def chemicalSimilarityOpenBabel(a,b):
from cinfony import pybel
#print a
#print b
mol1 = pybel.readstring("smi", a)
mol2 = pybel.readstring("smi", b)
return mol1.calcfp('maccs') | mol2.calcfp('maccs')
def read_fragment(self, name=None, fmt=None, handle=None,
zero_to_origin=True):
"""Read a molecular structure from a file. Guess at the file type from
extension if caller does not supply explicit fmt. If file handle is
provided, read data from it. Otherwise open file name for reading.
:param name: file to open
:type name : str
:param fmt: optional OpenBabel format code e.g. "xyz"
:type fmt : str
:param zero_to_origin: translate geometry to put atom 0 at origin
:type zero_to_origin : bool
:return: molecular fragment
:rtype : Fragment
"""
if not fmt:
try:
fmt = name.rsplit(".", 1)[-1]
except (IndexError, AttributeError):
msg = "No fmt given for {0} and unable to guess from file extension".format(repr(name))
if handle is None:
molecule = pybel.readfile(fmt, name).next()
else:
data = handle.read()
molecule = pybel.readstring(fmt, data)
fragment = Fragment(molecule)
if zero_to_origin:
fragment.set_zero_to_origin()
return fragment
def write(self, fmt):
"""Write all fragments into a single molecular system, by way of an
intermediate fused xyz. There might be a better way to do this,
but it's not obvious.
There may be strange results trying to write systems containing
multiple fragments as a linear format like SMILES or InChI
:param fmt: final format to write, e.g. "mopin" or "pdb"
:type fmt : str
"""
natoms = len(self.atoms)
xyzs = []
for f in self.fragments:
#clip header and get right to the atom geometry
xyz = f.write("xyz").strip().split("\n")[2:]
xyzs.append("\n".join(xyz))
geoblock = "\n".join(xyzs)
fused = "{0}\n\n{1}\n".format(natoms, geoblock)
reread = pybel.readstring("xyz", fused)
reread.title = self.title
written = reread.write(fmt)
return written
def write(self, fmt):
"""Write all fragments into a single molecular system, by way of an
intermediate fused xyz. There might be a better way to do this,
but it's not obvious.
There may be strange results trying to write systems containing
multiple fragments as a linear format like SMILES or InChI
:param fmt: final format to write, e.g. "mopin" or "pdb"
:type fmt : str
"""
natoms = len(self.atoms)
xyzs = []
for f in self.fragments:
#clip header and get right to the atom geometry
xyz = f.write("xyz").strip().split("\n")[2:]
xyzs.append("\n".join(xyz))
geoblock = "\n".join(xyzs)
fused = "{0}\n\n{1}\n".format(natoms, geoblock)
reread = pybel.readstring("xyz", fused)
reread.title = self.title
written = reread.write(fmt)
return written
def getFingerprint(a):
from cinfony import pybel
#print a
#print b
mol1 = pybel.readstring("smi", a)
return mol1.calcfp('maccs').bits
def make_fragment(self, representation, fmt="smiles"):
"""Take a linear representation of a molecule and add a title with
IUPAC and SMILES designations. Convert a linear molecular specification
to a 3D form.
:param representation: linear molecule encoding
:type representation : str
:param fmt: smiles, inchi, etc. (default smiles)
:type fmt : str
:return: 3D-form molecular fragment
:rtype: Fragment
"""
molecule = pybel.readstring(fmt, representation)
molecule.make3D()
fragment = Fragment(molecule)
fragment.set_zero_to_origin()
return fragment
def make_fragment(self, representation, fmt="smiles"):
"""Take a linear representation of a molecule and add a title with
IUPAC and SMILES designations. Convert a linear molecular specification
to a 3D form.
:param representation: linear molecule encoding
:type representation : str
:param fmt: smiles, inchi, etc. (default smiles)
:type fmt : str
:return: 3D-form molecular fragment
:rtype: Fragment
"""
molecule = pybel.readstring(fmt, representation)
molecule.make3D()
fragment = Fragment(molecule)
fragment.set_zero_to_origin()
return fragment
def read_fragment(self,
name=None,
fmt=None,
handle=None,
zero_to_origin=True):
"""Read a molecular structure from a file. Guess at the file type from
extension if caller does not supply explicit fmt. If file handle is
provided, read data from it. Otherwise open file name for reading.
:param name: file to open
:type name : str
:param fmt: optional OpenBabel format code e.g. "xyz"
:type fmt : str
:param zero_to_origin: translate geometry to put atom 0 at origin
:type zero_to_origin : bool
:return: molecular fragment
:rtype : Fragment
"""
if not fmt:
try:
fmt = name.rsplit(".", 1)[-1]
except (IndexError, AttributeError):
msg = "No fmt given for {0} and unable to guess from file extension".format(
repr(name))
if handle is None:
molecule = pybel.readfile(fmt, name).next()
else:
data = handle.read()
molecule = pybel.readstring(fmt, data)
fragment = Fragment(molecule)
if zero_to_origin:
fragment.set_zero_to_origin()
return fragment
#!/usr/bin/env python
from subprocess import Popen, PIPE
from cinfony import pybel
import math, sys
#smiles = raw_input("Enter the SMILES string for BBB permeability: ")
smiles = str(sys.argv[1])
entry = ""
try:
# Reads the molecule into pybel
pybelMol = pybel.readstring("smi", smiles);
pybelFP = pybelMol.calcfp()
pybelProperties = str(pybelFP).split(",")
properties = pybelProperties
properties = [p.strip() for p in properties]
for current in properties:
fixed = 0.0;
# Take log_2(property) (May change later)
if current != "0":
fixed = math.log(float(current), 2)
# Tack onto entry
entry = entry + str(fixed) + " "
command = "java Predictor " + entry
p1 = Popen([command], stdout=PIPE, shell=True)