def ch(x, y):
x = _convert(x)
y = _convert(y)
return g.CritAnd(c, mg.HasNeighbors(h, x, y))
def ipr(atom):
at = _convert(atom)
return g.CritAnd(c, mg.HasNeighbors(me(c), me(c), h, at))
# Dirty trick to silence warnings of confliciting
# modules on the HPC cluster and to silence NumPy
# warnings.
with warnings.catch_warnings():
warnings.simplefilter('ignore')
import molmod.graphs as g
import molmod.molecular_graphs as mg
h = mg.HasAtomNumber(1)
c = mg.HasAtomNumber(6)
n = mg.HasAtomNumber(7)
o = mg.HasAtomNumber(8)
s = mg.HasAtomNumber(16)
p = mg.HasAtomNumber(15)
csp3 = g.CritAnd(c, mg.HasNumNeighbors(4))
csp2 = g.CritAnd(c, mg.HasNumNeighbors(3))
csp = g.CritAnd(c, mg.HasNumNeighbors(2))
def _convert(atom):
try:
return mg.HasAtomNumber(utils.anum(atom))
except:
return atom
def me(atom):
'''
at can be 'C', 'c', 6 or a pattern
'''
def me(atom):
'''
at can be 'C', 'c', 6 or a pattern
'''
at = _convert(atom)
return g.CritAnd(mg.HasNeighbors(h, h, h, at), c)
def _classify(self):
p = OrderedDict()
self.geometry.initiate_match()
p['ph'] = gr.CritAnd(c, g.HasNeighbors(c, c, c))
self.geometry.set_matches(p)
if self.nucleophile == 'OPh':
# find the O just to check which ph was parsed
self.geometry.set_match('o', o)
# wrong phenyl group selected, select the other one
if self.geometry.dist(self.geometry.ph.n, self.geometry.o.n) < 3.0:
self.geometry.set_match('ph',
gr.CritAnd(c, g.HasNeighbors(c, c, c)))
# remove phenyl group to speed up pattern searching
phgroup = self.geometry.closest(6, self.geometry.ph.n, n=2)
phgroup += [
self.geometry.closest(6, i, exclude=[self.geometry.ph.n])
for i in phgroup
]
phgroup += [self.geometry.closest(6, phgroup[-1], exclude=phgroup)]
logging.debug('SixThreeBicyclic._classify(): phenyl group %s' %
(phgroup + [self.geometry.ph.n]))
for i in phgroup:
self.geometry.unparsed.remove(i)
self.geometry.set_match(
'c7',
self.geometry.closest(6,
self.geometry.ph.n,
only=self.geometry.unparsed))
self.geometry.set_match(
'me',
self.geometry.closest(6,
self.geometry.c7.n,
only=self.geometry.unparsed))
self.geometry.set_match(
'nplus',
self.geometry.closest(7,
self.geometry.c7.n,
only=self.geometry.unparsed))
nplus = gr.CritAnd(
n, gr.CritOr(g.HasNeighbors(c, c, c, c), g.HasNeighbors(c, c, c)))
c_nextto_nplus = g.HasNeighbors(nplus, h, h, c)
p['c2'] = g.HasNeighbors(c_nextto_nplus, h, h, c)
p['c3'] = g.HasNeighbors(p['c2'], h, h, c)
p['c4'] = g.HasNeighbors(p['c3'], h, h, c)
p['c1'] = g.HasNeighbors(nplus, h, h, p['c2'])
self.geometry.set_matches(p)
self.geometry.set_match(
'c5',
self.geometry.closest(6,
self.geometry.c4.n,
only=self.geometry.unparsed))
self.geometry.set_match(
'c6',
self.geometry.closest(6,
self.geometry.nplus.n,
only=self.geometry.unparsed))
if self.attacking_atom:
self.geometry.set_match(
'nu',
self.geometry.closest(self.attacking_atom,
self.geometry.c5.n,
only=self.geometry.unparsed))
else:
logging.debug(
'SixThreeBicyclic._classify(): nu not parsed, since no nucleophile was found.'
)