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# $Id: rough_test.py 997 2009-02-25 06:12:43Z glandrum $
#
# 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 unittest,os
from rdkit import RDConfig
from rdkit.RDLogger import logger
logger=logger()
from rdkit import Chem
from rdkit.Chem import FragmentCatalog
from rdkit import DataStructs
import cPickle
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()
assert(ctype == "Fragment Catalog Parameters")
assert(fparams.GetLowerFragLength() == 1)
assert(fparams.GetUpperFragLength() == 6)
ngps = fparams.GetNumFuncGroups()
assert 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)
assert(fcat.GetNumEntries() == 0)
assert( fcat.GetFPLength() == 0)
nparams = fcat.GetCatalogParams()
assert(nparams.GetLowerFragLength() == 1)
assert(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)
assert fcat.GetNumEntries()==21
assert fcat.GetFPLength()==21
for id in range(fcat.GetNumEntries()):
assert fcat.GetEntryBitId(id)==id
assert fcat.GetEntryOrder(id)==fcat.GetBitOrder(id)
assert fcat.GetEntryDescription(id)==fcat.GetBitDescription(id)
assert tuple(fcat.GetEntryFuncGroupIds(id))==tuple(fcat.GetBitFuncGroupIds(id))
def test3FPgenerator(self) :
smiLines = open(self.smiName,'r').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))
assert fcat.GetNumEntries()==21
assert fcat.GetFPLength()==21,fcat.GetFPLength()
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):
assert fp.GetNumOnBits()==obits[i],'%s: %s'%(smi,str(fp.GetOnBits()))
obl = fp.GetOnBits()
if i < len(obls):
assert tuple(obl)==obls[i],'%s: %s'%(smi,obl)
def test4Serialize(self) :
smiLines = open(self.smiName,'r').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))
assert fcat.GetNumEntries()==21
assert fcat.GetFPLength()==21,fcat.GetFPLength()
pkl = cPickle.dumps(fcat)
fcat2 = cPickle.loads(pkl)
assert fcat2.GetNumEntries()==21
assert fcat2.GetFPLength()==21,fcat2.GetFPLength()
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)
assert fp1.GetNumOnBits()==fp2.GetNumOnBits()
obl1 = fp1.GetOnBits()
obl2 = fp2.GetOnBits()
assert tuple(obl1)==tuple(obl2)
def test5FPsize(self) :
smiLines = open(self.smiName,'r').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)
assert fcat.GetFPLength()==1
for i in range(fcat.GetFPLength()):
assert fcat.GetBitOrder(i)==6
assert fcat.GetBitDescription(i)=="C1CCOC<-O>C1",fcat.GetBitDescription(i)
assert 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)
assert fcat.GetNumEntries()==21
assert fcat.GetFPLength()==21
assert tuple(fcat.GetEntryDownIds(0))==(2,8,9,16)
assert 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)
assert cat.GetFPLength()==2
assert cat.GetBitDescription(0)=='ccC'
fpgen = FragmentCatalog.FragFPGenerator()
mol = Chem.MolFromSmiles('Cc1ccccc1')
fp = fpgen.GetFPForMol(mol,cat)
assert fp[0]
assert fp[1]
mol = Chem.MolFromSmiles('c1ccccc1-c1ccccc1')
fp = fpgen.GetFPForMol(mol,cat)
assert not fp[0]
assert fp[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)
assert cat.GetFPLength()==1
assert cat.GetBitDescription(0)=='CCN(<-C(=O)N>)<-N=O>'
if __name__ == '__main__':
unittest.main()
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