def OEAddLabel_Predicate(disp):
ringhighlight = oedepict.OEHighlightByBallAndStick(oechem.OELightGreen)
oedepict.OEAddHighlighting(disp, ringhighlight,
oechem.OEAtomIsInRing(), oechem.OEBondIsInRing())
ringlabel = oedepict.OEHighlightLabel("ring", oechem.OELightGreen)
oedepict.OEAddLabel(disp, ringlabel, oechem.OEAtomIsInRing())
chainhighlight = oedepict.OEHighlightByBallAndStick(oechem.OEBlueTint)
oedepict.OEAddHighlighting(disp, chainhighlight,
oechem.OEAtomIsInChain(), oechem.OEBondIsInChain())
chainlabel = oedepict.OEHighlightLabel("chain", oechem.OEBlueTint)
oedepict.OEAddLabel(disp, chainlabel, oechem.OEAtomIsInChain())
def OEAddLabel_OEAtomBondSet(disp):
mol = disp.GetMolecule()
ringset = oechem.OEAtomBondSet(mol.GetAtoms(oechem.OEAtomIsInRing()),
mol.GetBonds(oechem.OEBondIsInRing()))
ringhighlight = oedepict.OEHighlightByBallAndStick(oechem.OELightGreen)
oedepict.OEAddHighlighting(disp, ringhighlight, ringset)
ringlabel = oedepict.OEHighlightLabel("ring", oechem.OELightGreen)
oedepict.OEAddLabel(disp, ringlabel, ringset)
chainset = oechem.OEAtomBondSet(mol.GetAtoms(oechem.OEAtomIsInChain()),
mol.GetBonds(oechem.OEBondIsInChain()))
chainhighlight = oedepict.OEHighlightByBallAndStick(oechem.OEBlueTint)
oedepict.OEAddHighlighting(disp, chainhighlight, chainset)
chainlabel = oedepict.OEHighlightLabel("chain", oechem.OEBlueTint)
oedepict.OEAddLabel(disp, chainlabel, chainset)
def OEAddHighlighting_OEAtomBondSet(disp):
mol = disp.GetMolecule()
abset = oechem.OEAtomBondSet(mol.GetAtoms(Pred6MemAromAtom()),
mol.GetBonds(Pred6MemAromBond()))
highlightstyle = oedepict.OEHighlightByBallAndStick(oechem.OELightGreen)
oedepict.OEAddHighlighting(disp, highlightstyle, abset)
def OEAddLabel_OEMatch(disp):
subs = oechem.OESubSearch("a1aaaaa1")
unique = True
highlightstyle = oedepict.OEHighlightByBallAndStick(oechem.OELightGreen)
for match in subs.Match(disp.GetMolecule(), unique):
oedepict.OEAddHighlighting(disp, highlightstyle, match)
label = oedepict.OEHighlightLabel("aromatic", oechem.OELightGreen)
oedepict.OEAddLabel(disp, label, match)
def smiles_to_image_grid_mod(
smiles: set,
output_path: str,
cols: int = 8,
cell_width: int = 200,
cell_height: int = 200,
):
from openeye import oechem, oedepict
itf = oechem.OEInterface()
PageByPage = True
suppress_h = True
rows = math.ceil(len(smiles) / cols)
image = oedepict.OEImage(cell_width * cols, cell_height * rows)
grid = oedepict.OEImageGrid(image, rows, cols)
opts = oedepict.OE2DMolDisplayOptions(
grid.GetCellWidth(), grid.GetCellHeight(), oedepict.OEScale_AutoScale
)
opts.SetAromaticStyle(oedepict.OEAromaticStyle_Circle)
opts.SetTitleLocation(oedepict.OETitleLocation_Bottom)
for i, (smi, cell) in enumerate(zip(smiles, grid.GetCells())):
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, smi)
center_bond = []
for atom in mol.GetAtoms():
if atom.GetMapIdx() >0:
center_bond.append(atom.GetIdx())
# print(smi, center_bond)
assert len(center_bond) == 2
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 NoBond(oechem.OEUnaryBondPred):
def __call__(self, bond):
return False
class CentralBondInTorsion(oechem.OEUnaryBondPred):
def __call__(self, bond):
return (bond.GetBgn().GetIdx() in center_bond) and (bond.GetEnd().GetIdx() in center_bond)
atoms = mol.GetAtoms(NoAtom())
bonds = mol.GetBonds(CentralBondInTorsion())
abset = oechem.OEAtomBondSet(atoms, bonds)
oedepict.OEAddHighlighting(disp, oechem.OEColor(oechem.OEMandarin), oedepict.OEHighlightStyle_BallAndStick, abset)
oedepict.OERenderMolecule(cell, disp)
oedepict.OEWriteImage(output_path, image)
def plot_dihedral(mol2, width=200, height=200):
mol = mol2.CreateCopy()
dihedralAtomIndices = [
int(x) - 1 for x in get_sd_data(mol, "TORSION_ATOMS_FRAGMENT").split()
]
dih, tor = get_dihedral(mol, dihedralAtomIndices)
opts = oedepict.OE2DMolDisplayOptions(width, height, oedepict.OEScale_AutoScale)
oedepict.OEPrepareDepiction(mol)
disp = oedepict.OE2DMolDisplay(mol, opts)
img = oedepict.OEImage(width, height)
hstyle = oedepict.OEHighlightByBallAndStick(oechem.OEBlueTint)
oedepict.OEAddHighlighting(disp, hstyle, dih)
hstyle = oedepict.OEHighlightByColor(oechem.OERed)
oedepict.OEAddHighlighting(disp, hstyle, tor)
oedepict.OERenderMolecule(img, disp)
return img
def show_oemol_struc(oemol,
torsions=False,
atom_indices=[],
width=500,
height=300):
from IPython.display import Image
from openeye import oechem, oedepict
# 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])
opts = oedepict.OE2DMolDisplayOptions(width, height,
oedepict.OEScale_AutoScale)
opts.SetAtomPropertyFunctor(oedepict.OEDisplayAtomIdx())
oedepict.OEPrepareDepiction(oemol)
img = oedepict.OEImage(width, height)
display = oedepict.OE2DMolDisplay(oemol, opts)
if torsions:
atoms = oemol.GetAtoms(AtomInTorsion())
bonds = oemol.GetBonds(NoBond())
abset = oechem.OEAtomBondSet(atoms, bonds)
oedepict.OEAddHighlighting(
display,
oechem.OEColor(oechem.OEYellow),
oedepict.OEHighlightStyle_BallAndStick,
abset,
)
oedepict.OERenderMolecule(img, display)
png = oedepict.OEWriteImageToString("png", img)
return Image(png)
def highlight_atoms_in_mol(mol2, dihedralAtomIndices, width=200, height=200):
mol = mol2.CreateCopy()
opts = oedepict.OE2DMolDisplayOptions(width, height, oedepict.OEScale_AutoScale)
oedepict.OEPrepareDepiction(mol)
disp = oedepict.OE2DMolDisplay(mol, opts)
img = oedepict.OEImage(width, height)
hstyle = oedepict.OEHighlightByBallAndStick(oechem.OEBlueTint)
for atom_idx in dihedralAtomIndices:
oedepict.OEAddHighlighting(disp, hstyle, oechem.OEHasAtomIdx(atom_idx))
oedepict.OERenderMolecule(img, disp)
return img
def depictMatch(mol, match, width=500, height=200):
from IPython.display import Image
dopt = oedepict.OEPrepareDepictionOptions()
dopt.SetDepictOrientation(oedepict.OEDepictOrientation_Horizontal)
dopt.SetSuppressHydrogens(True)
oedepict.OEPrepareDepiction(mol, dopt)
opts = oedepict.OE2DMolDisplayOptions(width, height,
oedepict.OEScale_AutoScale)
disp = oedepict.OE2DMolDisplay(mol, opts)
hstyle = oedepict.OEHighlightStyle_Color
hcolor = oechem.OEColor(oechem.OELightBlue)
oedepict.OEAddHighlighting(disp, hcolor, hstyle, match)
ofs = oechem.oeosstream()
oedepict.OERenderMolecule(ofs, 'png', disp)
ofs.flush()
return Image(data="".join(ofs.str()))
def DepictMoleculesWithHighlight(smiles, ss, highlight, basefilename):
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, smiles)
oedepict.OEPrepareDepiction(mol)
opts = oedepict.OE2DMolDisplayOptions(220, 160, oedepict.OEScale_AutoScale)
disp = oedepict.OE2DMolDisplay(mol, opts)
unique = True
for match in ss.Match(mol, unique):
oedepict.OEAddHighlighting(disp, highlight, match)
image = oedepict.OEImage(disp.GetWidth(), disp.GetHeight())
oedepict.OERenderMolecule(image, disp)
oedepict.OEWriteImage(basefilename + ".png", image)
oedepict.OEWriteImage(basefilename + ".pdf", image)
def draw_subsearch_highlights(mol, subsearch, width=400.0, height=400.0):
"""
Draws the hits for the substructure in a given molecule.
Copied from http://notebooks.eyesopen.com/substructure-search-pandas-oenotebook.html
"""
opts = oedepict.OE2DMolDisplayOptions(width, height, oedepict.OEScale_AutoScale)
mol = oechem.OEGraphMol(mol)
oedepict.OEPrepareDepiction(mol)
img = oedepict.OEImage(width, height)
hstyle = oedepict.OEHighlightByBallAndStick(oechem.OEBlueTint)
disp = oedepict.OE2DMolDisplay(mol, opts)
unique = True
for match in subsearch.Match(mol, unique):
oedepict.OEAddHighlighting(disp, hstyle, match)
oedepict.OERenderMolecule(img, disp)
# return oenb.draw_oeimage_to_img_tag(img)
return img
def gen_pdf(
tid_clusters_list: list,
output_path: str,
cols: int = 8,
cell_width: int = 200,
cell_height: int = 200,
):
from openeye import oechem, oedepict
from openforcefield.topology import Molecule
itf = oechem.OEInterface()
PageByPage = True
suppress_h = True
n = sum([len(clusters) for tid, clusters in tid_clusters_list.items()])
rows = math.ceil(n / cols)
image = oedepict.OEImage(cell_width * cols, cell_height * rows)
grid = oedepict.OEImageGrid(image, rows, cols)
opts = oedepict.OE2DMolDisplayOptions(grid.GetCellWidth(),
grid.GetCellHeight(),
oedepict.OEScale_AutoScale)
opts.SetAromaticStyle(oedepict.OEAromaticStyle_Circle)
opts.SetTitleLocation(oedepict.OETitleLocation_Bottom)
count = 0
for tid, clusters in tid_clusters_list.items():
for cluster in clusters:
torsions = cluster['torsions']
label = cluster['cluster_label']
torsions = cluster['torsions']
for torsion in torsions:
cell = grid.GetCell(count // cols + 1, count % cols + 1)
smi = torsion['mol_index']
atom_indices = torsion['indices']
# mol = oechem.OEGraphMol()
# oechem.OESmilesToMol(mol, smi)
off_mol = Molecule.from_smiles(smi,
allow_undefined_stereo=True)
off_mol = off_mol.canonical_order_atoms()
mol = Molecule.to_openeye(off_mol)
title = '{} ({})'.format(tid, set(torsion['covered_tids']))
mol.SetTitle(title)
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 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.OEMandarin),
oedepict.OEHighlightStyle_BallAndStick, abset)
oedepict.OERenderMolecule(cell, disp)
count += 1
oedepict.OEWriteImage(output_path, image)
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 DepictMoleculeWithFragmentCombinations(report, mol, frags, opts): #fragcombs, opts):
""" This function was taken from https://docs.eyesopen.com/toolkits/cookbook/python/depiction/enumfrags.html with some modification
"""
stag = "fragment idx"
itag = oechem.OEGetTag(stag)
for fidx, frag in enumerate(frags):
for bond in frags[frag].GetBonds():
bond.SetData(itag, fidx)
# setup depiction styles
nrfrags = len(frags)
colors = [c for c in oechem.OEGetLightColors()]
if len(colors) < nrfrags:
colors = [c for c in oechem.OEGetColors(oechem.OEYellowTint, oechem.OEDarkOrange, nrfrags)]
bondglyph = ColorBondByFragmentIndex(colors, itag)
lineWidthScale = 0.75
fadehighlight = oedepict.OEHighlightByColor(oechem.OEGrey, lineWidthScale)
# depict each fragment combinations
for frag in frags:
cell = report.NewCell()
disp = oedepict.OE2DMolDisplay(mol, opts)
fragatoms = oechem.OEIsAtomMember(frags[frag].GetAtoms())
fragbonds = oechem.OEIsBondMember(frags[frag].GetBonds())
notfragatoms = oechem.OENotAtom(fragatoms)
notfragbonds = oechem.OENotBond(fragbonds)
oedepict.OEAddHighlighting(disp, fadehighlight, notfragatoms, notfragbonds)
bond = mol.GetBond(oechem.OEHasBondIdx(frag))
atomBondSet = oechem.OEAtomBondSet()
atomBondSet.AddBond(bond)
atomBondSet.AddAtom(bond.GetBgn())
atomBondSet.AddAtom(bond.GetEnd())
hstyle = oedepict.OEHighlightStyle_BallAndStick
hcolor = oechem.OEColor(oechem.OELightBlue)
oedepict.OEAddHighlighting(disp, hcolor, hstyle, atomBondSet)
#oegrapheme.OEAddGlyph(disp, bondglyph, fragbonds)
oedepict.OERenderMolecule(cell, disp)
# depict original fragmentation in each header
cellwidth, cellheight = report.GetHeaderWidth(), report.GetHeaderHeight()
opts.SetDimensions(cellwidth, cellheight, oedepict.OEScale_AutoScale)
opts.SetAtomColorStyle(oedepict.OEAtomColorStyle_WhiteMonochrome)
bondlabel = LabelBondOrder()
opts.SetBondPropertyFunctor(bondlabel)
disp = oedepict.OE2DMolDisplay(mol, opts)
#oegrapheme.OEAddGlyph(disp, bondglyph, oechem.IsTrueBond())
headerpen = oedepict.OEPen(oechem.OEWhite, oechem.OELightGrey, oedepict.OEFill_Off, 2.0)
for header in report.GetHeaders():
oedepict.OERenderMolecule(header, disp)
oedepict.OEDrawBorder(header, headerpen)
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 i, mol in enumerate(oemols):
cell = report.NewCell()
mol_copy = oechem.OEMol(mol)
oedepict.OEPrepareDepiction(mol_copy, False, suppress_h)
disp = oedepict.OE2DMolDisplay(mol_copy, opts)
# Highlight element of interest
unique = False
if subs is not None:
for match in subs.Match(mol_copy, unique):
oedepict.OEAddHighlighting(disp, oechem.OEColor(oechem.OEYellow),
oedepict.OEHighlightStyle_BallAndStick,
match)
oedepict.OERenderMolecule(cell, disp)
oedepict.OEWriteReport(pdf_filename, report)
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)
from openeye import oechem
from openeye import oedepict
# @ <SNIPPET-HIGHLIGHT-MULTI>
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, "c1cncc2c1cc3c(cncc3)c2")
oedepict.OEPrepareDepiction(mol)
subs = oechem.OESubSearch("c1cc[c,n]cc1")
width, height = 350, 250
image = oedepict.OEImage(width, height)
rows, cols = 2, 2
grid = oedepict.OEImageGrid(image, rows, cols)
opts = oedepict.OE2DMolDisplayOptions(grid.GetCellWidth(),
grid.GetCellHeight(),
oedepict.OEScale_AutoScale)
unique = True
for match, cell in zip(subs.Match(mol, unique), grid.GetCells()):
disp = oedepict.OE2DMolDisplay(mol, opts)
oedepict.OEAddHighlighting(disp, oechem.OEColor(oechem.OEPink),
oedepict.OEHighlightStyle_Color, match)
oedepict.OERenderMolecule(cell, disp)
oedepict.OEWriteImage("HighlightMulti.png", image)
# @ </SNIPPET-HIGHLIGHT-MULTI>
oedepict.OEWriteImage("HighlightMulti.pdf", image)
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()
def OEAddHighlighting_AtomAndBondPredicate(disp):
oedepict.OEAddHighlighting(disp, oechem.OEDarkGreen, oedepict.OEHighlightStyle_Color,
Pred6MemAromAtom(), Pred6MemAromBond())
def OEAddHighlighting_OESubSearch(disp):
subsearch = oechem.OESubSearch("a1aaaaa1")
highlightstyle = oedepict.OEHighlightByBallAndStick(oechem.OELightGreen)
oedepict.OEAddHighlighting(disp, highlightstyle, subsearch)
def _oe_render_fragment(
parent: Molecule,
fragment: Molecule,
bond_indices: BondTuple,
image_width: int = 283,
image_height: int = 169,
) -> str:
from openeye import oechem, oedepict
# Map the OpenFF molecules into OE ones, making sure to explicitly set the atom
# map on the OE object as this is not handled by the OpenFF toolkit.
oe_parent = parent.to_openeye()
for atom in oe_parent.GetAtoms():
atom.SetMapIdx(get_map_index(parent, atom.GetIdx(), False))
oedepict.OEPrepareDepiction(oe_parent)
oe_fragment = fragment.to_openeye()
for atom in oe_fragment.GetAtoms():
atom.SetMapIdx(get_map_index(fragment, atom.GetIdx(), False))
oe_parent_bond = oe_parent.GetBond(
oe_parent.GetAtom(oechem.OEHasMapIdx(bond_indices[0])),
oe_parent.GetAtom(oechem.OEHasMapIdx(bond_indices[1])),
)
# Set-up common display options.
image = oedepict.OEImage(image_width, image_height)
display_options = oedepict.OE2DMolDisplayOptions(
image_width, image_height, oedepict.OEScale_AutoScale)
display_options.SetTitleLocation(oedepict.OETitleLocation_Hidden)
display_options.SetAtomColorStyle(
oedepict.OEAtomColorStyle_WhiteMonochrome)
display_options.SetAtomLabelFontScale(1.2)
# display_options.SetBondPropertyFunctor(_oe_wbo_label_display({bond_indices}))
display = oedepict.OE2DMolDisplay(oe_parent, display_options)
fragment_atom_predicate, fragment_bond_predicate = _oe_fragment_predicates(
{atom.GetMapIdx()
for atom in oe_fragment.GetAtoms()})
not_fragment_atoms = oechem.OENotAtom(fragment_atom_predicate)
not_fragment_bonds = oechem.OENotBond(fragment_bond_predicate)
oedepict.OEAddHighlighting(
display,
oedepict.OEHighlightByColor(oechem.OEGrey, 0.75),
not_fragment_atoms,
not_fragment_bonds,
)
rotatable_bond = oechem.OEAtomBondSet()
rotatable_bond.AddBond(oe_parent_bond)
rotatable_bond.AddAtom(oe_parent_bond.GetBgn())
rotatable_bond.AddAtom(oe_parent_bond.GetEnd())
oedepict.OEAddHighlighting(
display,
oechem.OEColor(oechem.OELimeGreen),
oedepict.OEHighlightStyle_BallAndStick,
rotatable_bond,
)
oedepict.OERenderMolecule(image, display)
svg_contents = oedepict.OEWriteImageToString("svg", image)
return svg_contents.decode()
def OEAddHighlighting_AtomAndBondPredicate(disp):
highlightstyle = oedepict.OEHighlightByBallAndStick(oechem.OELightGreen)
oedepict.OEAddHighlighting(disp, highlightstyle, Pred6MemAromAtom(),
Pred6MemAromBond())
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(mcss.GetPattern(), opts)
fitdisp = oedepict.OE2DMolDisplay(fitmol, opts)
if alignres.IsValid():
refabset = oechem.OEAtomBondSet(alignres.GetPatternAtoms(),
alignres.GetPatternBonds())
oedepict.OEAddHighlighting(refdisp, oechem.OEBlueTint,
oedepict.OEHighlightStyle_BallAndStick,
refabset)
fitabset = oechem.OEAtomBondSet(alignres.GetTargetAtoms(),
alignres.GetTargetBonds())
oedepict.OEAddHighlighting(fitdisp, oechem.OEBlueTint,
oedepict.OEHighlightStyle_BallAndStick,
fitabset)
refcell = grid.GetCell(1, 1)
oedepict.OERenderMolecule(refcell, refdisp)
fitcell = grid.GetCell(1, 2)
oedepict.OERenderMolecule(fitcell, fitdisp)
oedepict.OEWriteImage("MCSAlign.png", image)
def OEAddHighlighting_OEMatch(disp):
subs = oechem.OESubSearch("a1aaaaa1")
unique = True
for match in subs.Match(disp.GetMolecule(), unique):
oedepict.OEAddHighlighting(disp, oechem.OEDarkGreen, oedepict.OEHighlightStyle_Color, match)
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 OEAddHighlighting_OEAtomBondSet(disp):
abset = oechem.OEAtomBondSet(mol.GetAtoms(Pred6MemAromAtom()),
mol.GetBonds(Pred6MemAromBond()))
oedepict.OEAddHighlighting(disp, oechem.OEDarkGreen, oedepict.OEHighlightStyle_Color, abset)
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 OEAddHighlighting_OESubSearch(disp):
subsearch = oechem.OESubSearch("a1aaaaa1")
oedepict.OEAddHighlighting(disp, oechem.OEDarkGreen, oedepict.OEHighlightStyle_Color, subsearch)
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 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
