def _testformula(self, num):
smile1, sum_forms = self.formulas[num]
conv = smiles.converter()
mols = conv.read_text(smile1)
for i, mol in enumerate(mols):
self.assert_(i < len(sum_forms))
self.assertEqual(str(mol.get_formula_dict()), sum_forms[i])
def stereo2():
sms = ["C\C=C\C", "C\C=C/C"]
c = smiles.converter()
c.configuration['R_GENERATE_COORDS'] = True
for i, sm in enumerate(sms):
m = c.read_text(sm)[0]
print m.stereochemistry
def stereo2():
sms = ["C\C=C\C","C\C=C/C"]
c = smiles.converter()
c.configuration['R_GENERATE_COORDS'] = True
for i,sm in enumerate( sms):
m = c.read_text( sm)[0]
print m.stereochemistry
def _testformula(self, num):
def create_st_sum(st):
symbols = [a.symbol for a in (st.references[0], st.references[-1])]
symbols.sort()
return tuple(symbols + [st.value == st.SAME_SIDE and 1 or -1])
# round 1
smile1 = self.formulas[num]
conv = smiles.converter()
mols = conv.read_text(smile1)
self.assertEqual(len(mols), 1)
mol = mols[0]
sts1 = [create_st_sum(st) for st in mol.stereochemistry]
# round 2
mol.stereochemistry = []
mol.detect_stereochemistry_from_coords()
sts2 = [create_st_sum(st) for st in mol.stereochemistry]
for stsum in sts2:
if not stsum in sts1:
# not necessarily an error, we must count changes
changes = 0
for (v1, v2) in zip(stsum, sts1[0]):
if v1 != v2:
changes += 1
self.assertEqual(changes % 2, 0)
else:
self.assertEqual((stsum in sts1), True)
def test_rings_in_disconnected_mol():
import smiles
sc = smiles.converter()
mol = smiles.text_to_mol( "c1ccccc1.c1ccccc1.c1ccccc1CC=C")
mol.remove_zero_order_bonds()
print mol, mol.is_connected()
print [len( c) for c in mol.get_smallest_independent_cycles_e()]
def _testformula(self, num):
smile1, sum_forms = self.formulas[num]
conv = smiles.converter()
mols = conv.read_text( smile1)
for i,mol in enumerate( mols):
self.assert_( i < len( sum_forms))
self.assertEqual( str( mol.get_formula_dict()), sum_forms[i])
def test_rings_in_disconnected_mol():
import smiles
sc = smiles.converter()
mol = smiles.text_to_mol("c1ccccc1.c1ccccc1.c1ccccc1CC=C")
mol.remove_zero_order_bonds()
print mol, mol.is_connected()
print[len(c) for c in mol.get_smallest_independent_cycles_e()]
def _testformula(self, num):
def create_st_sum( st):
symbols = [a.symbol for a in (st.references[0],st.references[-1])]
symbols.sort()
return tuple( symbols + [st.value==st.SAME_SIDE and 1 or -1])
# round 1
smile1 = self.formulas[num]
conv = smiles.converter()
mols = conv.read_text( smile1)
self.assertEqual( len( mols), 1)
mol = mols[0]
sts1 = [create_st_sum( st) for st in mol.stereochemistry]
# round 2
mol.stereochemistry = []
mol.detect_stereochemistry_from_coords()
sts2 = [create_st_sum( st) for st in mol.stereochemistry]
for stsum in sts2:
if not stsum in sts1:
# not necessarily an error, we must count changes
changes = 0
for (v1,v2) in zip( stsum, sts1[0]):
if v1 != v2:
changes += 1
self.assertEqual( changes % 2, 0)
else:
self.assertEqual( (stsum in sts1), True)
def stereo():
sms = ["C\C=C\C","C\C=C/C"]
c = smiles.converter()
c.configuration['R_GENERATE_COORDS'] = True
for i,sm in enumerate( sms):
fname = "pokus%d.mol" % i
m = c.read_text( sm)[0]
print [(a.x,a.y) for a in m.vertices]
def test2(self):
"""test reactions with some empty parts"""
c = smiles.converter()
reacts = c.read_text("C=C.[H][H]>>CC")
self.assertEqual(len(reacts), 1)
react = reacts[0]
self.assertEqual(len(react.reagents), 0)
self.assertEqual(len(react.reactants), 2)
self.assertEqual(len(react.products), 1)
def _testformula(self, num):
smile1, charges = self.formulas[num]
conv = smiles.converter()
mols = conv.read_text(smile1)
comp_charges = [mol.charge for mol in mols]
comp_charges.sort()
charges = list(charges)
charges.sort()
self.assertEqual(comp_charges, charges)
def test2(self): """test reactions with some empty parts""" c = smiles.converter() reacts = c.read_text( "C=C.[H][H]>>CC") self.assertEqual( len( reacts), 1) react = reacts[0] self.assertEqual( len( react.reagents), 0) self.assertEqual( len( react.reactants), 2) self.assertEqual( len( react.products), 1)
def _testformula(self, num): smile1, charges = self.formulas[num] conv = smiles.converter() mols = conv.read_text( smile1) comp_charges = [mol.charge for mol in mols] comp_charges.sort() charges = list( charges) charges.sort() self.assertEqual( comp_charges, charges)
def _testformula(self, num): smile1, directions = self.formulas[num] conv = smiles.converter() mols = conv.read_text( smile1) self.assertEqual( len( mols), 1) mol = mols[0] sts = [st.value==st.SAME_SIDE and 1 or -1 for st in mol.stereochemistry] sts.sort() sts = tuple( sts) self.assertEqual( sts, directions)
def stereo():
sms = ["C\C=C\C", "C\C=C/C"]
c = smiles.converter()
c.configuration['R_GENERATE_COORDS'] = True
for i, sm in enumerate(sms):
fname = "pokus%d.mol" % i
m = c.read_text(sm)[0]
print[(a.x, a.y) for a in m.vertices]
f = file(fname, "w")
molfile.mol_to_file(m, f)
def test_sdf_processing():
import gzip
import molfile, smiles
m = molfile.converter()
m2 = smiles.converter()
f = gzip.open("00000001_00025000.sdf.gz", "r")
for mol in m.read_file(f):
mol.remove_unimportant_hydrogens()
mols = mol.get_disconnected_subgraphs()
print m2.mols_to_text(mols)
f.close()
def test_sdf_processing():
import gzip
import molfile, smiles
m = molfile.converter()
m2 = smiles.converter()
f = gzip.open("00000001_00025000.sdf.gz","r")
for mol in m.read_file( f):
mol.remove_unimportant_hydrogens()
mols = mol.get_disconnected_subgraphs()
print m2.mols_to_text( mols)
f.close()
def _testformula(self, num):
smile1, directions = self.formulas[num]
conv = smiles.converter()
mols = conv.read_text(smile1)
self.assertEqual(len(mols), 1)
mol = mols[0]
sts = [
st.value == st.SAME_SIDE and 1 or -1 for st in mol.stereochemistry
]
sts.sort()
sts = tuple(sts)
self.assertEqual(sts, directions)
def _testformula(self, num):
smile1, (explicit_hs, occupied_v, free_v) = self.formulas[num]
conv = smiles.converter()
mols = conv.read_text(smile1)
self.assertEqual(len(mols), 1)
mol = mols[0]
ns = [v for v in mol.vertices if v.symbol == 'N']
self.assertEqual(len(ns), 1)
n = ns[0]
self.assertEqual(n.explicit_hydrogens, explicit_hs)
self.assertEqual(n.free_valency, free_v)
self.assertEqual(n.occupied_valency, occupied_v)
def _testformula(self, num): smile1, (explicit_hs, occupied_v, free_v) = self.formulas[num] conv = smiles.converter() mols = conv.read_text( smile1) self.assertEqual( len( mols), 1) mol = mols[0] ns = [v for v in mol.vertices if v.symbol == 'N'] self.assertEqual( len( ns), 1) n = ns[0] self.assertEqual( n.explicit_hydrogens, explicit_hs) self.assertEqual( n.free_valency, free_v) self.assertEqual( n.occupied_valency, occupied_v)
def test1(self): """tests handling of reactions by the SMILES reader on a preparation of methyl-formate""" c = smiles.converter() reacts = c.read_text( "O=CO.CO>[H+]>O=COC.O") self.assertEqual( reacts, c.result) self.assertEqual( c.last_status, c.STATUS_OK) self.assertEqual( len( reacts), 1) react = reacts[0] self.assertEqual( len( react.reactants), 2) self.assertEqual( len( react.reactants[0].molecule.atoms), 3) self.assertEqual( len( react.reactants[1].molecule.atoms), 2) self.assertEqual( len( react.reagents[0].molecule.atoms), 1) self.assertEqual( len( react.products[0].molecule.atoms), 4) self.assertEqual( len( react.products[1].molecule.atoms), 1) self.assertEqual( str( react.products[0].molecule.get_formula_dict()), "C2H4O2")
def test1(self):
"""tests handling of reactions by the SMILES reader on a preparation of methyl-formate"""
c = smiles.converter()
reacts = c.read_text("O=CO.CO>[H+]>O=COC.O")
self.assertEqual(reacts, c.result)
self.assertEqual(c.last_status, c.STATUS_OK)
self.assertEqual(len(reacts), 1)
react = reacts[0]
self.assertEqual(len(react.reactants), 2)
self.assertEqual(len(react.reactants[0].molecule.atoms), 3)
self.assertEqual(len(react.reactants[1].molecule.atoms), 2)
self.assertEqual(len(react.reagents[0].molecule.atoms), 1)
self.assertEqual(len(react.products[0].molecule.atoms), 4)
self.assertEqual(len(react.products[1].molecule.atoms), 1)
self.assertEqual(str(react.products[0].molecule.get_formula_dict()),
"C2H4O2")
def smiles_from_db():
import structure_database
import time, sys
c = smiles.converter()
c.configuration['R_GENERATE_COORDS'] = True
i = 0
errors, ok = 0, 0
t = time.time()
for hit in structure_database.get_compounds_from_database():
i += 1
try:
mol = c.read_text( hit[3])
except:
print >> sys.stderr, "CRASH:", hit[3]
errors += 1
else:
ok += 1
if i % 100 == 0:
tm = time.time() - t
print "%d, %d ok, %d crashes; %.1f per second" % (i, ok, errors, i/tm)
def _testformula(self, num):
def create_st_sum( st):
symbols = [a.symbol for a in (st.references[0],st.references[-1])]
symbols.sort()
return tuple( symbols + [st.value==st.SAME_SIDE and 1 or -1])
# round 1
smile1 = self.formulas[num]
conv = smiles.converter()
mols = conv.read_text( smile1)
self.assertEqual( len( mols), 1)
mol = mols[0]
sts1 = [create_st_sum( st) for st in mol.stereochemistry]
# round 2
smile2 = conv.mols_to_text( [mol])
mols = conv.read_text( smile1)
self.assertEqual( len( mols), 1)
mol = mols[0]
sts2 = [create_st_sum( st) for st in mol.stereochemistry]
for stsum in sts2:
self.assertEqual( (stsum in sts1), True)
def smiles_from_db():
import structure_database
import time, sys
c = smiles.converter()
c.configuration['R_GENERATE_COORDS'] = True
i = 0
errors, ok = 0, 0
t = time.time()
for hit in structure_database.get_compounds_from_database():
i += 1
try:
mol = c.read_text(hit[3])
except:
print >> sys.stderr, "CRASH:", hit[3]
errors += 1
else:
ok += 1
if i % 100 == 0:
tm = time.time() - t
print "%d, %d ok, %d crashes; %.1f per second" % (i, ok, errors,
i / tm)
def _testformula(self, num):
def create_st_sum(st):
symbols = [a.symbol for a in (st.references[0], st.references[-1])]
symbols.sort()
return tuple(symbols + [st.value == st.SAME_SIDE and 1 or -1])
# round 1
smile1 = self.formulas[num]
conv = smiles.converter()
mols = conv.read_text(smile1)
self.assertEqual(len(mols), 1)
mol = mols[0]
sts1 = [create_st_sum(st) for st in mol.stereochemistry]
# round 2
smile2 = conv.mols_to_text([mol])
mols = conv.read_text(smile1)
self.assertEqual(len(mols), 1)
mol = mols[0]
sts2 = [create_st_sum(st) for st in mol.stereochemistry]
for stsum in sts2:
self.assertEqual((stsum in sts1), True)
def stereo_from_coords2():
f = file("cis_trans_cycles.mol", "r")
mol = molfile.file_to_mol(f)
f.close()
c = smiles.converter()
print c.mols_to_text([mol])
def test_empty_smiles(self):
conv = smiles.converter()
for text in ("", " "):
mols = conv.read_text("")
self.assertEqual(mols, [])
def test_empty_smiles( self):
conv = smiles.converter()
for text in ("", " "):
mols = conv.read_text( "")
self.assertEqual( mols, [])
def update_coords(self):
self.ff.UpdateCoordinates(self._amol.OBMol)
for patom in self._amol:
oatom = self._patom_idx2oatom[patom.idx]
oatom.coords = patom.coords
if __name__ == "__main__":
import time
pmol = pybel.readstring("smi", "CC(=O)O")
omol = PybelConverter.pybel_to_oasa_molecule(pmol)
print(omol)
import smiles
c = smiles.converter()
print(c.mols_to_text([omol]))
#print(get_supported_input_formats())
#print(get_supported_output_formats())
if False:
import molfile
with open("tbu-benzen.mol", 'r') as f:
mol = molfile.file_to_mol(f)
print(PybelConverter.oasa_to_pybel_molecule(mol))
t = time.time()
ff = ForceFieldOptimizer(mol)
gen = ff.conjugate_gradients()
def update_coords( self):
self.ff.UpdateCoordinates( self._amol.OBMol)
for patom in self._amol:
oatom = self._patom_idx2oatom[ patom.idx]
oatom.coords = patom.coords
if __name__ == "__main__":
import time
pmol = pybel.readstring("smi", "CC(=O)O")
omol = PybelConverter.pybel_to_oasa_molecule( pmol)
print(omol)
import smiles
c = smiles.converter()
print(c.mols_to_text([omol]))
#print(get_supported_input_formats())
#print(get_supported_output_formats())
if False:
import molfile
with open("tbu-benzen.mol", 'r') as f:
mol = molfile.file_to_mol(f)
print(PybelConverter.oasa_to_pybel_molecule(mol))
t = time.time()
ff = ForceFieldOptimizer( mol)
gen = ff.conjugate_gradients()
def stereo_from_coords2():
f = file( "cis_trans_cycles.mol", "r")
mol = molfile.file_to_mol( f)
f.close()
c = smiles.converter()
print c.mols_to_text( [mol])