parser.add_argument("--verbose", action="store_true",
help="Verbose logging")
opts = parser.parse_args()
store = DescriptaStore(opts.storage)
if opts.seperator == ",":
writer = csv.writer(sys.stdout)
elif opts.seperator == "\t":
writer = csv.writer(sys.stdout, dialiect=csv.excel_tab)
if opts.keep_missing_descriptors:
opts.keep_calculatedflags = True
if opts.output_name:
writer.writerow(['Name'] + store.getDescriptorNames(opts.keep_calculatedflags))
else:
writer.writerow(store.getDescriptorNames(opts.keep_calculatedflags))
if not opts.namefile:
indices = range(len(store))
else:
def idx_getter(namefile):
for line in open(namefile):
try:
idx = store.lookupName(line.strip())
yield idx
except:
logging.warning("Name %r not found in store", line.strip())
continue
indices = idx_getter(opts.namefile)
import sys
from rdkit import rdBase
rdBase.DisableLog("rdApp.*")
parser = argparse.ArgumentParser()
parser.add_argument("storage",
help="directory in which to store the descriptors")
parser.add_argument("storage2",
help="directory in which to store the descriptors")
opts = parser.parse_args()
store1 = DescriptaStore(opts.storage)
store2 = DescriptaStore(opts.storage2)
if store1.getDescriptorNames() != store2.getDescriptorNames():
logging.warning("Storages are not compatible, columns are different")
s1 = set(store1.getDescriptorNames())
s2 = set(store2.getDescriptorNames())
if s1 == s2:
logging.warning("Columns are the same but reordered")
else:
logging.warning("Extra columns in store1:\n\t%s", "\n\t".join(s1-s2))
logging.warning("Extra columns in store2:\n\t%s", "\n\t".join(s2-s1))
for i,(a,b) in enumerate(zip(store1.getDescriptorNames(),
store2.getDescriptorNames())):
if a != b:
logging.warning("First differing element at index %s (%s != %s)", i,a,b)
break