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 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 OEAddLabel_OEImage(image):
label = oedepict.OEHighlightLabel("Hello!")
oedepict.OEAddLabel(image, oedepict.OE2DPoint(50, 50), label)
label.SetBoundingBoxPen(oedepict.OETransparentPen)
oedepict.OEAddLabel(image, oedepict.OE2DPoint(100, 50), label)
label.SetBoundingBoxPen(oedepict.OELightGreyPen)
oedepict.OEAddLabel(image, oedepict.OE2DPoint(150, 50), label)
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 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 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 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 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 DrawFigure(image, pen):
w = image.GetWidth()
h = image.GetHeight()
image.Clear(oechem.OEWhite)
a = oedepict.OE2DPoint(10.0, 10.0)
b = oedepict.OE2DPoint(w - 10, h - 10.0)
image.DrawRectangle(a, b, pen)
a = oedepict.OE2DPoint(20.0, 20.0)
b = oedepict.OE2DPoint(w - 20, h - 20.0)
image.DrawLine(a, b, pen)
a = oedepict.OE2DPoint(60.0, 20.0)
b = oedepict.OE2DPoint(20.0, 60.0)
image.DrawLine(a, b, pen)
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 draw_color_gradient(image, colorg):
"""
Draws the color gradient used to color the circle in the middle of
the rotatable bond.
:type image: oedepict.OEImageBase
:type colorg: oechem.OEColorGradientBase
"""
width, height = image.GetWidth(), image.GetHeight()
frame = oedepict.OEImageFrame(
image, width * 0.8, height * 0.8,
oedepict.OE2DPoint(width * 0.1, height * 0.1))
opts = oegrapheme.OEColorGradientDisplayOptions()
opts.SetColorStopPrecision(1)
opts.SetColorStopLabelFontScale(0.5)
opts.SetColorStopVisibility(False)
opts.AddLabel(
oegrapheme.OEColorGradientLabel(colorg.GetMinValue(), "rigid"))
opts.AddLabel(
oegrapheme.OEColorGradientLabel(colorg.GetMaxValue(), "flexible"))
oegrapheme.OEDrawColorGradient(frame, colorg, opts)
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 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
| oechem.OESplitMolComplexSetup_CovLig)
if not oechem.OEParseCommandLine(itf, argv):
return 1
if itf.HasString("-complex") and (itf.HasString("-protein")
or itf.HasString("-ligand")):
oechem.OEThrow.Warning("Only complex in %s file fill be used!" %
itf.GetString("-complex"))
if not (itf.HasString("-complex")) ^ (itf.HasString("-protein")
and itf.HasString("-ligand")):
oechem.OEThrow.Fatal(
"Please specify either complex or ligand and protein input files!")
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!")
# initialize protein and ligand
protein = oechem.OEGraphMol()
ligand = oechem.OEGraphMol()
if not get_protein_and_ligands(protein, ligand, itf):
oechem.OEThrow.Fatal("Cannot initialize protein and/or ligand!")
# depict active site with interactions
width, height = oedepict.OEGetImageWidth(itf), oedepict.OEGetImageHeight(
itf)
image = oedepict.OEImage(width, height)
interactive_legend = False
magnify_residue = 1.0
if ext == 'svg':
interactive_legend = itf.GetBool("-interactive-legend")
magnify_residue = itf.GetFloat("-magnify-residue")
cwidth, cheight = width, height
if not interactive_legend:
cwidth = cwidth * 0.8
opts = oegrapheme.OE2DActiveSiteDisplayOptions(cwidth, cheight)
oedepict.OESetup2DMolDisplayOptions(opts, itf)
opts.SetRenderInteractiveLegend(interactive_legend)
opts.SetSVGMagnifyResidueInHover(magnify_residue)
if interactive_legend:
depict_complex(image, protein, ligand, opts)
else:
main_frame = oedepict.OEImageFrame(
image, width * 0.80, height, oedepict.OE2DPoint(width * 0.2, 0.0))
legend_frame = oedepict.OEImageFrame(
image, width * 0.20, height, oedepict.OE2DPoint(width * 0.0, 0.0))
depict_complex(main_frame, protein, ligand, opts, legend_frame)
if ext == 'svg' and (interactive_legend or magnify_residue > 1.0):
iconscale = 0.5
oedepict.OEAddInteractiveIcon(image, oedepict.OEIconLocation_TopRight,
iconscale)
oedepict.OEDrawCurvedBorder(image, oedepict.OELightGreyPen, 10.0)
oedepict.OEWriteImage(oname, image)
return 0
# 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
width, height = 100, 100
image = oedepict.OEImage(width, height)
# @ <SNIPPET-CREATE-CLASS>
svg_group_circ = image.NewSVGGroup("circle")
svg_group_rect = image.NewSVGGroup("rectangle")
svg_class_objs = image.NewSVGClass("object")
svg_group_circ.AddSVGClass(svg_class_objs)
svg_group_rect.AddSVGClass(svg_class_objs)
image.PushGroup(svg_group_circ)
image.DrawCircle(oedepict.OEGetCenter(image), 30, oedepict.OERedBoxPen)
image.PopGroup(svg_group_circ)
image.PushGroup(svg_group_rect)
image.DrawRectangle(oedepict.OE2DPoint(10, 10), oedepict.OE2DPoint(90, 90),
oedepict.OELightGreyPen)
image.PopGroup(svg_group_rect)
oedepict.OEWriteImage("CreateSVGClass.svg", image)
# @ </SNIPPET-CREATE-CLASS>
radius = (n_ring - ring_num) * RADIUS_BASE
if isinstance(value, str) and ">" in value:
value_for_color = 100
else:
value_for_color = value
gradient = gradients[ring_num]
color = gradient.GetColorAt(value_for_color)
pen = oedepict.OEPen(color, oechem.OEBlack, oedepict.OEFill_On, 1.0)
layer.DrawPie(r_coords, starting_angle, starting_angle + WEDGE_WIDTH,
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)
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)
def main(argv=[__name__]):
itf = oechem.OEInterface()
oechem.OEConfigure(itf, InterfaceData)
oedepict.OEConfigureImageWidth(itf, 600.0)
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()
oechem.OESplitMolComplex(ligand, protein, water, other, complexmol, sopts)
if ligand.NumAtoms() == 0:
oechem.OEThrow.Fatal("Cannot separate complex!")
# Calculate average BFactor of the whole complex
avgbfactor = GetAverageBFactor(complexmol)
# Calculate minimum and maximum BFactor of the ligand and its environment
minbfactor, maxbfactor = GetMinAndMaxBFactor(ligand, protein)
# Attach to each ligand atom the average BFactor of the nearby protein atoms
stag = "avg residue BFfactor"
itag = oechem.OEGetTag(stag)
SetAverageBFactorOfNearbyProteinAtoms(ligand, protein, itag)
oechem.OEThrow.Info("Average BFactor of the complex = %+.3f" % avgbfactor)
oechem.OEThrow.Info("Minimum BFactor of the ligand and its environment = %+.3f" % minbfactor)
oechem.OEThrow.Info("Maximum BFactor of the ligand and its environment = %+.3f" % maxbfactor)
# Create image
imagewidth, imageheight = oedepict.OEGetImageWidth(itf), oedepict.OEGetImageHeight(itf)
image = oedepict.OEImage(imagewidth, imageheight)
mframe = oedepict.OEImageFrame(image, imagewidth,
imageheight * 0.90, oedepict.OE2DPoint(0.0, 0.0))
lframe = oedepict.OEImageFrame(image, imagewidth, imageheight * 0.10,
oedepict.OE2DPoint(0.0, imageheight * 0.90))
opts = oedepict.OE2DMolDisplayOptions(mframe.GetWidth(), mframe.GetHeight(),
oedepict.OEScale_AutoScale)
oedepict.OESetup2DMolDisplayOptions(opts, itf)
opts.SetAtomColorStyle(oedepict.OEAtomColorStyle_WhiteMonochrome)
# Create BFactor color gradient
colorg = oechem.OELinearColorGradient()
colorg.AddStop(oechem.OEColorStop(0.0, oechem.OEDarkBlue))
colorg.AddStop(oechem.OEColorStop(10.0, oechem.OELightBlue))
colorg.AddStop(oechem.OEColorStop(25.0, oechem.OEYellowTint))
colorg.AddStop(oechem.OEColorStop(50.0, oechem.OERed))
colorg.AddStop(oechem.OEColorStop(100.0, oechem.OEDarkRose))
# Prepare ligand for depiction
oegrapheme.OEPrepareDepictionFrom3D(ligand)
arcfxn = BFactorArcFxn(colorg, itag)
for atom in ligand.GetAtoms():
oegrapheme.OESetSurfaceArcFxn(ligand, atom, arcfxn)
opts.SetScale(oegrapheme.OEGetMoleculeSurfaceScale(ligand, opts))
# Render ligand and visualize BFactor
disp = oedepict.OE2DMolDisplay(ligand, opts)
colorbfactor = ColorLigandAtomByBFactor(colorg)
oegrapheme.OEAddGlyph(disp, colorbfactor, oechem.OEIsTrueAtom())
oegrapheme.OEDraw2DSurface(disp)
oedepict.OERenderMolecule(mframe, disp)
# Draw color gradient
opts = oegrapheme.OEColorGradientDisplayOptions()
opts.SetColorStopPrecision(1)
opts.AddMarkedValue(avgbfactor)
opts.SetBoxRange(minbfactor, maxbfactor)
oegrapheme.OEDrawColorGradient(lframe, colorg, opts)
oedepict.OEWriteImage(oname, image)
return 0
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
# 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)
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
# @ <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)
# 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
width, height = 200, 100
image = oedepict.OEImage(width, height)
# @ <SNIPPET-ADD-SVG-HOVER>
hover_area = image.NewSVGGroup("hover_area")
target_area = image.NewSVGGroup("hover_target_area")
oedepict.OEAddSVGHover(hover_area, target_area)
image.PushGroup(hover_area)
image.DrawRectangle(oedepict.OE2DPoint(30, 30), oedepict.OE2DPoint(70, 70),
oedepict.OERedBoxPen)
image.PopGroup(hover_area)
image.PushGroup(target_area)
image.DrawCircle(oedepict.OE2DPoint(150, 50), 30, oedepict.OEBlueBoxPen)
image.PopGroup(target_area)
oedepict.OEAddInteractiveIcon(image)
oedepict.OEWriteImage("AddSVGHover.svg", image)
# @ <SNIPPET-ADD-SVG-HOVER>
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
for cell in grid.GetCells(row, 0):
pass
