def testSaveRead(self):
from decaf import Pharmacophore
from os import remove
filename = "test.p"
self.phar.save(filename)
p_copy = Pharmacophore.read(filename)
self.assertEqual(self.phar.numnodes, p_copy.numnodes)
self.assertEqual(self.phar.nodes, p_copy.nodes)
for i in range(p_copy.numnodes):
for j in range(p_copy.numnodes):
self.assertEqual(self.phar.edges[i, j], p_copy.edges[i, j])
self.assertEqual(self.phar.title, p_copy.title)
self.assertEqual(self.phar.molecules, p_copy.molecules)
remove(filename)
self.assertRaises(IOError, Pharmacophore.read, filename)
self.assertRaises(IOError, Pharmacophore.save, p_copy,
"nonexist/" + filename)
Created on Mon Mar 16 10:11:53 2015
@author: Marta Stepniewska
"""
from pybel import readfile
from decaf import Pharmacophore
from decaf.toolkits.ob import phar_from_mol
from decaf.utils import similarity
from multiprocessing import Process, Manager, cpu_count
from time import sleep
NUM_PROCESSES = cpu_count()
cutoff = 0.8
database = readfile("smi", "all.ism")
model = Pharmacophore.read("model.p")
print "Read model with %s nodes created from %s molecules." % (model.numnodes,
model.molecules)
manager = Manager()
similar = manager.list()
proc = [None] * NUM_PROCESSES
def check_mol(mol):
p = phar_from_mol(mol)
s, c = similarity(model, p)
#print s, c
if s > cutoff:
similar.append((mol.write(), s, c))
def setUp(self):
from decaf import Pharmacophore
self.phars = [Pharmacophore.read(fname) for fname in self.files]