def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
oedepict.OEConfigureReportOptions(itf)
oedepict.OEConfigurePrepareDepictionOptions(itf)
oedepict.OEConfigure2DMolDisplayOptions(itf)
if not oechem.OEParseCommandLine(itf, argv):
return 1
iname = itf.GetString("-in")
ifs = oechem.oemolistream()
ifs.SetConfTest(oechem.OEAbsoluteConfTest()) # VTL
if not ifs.open(iname):
oechem.OEThrow.Fatal("Cannot open input file!")
oname = itf.GetString("-out")
ext = oechem.OEGetFileExtension(oname)
if ext != "pdf":
oechem.OEThrow.Fatal("Output must be PDF format.")
ofs = oechem.oeofstream()
if not ofs.open(oname):
oechem.OEThrow.Fatal("Cannot open output file!")
if itf.HasString("-ringdict"):
rdfname = itf.GetString("-ringdict")
if not oechem.OEInit2DRingDictionary(rdfname):
oechem.OEThrow.Warning("Cannot use user-defined ring dictionary!")
ropts = oedepict.OEReportOptions()
oedepict.OESetupReportOptions(ropts, itf)
ropts.SetFooterHeight(25.0)
report = oedepict.OEReport(ropts)
popts = oedepict.OEPrepareDepictionOptions()
oedepict.OESetupPrepareDepictionOptions(popts, itf)
dopts = oedepict.OE2DMolDisplayOptions()
oedepict.OESetup2DMolDisplayOptions(dopts, itf)
dopts.SetDimensions(report.GetCellWidth(), report.GetCellHeight(),
oedepict.OEScale_AutoScale)
for mol in ifs.GetOEMols(): # VTL ignore confs; dont use GetOEGraphMols
print(mol.GetTitle()) # VTL
cell = report.NewCell()
oedepict.OEPrepareDepiction(mol, popts)
disp = oedepict.OE2DMolDisplay(mol, dopts)
oedepict.OERenderMolecule(cell, disp)
font = oedepict.OEFont(oedepict.OEFontFamily_Default,
oedepict.OEFontStyle_Bold, 12,
oedepict.OEAlignment_Center, oechem.OEBlack)
for pagenum, footer in enumerate(report.GetFooters()):
text = "Page %d of %d" % (pagenum + 1, report.NumPages())
oedepict.OEDrawTextToCenter(footer, text, font)
oedepict.OEWriteReport(ofs, ext, report)
return 0
def main(argv=[__name__]):
# import configuration file
itf = oechem.OEInterface()
oechem.OEConfigure(itf, InterfaceData)
# add configuration for image size and display options
oedepict.OEConfigureImageOptions(itf)
oedepict.OEConfigure2DMolDisplayOptions(itf)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
ifname = itf.GetString("-in")
ofname = itf.GetString("-out")
ifs = oechem.oemolistream(ifname)
mol = oechem.OEGraphMol()
oechem.OEReadMolecule(ifs, mol)
oedepict.OEPrepareDepiction(mol)
width, height = oedepict.OEGetImageWidth(itf), oedepict.OEGetImageHeight(itf)
opts = oedepict.OE2DMolDisplayOptions(width, height, oedepict.OEScale_AutoScale)
# set up display options from command line parameters
oedepict.OESetup2DMolDisplayOptions(opts, itf)
disp = oedepict.OE2DMolDisplay(mol, opts)
oedepict.OERenderMolecule(ofname, disp)
def ToPdf(mol, oname, frags):#, fragcombs):
"""
Parameters
----------
mol: charged OEMolGraph
oname: str
Output file name
Returns
-------
"""
itf = oechem.OEInterface()
oedepict.OEPrepareDepiction(mol)
ropts = oedepict.OEReportOptions()
oedepict.OESetupReportOptions(ropts, itf)
ropts.SetFooterHeight(25.0)
ropts.SetHeaderHeight(ropts.GetPageHeight() / 4.0)
report = oedepict.OEReport(ropts)
# setup decpiction options
opts = oedepict.OE2DMolDisplayOptions()
oedepict.OESetup2DMolDisplayOptions(opts, itf)
cellwidth, cellheight = report.GetCellWidth(), report.GetCellHeight()
opts.SetDimensions(cellwidth, cellheight, oedepict.OEScale_AutoScale)
opts.SetTitleLocation(oedepict.OETitleLocation_Hidden)
opts.SetAtomColorStyle(oedepict.OEAtomColorStyle_WhiteMonochrome)
opts.SetAtomLabelFontScale(1.2)
DepictMoleculeWithFragmentCombinations(report, mol, frags, opts)
return oedepict.OEWriteReport(oname, report)
def main(argv=[__name__]):
itf = oechem.OEInterface()
oechem.OEConfigure(itf, InterfaceData)
oedepict.OEConfigureImageWidth(itf, 400.0)
oedepict.OEConfigureImageHeight(itf, 400.0)
oedepict.OEConfigureImageGridParams(itf)
oedepict.OEConfigurePrepareDepictionOptions(itf)
oedepict.OEConfigure2DMolDisplayOptions(itf)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
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!")
width, height = oedepict.OEGetImageWidth(itf), oedepict.OEGetImageHeight(
itf)
image = oedepict.OEImage(width, height)
rows = oedepict.OEGetImageGridNumRows(itf)
cols = oedepict.OEGetImageGridNumColumns(itf)
grid = oedepict.OEImageGrid(image, rows, cols)
popts = oedepict.OEPrepareDepictionOptions()
oedepict.OESetupPrepareDepictionOptions(popts, itf)
dopts = oedepict.OE2DMolDisplayOptions()
oedepict.OESetup2DMolDisplayOptions(dopts, itf)
dopts.SetDimensions(grid.GetCellWidth(), grid.GetCellHeight(),
oedepict.OEScale_AutoScale)
celliter = grid.GetCells()
for iname in itf.GetStringList("-in"):
ifs = oechem.oemolistream()
if not ifs.open(iname):
oechem.OEThrow.Warning("Cannot open %s input file!" % iname)
continue
for mol in ifs.GetOEGraphMols():
if not celliter.IsValid():
break
oedepict.OEPrepareDepiction(mol, popts)
disp = oedepict.OE2DMolDisplay(mol, dopts)
oedepict.OERenderMolecule(celliter.Target(), disp)
celliter.Next()
oedepict.OEWriteImage(ofs, ext, image)
return 0
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 main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
oedepict.OEConfigureImageOptions(itf)
oedepict.OEConfigurePrepareDepictionOptions(itf)
oedepict.OEConfigure2DMolDisplayOptions(itf)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
iname = itf.GetString("-in")
oname = itf.GetString("-out")
ext = oechem.OEGetFileExtension(oname)
if not oedepict.OEIsRegisteredImageFile(ext):
oechem.OEThrow.Fatal("Unknown image type!")
ifs = oechem.oemolistream()
if not ifs.open(iname):
oechem.OEThrow.Fatal("Cannot open input file!")
ofs = oechem.oeofstream()
if not ofs.open(oname):
oechem.OEThrow.Fatal("Cannot open output file!")
mol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ifs, mol):
oechem.OEThrow.Fatal("Cannot read input file!")
if itf.HasString("-ringdict"):
rdfname = itf.GetString("-ringdict")
if not oechem.OEInit2DRingDictionary(rdfname):
oechem.OEThrow.Warning("Cannot use user-defined ring dictionary!")
popts = oedepict.OEPrepareDepictionOptions()
oedepict.OESetupPrepareDepictionOptions(popts, itf)
oedepict.OEPrepareDepiction(mol, popts)
width, height = oedepict.OEGetImageWidth(itf), oedepict.OEGetImageHeight(
itf)
dopts = oedepict.OE2DMolDisplayOptions(width, height,
oedepict.OEScale_AutoScale)
oedepict.OESetup2DMolDisplayOptions(dopts, itf)
disp = oedepict.OE2DMolDisplay(mol, dopts)
oedepict.OERenderMolecule(ofs, ext, disp)
return 0
def prep_pdf_writer():
itf = oechem.OEInterface()
ropts = oedepict.OEReportOptions()
oedepict.OESetupReportOptions(ropts, itf)
ropts.SetFooterHeight(25.0)
report = oedepict.OEReport(ropts)
popts = oedepict.OEPrepareDepictionOptions()
oedepict.OESetupPrepareDepictionOptions(popts, itf)
dopts = oedepict.OE2DMolDisplayOptions()
oedepict.OESetup2DMolDisplayOptions(dopts, itf)
dopts.SetDimensions(report.GetCellWidth(), report.GetCellHeight(), oedepict.OEScale_AutoScale)
return popts, dopts, report
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
oedepict.OEConfigureImageOptions(itf)
oedepict.OEConfigure2DMolDisplayOptions(itf)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
iname = itf.GetString("-in")
oname = itf.GetString("-out")
ext = oechem.OEGetFileExtension(oname)
if not oedepict.OEIsRegisteredImageFile(ext):
oechem.OEThrow.Fatal("Unknown image type!")
ifs = oechem.oemolistream()
if not ifs.open(iname):
oechem.OEThrow.Fatal("Cannot open input file!")
if ifs.GetFormat() != oechem.OEFormat_MDL:
oechem.OEThrow.Fatal("Input file is not an MDL query file")
ofs = oechem.oeofstream()
if not ofs.open(oname):
oechem.OEThrow.Fatal("Cannot open output file!")
mol = oechem.OEGraphMol()
if not oechem.OEReadMDLQueryFile(ifs, mol):
oechem.OEThrow.Fatal("Cannot read mdl query input file!")
clearcoords, suppressH = False, False
oedepict.OEPrepareDepiction(mol, clearcoords, suppressH)
width, height = oedepict.OEGetImageWidth(itf), oedepict.OEGetImageHeight(
itf)
opts = oedepict.OE2DMolDisplayOptions(width, height,
oedepict.OEScale_AutoScale)
oedepict.OESetup2DMolDisplayOptions(opts, itf)
disp = oedepict.OE2DMolDisplay(mol, opts)
oedepict.OERenderMolecule(ofs, ext, disp)
return 0
def to_pdf(molecules, oname, rows=5, cols=3):
itf = oechem.OEInterface()
PageByPage = True
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_AutoScale)
oedepict.OESetup2DMolDisplayOptions(opts, itf)
for mol in molecules:
cell = report.NewCell()
oedepict.OEPrepareDepiction(mol)
disp = oedepict.OE2DMolDisplay(mol, opts)
oedepict.OERenderMolecule(cell, disp)
oedepict.OEDrawCurvedBorder(cell, oedepict.OELightGreyPen, 10.0)
oedepict.OEWriteReport(oname, report)
def visualize_mols(smiles,
fname,
rows,
cols,
bond_idx,
wbos,
colors,
align_to=0):
"""
Visualize molecules with highlighted bond and labeled with WBO
Parameters
----------
smiles : list of SMILES to visualize.
bond atoms should have map indices
fname : str
filename
rows : int
cols : int
bond_idx : tuple of atom maps of bond to highlight.
wbos : list of floats
colors : list of hex values for colors
align_to: int, optional, default 0
index for which molecule to align to. If zero, will align to first molecules in SMILES list
"""
itf = oechem.OEInterface()
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_AutoScale)
oedepict.OESetup2DMolDisplayOptions(opts, itf)
# align to chosen molecule
ref_mol = oechem.OEGraphMol()
oechem.OESmilesToMol(ref_mol, smiles[align_to])
oedepict.OEPrepareDepiction(ref_mol)
mols = []
minscale = float("inf")
for s in smiles:
mol = oechem.OEMol()
oechem.OESmilesToMol(mol, s)
mols.append(mol)
oedepict.OEPrepareDepiction(mol, False, True)
minscale = min(minscale, oedepict.OEGetMoleculeScale(mol, opts))
print(minscale)
print(minscale)
opts.SetScale(minscale)
for i, mol in enumerate(mols):
cell = report.NewCell()
oedepict.OEPrepareDepiction(mol, False, True)
bond = get_bond(mol, bond_idx)
atom_bond_set = oechem.OEAtomBondSet()
atom_bond_set.AddAtoms([bond.GetBgn(), bond.GetEnd()])
atom_bond_set.AddBond(bond)
hstyle = oedepict.OEHighlightStyle_BallAndStick
hcolor = oechem.OEColor(*colors[i])
overlaps = oegraphsim.OEGetFPOverlap(
ref_mol, mol, oegraphsim.OEGetFPType(oegraphsim.OEFPType_Tree))
oedepict.OEPrepareMultiAlignedDepiction(mol, ref_mol, overlaps)
#opts.SetBondPropLabelFontScale(4.0)
disp = oedepict.OE2DMolDisplay(mol, opts)
oedepict.OEAddHighlighting(disp, hcolor, hstyle, atom_bond_set)
#font = oedepict.OEFont(oedepict.OEFontFamily_Default, oedepict.OEFontStyle_Bold, 12,
# oedepict.OEAlignment_Default, oechem.OEBlack)
bond_label = oedepict.OEHighlightLabel("{:.2f}".format((wbos[i])),
hcolor)
bond_label.SetFontScale(1.4)
#bond_label.SetFont(font)
oedepict.OEAddLabel(disp, bond_label, atom_bond_set)
oedepict.OERenderMolecule(cell, disp)
# oedepict.OEDrawCurvedBorder(cell, oedepict.OELightGreyPen, 10.0)
return (oedepict.OEWriteReport(fname, report))
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)
def render_atom_mapping(filename, molecule1, molecule2, new_to_old_atom_map, width=1200, height=600):
"""
Render the atom mapping to a PDF file.
Parameters
----------
filename : str
The PDF filename to write to.
molecule1 : openeye.oechem.OEMol
Initial molecule
molecule2 : openeye.oechem.OEMol
Final molecule
new_to_old_atom_map : dict of int
new_to_old_atom_map[molecule2_atom_index] is the corresponding molecule1 atom index
width : int, optional, default=1200
Width in pixels
height : int, optional, default=1200
Height in pixels
"""
from openeye import oechem, oedepict
# Make copies of the input molecules
molecule1, molecule2 = oechem.OEGraphMol(molecule1), oechem.OEGraphMol(molecule2)
oechem.OEGenerate2DCoordinates(molecule1)
oechem.OEGenerate2DCoordinates(molecule2)
# Add both to an OEGraphMol reaction
rmol = oechem.OEGraphMol()
rmol.SetRxn(True)
def add_molecule(mol):
# Add atoms
new_atoms = list()
old_to_new_atoms = dict()
for old_atom in mol.GetAtoms():
new_atom = rmol.NewAtom(old_atom.GetAtomicNum())
new_atoms.append(new_atom)
old_to_new_atoms[old_atom] = new_atom
# Add bonds
for old_bond in mol.GetBonds():
rmol.NewBond(old_to_new_atoms[old_bond.GetBgn()], old_to_new_atoms[old_bond.GetEnd()], old_bond.GetOrder())
return new_atoms, old_to_new_atoms
[new_atoms_1, old_to_new_atoms_1] = add_molecule(molecule1)
[new_atoms_2, old_to_new_atoms_2] = add_molecule(molecule2)
# Label reactant and product
for atom in new_atoms_1:
atom.SetRxnRole(oechem.OERxnRole_Reactant)
for atom in new_atoms_2:
atom.SetRxnRole(oechem.OERxnRole_Product)
core1 = oechem.OEAtomBondSet()
core2 = oechem.OEAtomBondSet()
# add all atoms to the set
core1.AddAtoms(new_atoms_1)
core2.AddAtoms(new_atoms_2)
# Label mapped atoms
core_change = oechem.OEAtomBondSet()
index =1
for (index2, index1) in new_to_old_atom_map.items():
new_atoms_1[index1].SetMapIdx(index)
new_atoms_2[index2].SetMapIdx(index)
# now remove the atoms that are core, so only uniques are highlighted
core1.RemoveAtom(new_atoms_1[index1])
core2.RemoveAtom(new_atoms_2[index2])
if new_atoms_1[index1].GetAtomicNum() != new_atoms_2[index2].GetAtomicNum():
# this means the element type is changing
core_change.AddAtom(new_atoms_1[index1])
core_change.AddAtom(new_atoms_2[index2])
index += 1
# Set up image options
itf = oechem.OEInterface()
oedepict.OEConfigureImageOptions(itf)
ext = oechem.OEGetFileExtension(filename)
if not oedepict.OEIsRegisteredImageFile(ext):
raise Exception('Unknown image type for filename %s' % filename)
ofs = oechem.oeofstream()
if not ofs.open(filename):
raise Exception('Cannot open output file %s' % filename)
# Setup depiction options
oedepict.OEConfigure2DMolDisplayOptions(itf, oedepict.OE2DMolDisplaySetup_AromaticStyle)
opts = oedepict.OE2DMolDisplayOptions(width, height, oedepict.OEScale_AutoScale)
oedepict.OESetup2DMolDisplayOptions(opts, itf)
opts.SetBondWidthScaling(True)
opts.SetAtomPropertyFunctor(oedepict.OEDisplayAtomMapIdx())
opts.SetAtomColorStyle(oedepict.OEAtomColorStyle_WhiteMonochrome)
# Depict reaction with component highlights
oechem.OEGenerate2DCoordinates(rmol)
rdisp = oedepict.OE2DMolDisplay(rmol, opts)
oedepict.OEAddHighlighting(rdisp, oechem.OEColor(oechem.OEPink),oedepict.OEHighlightStyle_Stick, core1)
oedepict.OEAddHighlighting(rdisp, oechem.OEColor(oechem.OEPurple),oedepict.OEHighlightStyle_Stick, core2)
oedepict.OEAddHighlighting(rdisp, oechem.OEColor(oechem.OEGreen),oedepict.OEHighlightStyle_Stick, core_change)
oedepict.OERenderMolecule(ofs, ext, rdisp)
ofs.close()
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)
# Highlight element of interest
class NoAtom(oechem.OEUnaryAtomPred):
def to_pdf(molecules, bond_map_idx, fname, rows=3, cols=2, align=None):
"""
Generate PDF of list of oemols or SMILES
Parameters
----------
molecules : list of OEMols
These mols need to have map indices on bond of interest and WBO attached to that bond's data
fname : str
Name of PDF
rows : int
How many rows of molecules per page
cols : int
How many columns of molecule per page
bond_map_idx : tuple of bond to highlight
align: oemol
molecule to align all other molecules in the list
"""
itf = oechem.OEInterface()
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_AutoScale)
oedepict.OESetup2DMolDisplayOptions(opts, itf)
if align:
if isinstance(align, str):
ref_mol = oechem.OEGraphMol()
oechem.OESmilesToMol(ref_mol, align)
elif isinstance(align,
(oechem.OEMol, oechem.OEMolBase, oechem.OEGraphMol)):
ref_mol = align
oedepict.OEPrepareDepiction(ref_mol)
for i, mol in enumerate(molecules):
cell = report.NewCell()
mol_copy = oechem.OEMol(mol)
oedepict.OEPrepareDepiction(mol_copy, False, True)
atom_bond_set = oechem.OEAtomBondSet()
a1 = mol_copy.GetAtom(oechem.OEHasMapIdx(bond_map_idx[0]))
a2 = mol_copy.GetAtom(oechem.OEHasMapIdx(bond_map_idx[1]))
b = mol_copy.GetBond(a1, a2)
opts.SetBondPropertyFunctor(fragmenter.chemi.LabelWibergBondOrder())
atom_bond_set.AddAtom(a1)
atom_bond_set.AddAtom(a2)
atom_bond_set.AddBond(b)
hstyle = oedepict.OEHighlightStyle_BallAndStick
hcolor = oechem.OEColor(oechem.OELightBlue)
overlaps = oegraphsim.OEGetFPOverlap(
ref_mol, mol_copy,
oegraphsim.OEGetFPType(oegraphsim.OEFPType_Tree))
oedepict.OEPrepareMultiAlignedDepiction(mol_copy, ref_mol, overlaps)
disp = oedepict.OE2DMolDisplay(mol_copy, opts)
oedepict.OEAddHighlighting(disp, hcolor, hstyle, atom_bond_set)
oedepict.OERenderMolecule(cell, disp)
oedepict.OEDrawCurvedBorder(cell, oedepict.OELightGreyPen, 10.0)
oedepict.OEWriteReport(fname, report)
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
def smiles_to_pdf(smiles, file_path, rows=10, columns=6):
"""Creates a PDF file containing images of a list of molecules
described by their SMILES patterns.
Parameters
----------
smiles: list of str or tuple of str
The SMILES patterns of the molecules. The list can either contain
a list of single SMILES strings, or a tuple of SMILES strings. If
tuples of SMILES are provided, these smiles will be grouped together
in the output. All tuples in the list must have the same length.
file_path: str
The file path to save the pdf to.
rows: int
The maximum number of rows of molecules to include per page.
columns: int
The maximum number of molecules to include per row.
"""
assert len(smiles) > 0
# Validate the input type.
assert all(isinstance(x, str)
for x in smiles) or all(isinstance(x, tuple) for x in smiles)
# Make sure the smiles tuples are the same length.
molecules_per_group = 1
if isinstance(smiles[0], tuple):
assert (len(x) == len(smiles[0]) for x in smiles)
molecules_per_group = len(smiles[0])
# Convert the list of tuple to list of strings.
if isinstance(smiles[0], tuple):
smiles = [".".join(sorted(x)) for x in smiles]
# Create OEMol objects for each unique smiles pattern provided.
oe_molecules = {}
unique_smiles = set(smiles)
for smiles_pattern in unique_smiles:
molecule = oechem.OEMol()
oechem.OEParseSmiles(molecule, smiles_pattern)
oe_molecules[smiles_pattern] = molecule
# Take into account that each group may have more than one molecule
columns = int(math.floor(columns / molecules_per_group))
report_options = oedepict.OEReportOptions(rows, columns)
report_options.SetHeaderHeight(25)
report_options.SetFooterHeight(25)
report_options.SetCellGap(4)
report_options.SetPageMargins(10)
report = oedepict.OEReport(report_options)
cell_width, cell_height = report.GetCellWidth(), report.GetCellHeight()
display_options = oedepict.OE2DMolDisplayOptions(
cell_width, cell_height, oedepict.OEScale_Default * 0.5)
display_options.SetAromaticStyle(oedepict.OEAromaticStyle_Circle)
pen = oedepict.OEPen(oechem.OEBlack, oechem.OEBlack, oedepict.OEFill_On,
1.0)
display_options.SetDefaultBondPen(pen)
interface = oechem.OEInterface()
oedepict.OESetup2DMolDisplayOptions(display_options, interface)
for i, smiles_pattern in enumerate(smiles):
cell = report.NewCell()
oe_molecule = oechem.OEMol(oe_molecules[smiles_pattern])
oedepict.OEPrepareDepiction(oe_molecule, False, True)
display = oedepict.OE2DMolDisplay(oe_molecule, display_options)
oedepict.OERenderMolecule(cell, display)
oedepict.OEWriteReport(file_path, report)
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():
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('-i', '--json', default='selected_torsions.json')
parser.add_argument('-o', '--outfile', default='selected_torsions.pdf')
args = parser.parse_args()
json_molecules = read_molecules(args.json)
# Generate a PDF of all molecules in the set
pdf_filename = args.outfile
from openeye import oedepict
itf = oechem.OEInterface()
PageByPage = True
suppress_h = True
rows = 7
cols = 3
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)
torsion_param = get_torsion_definition(ff_torsion_param_list,
json_molecule['tid'])
mol.SetTitle(f'{torsion_param.id} ({torsion_param.smirks})')
oedepict.OEPrepareDepiction(mol, False, suppress_h)
disp = oedepict.OE2DMolDisplay(mol, opts)
# Highlight element of interest
class NoAtom(oechem.OEUnaryAtomPred):
def __call__(self, atom):
return False
class AtomInTorsion(oechem.OEUnaryAtomPred):
def __call__(self, atom):
return atom.GetIdx() in atom_indices
class NoBond(oechem.OEUnaryBondPred):
def __call__(self, bond):
return False
class BondInTorsion(oechem.OEUnaryBondPred):
def __call__(self, bond):
return (bond.GetBgn().GetIdx()
in atom_indices) and (bond.GetEnd().GetIdx()
in atom_indices)
class CentralBondInTorsion(oechem.OEUnaryBondPred):
def __call__(self, bond):
return (bond.GetBgn().GetIdx()
in atom_indices[1:3]) and (bond.GetEnd().GetIdx()
in atom_indices[1:3])
atoms = mol.GetAtoms(AtomInTorsion())
bonds = mol.GetBonds(NoBond())
abset = oechem.OEAtomBondSet(atoms, bonds)
oedepict.OEAddHighlighting(disp, oechem.OEColor(oechem.OEYellow),
oedepict.OEHighlightStyle_BallAndStick,
abset)
atoms = mol.GetAtoms(NoAtom())
bonds = mol.GetBonds(CentralBondInTorsion())
abset = oechem.OEAtomBondSet(atoms, bonds)
oedepict.OEAddHighlighting(disp, oechem.OEColor(oechem.OEOrange),
oedepict.OEHighlightStyle_BallAndStick,
abset)
oedepict.OERenderMolecule(cell, disp)
#oedepict.OEDrawCurvedBorder(cell, oedepict.OELightGreyPen, 10.0)
oedepict.OEWriteReport(pdf_filename, report)
def main(argv=[__name__]):
itf = oechem.OEInterface(InterfaceData)
oedepict.OEConfigureImageOptions(itf)
oedepict.OEConfigurePrepareDepictionOptions(itf)
oedepict.OEConfigure2DMolDisplayOptions(itf)
oedepict.OEConfigureHighlightParams(itf)
if not oechem.OEParseCommandLine(itf, argv):
oechem.OEThrow.Fatal("Unable to interpret command line!")
iname = itf.GetString("-in")
oname = itf.GetString("-out")
ext = oechem.OEGetFileExtension(oname)
if not oedepict.OEIsRegisteredImageFile(ext):
oechem.OEThrow.Fatal("Unknown image type!")
ifs = oechem.oemolistream()
if not ifs.open(iname):
oechem.OEThrow.Fatal("Cannot open input file!")
ofs = oechem.oeofstream()
if not ofs.open(oname):
oechem.OEThrow.Fatal("Cannot open output file!")
mol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ifs, mol):
oechem.OEThrow.Fatal("Cannot read input file!")
smarts = itf.GetString("-smarts")
ss = oechem.OESubSearch()
if not ss.Init(smarts):
oechem.OEThrow.Fatal("Cannot parse smarts: %s" % smarts)
popts = oedepict.OEPrepareDepictionOptions()
oedepict.OESetupPrepareDepictionOptions(popts, itf)
oedepict.OEPrepareDepiction(mol, popts)
width, height = oedepict.OEGetImageWidth(itf), oedepict.OEGetImageHeight(
itf)
dopts = oedepict.OE2DMolDisplayOptions(width, height,
oedepict.OEScale_AutoScale)
oedepict.OESetup2DMolDisplayOptions(dopts, itf)
dopts.SetMargins(10.0)
disp = oedepict.OE2DMolDisplay(mol, dopts)
hstyle = oedepict.OEGetHighlightStyle(itf)
hcolor = oedepict.OEGetHighlightColor(itf)
oechem.OEPrepareSearch(mol, ss)
unique = True
for match in ss.Match(mol, unique):
oedepict.OEAddHighlighting(disp, hcolor, hstyle, match)
oedepict.OERenderMolecule(ofs, ext, disp)
return 0
def _create_openeye_pdf(molecules: List[Molecule], file_name: str,
columns: int):
"""Make the pdf of the molecules using OpenEye."""
from openeye import oechem, oedepict
itf = oechem.OEInterface()
suppress_h = True
rows = 10
cols = columns
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)
# now we load the molecules
for off_mol in molecules:
off_mol = copy.deepcopy(off_mol)
off_mol._conformers = []
off_mol.name = None
cell = report.NewCell()
mol = off_mol.to_openeye()
oedepict.OEPrepareDepiction(mol, False, suppress_h)
disp = oedepict.OE2DMolDisplay(mol, opts)
if "dihedrals" in off_mol.properties:
# work out if we have a double or single torsion
if len(off_mol.properties["dihedrals"]) == 1:
dihedrals = off_mol.properties["dihedrals"][0]
center_bonds = dihedrals[1:3]
else:
# double torsion case
dihedrals = [
*off_mol.properties["dihedrals"][0],
*off_mol.properties["dihedrals"][1],
]
center_bonds = [
*off_mol.properties["dihedrals"][0][1:3],
*off_mol.properties["dihedrals"][1][1:3],
]
# Highlight element of interest
class NoAtom(oechem.OEUnaryAtomPred):
def __call__(self, atom):
return False
class AtomInTorsion(oechem.OEUnaryAtomPred):
def __call__(self, atom):
return atom.GetIdx() in dihedrals
class NoBond(oechem.OEUnaryBondPred):
def __call__(self, bond):
return False
class CentralBondInTorsion(oechem.OEUnaryBondPred):
def __call__(self, bond):
return (bond.GetBgn().GetIdx()
in center_bonds) and (bond.GetEnd().GetIdx()
in center_bonds)
atoms = mol.GetAtoms(AtomInTorsion())
bonds = mol.GetBonds(NoBond())
abset = oechem.OEAtomBondSet(atoms, bonds)
oedepict.OEAddHighlighting(
disp,
oechem.OEColor(oechem.OEYellow),
oedepict.OEHighlightStyle_BallAndStick,
abset,
)
atoms = mol.GetAtoms(NoAtom())
bonds = mol.GetBonds(CentralBondInTorsion())
abset = oechem.OEAtomBondSet(atoms, bonds)
oedepict.OEAddHighlighting(
disp,
oechem.OEColor(oechem.OEOrange),
oedepict.OEHighlightStyle_BallAndStick,
abset,
)
oedepict.OERenderMolecule(cell, disp)
oedepict.OEWriteReport(file_name, report)
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(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
