def spectrophores(dataset, overwrite=True):
""" Compute the spectrophores for a dataset """
try:
print '\tSpectrophores'
specs = spec.spectrophores(pybel.readfile('sdf', dataset))
dataset_root, dataset_name = op.split(dataset)
dataset_name = op.splitext(dataset_name)[0]
#numpy.savetxt(op.join(dataset_root, dataset_name + '-ob-spectrophores.csv'),
#specs, fmt='%s %.6f', delimiter=',')
destfile = op.join(dataset_root, dataset_name + '-ob-spectrophores.csv')
if op.exists(destfile) and overwrite==False:
print '%s is already there and not overwriting requested' % destfile
return
else:
if op.exists(destfile) and overwrite==True:
print '%s is already there but overwriting requested' % destfile
os.remove(destfile)
f= open(destfile, 'a')
for molecule in specs:
f.write(molecule[0])
f.write(",")
for i in range(1,49):
f.write(str(molecule[i]))
f.write(",")
f.write("\n")
f.close()
print '\tSpectrophores computed succesfully'
return destfile
except Exception, e:
print 'Damn, there has been a problem computing the spectrophores...'
print 'Research into this...'
print e.message
def spectrophores(dataset):
""" Compute the spectrophores for a dataset """
try:
print '\tSpectrophores'
specs = ob.spectrophores(pybel.readfile('sdf', dataset))
dataset_root, dataset_name = op.split(dataset)
dataset_name = op.splitext(dataset_name)[0]
numpy.savetxt(op.join(dataset_root, dataset_name + '-ob-spectrophores.csv'),
specs, fmt='%.6f', delimiter=',')
print '\tSpectrophores computed succesfully'
except Exception, e:
print 'Damn, there has been a problem computing the pharmacophores...'
print 'Research into this...'
print e.message
