def test_ring_substituents(self):
"""Test finding ring substituents"""
tagged_rings, tagged_funcgroup = fragment.tag_molecule(charged)
bond = charged.GetBond(oechem.OEHasBondIdx(8))
next_bond = charged.GetBond(oechem.OEHasBondIdx(10))
ring_idx = next_bond.GetData('ringsystem')
rs_atoms, rs_bonds = fragment._ring_substiuents(
charged, next_bond, bond, tagged_rings, ring_idx, tagged_funcgroup)
self.assertEquals(rs_atoms, {5, 6, 7, 8, 10, 28, 29, 46, 47, 48})
self.assertEquals(rs_bonds, {5, 6, 7, 8, 30, 31, 49, 50, 51})
def test_is_ortho(self):
"""Test if substituent is ortho to rotatable bond"""
rot_bond = charged.GetBond(oechem.OEHasBondIdx(8))
next_bond = charged.GetBond(oechem.OEHasBondIdx(10))
ortho_bond = charged.GetBond(oechem.OEHasBondIdx(30))
self.assertTrue(
fragment._is_ortho(bond=ortho_bond,
rot_bond=rot_bond,
next_bond=next_bond))
other_bond = charged.GetBond(oechem.OEHasBondIdx(31))
self.assertFalse(
fragment._is_ortho(bond=other_bond,
rot_bond=rot_bond,
next_bond=next_bond))
def test_is_fgroup(self):
"""Test is functional group """
tagged_rings, taggged_funcgroup = fragment.tag_molecule(charged)
atom_idx = taggged_funcgroup['amide_0'][0].pop()
bond_idx = taggged_funcgroup['amide_0'][-1].pop()
atom = charged.GetAtom(oechem.OEHasAtomIdx(atom_idx))
bond = charged.GetBond(oechem.OEHasBondIdx(bond_idx))
self.assertTrue(fragment._is_fgroup(taggged_funcgroup, atom))
self.assertTrue(fragment._is_fgroup(taggged_funcgroup, bond))
def test_build_frag(self):
""" Test build fragment """
bond = charged.GetBond(oechem.OEHasBondIdx(2))
tagged_rings, tagged_funcgroup = fragment.tag_molecule(charged)
atoms, bonds = fragment._build_frag(bond, charged, tagged_funcgroup,
tagged_rings)
self.assertEquals(atoms, {0, 1, 2, 3, 4, 5, 6, 41, 42, 44})
self.assertEquals(bonds, {0, 1, 2, 3, 4})
def test_iterate_nbratoms(self):
"""Test iterate neighboring atoms"""
rotor_bond = charged.GetBond(oechem.OEHasBondIdx(2))
beg = rotor_bond.GetBgn()
end = rotor_bond.GetEnd()
tagged_rings, tagged_funcgroup = fragment.tag_molecule(charged)
atoms, bonds = fragment.iterate_nbratoms(charged, rotor_bond, beg, end,
tagged_funcgroup,
tagged_rings)
self.assertEquals(atoms, {0, 2})
self.assertEquals(bonds, {0, 1})
def get_molecule(self):
"""
Extracts the parent molecule this bond is in
Returns
-------
mol: chemper Mol
molecule this bond is stored in
"""
mol = oechem.OEMol(self.bond.GetParent())
self.bond = mol.GetBond(oechem.OEHasBondIdx(self._idx))
return Mol(mol)
def get_bond_by_index(self, idx):
"""
Parameters
----------
idx: ing
bond index
Returns
-------
bond: chemper Bond object
bond with index idx
"""
return Bond(self.mol.GetBond(oechem.OEHasBondIdx(idx)))
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 tag_conjugated_bond(mol, tautomers=None, tag=None, threshold=1.05):
"""
Add conjugated bond data tag. If the bond order is above the threshold, this tag will be True, otherwise it will be
False
Parameters
----------
mol: OEMol
tautomers: list of OEMols, optional, Default None
If a list is provided, the conjugation tag will be true if the bond in any of the set of molecules is double.
The list should consist of resonance structures of the molecules. You can get that from oequacpac.EnumerateTautomres
tag: str, optional, Default None
If provided, will use that bond order. Options are WibergBondOrder, Wiberg_psi4, Mayer_psi4
threshold: int, optional, Default is 1.05
The fractional bond order threshold above which the bond will be considered conjugated.
Returns
-------
atom_indices: list of atom indices in conjugated bonds.
"""
atom_indices = []
for bond in mol.GetBonds():
resonance = False
if tautomers is not None:
for tmol in tautomers:
t_bond = tmol.GetBond(oechem.OEHasBondIdx(bond.GetIdx()))
if t_bond.GetOrder() > 1:
resonance = True
break
elif bond.GetData()[tag] >= threshold:
resonance = True
# Add tag to bond
conj_tag = oechem.OEGetTag("conjugated")
bond.SetData(conj_tag, resonance)
if resonance:
a1 = bond.GetBgnIdx()
a2 = bond.GetEndIdx()
atom_indices.extend([a1, a2])
return atom_indices
# 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 openeye import oechem
# @ <SNIPPET-OEADDMOLS>
dstmol = oechem.OEGraphMol()
oechem.OESmilesToMol(dstmol, 'c1ccccc1 benzene')
srcmol = oechem.OEGraphMol()
oechem.OESmilesToMol(srcmol, 'c1cnccc1 pyridine')
amap, bmap = oechem.OEAddMols(dstmol, srcmol, "+")
print("%s %s" % (oechem.OEMolToSmiles(dstmol), dstmol.GetTitle()))
print(" ".join(str(a) for a in amap))
print(" ".join(str(b) for b in bmap))
# @ </SNIPPET-OEADDMOLS>
# @ <SNIPPET-OEADDMOL-ATOMMAP>
srcatom = srcmol.GetAtom(oechem.OEHasAtomicNum(oechem.OEElemNo_N))
dstatom = amap[srcatom.GetIdx()]
# @ </SNIPPET-OEADDMOL-ATOMMAP>
# @ <SNIPPET-OEADDMOL-BONDMAP>
srcbond = srcmol.GetBond(oechem.OEHasBondIdx(0))
dstbond = bmap[srcbond.GetIdx()]
# @ </SNIPPET-OEADDMOL-BONDMAP>
# @ </SNIPPET>
def get_bond_by_index(self, idx):
return Bond(self.mol.GetBond(oechem.OEHasBondIdx(idx)))
def get_molecule(self):
mol = oechem.OEMol(self.bond.GetParent())
self.bond = mol.GetBond(oechem.OEHasBondIdx(self._idx))
return Mol(mol)
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)