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 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)
# 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 oegraphsim
# @ <SNIPPET-FPOVERLAP>
pmol = oechem.OEGraphMol()
oechem.OESmilesToMol(pmol, "c1cnc2c(c1)CC(CC2O)CF")
tmol = oechem.OEGraphMol()
oechem.OESmilesToMol(tmol, "c1cc2c(cc1)CC(CCl)CC2N")
fptype = oegraphsim.OEGetFPType("Tree,ver=2.0.0,size=4096,bonds=5-5,"
"atype=AtmNum|HvyDeg|EqHalo,btype=Order")
for idx, match in enumerate(oegraphsim.OEGetFPOverlap(pmol, tmol, fptype)):
ostring = "match %2d: " % (idx + 1)
for mpair in match.GetAtoms():
p = mpair.pattern
t = mpair.target
ostring += "%d%s-%d%s " % (
p.GetIdx(), oechem.OEGetAtomicSymbol(p.GetAtomicNum()), t.GetIdx(),
oechem.OEGetAtomicSymbol(t.GetAtomicNum()))
print(ostring)
# @ </SNIPPET-FPOVERLAP>
# @ <SNIPPET-FINGERPRINT-ALIGN>
refmol = oechem.OEGraphMol()
oechem.OESmilesToMol(refmol, "C[C@H](C(=O)N1CCC[C@H]1C(=O)O)OC(=O)[C@@H](Cc2ccccc2)S")
oedepict.OEPrepareDepiction(refmol)
fitmol = oechem.OEGraphMol()
oechem.OESmilesToMol(fitmol, "C[C@H](C(=O)N1CCC[C@H]1C(=O)O)NC(=O)[C@@H](Cc2ccccn2)S")
oedepict.OEPrepareDepiction(fitmol)
image = oedepict.OEImage(500, 300)
rows, cols = 1, 2
grid = oedepict.OEImageGrid(image, rows, cols)
overlaps = oegraphsim.OEGetFPOverlap(refmol, fitmol,
oegraphsim.OEGetFPType(oegraphsim.OEFPType_Tree))
oedepict.OEPrepareMultiAlignedDepiction(fitmol, refmol, overlaps)
opts = oedepict.OE2DMolDisplayOptions(grid.GetCellWidth(), grid.GetCellHeight(),
oedepict.OEScale_AutoScale)
opts.SetTitleLocation(oedepict.OETitleLocation_Hidden)
refscale = oedepict.OEGetMoleculeScale(refmol, opts)
fitscale = oedepict.OEGetMoleculeScale(fitmol, opts)
opts.SetScale(min(refscale, fitscale))
refdisp = oedepict.OE2DMolDisplay(refmol, opts)
fitdisp = oedepict.OE2DMolDisplay(fitmol, opts)
refcell = grid.GetCell(1, 1)
oedepict.OERenderMolecule(refcell, refdisp)
