def Draw2DSurfacePartialCharge(image, mol):
oedepict.OEPrepareDepiction(mol)
oechem.OEMMFFAtomTypes(mol)
oechem.OEMMFF94PartialCharges(mol)
opts = oedepict.OE2DMolDisplayOptions(image.GetWidth(), image.GetHeight(),
oedepict.OEScale_AutoScale)
opts.SetTitleLocation(oedepict.OETitleLocation_Hidden)
opts.SetScale(oegrapheme.OEGetMoleculeSurfaceScale(mol, opts))
coloranion = oechem.OEColorStop(-1.0, oechem.OEColor(oechem.OEDarkRed))
colorcation = oechem.OEColorStop(+1.0, oechem.OEColor(oechem.OEDarkBlue))
colorg = oechem.OELinearColorGradient(coloranion, colorcation)
colorg.AddStop(oechem.OEColorStop(0.0, oechem.OEColor(oechem.OEWhite)))
arcfxn = AtomPartialChargeArcFxn(colorg)
for atom in mol.GetAtoms():
oegrapheme.OESetSurfaceArcFxn(mol, atom, arcfxn)
disp = oedepict.OE2DMolDisplay(mol, opts)
oegrapheme.OEDraw2DSurface(disp)
oedepict.OERenderMolecule(image, disp)
#
# TERMS FOR USE OF SAMPLE CODE The software below ("Sample Code") is
# provided to current licensees or subscribers of OpenEye products or
# SaaS offerings (each a "Customer").
# Customer is hereby permitted to use, copy, and modify the Sample Code,
# subject to these terms. OpenEye claims no rights to Customer's
# modifications. Modification of Sample Code is at Customer's sole and
# exclusive risk. Sample Code may require Customer to have a then
# current license or subscription to the applicable OpenEye offering.
# THE SAMPLE CODE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED. OPENEYE DISCLAIMS ALL WARRANTIES, INCLUDING, BUT
# NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
# PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall OpenEye be
# liable for any damages or liability in connection with the Sample Code
# or its use.
from openeye import oechem
from openeye import oedepict
from openeye import oegrapheme
# @ <SNIPPET-DRAW-COLOR-GRADIENT>
colorg = oechem.OELinearColorGradient(oechem.OEColorStop(0.0, oechem.OEYellow))
colorg.AddStop(oechem.OEColorStop(+1.0, oechem.OEOrange))
colorg.AddStop(oechem.OEColorStop(-1.0, oechem.OEGreen))
image = oedepict.OEImage(400, 100)
oegrapheme.OEDrawColorGradient(image, colorg)
oedepict.OEWriteImage("DrawColorGradient.png", image)
# @ </SNIPPET-DRAW-COLOR-GRADIENT>
oedepict.OEWriteImage("DrawColorGradient.pdf", image)
def main(argv=[__name__]):
itf = oechem.OEInterface()
oechem.OEConfigure(itf, InterfaceData)
oedepict.OEConfigureImageWidth(itf, 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
if atom.GetMapIdx() == 1:
r_coords = mdisp.GetAtomDisplay(atom).GetCoords()
# Create base image
image = oedepict.OEImage(300, 300)
# Draw pie segments
vals = [[100, ">99", 50, 12], [78, 12, 34, 77]]
n_ring = len(vals)
# Get the layer into which we will draw the pie chart
layer = mdisp.GetLayer(oedepict.OELayerPosition_Below)
# Set up gradients for segments
gradients = [
oechem.OELinearColorGradient(oechem.OEColorStop(0, oechem.OEWhite),
oechem.OEColorStop(100, oechem.OEGreen)),
oechem.OELinearColorGradient(oechem.OEColorStop(0, oechem.OEWhite),
oechem.OEColorStop(100, oechem.OERed))
]
# Draw rings from outside inwards
for ring_num in range(n_ring):
starting_angle = START_ANGLE
ring = vals[ring_num]
for value in ring:
radius = (n_ring - ring_num) * RADIUS_BASE
if isinstance(value, str) and ">" in value:
value_for_color = 100
else:
value_for_color = value
return True
def CreateCopy(self):
return ColorCharge(self.colorg).__disown__()
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, "Cc1cc(cc(c1[N+](=O)[O-])F)[N+]#C")
oechem.OEMMFFAtomTypes(mol)
oechem.OEMMFF94PartialCharges(mol)
oedepict.OEPrepareDepiction(mol)
opts = oedepict.OE2DMolDisplayOptions(350, 250, oedepict.OEScale_AutoScale)
opts.SetAtomColorStyle(oedepict.OEAtomColorStyle_WhiteMonochrome)
opts.SetTitleLocation(oedepict.OETitleLocation_Hidden)
disp = oedepict.OE2DMolDisplay(mol, opts)
coloranion = oechem.OEColorStop(-1.0, oechem.OEColor(oechem.OEDarkRed))
colorcation = oechem.OEColorStop(+1.0, oechem.OEColor(oechem.OEDarkBlue))
colorg = oechem.OELinearColorGradient(coloranion, colorcation)
colorg.AddStop(oechem.OEColorStop(0.0, oechem.OEColor(oechem.OEWhite)))
colorcharge = ColorCharge(colorg)
oegrapheme.OEAddGlyph(disp, colorcharge, oechem.OEIsTrueAtom())
oedepict.OERenderMolecule("AnnotatePartialCharge.png", disp)
# @ </SNIPPET-ANNOTATE-PARTIAL-CHARGE>
oedepict.OERenderMolecule("AnnotatePartialCharge.pdf", disp)
def ligand_to_svg_stmd(ligand, ligand_name):
class ColorLigandAtomByBFactor(oegrapheme.OEAtomGlyphBase):
def __init__(self, colorg):
oegrapheme.OEAtomGlyphBase.__init__(self)
self.colorg = colorg
def RenderGlyph(self, disp, atom):
adisp = disp.GetAtomDisplay(atom)
if adisp is None or not adisp.IsVisible():
return False
if not oechem.OEHasResidue(atom):
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)
circlestyle = oegrapheme.OECircleStyle_Default
oegrapheme.OEDrawCircle(layer, circlestyle, adisp.GetCoords(),
radius, pen)
return True
def CreateCopy(self):
return ColorLigandAtomByBFactor(self.colorg).__disown__()
with TemporaryDirectory() as output_directory:
lig_copy = oechem.OEMol(ligand)
if len(ligand_name) < 15:
lig_copy.SetTitle(ligand_name)
else:
lig_copy.SetTitle(ligand_name[0:13] + '...')
img_fn = os.path.join(output_directory, "img.svg")
oegrapheme.OEPrepareDepictionFrom3D(lig_copy)
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))
color_bfactor = ColorLigandAtomByBFactor(colorg)
width, height = 150, 150
opts = oedepict.OE2DMolDisplayOptions(width, height,
oedepict.OEScale_AutoScale)
opts.SetTitleLocation(oedepict.OETitleLocation_Bottom)
disp = oedepict.OE2DMolDisplay(lig_copy, opts)
oegrapheme.OEAddGlyph(disp, color_bfactor, oechem.OEIsTrueAtom())
oedepict.OERenderMolecule(img_fn, disp)
svg_lines = ""
marker = False
with open(img_fn, 'r') as file:
for line in file:
if marker:
svg_lines += line
if line.startswith("<svg"):
marker = True
svg_lines += line
svg_lines += """<title>{}</title>\n""".format(ligand_name)
if line.startswith("</svg>"):
marker = False
return svg_lines