def CreateScaleReportLayout(opts, scale):
opts = ScaleReportOptions(opts, scale)
report = oedepict.OEReport(opts)
borderpen = oedepict.OEPen(oechem.OEGrey, oechem.OEGrey,
oedepict.OEFill_Off, 1.0)
first = report.NewBody()
oedepict.OEDrawBorder(first, borderpen)
nrgridpages = 1
for p in range(0, nrgridpages):
for c in range(0, report.NumRowsPerPage() * report.NumColsPerPage()):
cell = report.NewCell()
oedepict.OEDrawBorder(cell, borderpen)
for page in report.GetPages():
oedepict.OEDrawBorder(page, oedepict.OEBlackPen)
if opts.GetHeaderHeight() > 0.0:
for header in report.GetHeaders():
oedepict.OEDrawBorder(header, borderpen)
if opts.GetFooterHeight() > 0.0:
for footer in report.GetFooters():
oedepict.OEDrawBorder(footer, borderpen)
return 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 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 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 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 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 CreateReportLayout():
rows, cols = 3, 2
reportopts = oedepict.OEReportOptions(rows, cols)
reportopts.SetPageWidth(100.0)
reportopts.SetPageHeight(150.0)
reportopts.SetPageMargins(5.0)
reportopts.SetCellGap(5.0)
reportopts.SetHeaderHeight(15.0)
reportopts.SetFooterHeight(15.0)
report = oedepict.OEReport(reportopts)
borderpen = oedepict.OEPen(oechem.OELightGrey, oechem.OELightGrey,
oedepict.OEFill_Off, 1.0)
first = report.NewBody()
oedepict.OEDrawBorder(first, borderpen)
nrgridpages = 3
for p in range(0, nrgridpages):
for c in range(0, report.NumRowsPerPage() * report.NumColsPerPage()):
cell = report.NewCell()
oedepict.OEDrawBorder(cell, borderpen)
last = report.NewBody()
oedepict.OEDrawBorder(last, borderpen)
for page in report.GetPages():
oedepict.OEDrawBorder(page, oedepict.OEBlackPen)
for header in report.GetHeaders():
oedepict.OEDrawBorder(header, borderpen)
for footer in report.GetFooters():
oedepict.OEDrawBorder(footer, borderpen)
return report
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 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 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 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)
# 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.
import sys
from openeye import oechem
from openeye import oedepict
from openeye import oegrapheme
###############################################################
# USED TO GENERATE CODE SNIPPETS FOR THE GRAPHEME DOCUMENTATION
###############################################################
if len(sys.argv) != 2:
oechem.OEThrow.Usage("%s <design unit>" % sys.argv[0])
filename = sys.argv[1]
# @ <SNIPPET-DRAW-IRIDIUM-DATA>
du = oechem.OEDesignUnit()
if not oechem.OEReadDesignUnit(filename, du):
oechem.OEThrow.Fatal("Cannot read design unit!")
image = oedepict.OEImage(250, 250)
oegrapheme.OEDrawIridiumData(image, du)
oedepict.OEDrawBorder(image, oedepict.OELightGreyPen)
oedepict.OEWriteImage("DrawIridiumData.svg", image)
# @ </SNIPPET-DRAW-IRIDIUM-DATA>
oedepict.OEWriteImage("DrawIridiumData.pdf", image)
# 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-OEDrawBorder>
width, height = 100, 50
image = oedepict.OEImage(width, height)
pen = oedepict.OEPen(oechem.OEWhite, oechem.OELightGreen, oedepict.OEFill_Off,
4.0)
oedepict.OEDrawBorder(image, pen)
oedepict.OEWriteImage("OEDrawBorder.png", image)
# @ </SNIPPET-OEDrawBorder>
oedepict.OEWriteImage("OEDrawBorder.pdf", image)
# @ <SNIPPET-OEDrawCurvedBorder>
width, height = 100, 50
image = oedepict.OEImage(width, height)
pen = oedepict.OEPen(oechem.OEWhite, oechem.OELightGreen, oedepict.OEFill_Off,
4.0)
oedepict.OEDrawCurvedBorder(image, pen, 15)
oedepict.OEWriteImage("OEDrawCurvedBorder.png", image)
# @ </SNIPPET-OEDrawCurvedBorder>
def DepictMoleculeWithFragmentCombinations(report, mol, frags, opts): #fragcombs, opts):
""" This function was taken from https://docs.eyesopen.com/toolkits/cookbook/python/depiction/enumfrags.html with some modification
"""
stag = "fragment idx"
itag = oechem.OEGetTag(stag)
for fidx, frag in enumerate(frags):
for bond in frags[frag].GetBonds():
bond.SetData(itag, fidx)
# setup depiction styles
nrfrags = len(frags)
colors = [c for c in oechem.OEGetLightColors()]
if len(colors) < nrfrags:
colors = [c for c in oechem.OEGetColors(oechem.OEYellowTint, oechem.OEDarkOrange, nrfrags)]
bondglyph = ColorBondByFragmentIndex(colors, itag)
lineWidthScale = 0.75
fadehighlight = oedepict.OEHighlightByColor(oechem.OEGrey, lineWidthScale)
# depict each fragment combinations
for frag in frags:
cell = report.NewCell()
disp = oedepict.OE2DMolDisplay(mol, opts)
fragatoms = oechem.OEIsAtomMember(frags[frag].GetAtoms())
fragbonds = oechem.OEIsBondMember(frags[frag].GetBonds())
notfragatoms = oechem.OENotAtom(fragatoms)
notfragbonds = oechem.OENotBond(fragbonds)
oedepict.OEAddHighlighting(disp, fadehighlight, notfragatoms, notfragbonds)
bond = mol.GetBond(oechem.OEHasBondIdx(frag))
atomBondSet = oechem.OEAtomBondSet()
atomBondSet.AddBond(bond)
atomBondSet.AddAtom(bond.GetBgn())
atomBondSet.AddAtom(bond.GetEnd())
hstyle = oedepict.OEHighlightStyle_BallAndStick
hcolor = oechem.OEColor(oechem.OELightBlue)
oedepict.OEAddHighlighting(disp, hcolor, hstyle, atomBondSet)
#oegrapheme.OEAddGlyph(disp, bondglyph, fragbonds)
oedepict.OERenderMolecule(cell, disp)
# depict original fragmentation in each header
cellwidth, cellheight = report.GetHeaderWidth(), report.GetHeaderHeight()
opts.SetDimensions(cellwidth, cellheight, oedepict.OEScale_AutoScale)
opts.SetAtomColorStyle(oedepict.OEAtomColorStyle_WhiteMonochrome)
bondlabel = LabelBondOrder()
opts.SetBondPropertyFunctor(bondlabel)
disp = oedepict.OE2DMolDisplay(mol, opts)
#oegrapheme.OEAddGlyph(disp, bondglyph, oechem.IsTrueBond())
headerpen = oedepict.OEPen(oechem.OEWhite, oechem.OELightGrey, oedepict.OEFill_Off, 2.0)
for header in report.GetHeaders():
oedepict.OERenderMolecule(header, disp)
oedepict.OEDrawBorder(header, headerpen)
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
oedepict.OEConfigureReportOptions(itf)
oedepict.OEConfigure2DMolDisplayOptions(itf)
oedepict.OEConfigureHighlightParams(itf)
if not oechem.OEParseCommandLine(itf, argv):
return 1
qname = itf.GetString("-query")
tname = itf.GetString("-target")
oname = itf.GetString("-out")
ext = oechem.OEGetFileExtension(oname)
if not oedepict.OEIsRegisteredMultiPageImageFile(ext):
oechem.OEThrow.Fatal("Unknown multipage image type!")
qfile = oechem.oemolistream()
if not qfile.open(qname):
oechem.OEThrow.Fatal("Cannot open mdl query file!")
if qfile.GetFormat() != oechem.OEFormat_MDL and qfile.GetFormat(
) != oechem.OEFormat_SDF:
oechem.OEThrow.Fatal("Query file has to be an MDL file!")
ifs = oechem.oemolistream()
if not ifs.open(tname):
oechem.OEThrow.Fatal("Cannot open target input file!")
depictquery = oechem.OEGraphMol()
if not oechem.OEReadMDLQueryFile(qfile, depictquery):
oechem.OEThrow.Fatal("Cannot read query molecule!")
oedepict.OEPrepareDepiction(depictquery)
queryopts = oechem.OEMDLQueryOpts_Default | oechem.OEMDLQueryOpts_SuppressExplicitH
qmol = oechem.OEQMol()
oechem.OEBuildMDLQueryExpressions(qmol, depictquery, queryopts)
ss = oechem.OESubSearch()
if not ss.Init(qmol):
oechem.OEThrow.Fatal("Cannot initialize substructure search!")
hstyle = oedepict.OEGetHighlightStyle(itf)
hcolor = oedepict.OEGetHighlightColor(itf)
align = itf.GetBool("-align")
ropts = oedepict.OEReportOptions()
oedepict.OESetupReportOptions(ropts, itf)
ropts.SetHeaderHeight(140.0)
report = oedepict.OEReport(ropts)
dopts = oedepict.OE2DMolDisplayOptions()
oedepict.OESetup2DMolDisplayOptions(dopts, itf)
cellwidth, cellheight = report.GetCellWidth(), report.GetCellHeight()
dopts.SetDimensions(cellwidth, cellheight, oedepict.OEScale_AutoScale)
unique = True
for mol in ifs.GetOEGraphMols():
oechem.OEPrepareSearch(mol, ss)
miter = ss.Match(mol, unique)
if not miter.IsValid():
continue # no match
alignres = oedepict.OEAlignmentResult(miter.Target())
if align:
alignres = oedepict.OEPrepareAlignedDepiction(mol, ss)
else:
oedepict.OEPrepareDepiction(mol)
cell = report.NewCell()
disp = oedepict.OE2DMolDisplay(mol, dopts)
if alignres.IsValid():
oedepict.OEAddHighlighting(disp, hcolor, hstyle, alignres)
oedepict.OERenderMolecule(cell, disp)
oedepict.OEDrawBorder(cell, oedepict.OELightGreyPen)
# render query structure in each header
headwidth, headheight = report.GetHeaderWidth(), report.GetHeaderHeight()
dopts.SetDimensions(headwidth, headheight, oedepict.OEScale_AutoScale)
disp = oedepict.OE2DMolDisplay(depictquery, dopts)
for header in report.GetHeaders():
oedepict.OERenderMolecule(header, disp)
oedepict.OEDrawBorder(header, oedepict.OELightGreyPen)
oedepict.OEWriteReport(oname, report)
return 0
opts = oedepict.OE2DMolDisplayOptions()
rows, cols = 2, 2
grid = oedepict.OEImageGrid(image, rows, cols)
grid.SetCellGap(20)
grid.SetMargins(20)
citer = grid.GetCells()
for smi in smiles:
if not citer.IsValid():
# go to next page
image = multi.NewPage()
grid = oedepict.OEImageGrid(image, rows, cols)
grid.SetCellGap(20)
grid.SetMargins(20)
citer = grid.GetCells()
cell = citer.Target()
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, smi)
oedepict.OEPrepareDepiction(mol)
opts.SetDimensions(cell.GetWidth(), cell.GetHeight(), oedepict.OEScale_AutoScale)
disp = oedepict.OE2DMolDisplay(mol, opts)
oedepict.OERenderMolecule(cell, disp)
oedepict.OEDrawBorder(cell, oedepict.OEPen(oedepict.OERedPen))
citer.Next()
oedepict.OEWriteMultiPageImage("MultiPage.pdf", multi)
# @ </SNIPPET-MULTIPAGE>
return grid
pen = oedepict.OEPen(oechem.OEColor(225, 200, 200), oechem.OERed,
oedepict.OEFill_On, 1.0)
image = oedepict.OEImage(100, 100)
image.Clear(oechem.OELightGrey)
grid = CreateGrid(image)
i = 1
# @ <SNIPPET-OEIMAGEGRID-GETCELLS-ALL>
for cell in grid.GetCells():
pass
# @ </SNIPPET-OEIMAGEGRID-GETCELLS-ALL>
oedepict.OEDrawBorder(cell, pen)
font = oedepict.OEFont()
c = oedepict.OE2DPoint(cell.GetWidth(), cell.GetHeight() + font.GetSize())
cell.DrawText(c / 2.0, "(%d)" % i, font)
i += 1
oedepict.OEWriteImage("ImageGridIter-all.png", image)
oedepict.OEWriteImage("ImageGridIter-all.pdf", image)
image = oedepict.OEImage(100, 100)
image.Clear(oechem.OELightGrey)
grid = CreateGrid(image)
i = 1
# @ <SNIPPET-OEIMAGEGRID-GETCELLS-ROW>
row = 2
