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get the timing benchmarks working on py3

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This commit is contained in:
Greg Landrum
2015-11-05 03:25:34 +01:00
parent 5992c6fd23
commit b8d25f431f
2 changed files with 7 additions and 7 deletions
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6
Regress/Scripts/new_timings.py
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@@ -14,7 +14,7 @@ if len(sys.argv)>1:
tests[x] = 1
ts = []
mols = []
lines = gzip.open('../Data/znp.50k.smi.gz','rb').readlines()
lines = gzip.open('../Data/znp.50k.smi.gz','rt').readlines()
logger.info('mols from smiles')
nMols=0
nBad=0
@@ -61,7 +61,7 @@ if tests[2]:
ts.append(t2-t1)
if tests[3] or tests[4] or tests[5]:
pattData = gzip.open('../Data/queries.txt.gz','rb').readlines()
pattData = gzip.open('../Data/queries.txt.gz','rt').readlines()
pattData = [x.strip().replace('[H]','').replace('()','') for x in pattData]
logger.info('patterns from smiles')
patts = []
@@ -104,7 +104,7 @@ if tests[6] or tests[7] or tests[8]:
logger.info('reading SMARTS')
patts=[]
t1=time.time()
for line in file('../Data/RLewis_smarts.txt'):
for line in open('../Data/RLewis_smarts.txt'):
line = line.strip()
if line=='' or line[0]=='#':
continue

8
Regress/Scripts/timings.py
View File

@@ -15,7 +15,7 @@ if len(sys.argv)>1:
tests[x] = 1
ts = []
sdData = gzip.open('../Data/mols.1000.sdf.gz','rb').read()
sdData = gzip.open('../Data/mols.1000.sdf.gz','rt').read()
logger.info('mols from sdf')
suppl = Chem.SDMolSupplier()
suppl.SetData(sdData)
@@ -34,7 +34,7 @@ logger.info('Results1: %.2f seconds, %d passed, %d failed'%(t2-t1,nMols,nBad))
ts.append(t2-t1)
if tests[2]:
lines = gzip.open('../Data/mols.1000.txt.gz','rb').readlines()
lines = gzip.open('../Data/mols.1000.txt.gz','rt').readlines()
logger.info('mols from smiles')
nMols=0
nBad=0
@@ -51,7 +51,7 @@ if tests[2]:
ts.append(t2-t1)
if tests[3] or tests[4] or tests[5]:
pattData = gzip.open('../Data/queries.txt.gz','rb').readlines()
pattData = gzip.open('../Data/queries.txt.gz','rt').readlines()
pattData = [x.strip().replace('[H]','').replace('()','') for x in pattData]
logger.info('patterns from smiles')
patts = []
@@ -94,7 +94,7 @@ if tests[6] or tests[7] or tests[8]:
logger.info('reading SMARTS')
patts=[]
t1=time.time()
for line in file('../Data/RLewis_smarts.txt'):
for line in open('../Data/RLewis_smarts.txt'):
line = line.strip()
if line=='' or line[0]=='#':
continue