, oechem.OEDarkRed)
tableopts.SetCellFont(font)
# @ </SNIPPET-OEIMAGETABLEOPTIONS-SETCELLFONT>
WriteTable(tableopts, "OEImageTableOptions_SetCellFont")
# @ <SNIPPET-OEIMAGETABLEOPTIONS-SETHEADER>
tableopts = oedepict.OEImageTableOptions(4, 4, oedepict.OEImageTableStyle_MediumBlue)
tableopts.SetHeader(False)
# @ </SNIPPET-OEIMAGETABLEOPTIONS-SETHEADER>
WriteTable(tableopts, "OEImageTableOptions_SetHeader")
# @ <SNIPPET-OEIMAGETABLEOPTIONS-SETHEADERCOLOR>
tableopts = oedepict.OEImageTableOptions(4, 4, oedepict.OEImageTableStyle_MediumBlue)
tableopts.SetHeaderColor(oechem.OELightGrey)
# @ </SNIPPET-OEIMAGETABLEOPTIONS-SETHEADERCOLOR>
radius, pen)
# Write value in segment - based on
# https://docs.eyesopen.com/toolkits/cookbook/python/_downloads/properties2img.py
p = oedepict.OE2DPoint(0, -radius * 0.75)
midangle = (starting_angle + starting_angle + WEDGE_WIDTH) / 2.0
rad = math.radians(midangle)
cosrad = math.cos(rad)
sinrad = math.sin(rad)
txt_coord = r_coords + oedepict.OE2DPoint(
cosrad * p.GetX() - sinrad * p.GetY(),
sinrad * p.GetX() + cosrad * p.GetY())
fontsize = int(SEGMENT_LABEL_SCALE_FACTOR * math.sqrt(radius))
font = oedepict.OEFont(oedepict.OEFontFamily_Default,
oedepict.OEFontStyle_Bold, fontsize,
oedepict.OEAlignment_Center, oechem.OEBlack)
label = oedepict.OEHighlightLabel(str(value), font)
label.SetBoundingBoxPen(oedepict.OETransparentPen)
oedepict.OEAddLabel(layer, txt_coord, label)
starting_angle += WEDGE_WIDTH
# Draw circle round R atom on top of pie chart center
pen = oedepict.OEPen(OEWhite, OEBlack, oedepict.OEFill_On, 1)
glyph = oegrapheme.OEAtomGlyphCircle(pen, oegrapheme.OECircleStyle_Default,
1.5)
oegrapheme.OEAddGlyph(mdisp, glyph, oechem.OEHasMapIdx(1))
# Render molecule
oedepict.OERenderMolecule(image, mdisp)
# or its use.
from openeye import oechem
from openeye import oedepict
# @ <SNIPPET-TOGGLEATOMTEXT>
width, height = 400, 200
image = oedepict.OEImage(width, height)
mol = oechem.OEGraphMol()
smiles = "Cc1cccnc1/C=C/[C@H](C(=O)O)O"
oechem.OESmilesToMol(mol, smiles)
oedepict.OEPrepareDepiction(mol)
opts = oedepict.OE2DMolDisplayOptions(width, height,
oedepict.OEScale_AutoScale)
opts.SetMargins(10)
disp = oedepict.OE2DMolDisplay(mol, opts)
font = oedepict.OEFont(oedepict.OEFontFamily_Default,
oedepict.OEFontStyle_Default, 12,
oedepict.OEAlignment_Center, oechem.OEDarkRed)
for adisp in disp.GetAtomDisplays():
atom = adisp.GetAtom()
toggletext = "atom idx=%s" % atom.GetIdx()
oedepict.OEDrawSVGToggleText(disp, adisp, toggletext, font)
oedepict.OERenderMolecule("ToggleAtomText.svg", disp)
# @ </SNIPPET-TOGGLEATOMTEXT>
# 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
# @ <SNIPPET-ATOM-PROP-INDEX>
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, "c1cc(N)cc(S(=O)(=O)O)c1")
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)
oedepict.OERenderMolecule("AtomPropIndex.png", disp)
# @ </SNIPPET-ATOM-PROP-INDEX>
oedepict.OERenderMolecule("AtomPropIndex.pdf", disp)
