def cansmiles(self, isomeric=0):
if isomeric: draw = Traverse.drawIsomeric
else: draw = Traverse.draw
if self.dirty:
# XXX FIX ME
# Move equivalence_class setter outside?
# recompute the equivalence classes
for atom in self.atoms:
atom.equiv_class = compute_equiv_class(atom)
Disambiguate.FreedDisambiguate(self)
self._canonical, self.canonical_list = Traverse.draw(self)
self.dirty = 0
if isomeric:
return Traverse.drawIsomeric(self)[0]
return self._canonical
def cansmiles(self, isomeric=0):
if isomeric: draw = Traverse.drawIsomeric
else: draw = Traverse.draw
if self.dirty:
# XXX FIX ME
# Move equivalence_class setter outside?
# recompute the equivalence classes
for atom in self.atoms:
atom.equiv_class = compute_equiv_class(atom)
Disambiguate.FreedDisambiguate(self)
self._canonical, self.canonical_list = Traverse.draw(self)
self.dirty = 0
if isomeric:
return Traverse.drawIsomeric(self)[0]
return self._canonical
def arbsmarts(self, isomeric=0):
# XXX FIX ME
# compute canonicalization smarts
# without hydrogens and charges
canonical, canonical_list = Traverse.drawSmarts(self)
return canonical
def arbsmarts(self, isomeric=0):
# XXX FIX ME
# compute canonicalization smarts
# without hydrogens and charges
canonical, canonical_list = Traverse.drawSmarts(self)
return canonical
def test():
from frowns import Smiles
import RingDetection
import sssr as sssr2
import time
from frowns.Canonicalization import Disambiguate, Traverse
##mol = Smiles.smilin("C12C3C4C1C5C4C3C25CCCCCC12C3C4C1C5C4C3C25")
##mol1 = Smiles.smilin("C1O[CH]1C2=CC=CC=C2",
## transforms = [])
##print mol1.cansmiles()
smiles = "COC(=O)[CH]1C2CCC(CC2)[CH]1C(=O)OCC"
smiles = "CC1(C)[CH]2CC[CH](CC(O)=O)[CH]1C2"
smiles = "C[CH]1C(=O)O[CH]2CCN3CC=C(COC(=O)[C](C)(O)[C]1(C)O)[CH]23"
#smiles = "CC1=CC(=O)C=CC1=O"
smiles = "NC1=CC2=C(C=C1)C(=O)C3=C(C=CC=C3)C2=O"
smiles = "COC1=CC2=C(C=C1OC)[C]34CCN5CC6=CCO[CH]7CC(=O)N2[CH]3[CH]7[CH]6C[CH]45.OS(O)(=O)=O"
mol1 = Smiles.smilin(smiles, transforms=[])
print mol1.cansmiles()
NUM = 1
t1 = time.time()
for i in range(NUM):
sssr(mol1)
t2 = time.time()
print(t2 - t1) / NUM
symbols = []
for atom in mol1.atoms:
symbols.append(atom.symbol)
for atom in mol1.atoms:
atom.symbol += ".%s." % atom.index
atom.symorder = mol1.atoms.index(atom)
index = 0
for cycle in mol1.cycles:
print cycle.atoms
print cycle.bonds
for atom in cycle.atoms:
atom.symbol += "<%s>" % index
index += 1
print Traverse.draw(mol1)[0]
for atom, symbol in zip(mol1.atoms, symbols):
atom.symbol = symbol
for atom in mol1.atoms:
atom.symbol += ".%s." % atom.index
atom.symorder = mol1.atoms.index(atom)
t1 = time.time()
for i in range(NUM):
RingDetection.sssr(mol1)
t2 = time.time()
print(t2 - t1) / NUM
index = 0
for cycle in mol1.cycles:
print cycle.atoms
print cycle.bonds
for atom in cycle.atoms:
atom.symbol += "<%s>" % index
index += 1
print Traverse.draw(mol1)[0]
def test():
from frowns import Smiles
import RingDetection
import sssr as sssr2
import time
from frowns.Canonicalization import Disambiguate, Traverse
##mol = Smiles.smilin("C12C3C4C1C5C4C3C25CCCCCC12C3C4C1C5C4C3C25")
##mol1 = Smiles.smilin("C1O[CH]1C2=CC=CC=C2",
## transforms = [])
##print mol1.cansmiles()
smiles = "COC(=O)[CH]1C2CCC(CC2)[CH]1C(=O)OCC"
smiles = "CC1(C)[CH]2CC[CH](CC(O)=O)[CH]1C2"
smiles = "C[CH]1C(=O)O[CH]2CCN3CC=C(COC(=O)[C](C)(O)[C]1(C)O)[CH]23"
#smiles = "CC1=CC(=O)C=CC1=O"
smiles = "NC1=CC2=C(C=C1)C(=O)C3=C(C=CC=C3)C2=O"
smiles = "COC1=CC2=C(C=C1OC)[C]34CCN5CC6=CCO[CH]7CC(=O)N2[CH]3[CH]7[CH]6C[CH]45.OS(O)(=O)=O"
mol1 = Smiles.smilin(smiles,
transforms = [])
print mol1.cansmiles()
NUM = 1
t1 = time.time()
for i in range(NUM):
sssr(mol1)
t2 = time.time()
print (t2-t1)/NUM
symbols = []
for atom in mol1.atoms:
symbols.append(atom.symbol)
for atom in mol1.atoms:
atom.symbol += ".%s."%atom.index
atom.symorder = mol1.atoms.index(atom)
index = 0
for cycle in mol1.cycles:
print cycle.atoms
print cycle.bonds
for atom in cycle.atoms:
atom.symbol += "<%s>"%index
index += 1
print Traverse.draw(mol1)[0]
for atom, symbol in zip(mol1.atoms, symbols):
atom.symbol = symbol
for atom in mol1.atoms:
atom.symbol += ".%s."%atom.index
atom.symorder = mol1.atoms.index(atom)
t1 = time.time()
for i in range(NUM):
RingDetection.sssr(mol1)
t2 = time.time()
print (t2-t1)/NUM
index = 0
for cycle in mol1.cycles:
print cycle.atoms
print cycle.bonds
for atom in cycle.atoms:
atom.symbol += "<%s>"%index
index += 1
print Traverse.draw(mol1)[0]
