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 CombineAndConnectAtomBondSets(fraglist):
"""
This function was taken from OpeneEye Cookbook
https://docs.eyesopen.com/toolkits/cookbook/python/cheminfo/enumfrags.html
"""
# combine atom and bond sets
combined = oechem.OEAtomBondSet()
for frag in fraglist:
for atom in frag.GetAtoms():
combined.AddAtom(atom)
for bond in frag.GetBonds():
combined.AddBond(bond)
# add connecting bonds
for atomA in combined.GetAtoms():
for atomB in combined.GetAtoms():
if atomA.GetIdx() < atomB.GetIdx():
continue
bond = atomA.GetBond(atomB)
if bond is None:
continue
if combined.HasBond(bond):
continue
combined.AddBond(bond)
return combined
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 CombineAndConnectAtomBondSets(fraglist):
# combine atom and bond sets
combined = oechem.OEAtomBondSet()
for frag in fraglist:
for atom in frag.GetAtoms():
combined.AddAtom(atom)
for bond in frag.GetBonds():
combined.AddBond(bond)
# add connecting bonds
for atomA in combined.GetAtoms():
for atomB in combined.GetAtoms():
if atomA.GetIdx() < atomB.GetIdx():
continue
bond = atomA.GetBond(atomB)
if bond is None:
continue
if combined.HasBond(bond):
continue
combined.AddBond(bond)
return combined
def OEAddHighlighting_OEAtomBondSet(adisp):
ligand = adisp.GetDisplayedLigand()
highlight = oedepict.OEHighlightByCogwheel(oechem.OEPinkTint)
highlight.SetInnerContour(False)
abset = oechem.OEAtomBondSet(ligand.GetAtoms(Pred6MemAromAtom()),
ligand.GetBonds(Pred6MemAromBond()))
oegrapheme.OEAddLigandHighlighting(adisp, highlight, abset)
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 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 get_dihedral(mol, dihedralAtomIndices):
"""Get the dihedral corresponding to the indices in dihedralAtomIndices.
Note that the indices are zero-indexed. The torsion of interest is the bond
between atoms with indices 1 and 2.
"""
# dihedralAtomIndices = [int(x) for x in get_sd_data(mol, 'TORSION_ATOMS_FRAGMENT').split()]
dih = oechem.OEAtomBondSet()
tor = oechem.OEAtomBondSet()
for i in range(3):
srcIdx = dihedralAtomIndices[i]
destIdx = dihedralAtomIndices[i + 1]
src = mol.GetAtom(oechem.OEHasAtomIdx(srcIdx))
dest = mol.GetAtom(oechem.OEHasAtomIdx(destIdx))
dih.AddAtom(src)
bond = mol.GetBond(src, dest)
dih.AddBond(bond)
if i == 1:
tor.AddBond(bond)
dih.AddAtom(dest)
return dih, tor
def to_atom_bond_set(oemol, atoms, bonds):
from openeye import oechem
atom_bond_set = oechem.OEAtomBondSet()
for a_idx in atoms:
atom = oemol.GetAtom(oechem.OEHasAtomIdx(a_idx))
atom_bond_set.AddAtom(atom)
for b_tuple in bonds:
a1 = oemol.GetAtom(oechem.OEHasAtomIdx(b_tuple[0]))
a2 = oemol.GetAtom(oechem.OEHasAtomIdx(b_tuple[-1]))
bond = oemol.GetBond(a1, a2)
if not bond:
raise ValueError("{} is a disconnected bond".format(b_tuple))
atom_bond_set.AddBond(bond)
return atom_bond_set
def GetFuncGroups(mol):
'''
:param mol:
:return:
'''
funcGrps = []
for funcGrp in oemedchem.OEGetFuncGroupFragments(mol):
if oechem.OECount(funcGrp, oechem.OEIsHeavy()) > 5:
continue
if oechem.OECount(funcGrp, oechem.OEIsHetero()) == 0:
continue
if oechem.OECount(funcGrp, oechem.OEAtomIsInRing()) > 0:
continue
funcGrps.append(oechem.OEAtomBondSet(funcGrp))
return funcGrps
def _to_AtomBondSet(mol, atoms, bonds):
"""
Builds OpeneyeAtomBondet from atoms and bonds set of indices
Parameters
----------
mol: Openeye OEMolGraph
atoms: Set of atom indices
bonds: Set of bond indices
Returns
-------
AtomBondSet: Openeye AtomBondSet of fragment
"""
AtomBondSet = oechem.OEAtomBondSet()
for a_idx in atoms:
AtomBondSet.AddAtom(mol.GetAtom(oechem.OEHasAtomIdx(a_idx)))
for b_idx in bonds:
AtomBondSet.AddBond(mol.GetBond(oechem.OEHasBondIdx(b_idx)))
return AtomBondSet
def subgraphToAtomBondSet(graph, subgraph, oemol):
"""
Build Openeye AtomBondSet from subrgaphs for enumerating fragments recipe
Parameters
----------
graph: NetworkX graph
subgraph: NetworkX subgraph
oemol: Openeye OEMolGraph
Returns
------
atomBondSet: Openeye oechem atomBondSet
"""
# Build openeye atombondset from subgraphs
atomBondSet = oechem.OEAtomBondSet()
for node in subgraph.node:
atomBondSet.AddAtom(oemol.GetAtom(oechem.OEHasAtomIdx(node)))
for node1, node2 in subgraph.edges():
index = graph.edge[node1][node2]['index']
atomBondSet.AddBond(oemol.GetBond(oechem.OEHasBondIdx(index)))
return atomBondSet
def depict_dihedrals(image, dimage, mol1, mol2, refmol, opts, itag, nrbins,
colorg):
"""
Highlights the dihedral atoms of a torsion and the depicts the
corresponding dihedral angle histogram when hovering over
the center of the torsion on the molecule display.
:type image: oedepict.OEImageBase
:type dimage: oedepict.OEImageBase
:type mol: oechem.OEMol
:type refmol: oechem.OEMol
:type opts: oedepict.OE2DMolDisplayOptions
:type itag: int
:type nrbins: int
:type oechem.OEColorGradientBase
"""
nrconfs = mol1.NumConfs()
center = oedepict.OEGetCenter(dimage)
radius = min(dimage.GetWidth(), dimage.GetHeight()) * 0.40
draw_dihedral_circle(dimage, center, radius, nrbins, nrconfs)
suppressH = True
oegrapheme.OEPrepareDepictionFrom3D(mol1, suppressH)
if refmol is not None:
oegrapheme.OEPrepareDepictionFrom3D(refmol, suppressH)
disp = oedepict.OE2DMolDisplay(mol1, opts)
dihedrals = []
ref_dihedrals = []
centers = []
agroups = []
dgroups = []
dihedrals_ref_dist = []
for group in mol2.GetGroups(oechem.OEHasGroupType(itag)):
dihedrals_ref_dist.append(group)
nrdihedrals = 0
for group in mol1.GetGroups(oechem.OEHasGroupType(itag)):
uniqueid = uuid.uuid4().hex
agroup = image.NewSVGGroup("torsion_area_" + uniqueid)
dgroup = image.NewSVGGroup("torsion_data_" + uniqueid)
oedepict.OEAddSVGHover(agroup, dgroup)
dihedrals.append(group)
if refmol is not None:
ref_dihedrals.append(get_reference_dihedral(group, refmol, itag))
centers.append(get_center(disp, group))
agroups.append(agroup)
dgroups.append(dgroup)
nrdihedrals += 1
for didx in range(0, nrdihedrals):
image.PushGroup(dgroups[didx])
dihedral = dihedrals[didx]
abset = oechem.OEAtomBondSet(dihedral.GetAtoms(), dihedral.GetBonds())
draw_highlight(image, disp, abset)
dihedral_histogram = dihedral.GetData(itag)
dihedral_histogram_ref = dihedrals_ref_dist[didx].GetData(itag)
print(dihedral_histogram)
print(dihedral_histogram_ref)
draw_dihedral_histogram(dimage, dihedral_histogram,
dihedral_histogram_ref, center, radius, nrbins,
nrconfs)
image.PopGroup(dgroups[didx])
clearbackground = True
oedepict.OERenderMolecule(image, disp, not clearbackground)
markpen = oedepict.OEPen(oechem.OEBlack, oechem.OEWhite,
oedepict.OEFill_On, 1.0)
farpen = oedepict.OEPen(oechem.OEBlack, oechem.OERed, oedepict.OEFill_Off,
2.0)
angleinc = 360.0 / float(nrbins)
for didx in range(0, nrdihedrals):
image.PushGroup(agroups[didx])
dihedral = dihedrals[didx]
dihedral_histogram = dihedral.GetData(itag)
flexibility = determine_flexibility(dihedral_histogram)
color = colorg.GetColorAt(flexibility)
markpen.SetBackColor(color)
markradius = disp.GetScale() / 8.0
image.DrawCircle(centers[didx], markradius, markpen)
if refmol is not None and ref_dihedrals[didx] is not None:
ref_dihedral = ref_dihedrals[didx]
if get_closest_dihedral_angle(mol1, dihedral, ref_dihedral,
itag) > angleinc:
image.DrawCircle(centers[didx], markradius, farpen)
radius = disp.GetScale() / 4.0
image.DrawCircle(centers[didx], radius, oedepict.OESVGAreaPen)
image.PopGroup(agroups[didx])
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 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 highlight_torsion(mapped_molecule,
dihedrals,
fname,
width=600,
height=400,
combine_central_bond=True,
color=None):
mol = oechem.OEMol(mapped_molecule)
atom_bond_sets = []
if combine_central_bond:
central_bonds = [(tor[1], tor[2]) for tor in dihedrals]
eq_torsions = {
cb: [
tor for tor in dihedrals
if cb == (tor[1], tor[2]) or cb == (tor[2], tor[1])
]
for cb in central_bonds
}
for cb in eq_torsions:
atom_bond_set = oechem.OEAtomBondSet()
for dihedral in eq_torsions[cb]:
a = mol.GetAtom(oechem.OEHasMapIdx(dihedral[0] + 1))
atom_bond_set.AddAtom(a)
for idx in dihedral[1:]:
a2 = mol.GetAtom(oechem.OEHasMapIdx(idx + 1))
atom_bond_set.AddAtom((a2))
bond = mol.GetBond(a, a2)
atom_bond_set.AddBond(bond)
a = a2
atom_bond_sets.append(atom_bond_set)
if not combine_central_bond:
for dihedral in dihedrals:
atom_bond_set = oechem.OEAtomBondSet()
a = mol.GetAtom(oechem.OEHasMapIdx(dihedral[0] + 1))
atom_bond_set.AddAtom(a)
for idx in dihedral[1:]:
a2 = mol.GetAtom(oechem.OEHasMapIdx(idx + 1))
atom_bond_set.AddAtom((a2))
bond = mol.GetBond(a, a2)
atom_bond_set.AddBond(bond)
a = a2
atom_bond_sets.append(atom_bond_set)
dopt = oedepict.OEPrepareDepictionOptions()
dopt.SetSuppressHydrogens(False)
oedepict.OEPrepareDepiction(mol, dopt)
opts = oedepict.OE2DMolDisplayOptions(width, height,
oedepict.OEScale_AutoScale)
opts.SetTitleLocation(oedepict.OETitleLocation_Hidden)
disp = oedepict.OE2DMolDisplay(mol, opts)
aroStyle = oedepict.OEHighlightStyle_Color
aroColor = oechem.OEColor(oechem.OEBlack)
oedepict.OEAddHighlighting(disp, aroColor, aroStyle,
oechem.OEIsAromaticAtom(),
oechem.OEIsAromaticBond())
hstyle = oedepict.OEHighlightStyle_BallAndStick
if color:
highlight = oechem.OEColor(color)
# combine all atom_bond_sets
atom_bond_set = oechem.OEAtomBondSet()
for ab_set in atom_bond_sets:
for a in ab_set.GetAtoms():
atom_bond_set.AddAtom(a)
for b in ab_set.GetBonds():
atom_bond_set.AddBond(b)
oedepict.OEAddHighlighting(disp, highlight, hstyle, atom_bond_set)
else:
highlight = oedepict.OEHighlightOverlayByBallAndStick(
oechem.OEGetContrastColors())
oedepict.OEAddHighlightOverlay(disp, highlight, atom_bond_sets)
#hcolor = oechem.OEColor(oechem.OELightBlue)
#oedepict.OEAddHighlighting(disp, hcolor, hstyle, atom_bond_sets)
return oedepict.OERenderMolecule(fname, disp)
def highlight_bonds(mol_copy,
fname,
conjugation=True,
rotor=False,
width=600,
height=400,
label=None):
"""
Generate image of molecule with highlighted bonds. The bonds can either be highlighted with a conjugation tag
or if it is rotatable.
Parameters
----------
mol_copy: OEMol
fname: str
Name of image file
conjugation: Bool, optional, Default is True
If True, the bonds with conjugation tag set to True will be highlighted
rotor: Bool, optional, Default is False
If True, the rotatable bonds will be highlighted.
width: int
height: int
label: string. Optional, Default is None
The bond order label. The options are WibergBondOrder, Wiberg_psi4, Mayer_psi4.
"""
mol = oechem.OEMol(mol_copy)
bond_index_list = []
for bond in mol.GetBonds():
if conjugation:
try:
if bond.GetData('conjugated'):
bond_index_list.append(bond.GetIdx())
except ValueError:
pass
if rotor:
if bond.IsRotor():
bond_index_list.append(bond.GetIdx())
atomBondSet = oechem.OEAtomBondSet()
for bond in mol.GetBonds():
if bond.GetIdx() in bond_index_list:
atomBondSet.AddBond(bond)
atomBondSet.AddAtom(bond.GetBgn())
atomBondSet.AddAtom(bond.GetEnd())
dopt = oedepict.OEPrepareDepictionOptions()
dopt.SetSuppressHydrogens(True)
oedepict.OEPrepareDepiction(mol, dopt)
opts = oedepict.OE2DMolDisplayOptions(width, height,
oedepict.OEScale_AutoScale)
opts.SetTitleLocation(oedepict.OETitleLocation_Hidden)
if label is not None:
bond_label = {
'WibergBondOrder': LabelWibergBondOrder,
'Wiberg_psi4': LabelWibergPsiBondOrder,
'Mayer_psi4': LabelMayerPsiBondOrder
}
bondlabel = bond_label[label]
opts.SetBondPropertyFunctor(bondlabel())
disp = oedepict.OE2DMolDisplay(mol, opts)
aroStyle = oedepict.OEHighlightStyle_Color
aroColor = oechem.OEColor(oechem.OEBlack)
oedepict.OEAddHighlighting(disp, aroColor, aroStyle,
oechem.OEIsAromaticAtom(),
oechem.OEIsAromaticBond())
hstyle = oedepict.OEHighlightStyle_BallAndStick
hcolor = oechem.OEColor(oechem.OELightBlue)
oedepict.OEAddHighlighting(disp, hcolor, hstyle, atomBondSet)
return oedepict.OERenderMolecule(fname, disp)
def highltigh_torsion_by_cluster(mapped_molecule,
clustered_dihedrals,
fname,
width=600,
height=400):
"""
Highlight torsion by cluster. This is used to visualize clustering output.
Parameters
----------
mapped_molecule: oemol with map indices
clustered_dihedrals
fname
width
height
Returns
-------
"""
mol = oechem.OEMol(mapped_molecule)
atom_bond_sets = []
for cluster in clustered_dihedrals:
atom_bond_set = oechem.OEAtomBondSet()
for dihedral in clustered_dihedrals[cluster]:
a = mol.GetAtom(oechem.OEHasMapIdx(dihedral[0] + 1))
atom_bond_set.AddAtom(a)
for idx in dihedral[1:]:
a2 = mol.GetAtom(oechem.OEHasMapIdx(idx + 1))
atom_bond_set.AddAtom(a2)
bond = mol.GetBond(a, a2)
atom_bond_set.AddBond(bond)
a = a2
atom_bond_sets.append(atom_bond_set)
dopt = oedepict.OEPrepareDepictionOptions()
dopt.SetSuppressHydrogens(False)
oedepict.OEPrepareDepiction(mol, dopt)
opts = oedepict.OE2DMolDisplayOptions(width, height,
oedepict.OEScale_AutoScale)
opts.SetTitleLocation(oedepict.OETitleLocation_Hidden)
disp = oedepict.OE2DMolDisplay(mol, opts)
aroStyle = oedepict.OEHighlightStyle_Color
aroColor = oechem.OEColor(oechem.OEBlack)
oedepict.OEAddHighlighting(disp, aroColor, aroStyle,
oechem.OEIsAromaticAtom(),
oechem.OEIsAromaticBond())
hstyle = oedepict.OEHighlightStyle_BallAndStick
# if color:
# highlight = oechem.OEColor(color)
# # combine all atom_bond_sets
# atom_bond_set = oechem.OEAtomBondSet()
# for ab_set in atom_bond_sets:
# for a in ab_set.GetAtoms():
# atom_bond_set.AddAtom(a)
# for b in ab_set.GetBonds():
# atom_bond_set.AddBond(b)
# oedepict.OEAddHighlighting(disp, highlight, hstyle, atom_bond_set)
# else:
highlight = oedepict.OEHighlightOverlayByBallAndStick(
oechem.OEGetContrastColors())
oedepict.OEAddHighlightOverlay(disp, highlight, atom_bond_sets)
#hcolor = oechem.OEColor(oechem.OELightBlue)
#oedepict.OEAddHighlighting(disp, hcolor, hstyle, atom_bond_sets)
return oedepict.OERenderMolecule(fname, disp)
def OEAddHighlighting_OEAtomBondSet(disp):
abset = oechem.OEAtomBondSet(mol.GetAtoms(Pred6MemAromAtom()),
mol.GetBonds(Pred6MemAromBond()))
oedepict.OEAddHighlighting(disp, oechem.OEDarkGreen, oedepict.OEHighlightStyle_Color, abset)
grid = oedepict.OEImageGrid(image, rows, cols)
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(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)
def applyffExcipients(excipients, opt):
"""
This function applies the selected force field to the
excipients
Parameters:
-----------
excipients: OEMol molecule
The excipients molecules to parametrize
opt: python dictionary
The options used to parametrize the excipients
Return:
-------
excipient_structure: Parmed structure instance
The parametrized excipient parmed structure
"""
# OpenMM topology and positions from OEMol
topology, positions = oeommutils.oemol_to_openmmTop(excipients)
# Try to apply the selected FF on the excipients
forcefield = app.ForceField(opt['protein_forcefield'])
# List of the unrecognized excipients
unmatched_res_list = forcefield.getUnmatchedResidues(topology)
# Unique unrecognized excipient names
templates = set()
for res in unmatched_res_list:
templates.add(res.name)
if templates: # Some excipients are not recognized
oechem.OEThrow.Info("The following excipients are not recognized "
"by the protein FF: {}"
"\nThey will be parametrized by using the FF: {}".format(templates, opt['other_forcefield']))
# Create a bit vector mask used to split recognized from un-recognize excipients
bv = oechem.OEBitVector(excipients.GetMaxAtomIdx())
bv.NegateBits()
# Dictionary containing the name and the parmed structures of the unrecognized excipients
unrc_excipient_structures = {}
# Dictionary used to skip already selected unrecognized excipients and count them
unmatched_excp = {}
# Ordered list of the unrecognized excipients
unmatched_res_order = []
for r_name in templates:
unmatched_excp[r_name] = 0
hv = oechem.OEHierView(excipients)
for chain in hv.GetChains():
for frag in chain.GetFragments():
for hres in frag.GetResidues():
r_name = hres.GetOEResidue().GetName()
if r_name not in unmatched_excp:
continue
else:
unmatched_res_order.append(r_name)
if unmatched_excp[r_name]: # Test if we have selected the unknown excipient
# Set Bit mask
atms = hres.GetAtoms()
for at in atms:
bv.SetBitOff(at.GetIdx())
unmatched_excp[r_name] += 1
else:
unmatched_excp[r_name] = 1
# Create AtomBondSet to extract from the whole excipient system
# the current selected FF unknown excipient
atms = hres.GetAtoms()
bond_set = set()
for at in atms:
bv.SetBitOff(at.GetIdx())
bonds = at.GetBonds()
for bond in bonds:
bond_set.add(bond)
atom_bond_set = oechem.OEAtomBondSet(atms)
for bond in bond_set:
atom_bond_set.AddBond(bond)
# Create the unrecognized excipient OEMol
unrc_excp = oechem.OEMol()
if not oechem.OESubsetMol(unrc_excp, excipients, atom_bond_set):
oechem.OEThrow.Fatal("Is was not possible extract the residue: {}".format(r_name))
# Charge the unrecognized excipient
if not oequacpac.OEAssignCharges(unrc_excp,
oequacpac.OEAM1BCCCharges(symmetrize=True)):
oechem.OEThrow.Fatal("Is was not possible to "
"charge the extract residue: {}".format(r_name))
# If GAFF or GAFF2 is selected as FF check for tleap command
if opt['other_forcefield'] in ['GAFF', 'GAFF2']:
ff_utils.ParamLigStructure(oechem.OEMol(), opt['other_forcefield']).checkTleap
if opt['other_forcefield'] == 'SMIRNOFF':
unrc_excp = oeommutils.sanitizeOEMolecule(unrc_excp)
# Parametrize the unrecognized excipient by using the selected FF
pmd = ff_utils.ParamLigStructure(unrc_excp, opt['other_forcefield'],
prefix_name=opt['prefix_name']+'_'+r_name)
unrc_excp_struc = pmd.parameterize()
unrc_excp_struc.residues[0].name = r_name
unrc_excipient_structures[r_name] = unrc_excp_struc
# Recognized FF excipients
pred_rec = oechem.OEAtomIdxSelected(bv)
rec_excp = oechem.OEMol()
oechem.OESubsetMol(rec_excp, excipients, pred_rec)
if rec_excp.NumAtoms() > 0:
top_known, pos_known = oeommutils.oemol_to_openmmTop(rec_excp)
ff_rec = app.ForceField(opt['protein_forcefield'])
try:
omm_system = ff_rec.createSystem(top_known, rigidWater=False)
rec_struc = parmed.openmm.load_topology(top_known, omm_system, xyz=pos_known)
except:
oechem.OEThrow.Fatal("Error in the recognised excipient parametrization")
# Unrecognized FF excipients
bv.NegateBits()
pred_unrc = oechem.OEAtomIdxSelected(bv)
unrc_excp = oechem.OEMol()
oechem.OESubsetMol(unrc_excp, excipients, pred_unrc)
# Unrecognized FF excipients coordinates
oe_coord_dic = unrc_excp.GetCoords()
unrc_coords = np.ndarray(shape=(unrc_excp.NumAtoms(), 3))
for at_idx in oe_coord_dic:
unrc_coords[at_idx] = oe_coord_dic[at_idx]
# It is important the order used to assemble the structures. In order to
# avoid mismatch between the coordinates and the structures, it is convenient
# to use the unrecognized residue order
unmatched_res_order_count = []
i = 0
while i < len(unmatched_res_order):
res_name = unmatched_res_order[i]
for j in range(i+1, len(unmatched_res_order)):
if unmatched_res_order[j] == res_name:
continue
else:
break
if i == (len(unmatched_res_order) - 1):
num = 1
unmatched_res_order_count.append((res_name, num))
break
else:
num = j - i
unmatched_res_order_count.append((res_name, num))
i = j
# Merge all the unrecognized Parmed structure
unrc_struc = parmed.Structure()
for pair in unmatched_res_order_count:
res_name = pair[0]
nums = pair[1]
unrc_struc = unrc_struc + nums*unrc_excipient_structures[res_name]
# Set the unrecognized coordinates
unrc_struc.coordinates = unrc_coords
# Set the parmed excipient structure merging
# the unrecognized and recognized parmed
# structures together
if rec_excp.NumAtoms() > 0:
excipients_structure = unrc_struc + rec_struc
else:
excipients_structure = unrc_struc
return excipients_structure
else: # All the excipients are recognized by the selected FF
omm_system = forcefield.createSystem(topology, rigidWater=False)
excipients_structure = parmed.openmm.load_topology(topology, omm_system, xyz=positions)
return excipients_structure
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)
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()
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 _extract_oe_fragment(
molecule: Molecule, atom_indices: Set[int], bond_indices: Set[Tuple[int, int]]
) -> Molecule:
from openeye import oechem
oe_molecule = molecule.to_openeye()
# Restore the map indices as to_openeye does not automatically add them.
for atom_index, map_index in molecule.properties["atom_map"].items():
oe_atom = oe_molecule.GetAtom(oechem.OEHasAtomIdx(atom_index))
oe_atom.SetMapIdx(map_index)
# Include any Hs bonded to the included atom set so we can retain their map
# indices.
for map_index in {*atom_indices}:
oe_atom = oe_molecule.GetAtom(oechem.OEHasMapIdx(map_index))
for neighbour in oe_atom.GetAtoms():
if (
neighbour.GetAtomicNum() != 1
or neighbour.GetMapIdx() < 1
or neighbour.GetMapIdx() in atom_indices
):
continue
atom_indices.add(neighbour.GetMapIdx())
bond_indices.add((map_index, neighbour.GetMapIdx()))
atom_bond_set = oechem.OEAtomBondSet()
for map_index in atom_indices:
atom = oe_molecule.GetAtom(oechem.OEHasMapIdx(map_index))
atom_bond_set.AddAtom(atom)
for map_index_1, map_index_2 in bond_indices:
atom_1 = oe_molecule.GetAtom(oechem.OEHasMapIdx(map_index_1))
atom_2 = oe_molecule.GetAtom(oechem.OEHasMapIdx(map_index_2))
bond = oe_molecule.GetBond(atom_1, atom_2)
if not bond:
raise ValueError(f"{(map_index_1, map_index_2)} is a disconnected bond")
atom_bond_set.AddBond(bond)
atom_predicate = oechem.OEIsAtomMember(atom_bond_set.GetAtoms())
bond_predicate = oechem.OEIsBondMember(atom_bond_set.GetBonds())
fragment = oechem.OEMol()
oechem.OESubsetMol(fragment, oe_molecule, atom_predicate, bond_predicate, True)
oechem.OEAddExplicitHydrogens(fragment)
oechem.OEPerceiveChiral(fragment)
# Always restore map?
# if restore_maps:
# In some cases (symmetric molecules) this changes the atom map so skip it
# restore_atom_map(fragment)
# atom map should be restored for combinatorial fragmentation
# Perceive stereo and check that defined stereo did not change
oechem.OEPerceiveChiral(fragment)
oechem.OE3DToAtomStereo(fragment)
oechem.OE3DToBondStereo(fragment)
return Molecule.from_openeye(fragment, allow_undefined_stereo=True)
# 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.
# @ <SNIPPET>
from __future__ import print_function
from openeye import oechem
# @ <SNIPPET-CREATE-ROLE-OBJECT>
role = oechem.OERole("my:analysis:active-site")
print(role.GetName())
# @ </SNIPPET-CREATE-ROLE-OBJECT>
# @ <SNIPPET-ADD-ROLE-OBJECT>
frag = oechem.OEAtomBondSet() # isa OERoleSet
frag.AddRole(role)
# @ </SNIPPET-ADD-ROLE-OBJECT>
# @ <SNIPPET-ADD-ROLE-STRING>
frag.AddRole("my:analysis:low-energy")
# @ </SNIPPET-ADD-ROLE-STRING>
# @ <SNIPPET-HAS-ROLE-OBJECT>
role2 = oechem.OERole("my:analysis:low-energy")
print(frag.HasRole(role2))
# @ </SNIPPET-HAS-ROLE-OBJECT>
# @ <SNIPPET-HAS-ROLE-STRING>
print(frag.HasRole("my:analysis:small"))
# @ </SNIPPET-HAS-ROLE-STRING>
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 _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 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():
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)