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import os, sys, unittest, doctest
import gzip
from rdkit import RDConfig, rdBase
from rdkit import Chem
from rdkit import __version__
import sys
class TestCase(unittest.TestCase):
def testMultiSmiMolSupplier(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol',
'FileParsers', 'test_data', 'first_200.tpsa.csv')
# fileN = "../FileParsers/test_data/first_200.tpsa.csv"
smiSup = Chem.MultithreadedSmilesMolSupplier(fileN, ",", 0, - 1)
i = 0
while not smiSup.atEnd():
mol = next(smiSup)
if(mol):
i += 1
self.assertTrue(i == 200)
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol',
'FileParsers', 'test_data', 'fewSmi.csv')
# fileN = "../FileParsers/test_data/fewSmi.csv"
smiSup = Chem.MultithreadedSmilesMolSupplier(
fileN, delimiter=",", smilesColumn=1, nameColumn=0, titleLine=0)
names = ["1", "2", "3", "4", "5", "6", "7", "8", "9", "10"]
props = ["34.14", "25.78", "106.51", "82.78", "60.16",
"87.74", "37.38", "77.28", "65.18", "0.00"]
confusedNames = []
confusedProps = []
i = 0
for mol in smiSup:
if mol is not None:
self.assertTrue(mol.HasProp("_Name"))
self.assertTrue(mol.HasProp("Column_2"))
prop = mol.GetProp("Column_2")
name = mol.GetProp("_Name")
confusedProps.append(prop)
confusedNames.append(name)
i += 1
self.assertTrue(i == 10)
self.assertTrue(sorted(confusedNames) == sorted(names))
self.assertTrue(sorted(confusedProps) == sorted(props))
# context manager
confusedNames = []
confusedProps = []
i = 0
with Chem.MultithreadedSmilesMolSupplier(fileN,delimiter=",", smilesColumn=1,
nameColumn=0, titleLine=0) as smiSup:
for mol in smiSup:
if mol is not None:
self.assertTrue(mol.HasProp("_Name"))
self.assertTrue(mol.HasProp("Column_2"))
prop = mol.GetProp("Column_2")
name = mol.GetProp("_Name")
confusedProps.append(prop)
confusedNames.append(name)
i += 1
self.assertTrue(i == 10)
self.assertTrue(sorted(confusedNames) == sorted(names))
self.assertTrue(sorted(confusedProps) == sorted(props))
def testMultiSDMolSupplier(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol',
'FileParsers', 'test_data', 'NCI_aids_few.sdf')
# fileN = "../FileParsers/test_data/NCI_aids_few.sdf"
sdSup = Chem.MultithreadedSDMolSupplier(fileN)
molNames = ["48", "78", "128", "163", "164", "170", "180", "186",
"192", "203", "210", "211", "213", "220", "229", "256"]
confusedMolNames = []
i = 0
for mol in sdSup:
if mol is not None:
confusedMolNames.append(mol.GetProp("_Name"))
i += 1
self.assertTrue(len(molNames) == i)
self.assertTrue(sorted(confusedMolNames) == sorted(molNames))
# context manager
confusedMolNames = []
i = 0
with Chem.MultithreadedSDMolSupplier(fileN) as sdSup:
for mol in sdSup:
if mol is not None:
confusedMolNames.append(mol.GetProp("_Name"))
i += 1
self.assertTrue(len(molNames) == i)
self.assertTrue(sorted(confusedMolNames) == sorted(molNames))
# NOTE these are disabled until we rewrite the code to construct a
# MultithreadedSDMolSupplier from a python stream
@unittest.skip("Skipping construction from stream")
def testMultiSDMolSupplierFromStream(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol',
'FileParsers', 'test_data', 'NCI_aids_few.sdf')
molNames = ["48", "78", "128", "163", "164", "170", "180", "186",
"192", "203", "210", "211", "213", "220", "229", "256"]
# try opening with streambuf
inf = open(fileN,'rb')
if(inf):
gSup = Chem.SDMolSupplierFromStream(inf)
confusedMolNames = []
i = 0
for mol in gSup:
# print("!!",i,file=sys.stderr);sys.stderr.flush()
if(mol):
confusedMolNames.append(mol.GetProp("_Name"))
i += 1
self.assertTrue(len(molNames) == i)
self.assertTrue(sorted(confusedMolNames) == sorted(molNames))
# print("done!",file=sys.stderr);sys.stderr.flush()
# try opening with streambuf
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'NCI_aids_few.sdf.gz')
# try opening with gzip
inf = gzip.open(fileN)
if(inf):
gSup = Chem.SDMolSupplierFromStream(inf)
confusedMolNames = []
i = 0
for mol in gSup:
# print("!",i,file=sys.stderr);sys.stderr.flush()
if(mol):
confusedMolNames.append(mol.GetProp("_Name"))
i += 1
self.assertTrue(len(molNames) == i)
self.assertTrue(sorted(confusedMolNames) == sorted(molNames))
if __name__ == '__main__':
print("Testing Smiles and SD MultithreadedMolSupplier")
unittest.main()
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