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 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 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 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 __call__(self, image, arc):
adisp = arc.GetAtomDisplay()
if adisp is None or not adisp.IsVisible():
return False
atom = adisp.GetAtom()
if atom is None:
return False
charge = atom.GetPartialCharge()
if charge == 0.0:
return True
color = self.colorg.GetColorAt(charge)
pen = oedepict.OEPen()
pen.SetForeColor(color)
pen.SetLineWidth(2.0)
center = arc.GetCenter()
radius = arc.GetRadius()
bAngle = arc.GetBgnAngle()
eAngle = arc.GetEndAngle()
edgeAngle = 5.0
dir = oegrapheme.OEPatternDirection_Outside
patternAngle = 10.0
oegrapheme.OEDrawBrickRoadSurfaceArc(image, center, bAngle, eAngle,
radius, pen, edgeAngle, dir,
patternAngle)
return True
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 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 __call__(self, image, arc):
pen = oedepict.OEPen(oechem.OEGrey, oechem.OEGrey)
pen.SetLineWidth(2.0)
oegrapheme.OEDrawDefaultSurfaceArc(image, arc.GetCenter(),
arc.GetBgnAngle(),
arc.GetEndAngle(), arc.GetRadius(),
pen)
return True
def Draw2DSurface(disp, atompred, radius, color):
penA = oedepict.OEPen(color, color, oedepict.OEFill_Off, 2.0)
arcfxnA = oegrapheme.OEDefaultArcFxn(penA)
penB = oedepict.OEPen(oechem.OELightGrey, oechem.OELightGrey,
oedepict.OEFill_Off, 2.0,
oedepict.OEStipple_ShortDash)
arcfxnB = oegrapheme.OEDefaultArcFxn(penB)
layer = disp.GetLayer(oedepict.OELayerPosition_Below)
for adisp in disp.GetAtomDisplays():
for arc in oegrapheme.OEGet2DSurfaceArcs(disp, adisp, radius):
if atompred(adisp.GetAtom()):
arcfxnA(layer, arc)
else:
arcfxnB(layer, arc)
def DrawHelloWorld(image, font):
w = image.GetWidth()
h = image.GetHeight()
image.Clear(oechem.OEWhite)
pen = oedepict.OEPen()
image.DrawRectangle(oedepict.OE2DPoint(1.0, 1.0),
oedepict.OE2DPoint(w - 1.0, h - 1.0), pen)
image.DrawText(oedepict.OE2DPoint(w / 2.0, h / 2.0), "Hello World!", font)
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 DrawSurfaces(image, mol):
oechem.OEAssignCovalentRadii(mol)
minradius = oechem.OEGetCovalentRadius(oechem.OEElemNo_H)
radiusScales = oechem.OEDoubleVector(mol.GetMaxAtomIdx(), 0.0)
maxrscale = float("-inf")
for atom in mol.GetAtoms():
rscale = (atom.GetRadius() -
minradius) + oegrapheme.OESurfaceArcScale_Minimum
radiusScales[atom.GetIdx()] = rscale
maxrscale = max(maxrscale, rscale)
opts = oedepict.OE2DMolDisplayOptions(image.GetWidth(), image.GetHeight(),
oedepict.OEScale_AutoScale)
opts.SetTitleLocation(oedepict.OETitleLocation_Hidden)
opts.SetScale(oegrapheme.OEGetMoleculeSurfaceScale(mol, opts, maxrscale))
disp = oedepict.OE2DMolDisplay(mol, opts)
layer = disp.GetLayer(oedepict.OELayerPosition_Below)
penA = oedepict.OEPen(oechem.OELightGrey, oechem.OELightGrey,
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)
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 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 draw_highlight(image, disp, abset):
"""
Highlights the atoms of the dihedral angle on the molecule display.
:type image: oedepict.OEImageBase
:type disp: oedepict.OE2DMolDisplay
:type abset: oechem.OEAtomBondSet
"""
linewidth = disp.GetScale() / 2.0
pen = oedepict.OEPen(oechem.OEBlueTint, oechem.OEBlueTint,
oedepict.OEFill_On, linewidth)
for bond in abset.GetBonds():
adispB = disp.GetAtomDisplay(bond.GetBgn())
adispE = disp.GetAtomDisplay(bond.GetEnd())
image.DrawLine(adispB.GetCoords(), adispE.GetCoords(), pen)
def __call__(self, image, arc):
adisp = arc.GetAtomDisplay()
if adisp is None or not adisp.IsVisible():
return False
color = adisp.GetLabelFont().GetColor()
pen = oedepict.OEPen(color, color, oedepict.OEFill_Off, 1.0)
center = arc.GetCenter()
radius = arc.GetRadius()
bgnAngle = arc.GetBgnAngle()
endAngle = arc.GetEndAngle()
oegrapheme.OEDrawEyelashSurfaceArc(image, center, bgnAngle, endAngle,
radius, pen)
return True
def RenderGlyph(self, disp, atom):
adisp = disp.GetAtomDisplay(atom)
if adisp is None or not adisp.IsVisible():
return False
res = oechem.OEAtomGetResidue(atom)
bfactor = res.GetBFactor()
color = self.colorg.GetColorAt(bfactor)
pen = oedepict.OEPen(color, color, oedepict.OEFill_On, 1.0)
radius = disp.GetScale() / 3.0
layer = disp.GetLayer(oedepict.OELayerPosition_Below)
oegrapheme.OEDrawCircle(layer, oegrapheme.OECircleStyle_Default,
adisp.GetCoords(), radius, pen)
return True
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 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 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 RenderGlyph(self, disp, bond):
bdisp = disp.GetBondDisplay(bond)
if bdisp is None or not bdisp.IsVisible():
return False
if not bond.HasData(self.tag):
return False
linewidth = disp.GetScale() / 2.0
color = self.colorlist[bond.GetData(self.tag)]
pen = oedepict.OEPen(color, color, oedepict.OEFill_Off, linewidth)
adispB = disp.GetAtomDisplay(bond.GetBgn())
adispE = disp.GetAtomDisplay(bond.GetEnd())
layer = disp.GetLayer(oedepict.OELayerPosition_Below)
layer.DrawLine(adispB.GetCoords(), adispE.GetCoords(), pen)
return True
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 RenderGlyph(self, disp, atom):
adisp = disp.GetAtomDisplay(atom)
if adisp is None or not adisp.IsVisible():
return False
charge = atom.GetPartialCharge()
if charge == 0.0:
return True
color = self.colorg.GetColorAt(charge)
pen = oedepict.OEPen()
pen.SetForeColor(oechem.OEColor(color))
color.SetA(100)
pen.SetBackColor(oechem.OEColor(color))
pen.SetFill(oedepict.OEFill_On)
radius = disp.GetScale() / 2.5
layer = disp.GetLayer(oedepict.OELayerPosition_Below)
oegrapheme.OEDrawCircle(layer, oegrapheme.OECircleStyle_Simpson,
adisp.GetCoords(), radius, pen)
return True
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()))
def __call__(self, image, arc):
adisp = arc.GetAtomDisplay()
if adisp is None or not adisp.IsVisible():
return False
atom = adisp.GetAtom()
if atom is None:
return False
avgresiduebfactor = atom.GetDoubleData(self.itag)
if avgresiduebfactor == 0.0:
return True
color = self.colorg.GetColorAt(avgresiduebfactor)
pen = oedepict.OEPen(color, color, oedepict.OEFill_Off, 5.0)
center = arc.GetCenter()
bAngle = arc.GetBgnAngle()
eAngle = arc.GetEndAngle()
radius = arc.GetRadius()
oegrapheme.OEDrawDefaultSurfaceArc(image, center, bAngle, eAngle, radius, pen)
return True
def visualize_bond_atom_sensitivity(mols,
bonds,
scores,
fname,
rows,
cols,
atoms=None,
min_scale=True):
"""
Parameters
----------
mols :
bonds :
scores :
fname :
wbos :
rows :
cols :
atoms :
height :
width :
Returns
-------
"""
itf = oechem.OEInterface()
ropts = oedepict.OEReportOptions(rows, cols)
ropts.SetHeaderHeight(0.01)
ropts.SetFooterHeight(0.01)
ropts.SetCellGap(0.0001)
ropts.SetPageMargins(0.01)
report = oedepict.OEReport(ropts)
cellwidth, cellheight = report.GetCellWidth(), report.GetCellHeight()
opts = oedepict.OE2DMolDisplayOptions(cellwidth, cellheight,
oedepict.OEScale_AutoScale)
oedepict.OESetup2DMolDisplayOptions(opts, itf)
opts.SetAromaticStyle(oedepict.OEAromaticStyle_Circle)
opts.SetAtomColorStyle(oedepict.OEAtomColorStyle_WhiteMonochrome)
pen = oedepict.OEPen(oechem.OEBlack, oechem.OEBlack, oedepict.OEFill_Off,
0.9)
opts.SetDefaultBondPen(pen)
oedepict.OESetup2DMolDisplayOptions(opts, itf)
if min_scale:
minscale = float("inf")
for m in mols:
oedepict.OEPrepareDepiction(m, False, True)
minscale = min(minscale, oedepict.OEGetMoleculeScale(m, opts))
opts.SetScale(minscale)
for i, mol in enumerate(mols):
cell = report.NewCell()
oedepict.OEPrepareDepiction(mol, False, True)
atom_bond_sets = []
for j, bond in enumerate(bonds[i]):
bo = get_bond(mol, bond)
atom_bond_set = oechem.OEAtomBondSet()
atom_bond_set.AddBond(bo)
atom_bond_sets.append(atom_bond_set)
opts.SetTitleLocation(oedepict.OETitleLocation_Hidden)
disp = oedepict.OE2DMolDisplay(mol, opts)
hstyle = oedepict.OEHighlightStyle_Stick
hstyle_2 = oedepict.OEHighlightStyle_Color
score = scores[i]
norm = plt.Normalize(0, max(score))
colors = plt.cm.coolwarm(norm(score))
colors_oe = [rbg_to_int(c, 200) for c in colors]
for j, atom_bond_set in enumerate(atom_bond_sets):
highlight = oechem.OEColor(*colors_oe[j])
oedepict.OEAddHighlighting(disp, highlight, hstyle, atom_bond_set)
oedepict.OEAddHighlighting(disp, highlight, hstyle_2,
atom_bond_set)
highlight = oedepict.OEHighlightByCogwheel(oechem.OEDarkPurple)
highlight.SetBallRadiusScale(5.0)
if not atoms is None:
for a_b in atoms[i]:
if isinstance(a_b[-1], list):
for k, c in enumerate(a_b[-1]):
print(c)
color = oechem.OEColor(*colors_oe[c])
highlight.SetBallRadiusScale(5.0 - 2.5 * k)
highlight.SetColor(color)
atom_bond_set_a = oechem.OEAtomBondSet()
if len(a_b[0]) == 1:
a = mol.GetAtom(oechem.OEHasMapIdx(a_b[0][0]))
atom_bond_set_a.AddAtom(a)
oedepict.OEAddHighlighting(disp, highlight,
atom_bond_set_a)
else:
color = oechem.OEColor(*colors_oe[a_b[-1]])
highlight.SetColor(color)
atom_bond_set_a = oechem.OEAtomBondSet()
if len(a_b[0]) == 1:
a = mol.GetAtom(oechem.OEHasMapIdx(a_b[0][0]))
atom_bond_set_a.AddAtom(a)
else:
for b in itertools.combinations(a_b[0], 2):
bo = get_bond(mol, b)
if not bo:
continue
atom_bond_set_a.AddAtom(bo.GetBgn())
atom_bond_set_a.AddAtom(bo.GetEnd())
atom_bond_set_a.AddBond(bo)
oedepict.OEAddHighlighting(disp, highlight,
atom_bond_set_a)
oedepict.OERenderMolecule(cell, disp)
# oedepict.OEDrawCurvedBorder(cell, oedepict.OELightGreyPen, 10.0)
return oedepict.OEWriteReport(fname, report)
a = oedepict.OE2DPoint(60.0, 20.0)
b = oedepict.OE2DPoint(20.0, 60.0)
image.DrawLine(a, b, pen)
def DrawFigures(pen, basefilename):
image = oedepict.OEImage(80, 80)
DrawFigure(image, pen)
oedepict.OEWriteImage(basefilename + ".png", image)
oedepict.OEWriteImage(basefilename + ".pdf", image)
pen = oedepict.OEPen()
DrawFigures(pen, "OEPen_Default")
# @ <SNIPPET-OEPEN-SET-FORECOLOR>
pen = oedepict.OEPen()
pen.SetForeColor(oechem.OERed)
# @ </SNIPPET-OEPEN-SET-FORECOLOR>
DrawFigures(pen, "OEPen_SetForeColor")
# @ <SNIPPET-OEPEN-SET-BACKCOLOR>
pen = oedepict.OEPen()
pen.SetFill(oedepict.OEFill_On)
pen.SetBackColor(oechem.OEBlueTint)
# @ </SNIPPET-OEPEN-SET-BACKCOLOR>
DrawFigures(pen, "OEPen_SetBackColor")
itf = oechem.OEInterface()
PageByPage = True
suppress_h = True
rows = 10
cols = 6
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)
for json_molecule in json_molecules.values():
# Create oemol
oemol = cmiles.utils.load_molecule(json_molecule['initial_molecules'][0])
# Get atom indices
atom_indices = json_molecule['atom_indices'][0]
# Render molecule
cell = report.NewCell()
mol = oechem.OEMol(oemol)
oedepict.OEPrepareDepiction(mol, False, suppress_h)
disp = oedepict.OE2DMolDisplay(mol, opts)
def depict_dihedrals(image, dimage, mol1, mol2, refmol, opts, itag, nrbins,
colorg):
"""
Highlights the dihedral atoms of a torsion and the depicts the
corresponding dihedral angle histogram when hovering over
the center of the torsion on the molecule display.
:type image: oedepict.OEImageBase
:type dimage: oedepict.OEImageBase
:type mol: oechem.OEMol
:type refmol: oechem.OEMol
:type opts: oedepict.OE2DMolDisplayOptions
:type itag: int
:type nrbins: int
:type oechem.OEColorGradientBase
"""
nrconfs = mol1.NumConfs()
center = oedepict.OEGetCenter(dimage)
radius = min(dimage.GetWidth(), dimage.GetHeight()) * 0.40
draw_dihedral_circle(dimage, center, radius, nrbins, nrconfs)
suppressH = True
oegrapheme.OEPrepareDepictionFrom3D(mol1, suppressH)
if refmol is not None:
oegrapheme.OEPrepareDepictionFrom3D(refmol, suppressH)
disp = oedepict.OE2DMolDisplay(mol1, opts)
dihedrals = []
ref_dihedrals = []
centers = []
agroups = []
dgroups = []
dihedrals_ref_dist = []
for group in mol2.GetGroups(oechem.OEHasGroupType(itag)):
dihedrals_ref_dist.append(group)
nrdihedrals = 0
for group in mol1.GetGroups(oechem.OEHasGroupType(itag)):
uniqueid = uuid.uuid4().hex
agroup = image.NewSVGGroup("torsion_area_" + uniqueid)
dgroup = image.NewSVGGroup("torsion_data_" + uniqueid)
oedepict.OEAddSVGHover(agroup, dgroup)
dihedrals.append(group)
if refmol is not None:
ref_dihedrals.append(get_reference_dihedral(group, refmol, itag))
centers.append(get_center(disp, group))
agroups.append(agroup)
dgroups.append(dgroup)
nrdihedrals += 1
for didx in range(0, nrdihedrals):
image.PushGroup(dgroups[didx])
dihedral = dihedrals[didx]
abset = oechem.OEAtomBondSet(dihedral.GetAtoms(), dihedral.GetBonds())
draw_highlight(image, disp, abset)
dihedral_histogram = dihedral.GetData(itag)
dihedral_histogram_ref = dihedrals_ref_dist[didx].GetData(itag)
print(dihedral_histogram)
print(dihedral_histogram_ref)
draw_dihedral_histogram(dimage, dihedral_histogram,
dihedral_histogram_ref, center, radius, nrbins,
nrconfs)
image.PopGroup(dgroups[didx])
clearbackground = True
oedepict.OERenderMolecule(image, disp, not clearbackground)
markpen = oedepict.OEPen(oechem.OEBlack, oechem.OEWhite,
oedepict.OEFill_On, 1.0)
farpen = oedepict.OEPen(oechem.OEBlack, oechem.OERed, oedepict.OEFill_Off,
2.0)
angleinc = 360.0 / float(nrbins)
for didx in range(0, nrdihedrals):
image.PushGroup(agroups[didx])
dihedral = dihedrals[didx]
dihedral_histogram = dihedral.GetData(itag)
flexibility = determine_flexibility(dihedral_histogram)
color = colorg.GetColorAt(flexibility)
markpen.SetBackColor(color)
markradius = disp.GetScale() / 8.0
image.DrawCircle(centers[didx], markradius, markpen)
if refmol is not None and ref_dihedrals[didx] is not None:
ref_dihedral = ref_dihedrals[didx]
if get_closest_dihedral_angle(mol1, dihedral, ref_dihedral,
itag) > angleinc:
image.DrawCircle(centers[didx], markradius, farpen)
radius = disp.GetScale() / 4.0
image.DrawCircle(centers[didx], radius, oedepict.OESVGAreaPen)
image.PopGroup(agroups[didx])
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)
