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# $Id$
#
# Copyright (C) 2003-2005 Rational Discovery LLC
# All Rights Reserved
#
""" This is a rough coverage test of the python wrapper
it's intended to be shallow, but broad
"""
import os
import pickle
import unittest
from rdkit import RDConfig
from rdkit.RDLogger import logger
logger = logger()
from rdkit import Chem, DataStructs
from rdkit.Chem import FragmentCatalog
class TestCase(unittest.TestCase):
def setUp(self):
self.fName = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FragCatalog', 'test_data',
'funcGroups.txt')
self.smiName = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FragCatalog', 'test_data',
'mols.smi')
def test0Params(self):
fparams = FragmentCatalog.FragCatParams(1, 6, self.fName, 1.0e-8)
ctype = fparams.GetTypeString()
self.assertEqual(ctype, "Fragment Catalog Parameters")
self.assertEqual(fparams.GetLowerFragLength(), 1)
self.assertEqual(fparams.GetUpperFragLength(), 6)
ngps = fparams.GetNumFuncGroups()
self.assertEqual(ngps, 15)
for i in range(ngps):
mol = fparams.GetFuncGroup(i)
def test1Catalog(self):
fparams = FragmentCatalog.FragCatParams(1, 6, self.fName, 1.0e-8)
fcat = FragmentCatalog.FragCatalog(fparams)
self.assertEqual(fcat.GetNumEntries(), 0)
self.assertEqual(fcat.GetFPLength(), 0)
nparams = fcat.GetCatalogParams()
self.assertEqual(nparams.GetLowerFragLength(), 1)
self.assertEqual(nparams.GetUpperFragLength(), 6)
def test2Generator(self):
fparams = FragmentCatalog.FragCatParams(1, 6, self.fName, 1.0e-8)
fcat = FragmentCatalog.FragCatalog(fparams)
fgen = FragmentCatalog.FragCatGenerator()
suppl = Chem.SmilesMolSupplier(self.smiName, " ", 0, 1, 0)
for mol in suppl:
nent = fgen.AddFragsFromMol(mol, fcat)
self.assertEqual(fcat.GetNumEntries(), 21)
self.assertEqual(fcat.GetFPLength(), 21)
for id in range(fcat.GetNumEntries()):
self.assertEqual(fcat.GetEntryBitId(id), id)
self.assertEqual(fcat.GetEntryOrder(id), fcat.GetBitOrder(id))
self.assertEqual(fcat.GetEntryDescription(id), fcat.GetBitDescription(id))
self.assertEqual(tuple(fcat.GetEntryFuncGroupIds(id)), tuple(fcat.GetBitFuncGroupIds(id)))
def test3FPgenerator(self):
with open(self.smiName, 'r') as smiF:
smiLines = smiF.readlines()
fparams = FragmentCatalog.FragCatParams(1, 6, self.fName)
fcat = FragmentCatalog.FragCatalog(fparams)
fgen = FragmentCatalog.FragCatGenerator()
suppl = Chem.SmilesMolSupplier(self.smiName, " ", 0, 1, 0)
smiles = []
for mol in suppl:
nent = fgen.AddFragsFromMol(mol, fcat)
smiles.append(Chem.MolToSmiles(mol))
self.assertEqual(fcat.GetNumEntries(), 21)
self.assertEqual(fcat.GetFPLength(), 21)
fpgen = FragmentCatalog.FragFPGenerator()
obits = [3, 2, 3, 3, 2, 3, 5, 5, 5, 4, 5, 6]
obls = [(0, 1, 2), (1, 3), (1, 4, 5), (1, 6, 7), (0, 8), (0, 6, 9), (0, 1, 2, 3, 10),
(0, 1, 2, 8, 11), (1, 3, 4, 5, 12), (1, 4, 5, 13), (1, 3, 6, 7, 14),
(0, 1, 6, 7, 9, 15)]
for i in range(len(smiles)):
smi = smiles[i]
mol = Chem.MolFromSmiles(smi)
fp = fpgen.GetFPForMol(mol, fcat)
if i < len(obits):
self.assertEqual(fp.GetNumOnBits(), obits[i])
obl = fp.GetOnBits()
if i < len(obls):
self.assertEqual(tuple(obl), obls[i])
def test4Serialize(self):
with open(self.smiName, 'r') as smiF:
smiLines = smiF.readlines()
fparams = FragmentCatalog.FragCatParams(1, 6, self.fName)
fcat = FragmentCatalog.FragCatalog(fparams)
fgen = FragmentCatalog.FragCatGenerator()
suppl = Chem.SmilesMolSupplier(self.smiName, " ", 0, 1, 0)
smiles = []
for mol in suppl:
nent = fgen.AddFragsFromMol(mol, fcat)
smiles.append(Chem.MolToSmiles(mol))
self.assertEqual(fcat.GetNumEntries(), 21)
self.assertEqual(fcat.GetFPLength(), 21)
pkl = pickle.dumps(fcat)
fcat2 = pickle.loads(pkl)
self.assertEqual(fcat2.GetNumEntries(), 21)
self.assertEqual(fcat2.GetFPLength(), 21)
fpgen = FragmentCatalog.FragFPGenerator()
for i in range(len(smiles)):
smi = smiles[i]
mol = Chem.MolFromSmiles(smi)
fp1 = fpgen.GetFPForMol(mol, fcat)
fp2 = fpgen.GetFPForMol(mol, fcat2)
self.assertEqual(fp1.GetNumOnBits(), fp2.GetNumOnBits())
obl1 = fp1.GetOnBits()
obl2 = fp2.GetOnBits()
self.assertEqual(tuple(obl1), tuple(obl2))
def test5FPsize(self):
with open(self.smiName, 'r') as smiF:
smiLines = smiF.readlines()
fparams = FragmentCatalog.FragCatParams(6, 6, self.fName)
fcat = FragmentCatalog.FragCatalog(fparams)
fgen = FragmentCatalog.FragCatGenerator()
suppl = [Chem.MolFromSmiles('C1CCCOC1O')]
for mol in suppl:
nent = fgen.AddFragsFromMol(mol, fcat)
self.assertEqual(fcat.GetFPLength(), 1)
for i in range(fcat.GetFPLength()):
self.assertEqual(fcat.GetBitOrder(i), 6)
self.assertEqual(fcat.GetBitDescription(i), "C1CC<-O>OCC1")
self.assertEqual(tuple(fcat.GetBitFuncGroupIds(i)), (1, ))
def test6DownEntries(self):
fparams = FragmentCatalog.FragCatParams(1, 6, self.fName, 1.0e-8)
fcat = FragmentCatalog.FragCatalog(fparams)
fgen = FragmentCatalog.FragCatGenerator()
suppl = Chem.SmilesMolSupplier(self.smiName, " ", 0, 1, 0)
for mol in suppl:
nent = fgen.AddFragsFromMol(mol, fcat)
self.assertEqual(fcat.GetNumEntries(), 21)
self.assertEqual(fcat.GetFPLength(), 21)
self.assertEqual(tuple(fcat.GetEntryDownIds(0)), (2, 8, 9, 16))
self.assertEqual(tuple(fcat.GetEntryDownIds(1)), (2, 3, 5, 7))
def test7Issue116(self):
smiList = ['Cc1ccccc1']
suppl = Chem.SmilesMolSupplierFromText('\n'.join(smiList), ',', 0, -1, 0)
fparams = FragmentCatalog.FragCatParams(2, 2, self.fName, 1.0e-8)
cat = FragmentCatalog.FragCatalog(fparams)
fgen = FragmentCatalog.FragCatGenerator()
for mol in suppl:
nent = fgen.AddFragsFromMol(mol, cat)
self.assertEqual(cat.GetFPLength(), 2)
self.assertEqual(cat.GetBitDescription(0), 'ccC')
fpgen = FragmentCatalog.FragFPGenerator()
mol = Chem.MolFromSmiles('Cc1ccccc1')
fp = fpgen.GetFPForMol(mol, cat)
self.assertEqual(fp[0], 1)
self.assertEqual(fp[1], 1)
mol = Chem.MolFromSmiles('c1ccccc1-c1ccccc1')
fp = fpgen.GetFPForMol(mol, cat)
self.assertEqual(fp[0], 0)
self.assertEqual(fp[1], 1)
def test8Issue118(self):
smiList = ['CCN(C(N)=O)N=O']
fName = os.path.join(RDConfig.RDDataDir, 'FunctionalGroups.txt')
suppl = Chem.SmilesMolSupplierFromText('\n'.join(smiList), ',', 0, -1, 0)
fparams = FragmentCatalog.FragCatParams(2, 4, fName, 1.0e-8)
cat = FragmentCatalog.FragCatalog(fparams)
fgen = FragmentCatalog.FragCatGenerator()
for mol in suppl:
nent = fgen.AddFragsFromMol(mol, cat)
self.assertEqual(cat.GetFPLength(), 1)
self.assertEqual(cat.GetBitDescription(0), 'CCN(<-C(=O)N>)<-N=O>')
if __name__ == '__main__':
unittest.main()
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