def getStructuralClusters(data,
threshold,
minClusterSize,
minClusterSaveSize=0,
minMolSize=3,
minSaveSDFsize=0,
numThreads=1,
timeout=20):
""" just the clustering
returns a list (of clusters)
of lists (which contain the smiles string of the cluster members)
"""
clusters = []
isSuccess = False
tries = 0
while (not isSuccess and tries < 10):
tries += 1
sdf_tempName = dataUtilities.makeTempSDF(data, smilesAsName=1)
# create tempdir for usage as 6) outputpath
temp_dir = tempfile.mkdtemp(prefix="AZorangeTMP_")
# call clustering routine
# Example command line call; gspan files are available in the same folder as the jar executable
#java -jar structuralClustering.jar /home/girschic/proj/AZ/SAR/631.sdf 0.5 3 0 5 /home/girschic/proj/test/ . 2 20
jarpath = os.path.join(AZOC.STRUCTCLUSTDIR, 'structuralClustering.jar')
opt = '-jar ' + jarpath + ' ' + sdf_tempName + ' ' + str(
threshold) + ' ' + str(minMolSize) + ' ' + str(
minClusterSaveSize) + ' ' + str(
minClusterSize) + ' ' + temp_dir + '/ ' + str(
AZOC.STRUCTCLUSTDIR) + ' ' + str(
numThreads) + ' ' + str(timeout)
cmd = 'java ' + opt
p = Popen(cmd, shell=True, close_fds=True, stdout=PIPE)
stdout = p.communicate()
# parse output
outfile = os.path.join(temp_dir, 'output_clusters.txt')
try:
if os.path.isfile(outfile):
output = open(outfile, 'r')
# 1,CCC(C)NC(=O)CSC1=NC2=C(C=CC(=C2)OCC)C=C1C#N COC1=CC2=C(C=C1)N=C(C(=C2)C#N)SCC(=O)NC3=CC=C(C=C3)S(=O)(=O)N4CCCC4 CCC1=C(N=C2C=C3C(=CC2=C1)OCO3)SCC(=O)NC4=NOC(=C4)C
for line in output:
tmp = line.strip()
split = tmp.partition(',')
smilesList = split[2].split('\t')
clusters.append(smilesList)
else:
print str(outfile) + " does not exist!"
continue
except IOError as (errno, strerror):
print "I/O error({0}): {1}".format(errno, strerror)
continue
shutil.rmtree(temp_dir)
isSuccess = True
def test_mkTMPfile(self):
"""Test if temporary SDF files can be written """
import tempfile
from subprocess import Popen, PIPE
from cinfony import rdk
sdf_mols = dataUtilities.makeTempSDF(self.data)
cmd = 'cat ' + sdf_mols + ' | grep \'\$\$\$\$\' | wc'
p = Popen(cmd, shell=True, close_fds=True, stdout=PIPE)
stdout = p.communicate()
counts = stdout[0].strip().split()
self.assertEqual(counts[0].strip(),'100')
self.assertEqual(counts[1].strip(),'100')
self.assertEqual(counts[2].strip(),'500')
def getStructuralClusters(data, threshold, minClusterSize, minClusterSaveSize = 0, minMolSize = 3, minSaveSDFsize = 0, numThreads=1, timeout=20):
""" just the clustering
returns a list (of clusters)
of lists (which contain the smiles string of the cluster members)
"""
clusters = []
isSuccess = False
tries = 0
while (not isSuccess and tries < 10):
tries += 1
sdf_temp = dataUtilities.makeTempSDF(data, smilesAsName=1)
# create tempdir for usage as 6) outputpath
temp_dir = tempfile.mkdtemp(prefix="AZorangeTMP_")
# call clustering routine
# Example command line call; gspan files are available in the same folder as the jar executable
#java -jar structuralClustering.jar /home/girschic/proj/AZ/SAR/631.sdf 0.5 3 0 5 /home/girschic/proj/test/ . 2 20
jarpath = os.path.join(AZOC.STRUCTCLUSTDIR,'structuralClustering.jar')
opt = '-jar ' + jarpath + ' ' + sdf_temp.name + ' ' + str(threshold) + ' ' + str(minMolSize) + ' ' + str(minClusterSaveSize) + ' ' + str(minClusterSize) + ' ' + temp_dir + '/ ' + str(AZOC.STRUCTCLUSTDIR) + ' ' + str(numThreads) + ' ' + str(timeout)
cmd = 'java ' + opt
p = Popen(cmd, shell=True, close_fds=True, stdout=PIPE)
stdout = p.communicate()
# parse output
outfile = os.path.join(temp_dir,'output_clusters.txt')
try:
if os.path.isfile(outfile):
output = open(outfile, 'r')
# 1,CCC(C)NC(=O)CSC1=NC2=C(C=CC(=C2)OCC)C=C1C#N COC1=CC2=C(C=C1)N=C(C(=C2)C#N)SCC(=O)NC3=CC=C(C=C3)S(=O)(=O)N4CCCC4 CCC1=C(N=C2C=C3C(=CC2=C1)OCO3)SCC(=O)NC4=NOC(=C4)C
for line in output:
tmp = line.strip()
split = tmp.partition(',')
smilesList = split[2].split('\t')
clusters.append(smilesList)
else:
print str(outfile) + " does not exist!"
continue
except IOError as (errno, strerror):
print "I/O error({0}): {1}".format(errno, strerror)
continue
shutil.rmtree(temp_dir)
sdf_temp.close()
isSuccess = True
