def setUp(self):
self.defaultAbbrevs = rdAbbreviations.GetDefaultAbbreviations()
self.defaultLinkers = rdAbbreviations.GetDefaultLinkers()
self.customLinkers = rdAbbreviations.ParseLinkers(
'''PEG3 *OCCOCCOCC* PEG3
Pent *CCCCC*
Cy *C1CCC(*)CC1 Cy''')
def setUp(self):
self.defaultAbbrevs = rdAbbreviations.GetDefaultAbbreviations()
self.defaultLinkers = rdAbbreviations.GetDefaultLinkers()
self.customLinkers = rdAbbreviations.ParseLinkers('''PEG3 *OCCOCCOCC* PEG3
Pent *CCCCC*
Cy *C1CCC(*)CC1 Cy''')
self.parseMapping = lambda mapping: tuple(map(int, mapping.strip('[],').split(',')))
def testGithub3692(self):
defaults = rdAbbreviations.GetDefaultAbbreviations()
self.assertIsNotNone(defaults[0].mol)
lbls = [x.label for x in defaults]
self.assertIn('CO2Et', lbls)
idx = lbls.index('CO2Et')
self.assertEqual(Chem.MolToSmiles(defaults[idx].mol), '*C(=O)OCC')
def _drawHelper(mol, drawer, **kwargs):
tgt = request.get_json()
if tgt is None:
tgt = request.values
sanit = _stringtobool(tgt.get('sanitize', True))
kekulize = _stringtobool(tgt.get('kekulize', True))
for arg in ('highlightAtomColors', 'highlightBondColors'):
if arg not in kwargs:
tmp = _loadJSONParam(tgt.get(arg, None))
if tmp:
for k in list(tmp):
tmp[int(k)] = tuple(tmp[k])
del tmp[k]
kwargs[arg] = tmp
for arg in ('highlightAtoms', 'highlightBonds'):
if arg not in kwargs:
tmp = _loadJSONParam(tgt.get(arg, None))
if tmp:
kwargs[arg] = tmp
if 'legend' not in kwargs:
kwargs['legend'] = tgt.get('legend', '')
# if 'lw' not in kwargs and 'lw' in request.values:
# kwargs['lw'] = int(request.values['lw'])
if 'highlightSubstruct' not in kwargs:
if 'highlightColor' not in kwargs:
hcolor = _loadJSONParam(tgt.get('highlightColor', None))
if hcolor:
highlightColor = tuple(hcolor)
else:
highlightColor = None
else:
highlightColor = kwargs['highlightColor']
del kwargs['higlightColor']
if _stringtobool(tgt.get('highlightSubstruct', False)) or \
'smiles_highlight' in tgt or \
'smarts_highlight' in tgt or \
'mol_highlight' in tgt:
qmol = _queryfromrequest(suffix='_highlight')
if qmol is not None:
qMatches = mol.GetSubstructMatches(qmol)
highlights = kwargs.get('highlightAtoms', [])
if highlightColor is not None:
highlightBonds = kwargs.get('highlightBonds', [])
else:
highlightBonds = None
for entry in qMatches:
if highlightColor is not None:
had = kwargs.get('highlightAtomColors', {})
for v in entry:
had[v] = highlightColor
kwargs['highlightAtomColors'] = had
hbd = kwargs.get('highlightBondColors', {})
emap = dict(enumerate(entry))
for bond in qmol.GetBonds():
mbond = mol.GetBondBetweenAtoms(
emap[bond.GetBeginAtomIdx()],
emap[bond.GetEndAtomIdx()])
highlightBonds.append(mbond.GetIdx())
hbd[mbond.GetIdx()] = highlightColor
kwargs['highlightBondColors'] = hbd
highlights.extend(list(entry))
if highlights:
kwargs['highlightAtoms'] = highlights
if highlightBonds is not None:
kwargs['highlightBonds'] = highlightBonds
from rdkit.Chem.Draw import rdDepictor
rdDepictor.SetPreferCoordGen(True)
# print(Chem.MolToMolBlock(mc))
drawo = drawer.drawOptions()
for opt, default in (('dummiesAreAttachments', False),
('comicMode', False), ('addAtomIndices', False),
('addBondIndices', False), ('isotopeLabels', True),
('addStereoAnnotation',
False), ('explicitMethyl',
False), ('includeChiralFlagLabel', False),
('simplifiedStereoGroupLabel', False)):
setattr(drawo, opt, _stringtobool(tgt.get(opt, default)))
if drawo.comicMode:
drawo.fontFile = os.path.join(RDConfig.RDDataDir, "Fonts",
"ComicNeue-Regular.ttf")
if drawo.addStereoAnnotation:
Chem.FindMolChiralCenters(mol,
force=True,
useLegacyImplementation=False)
if 'backgroundColor' in tgt:
tmp = _loadJSONParam(tgt.get('backgroundColor', None))
drawo.SetBackgroundColor(tuple)
if _stringtobool(tgt.get('atomIndices', False)):
drawo.addAtomIndices = True
if _stringtobool(tgt.get('bondIndices', False)):
drawo.addBondIndices = True
if _stringtobool(tgt.get('useBW', False)):
drawo.useBWAtomPalette()
if _stringtobool(tgt.get('useGrid', '0')):
frags = []
for frag in Chem.GetMolFrags(mol, asMols=True):
frags.append(
rdMolDraw2D.PrepareMolForDrawing(frag,
kekulize=kekulize & sanit,
addChiralHs=sanit))
drawer.DrawMolecules(frags)
elif _stringtobool(tgt.get('asRxn', False)):
drawer.DrawReaction(mol)
else:
mc = rdMolDraw2D.PrepareMolForDrawing(mol,
kekulize=kekulize & sanit,
addChiralHs=sanit)
mc.SetProp("_Name", "temp")
if _stringtobool(tgt.get('collapseAbbreviations',False)) and \
len(Chem.GetMolSubstanceGroups(mc)):
mc = rdAbbreviations.CondenseAbbreviationSubstanceGroups(mc)
elif _stringtobool(tgt.get('findAbbreviations', False)):
mc = rdAbbreviations.CondenseMolAbbreviations(
mc,
rdAbbreviations.GetDefaultAbbreviations(),
maxCoverage=float(tgt.get('maxAbbreviationCoverage', 0.4)))
drawer.DrawMolecule(mc, **kwargs)
drawer.FinishDrawing()