def get_bond(mol, bond_idx):
a1 = mol.GetAtom(oechem.OEHasMapIdx(bond_idx[0]))
a2 = mol.GetAtom(oechem.OEHasMapIdx(bond_idx[1]))
bond = mol.GetBond(a1, a2)
if not bond:
raise ValueError("({}) atoms are not connected".format(bond_idx))
return bond
def test_tag_fgroups():
from openeye import oechem
import itertools
smiles = '[H:40][c:3]1[c:8]([c:20]2[n:30][c:12]([c:14]([n:32]2[n:31][c:11]1[H:48])[C:2]#[C:1][c:13]3[c:9]([c:15]([c:4]([c:5]([c:16]3[C:26]' \
'([H:58])([H:59])[H:60])[H:42])[H:41])[C:21](=[O:36])[N:35]([H:66])[c:19]4[c:7]([c:6]([c:17]([c:18]([c:10]4[H:47])[C:29]([F:37])([F:38])' \
'[F:39])[C:28]([H:64])([H:65])[N:34]5[C:24]([C:22]([N:33]([C:23]([C:25]5([H:56])[H:57])([H:52])[H:53])[C:27]([H:61])([H:62])[H:63])([H:50])' \
'[H:51])([H:54])[H:55])[H:43])[H:44])[H:46])[H:49])[H:45]'
mol = oechem.OEMol()
oechem.OESmilesToMol(mol, smiles)
frags = fragmenter.fragment.CombinatorialFragmenter(mol)
fgroups = {}
fgroups['alkyne_0'] = [1, 2]
fgroups['carbonyl_0'] = [21, 36]
fgroups['amide_0'] = [35]
fgroups['tri_halide_0'] = [29, 37, 38, 39]
for group in fgroups:
for i in fgroups[group]:
a = frags.molecule.GetAtom(oechem.OEHasMapIdx(i))
assert a.GetData('fgroup') == group
for group in fgroups:
atoms = [
frags.molecule.GetAtom(oechem.OEHasMapIdx(i))
for i in fgroups[group]
]
for atom in itertools.combinations(atoms, 2):
# Check for bond
b = frags.molecule.GetBond(atom[0], atom[1])
if b:
assert b.GetData('fgroup') == group
def get_bond(mol, bond_tuple):
a1 = mol.GetAtom(oechem.OEHasMapIdx(bond_tuple[0]))
a2 = mol.GetAtom(oechem.OEHasMapIdx(bond_tuple[1]))
if not a1 or not a2:
print('no atoms')
return False
bond = mol.GetBond(a1, a2)
if not bond:
print('no bond')
return False
return bond
def bond_order_to_bond_graph(bond_order,
threshold=0.8,
hydrogen_bond=True,
molecule=None,
atom_map=None):
"""
Get bond graph from bond orders. This function returns a set of bonds where the bond order is above a threshold
Parameters
----------
bond_order: np array
threshold: int
Returns
-------
bonds: set
"""
bonds = set()
for i in range(bond_order.shape[0]):
for j in range(bond_order.shape[1]):
if bond_order[i, j] >= threshold:
if not hydrogen_bond:
idx_1 = atom_map[i + 1]
idx_2 = atom_map[j + 1]
atom_1 = molecule.GetAtom(oechem.OEHasMapIdx(idx_1))
atom_2 = molecule.GetAtom(oechem.OEHasAtomIdx(idx_2))
if atom_1.IsHydrogen() or atom_2.IsHydrogen():
continue
if (j + 1, i + 1) in bonds:
continue
bonds.add((i + 1, j + 1))
return bonds
def get_wbo_growth(fragmenter, fragment_mol, atoms, bonds, target_bond,
heuristic):
wbos = []
fragments = []
fragment_mol = fragmenter.fragments[target_bond]
oechem.OEAddExplicitHydrogens(fragment_mol)
try:
charged_fragment = chemi.get_charges(fragment_mol,
strict_stereo=False,
strict_types=False)
a1 = charged_fragment.GetAtom(oechem.OEHasMapIdx(target_bond[0]))
a2 = charged_fragment.GetAtom(oechem.OEHasMapIdx(target_bond[-1]))
bond = charged_fragment.GetBond(a1, a2)
wbos.append(bond.GetData('WibergBondOrder'))
fragments.append(charged_fragment)
except RuntimeError:
print('Bad fragment. Continuing to adding the next bond')
pass
while fragment_mol.GetMaxAtomIdx() < fragmenter.molecule.GetMaxAtomIdx():
atoms, bonds = add_one_bond(
molecule=fragmenter.molecule,
atoms=atoms,
bonds=bonds,
functional_groups=fragmenter.functional_groups,
ring_systems=fragmenter.ring_systems,
target_bond=target_bond,
heuristic=heuristic)
ab_set = fragmenter._to_atom_bond_set(atoms, bonds)
fragment_mol = fragmenter.atom_bond_set_to_mol(
ab_set, expand_stereoisomers=False)
oechem.OEAddExplicitHydrogens(fragment_mol)
try:
charged_fragment = chemi.get_charges(fragment_mol,
strict_stereo=False,
strict_types=False)
a1 = charged_fragment.GetAtom(oechem.OEHasMapIdx(target_bond[0]))
a2 = charged_fragment.GetAtom(oechem.OEHasMapIdx(target_bond[-1]))
bond = charged_fragment.GetBond(a1, a2)
fragment_wbo = bond.GetData('WibergBondOrder')
wbos.append(fragment_wbo)
mol_copy = copy.deepcopy(charged_fragment)
fragments.append(mol_copy)
except RuntimeError:
pass
return wbos, fragments
def to_mapped_xyz(molecule,
atom_map=None,
conformer=None,
xyz_format=True,
filename=None):
"""
Generate xyz coordinates for molecule in the order given by the atom_map. atom_map is a dictionary that maps the
tag on the SMILES to the atom idex in OEMol.
Parameters
----------
molecule: OEMol with conformers
atom_map: dict
maps tag in SMILES to atom index
conformer: int
Which conformer to write xyz file for. If None, write out all conformers. Default is None
xyz_format: bool
If True, will write out number of atoms and molecule name. If false, will only write out elements and coordinates
filename: str
Name of file to save to. If None, only returns a string.
Returns
-------
str: elements and xyz coordinates (in angstroms) in order of tagged SMILES
"""
if not atom_map and not cmiles.utils.has_atom_map(molecule):
raise ValueError(
"If molecule does not have atom map, you must provide an atom map")
if not has_conformer(molecule, check_two_dimension=True):
raise ValueError("Molecule must have conformers")
xyz = ""
for k, mol in enumerate(molecule.GetConfs()):
if k == conformer or conformer is None:
if xyz_format:
xyz += "{}\n".format(mol.GetMaxAtomIdx())
xyz += "{}\n".format(mol.GetTitle())
coords = oechem.OEFloatArray(mol.GetMaxAtomIdx() * 3)
mol.GetCoords(coords)
if k != 0 and not xyz_format:
xyz += "*"
for mapping in range(1, molecule.NumAtoms() + 1):
if not atom_map:
atom = molecule.GetAtom(oechem.OEHasMapIdx(mapping))
idx = atom.GetIdx()
else:
idx = atom_map[mapping]
atom = mol.GetAtom(oechem.OEHasAtomIdx(idx))
syb = oechem.OEGetAtomicSymbol(atom.GetAtomicNum())
xyz += " {} {:05.3f} {:05.3f} {:05.3f}\n".format(
syb, coords[idx * 3], coords[idx * 3 + 1],
coords[idx * 3 + 2])
if filename:
file = open("{}.xyz".format(filename), 'w')
file.write(xyz)
file.close()
else:
return xyz
def test_cap_open_valance(input, bond, output):
from openeye import oechem
mol = chemi.smiles_to_oemol(input)
f = fragmenter.fragment.PfizerFragmenter(mol)
atoms, bonds = f._get_torsion_quartet(bond)
atoms, bonds = f._get_ring_and_fgroups(atoms, bonds)
f._cap_open_valence(atoms, bonds, bond)
# Check that carbon bonded to N was added
assert f.molecule.GetAtom(oechem.OEHasMapIdx(output))
def sort_by_wbo(molecule, atoms, bonds):
sort_by = []
atoms_to_add = []
for m_idx in atoms:
a = molecule.GetAtom(oechem.OEHasMapIdx(m_idx))
for nbr in a.GetAtoms():
nbr_m_idx = nbr.GetMapIdx()
if not nbr.IsHydrogen() and not nbr_m_idx in atoms:
b = molecule.GetBond(a, nbr)
atoms_to_add.append((nbr_m_idx, (m_idx, nbr_m_idx)))
sort_by.append(b.GetData('WibergBondOrder'))
return atoms_to_add, sort_by
def get_bond(mol, bond_tuple):
"""
Get bond in molecule
Parameters
----------
mol : oemole with map indices
bond_tuple : tuple with map indices of bond
Returns
-------
bond if found, False otherwise
"""
a1 = mol.GetAtom(oechem.OEHasMapIdx(bond_tuple[0]))
a2 = mol.GetAtom(oechem.OEHasMapIdx(bond_tuple[1]))
if not a1 or not a2:
return False
bond = mol.GetBond(a1, a2)
if not bond:
return False
return bond
def frags_with_nbrs(parent, frags, nbrs):
return_frags = {}
for f in frags:
keep = True
mol = oechem.OEMol()
oechem.OESmilesToMol(mol, frags[f]['map_to_parent'])
for n in nbrs:
a = mol.GetAtom(oechem.OEHasMapIdx(n))
if not a:
keep = False
if keep:
return_frags[f] = frags[f]
return return_frags
def SetSDData(A_IDX, B_IDX, C_IDX, D_IDX, torsion, torsionMol):
taIdx = torsionMol.GetAtom(oechem.OEHasMapIdx(A_IDX)).GetIdx() + 1
tbIdx = torsionMol.GetAtom(oechem.OEHasMapIdx(B_IDX)).GetIdx() + 1
tcIdx = torsionMol.GetAtom(oechem.OEHasMapIdx(C_IDX)).GetIdx() + 1
tdIdx = torsionMol.GetAtom(oechem.OEHasMapIdx(D_IDX)).GetIdx() + 1
apStr = "cs1:0:1;1%{}:1%{}:1%{}:1%{}".format(taIdx, tbIdx, tcIdx,
tdIdx)
oechem.OESetSDData(torsionMol, "TORSION_ATOMPROP", apStr)
fragTorAtoms = "{} {} {} {}".format(taIdx, tbIdx, tcIdx, tdIdx)
oechem.OESetSDData(torsionMol, TORSION_ATOMS_FRAG_KEY, fragTorAtoms)
parentTorAtoms = "{} {} {} {}".format(torsion.a.GetIdx() + 1,
torsion.b.GetIdx() + 1,
torsion.c.GetIdx() + 1,
torsion.d.GetIdx() + 1)
oechem.OESetSDData(torsionMol, TORSION_ATOMS_PARENT_MOL_KEY,
parentTorAtoms)
atom_map = ""
for atom in torsionMol.GetAtoms():
atom_map += str(atom.GetIdx() + 1) + "_" + str(
atom.GetData("idx")) + "-"
atom_map = atom_map[:-1]
oechem.OESetSDData(torsionMol, FRAGMENT_TO_PARENT_ATOMS_KEY, atom_map)
def generate_grid_conformers(molecule,
dihedrals,
intervals,
max_rotation=360,
copy_mol=True):
"""
Generate conformers using torsion angle grids.
Parameters
----------
molecule: OEMol
dihedrals: list of
intervals
Returns
-------
"""
# molecule must be mapped
if copy_mol:
molecule = copy.deepcopy(molecule)
if cmiles.utils.has_atom_map(molecule):
remove_map(molecule)
else:
raise ValueError("Molecule must have map indices")
# Check length of dihedrals match length of intervals
conf_mol = generate_conformers(molecule, max_confs=1)
conf = conf_mol.GetConfs().next()
coords = oechem.OEFloatArray(conf.GetMaxAtomIdx() * 3)
conf.GetCoords(coords)
torsions = [[conf_mol.GetAtom(oechem.OEHasMapIdx(i + 1)) for i in dih]
for dih in dihedrals]
for i, tor in enumerate(torsions):
copy_conf_mol = copy.deepcopy(conf_mol)
conf_mol.DeleteConfs()
for conf in copy_conf_mol.GetConfs():
coords = oechem.OEFloatArray(conf.GetMaxAtomIdx() * 3)
conf.GetCoords(coords)
for angle in range(5, max_rotation + 5, intervals[i]):
newconf = conf_mol.NewConf(coords)
oechem.OESetTorsion(newconf, tor[0], tor[1], tor[2], tor[3],
radians(angle))
restore_map(conf_mol)
return conf_mol
def AddRelevantRingAtoms(mol, torsion, torsionSet):
atom1or2 = oechem.OEOrAtom(oechem.OEHasMapIdx(1),
oechem.OEHasMapIdx(2))
ringNbrs = []
for atom in mol.GetAtoms(
oechem.OEAndAtom(oechem.OEAtomIsInRing(), atom1or2)):
for nbr in atom.GetAtoms(
oechem.OEAndAtom(oechem.OENotAtom(atom1or2),
oechem.OENotAtom(
oechem.OEAtomIsInRing()))):
if nbr.IsHydrogen():
ringNbrs.append(nbr)
continue
if nbr.IsOxygen() and mol.GetBond(atom, nbr).GetOrder() == 2:
ringNbrs.append(nbr)
continue
if TorsionGenerator.IsOrtho(nbr, torsion):
ringNbrs.append(nbr)
for nbr in ringNbrs:
if not torsionSet.HasAtom(nbr):
nbr.SetMapIdx(2)
torsionSet.AddAtom(nbr)
def MarkBridgingAtoms(BRIDGE_ATOM_IDX, mol, torsionSet):
NorOorS = oechem.OEOrAtom(
oechem.OEOrAtom(oechem.OEIsNitrogen(), oechem.OEIsOxygen()),
oechem.OEIsSulfur())
for atom in mol.GetAtoms(
oechem.OEAndAtom(oechem.OEHasMapIdx(2), NorOorS)):
for nbr in atom.GetAtoms(oechem.OEIsHeavy()):
if not torsionSet.HasAtom(nbr):
if nbr.GetMapIdx() == 0:
torsionSet.AddAtom(nbr)
if nbr.GetHvyDegree() == 1:
nbr.SetMapIdx(3)
continue
nbr.SetMapIdx(BRIDGE_ATOM_IDX)
def generate_torsion_index(fb_mol, torsion):
assert hasattr(
fb_mol, 'oe_mol'
), 'fb_mol does not have oe_mol attr, did you create it using read_sdf_to_fb_mol?'
oe_mol = fb_mol.oe_mol
mapped_smiles = cmiles.utils.mol_to_smiles(oe_mol)
# create a new mol and convert mapped smiles back to mol
mol = oechem.OEMol()
oechem.OESmilesToMol(mol, mapped_smiles)
for a in mol.GetAtoms():
if not a.GetMapIdx() - 1 in torsion:
a.SetMapIdx(0)
for i, t in enumerate(torsion):
a = mol.GetAtom(oechem.OEHasMapIdx(t + 1))
a.SetMapIdx(i + 1)
return oechem.OEMolToSmiles(mol)
def assign_canonical_idx(mol):
for atom in mol.GetAtoms():
atom.SetMapIdx(0)
for map_idx, atom in enumerate(mol.GetAtoms(oechem.OEIsHeavy())):
atom.SetMapIdx(map_idx + 1)
can_smiles = oechem.OEMolToSmiles(mol)
can_mol = oechem.OEGraphMol()
# smiles_opt = OEParseSmilesOptions(canon=True)
# OEParseSmiles(can_mol, can_smiles, smiles_opt)
oechem.OESmilesToMol(can_mol, can_smiles)
for can_atom in can_mol.GetAtoms(oechem.OEIsHeavy()):
atom = mol.GetAtom(oechem.OEHasMapIdx(can_atom.GetMapIdx()))
atom.SetData(CANONICAL_IDX_TAG, can_atom.GetIdx())
def get_bond(mol, bond_idx):
"""
Get oebond object
Parameters
----------
mol : oemol
Molecule to extract bond from
bond_idx : tuple of ints
tuple of map indices of atoms in bond
Returns
-------
bond: oebond
"""
atoms = [mol.GetAtom(oechem.OEHasMapIdx(i)) for i in bond_idx]
bond = mol.GetBond(atoms[0], atoms[1])
return bond
def generate_index(mol, labeled_atoms):
"""
Generate SMILES with labeled atoms
Parameters
----------
mol : oechem.OEMol
Must have atom indices that correspond to labeled atoms
labeled_atoms : tuple of ints
ints should be -1 of atom map
Returns
-------
labeled SMILES
"""
for a in mol.GetAtoms():
if not a.GetMapIdx() - 1 in labeled_atoms:
a.SetMapIdx(0)
for i, l in enumerate(labeled_atoms):
a = mol.GetAtom(oechem.OEHasMapIdx(l + 1))
a.SetMapIdx(i + 1)
return oechem.OEMolToSmiles(mol)
#for i in range(chunk):
# for j in range(6)
extra = n % (plots - 2)
for i in range(int(chunk)):
for j in range(plots - 2):
try:
key = keys[(plots - 2) * i + j]
except IndexError:
continue
figure = plt.subplot2grid((3, 2), (0, 0), rowspan=2)
img = mpimg.imread('{}_mapped.png'.format(ki))
imgplot = plt.imshow(img, interpolation='none')
plt.xticks([])
plt.yticks([])
bond = bond_order_wiberg[key]
atom_1 = molecule_charged.GetAtom(oechem.OEHasMapIdx(key[0]))
atom_2 = molecule_charged.GetAtom(oechem.OEHasMapIdx(key[1]))
bond_oe = molecule_charged.GetBond(atom_1, atom_2)
wiberg_oe = bond_oe.GetData('WibergBondOrder')
if j == 0:
plt.subplot2grid((3, 2), (0, 1))
#plt.(bond_order_wiberg[key], label='Wiberg_psi4', kde=True)
plt.hist(bond_order_wiberg[key],
label='Wiberg_psi4',
alpha=1.0)
plt.hist(bond_order_mayer[key],
label='Mayer_psi4',
alpha=1.0)
plt.vlines(wiberg_oe,
ymin=0,
ymax=len(bond_order_wiberg[key]) / 2.5,
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 visualize_mols(smiles,
fname,
rows,
cols,
bond_idx,
wbos,
colors,
align_to=0,
circle=None):
"""
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))
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
if i == 3:
hcolor = oechem.OERed
else:
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_Default, 24,
oedepict.OEAlignment_Default, oechem.OEBlack)
bond_label = oedepict.OEHighlightLabel("{:.2f}".format(wbos[i]),
hcolor)
bond_label.SetFontScale(4.0)
bond_label.SetFont(font)
# generate circle
atom_bond_set_circle = oechem.OEAtomBondSet()
if circle is not None:
color = oechem.OEColor(*colors[i])
highlight = oedepict.OEHighlightByCogwheel(color)
highlight.SetBallRadiusScale(5.0)
for m in circle:
print(m)
if m == 1:
continue
atom = mol.GetAtom(oechem.OEHasMapIdx(m))
print(atom)
atom_bond_set_circle.AddAtom(atom)
for bond_tuple in itertools.combinations(circle, 2):
bond_test = get_bond(mol, bond_tuple)
if bond_test:
atom_bond_set_circle.AddBond(bond_test)
#highlight.SetColor(color)
oedepict.OEAddHighlighting(disp, highlight, atom_bond_set_circle)
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 add_one_bond(molecule, atoms, bonds, functional_groups, ring_systems,
target_bond, heuristic):
bond_atom_1 = molecule.GetAtom(oechem.OEHasMapIdx(target_bond[0]))
bond_atom_2 = molecule.GetAtom(oechem.OEHasMapIdx(target_bond[1]))
atoms_to_add = []
sort_by_1 = []
sort_by_2 = []
sort_by = []
for m_idx in atoms:
a = molecule.GetAtom(oechem.OEHasMapIdx(m_idx))
if a is None:
print('{} is none'.format(m_idx))
continue
for nbr in a.GetAtoms():
nbr_m_idx = nbr.GetMapIdx()
if not nbr.IsHydrogen() and not nbr_m_idx in atoms:
b = molecule.GetBond(a, nbr)
atoms_to_add.append((nbr_m_idx, (m_idx, nbr_m_idx)))
if heuristic == 'wbo':
sort_by.append(b.GetData('WibergBondOrder'))
reverse = True
elif heuristic == 'path_length':
sort_by_1.append(oechem.OEGetPathLength(bond_atom_1, nbr))
sort_by_2.append(oechem.OEGetPathLength(bond_atom_2, nbr))
#sort_by.append(oechem.OEGetPathLength(bond_atom, nbr))
reverse = False
else:
raise ValueError(
'Only wbo and path_lenght are supported heuristics')
if heuristic == 'path_length':
min_1 = min(sort_by_1)
min_2 = min(sort_by_2)
if min_1 < min_2:
sort_by = sort_by_1
elif min_2 < min_1:
sort_by = sort_by_2
elif min_1 == min_2:
# Find the equivalent atoms and take the one with higher WBO
indices = []
for l in [sort_by_1, sort_by_2]:
indices.extend([i for i, x in enumerate(l) if x == min_1])
atoms_to_add = [atoms_to_add[i] for i in indices]
for a, b in atoms_to_add:
a1 = molecule.GetAtom(oechem.OEHasMapIdx(b[0]))
a2 = molecule.GetAtom(oechem.OEHasMapIdx(b[1]))
bond = molecule.GetBond(a1, a2)
sort_by.append(bond.GetData('WibergBondOrder'))
reverse = True
sorted_atoms = [
a for _, a in sorted(zip(sort_by, atoms_to_add), reverse=reverse)
]
a = molecule.GetAtom(oechem.OEHasMapIdx(sorted_atoms[0][0]))
if 'ringsystem' in a.GetData():
ring_idx = a.GetData('ringsystem')
atoms.update(ring_systems[ring_idx][0])
bonds.update(ring_systems[ring_idx][1])
if 'fgroup' in a.GetData():
fgroup = a.GetData('fgroup')
atoms.update(functional_groups[fgroup][0])
bonds.update(functional_groups[fgroup][1])
atoms.add(sorted_atoms[0][0])
bonds.add(sorted_atoms[0][1])
return atoms, bonds
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()
cmiles_ids = cmiles.get_molecule_ids(smiles, strict=False)
mapped_smiles = cmiles_ids[
'canonical_isomeric_explicit_hydrogen_mapped_smiles']
qcarchive_mols = [
cmiles.utils.mol_to_map_ordered_qcschema(conf, mapped_smiles)
for conf in conformers.GetConfs()
]
job_idx = cmiles.utils.to_canonical_label(smiles, torsion)
# Map torsion indices to canonical ordered mapped SMILES
mol_copy = oechem.OEMol(oemol)
oechem.OEAddExplicitHydrogens(mol_copy)
cmiles._cmiles_oe.canonical_order_atoms(mol_copy)
dih = []
for m_idx in torsion:
atom = mol_copy.GetAtom(oechem.OEHasMapIdx(m_idx + 1))
dih.append(atom.GetIdx())
torsion_dict[job_idx] = {
'initial_molecules': qcarchive_mols,
'dihedral': [dih],
'grid': [15],
'cmiles_identifiers': cmiles_ids
}
if mol not in keep_track:
keep_track[mol] = {}
if bond not in keep_track[mol]:
keep_track[mol][bond] = {}
keep_track[mol][bond][frag] = job_idx
frag = 'pfizer'
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)
continue
if a1.IsHalogen() or a2.IsHalogen():
continue
if bond.GetOrder() > 1:
continue
if bond.IsInRing():
continue
key = (a1.GetMapIdx(), a2.GetMapIdx())
if key not in frag_with_bond and tuple(reversed(key)) not in frag_with_bond:
frag_with_bond[key] = {}
r_bonds.append(key)
#r_bonds = [(b.GetBgn().GetMapIdx(), b.GetEnd().GetMapIdx()) for b in oemol.GetBonds() if b.IsRotor()]
for b in r_bonds:
terminal = False
# check if it's terminal
bond = oemol.GetBond(oemol.GetAtom(oechem.OEHasMapIdx(b[0])), oemol.GetAtom(oechem.OEHasMapIdx(b[1])))
if not bond.IsRotor():
# This is terminal
terminal = True
reverse = tuple(reversed(b))
if b not in oe_wbo_deserialized[frag]:
# Try reverse
bo = oe_wbo_deserialized[frag][reverse]
else:
bo = oe_wbo_deserialized[frag][b]
if terminal:
frag_key = frag + '_term'
else:
frag_key = frag
try:
frag_with_bond[b][frag_key] = bo
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 get_bond(mol, bond_idx):
atoms = [mol.GetAtom(oechem.OEHasMapIdx(i)) for i in bond_idx]
bond = mol.GetBond(atoms[0], atoms[1])
return bond
def generate_constraint_opt_input(qc_molecule, dihedrals, maximum_rotation=30, interval=5, filename=None):
"""
Parameters
----------
qc_molecule
dihedrals
Returns
-------
QCFractal optimization jobs input
"""
from openeye import oechem
optimization_jobs = {}
tagged_smiles = qc_molecule['identifiers']['canonical_isomeric_explicit_hydrogen_mapped_smiles']
mol = oechem.OEMol()
oechem.OESmilesToMol(mol, tagged_smiles)
atom_map = get_atom_map(mol, tagged_smiles)
coords = chemi.from_mapped_xyz_to_mol_idx_order(qc_molecule['geometry'], atom_map)
# convert coord to Angstrom
coords = coords * utils.BOHR_2_ANGSTROM
conf = mol.GetConfs().next()
conf.SetCoords(oechem.OEFloatArray(coords))
# new molecule for setting dihedral angles
mol_2 = oechem.OEMol(mol)
conf_2 = mol_2.GetConfs().next()
coords_2 = oechem.OEFloatArray(conf_2.GetMaxAtomIdx()*3)
conf.GetCoords(coords_2)
mol_2.DeleteConfs()
interval = radians(interval)
max_rot = radians(maximum_rotation)
for dihedral in dihedrals:
#j = 0
dih_idx = dihedrals[dihedral]
tor = []
for i in dih_idx:
a = mol.GetAtom(oechem.OEHasMapIdx(i+1))
tor.append(a)
dih_angle = oechem.OEGetTorsion(conf, tor[0], tor[1], tor[2], tor[3])
for i, angle in enumerate(np.arange(dih_angle-max_rot, dih_angle+max_rot, interval)):
newconf = mol.NewConf(coords_2)
oechem.OESetTorsion(newconf, tor[0], tor[1], tor[2], tor[3], angle)
#new_angle = oechem.OEGetTorsion(newconf, tor[0], tor[1], tor[2], tor[3])
# if new_angle == dih_angle:
# j += 1
# if j > 1:
# # One equivalent angle should be generated.
# logger().warning("Openeye did not generate a new conformer for torsion and angle {} {}. Will not generate"
# "qcfractal optimizaiton input".format(dih_idx, angle))
# break
if filename:
pdb = oechem.oemolostream("{}_{}.pdb".format(filename, i))
oechem.OEWritePDBFile(pdb, newconf)
symbols, geometry = chemi.to_mapped_geometry(newconf, atom_map)
qc_molecule = copy.deepcopy(qc_molecule)
qc_molecule['geometry'] = geometry
qc_molecule['symbols'] = symbols
degree = degrees(angle)
optimization_jobs['{}_{}'.format(dih_idx, int(round(degree)))] = {
'type': 'optimization_input',
'initial_molecule': qc_molecule,
'dihedral': dih_idx,
'constraints': {
"set": [{
"type": "dihedral",
"indices": dih_idx,
"value": degree
}]
}
}
return optimization_jobs