本文整理汇总了Python中frowns.Smiles类的典型用法代码示例。如果您正苦于以下问题：Python Smiles类的具体用法？Python Smiles怎么用？Python Smiles使用的例子？那么, 这里精选的类代码示例或许可以为您提供帮助。
在下文中一共展示了Smiles类的15个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: test2
def test2():
smiles, id = "OC1=C(Cl)C=CC=C1[N+]", 1
mol = Smiles.smilin(smiles)
print mol.cansmiles()
for atom in mol.atoms:
print atom.index示例2: cansmiles
def cansmiles(self) :
"""
affiche en canonical smiles une brique
"""
# sys.stderr.write("Brique.cansmiles: will call molecule.cansmiles() ...\n")
a = self.molecule.cansmiles()
m = Smiles.smilin("".join(re.split("[\[\]+-]","".join(re.split("H[0-9]*",a)))))
return m.cansmiles()示例3: checkSmiles
def checkSmiles(fname):
from frowns import Smiles
try:
fSmiles = open(fname, "r")
lines = fSmiles.readlines()
fSmiles.close()
asmiles = Smiles.smilin(lines[0].split()[0])
return True
except:
return False示例4: test
def test():
from frowns import Smiles
import time
smiles, id = "OC1=C(Cl)C=CC=C1[N+]C2CCC3CC3CCC2", 1
mol = Smiles.smilin(smiles, transforms=[])
t1 = time.time()
for i in range(100):
atoms, bonds = getAtomsBondsInRings(mol)
print (time.time() - t1)/100示例5: test
def test():
from frowns import Smiles
import time
smiles, id = "OC1=C(Cl)C=CC=C1[N+]C2CCC3CC3CCC2", 1
mol = Smiles.smilin(smiles, transforms=[])
assert frerejaqueNumber(mol) == 3
t1 = time.time()
for i in range(100):
frerejaqueNumber(mol)
print (time.time() - t1)/100 示例6: next
def next(self):
if not self.smiles:
return None
smile = self.smiles.pop()
m = Smiles.smilin(smile)
#addCoords(m)
#toplevel = Toplevel(self.tk)
if self.drawer:
self.drawer.frame.pack_forget()
drawer = self.drawer=TkMoleculeDrawer.MoleculeDrawer(self.tk, m, name=smile)
drawer.pack(expand=1, fill=BOTH)示例7: test
def test():
from frowns import Smiles
strings = ["Cl/C(F)=C(Br)/I",
#"Cl\C)(F)=C(Br)\I", <- fix parsing bug
#"Cl\C(\F)=C(/Br)\I",
"Cl\C(F)=C(Br)\I",
"Cl\C(F)=C(Br)/I",
"Cl/C(F)=C(Br)\I"
]
for s in strings:
print s
m = Smiles.smilin(s)
assignStereo(m)示例8: test
def test():
from frowns import Smiles
import time
h = BuildMatcher()
for smi in ["C",
"CC",
"c",
"C(N)O",
"[O]",
"c1ccccc1",
]:
matcher = compile(smi)
print matcher.dump()
smiles = Smiles.smilin(smi)
pathset = matcher.match(smiles)示例9: testPath
def testPath():
from frowns import Smiles
mol = Smiles.smilin("C1CCCC1CCCC2CCCC3CCC3CCC2")
rings = {}
spans = [Path(mol.atoms[0], rings)]
while spans:
new = []
for span in spans:
new += span.next()
if len(rings) == 1:
break
if len(rings) == 1:
break
spans = new
print rings示例10: len
atom.hybrid = SP2
continue
symbol = atom.symbol
hcount = atom.valences[0] - atom.sumBondOrders()
connections = len(atom.bonds) + hcount
charge = atom.charge
if atom.symbol in ["C", "N"] and connections == 2:
charge = ANY
atom.hybrid = _hybrid.get((symbol, connections, charge), "")
#print atom, `atom`, hcount, atom.hybrid
if __name__ == "__main__":
from frowns import Smiles
from frowns.perception import TrustedSmiles, sssr
smiles = "CC(=O)OC1C(N(c2c(CC1c1ccc(OC)cc1)cc(cc2)Oc1ccccc1)CCN(C)C)=O"
smiles = "O=C1NC(N)=NC2=C1N=CNC2"
#smiles = "O=C1C=CC(=O)C=C1"
print smiles
mol = Smiles.smilin(smiles, [sssr.sssr])
getHybridAtoms(mol)
for cycle in mol.cycles:
print [(atom, atom.symbol, atom.hybrid) for atom in cycle.atoms]
示例11:
from frowns import Smiles
print "*"*33
print "benzene with default transforms"
mol = Smiles.smilin("c1ccccc1")
print mol.cansmiles()
print "atoms"
for atom in mol.atoms:
print "\tsymbol %s hcount %s aromatic %s"%(
atom.symbol, atom.hcount, atom.aromatic)
print "bonds"
for bond in mol.bonds:
print "\tbondorder %s, bondtype %s fixed %s"%(
bond.bondorder, bond.bondtype, bond.fixed)
print "*"*33
print "benzene with no transforms"
mol = Smiles.smilin("c1ccccc1", transforms=[])
print mol.cansmiles()
print "atoms"
for atom in mol.atoms:
print "\tsymbol %s hcount %s aromatic %s"%(
atom.symbol, atom.hcount, atom.aromatic)
print "bonds"
for bond in mol.bonds:
print "\tbondorder %s, bondtype %s fixed %s"%(
bond.bondorder, bond.bondtype, bond.fixed)示例12: len
import time
from frowns import Smiles
from frowns import Smarts
mol = Smiles.smilin("CCCCC(C)CCCC(C)CCCCCC(C)C(C)CCCCCC(C)CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCN")
pat = Smarts.compile("C*")
print len(pat.match(mol))
pat2 = Smarts.compile("[#6]")
t1 = time.time()
print len(pat2.match(mol))
t2 = time.time()
print t2-t1
t1 = time.time()
print len(pat2.match(mol))
t2 = time.time()
print t2-t1
print mol.vfgraph
示例13:
from frowns import Smiles
m = Smiles.smilin("N[[email protected]](C)(F)C(=O)O")
print "initial smiles:", m.arbsmiles(isomeric=1)
print "canonical smiles:", m.cansmiles(isomeric=1)
print
m = Smiles.smilin("[[email protected]](C)(F)(O)")
print "initial smiles:", m.arbsmiles(isomeric=1)
print "canonical smiles:", m.cansmiles(isomeric=1)
示例14: generatePaths
def generatePaths(molecule, maxdepth=5,
name_atom=name_atom, name_bond=name_bond,
name_ring_atom=name_ring_atom, name_ring_bond=name_ring_bond,
make_rpath=0):
"""(molecule, maxdepth, *name_atom, *name_bond) -> linear paths
Generate all linear paths through a molecule up to maxdepth
change name_atom and name_bond to name the atoms and bonds
in the molecule
name_atom and name_bond must return a stringable value"""
paths = {}
for atom in molecule.atoms:
_bfswalk(atom, {atom:1}, [name_atom(atom)], [name_ring_atom(atom)], paths, 1, maxdepth,
name_atom, name_bond, name_ring_atom, name_ring_bond, make_rpath)
return paths.keys()
if __name__ == "__main__":
from frowns import Smiles
mol = Smiles.smilin("CCNc1cccc1")
paths = generatePaths(mol)
print len(paths)
print paths
ONE_STRING_PER_PATH = 1
paths = generatePaths(mol)
print len(paths)
print paths
示例15:
from frowns import Smiles
mol = Smiles.smilin("C1CC=1")
print mol.arbsmiles()