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 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 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 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
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
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)
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