do_append = False
if options.do_append: do_append = options.do_append
simil_metric = 'Dice'
if options.simil: simil_metric = options.simil
outpath = path
outpath_set = False
if options.outpath:
outpath_set = True
outpath = path+options.outpath
# check for sensible input
fp_names = scor.checkFPFile(fp_file)
if not fp_names: raise ValueError('No fingerprints given in', fp_file)
if outpath_set: scor.checkPath(outpath, 'output')
scor.checkSimil(simil_metric)
scor.checkQueryMols(num_query_mols, conf.list_num_query_mols)
# loop over data-set sources
for dataset in conf.set_data.keys():
print dataset
# loop over targets
for target in conf.set_data[dataset]['ids']:
print target
# read in actives and calculate fps
actives = []
for line in gzip.open(inpath_cmp+dataset+'/cmp_list_'+dataset+'_'+str(target)+'_actives.dat.gz', 'r'):
if line[0] != '#':
# structure of line: [external ID, internal ID, SMILES]]
line = line.rstrip().split()
fp_dict = scor.getFPDict(fp_names, line[2])
do_append = False
if options.do_append: do_append = options.do_append
simil_metric = 'Dice'
if options.simil: simil_metric = options.simil
outpath = path
outpath_set = False
if options.outpath:
outpath_set = True
outpath = path + options.outpath
# check for sensible input
fp_names = scor.checkFPFile(fp_file)
if not fp_names: raise ValueError('No fingerprints given in', fp_file)
if outpath_set: scor.checkPath(outpath, 'output')
scor.checkSimil(simil_metric)
scor.checkQueryMols(num_query_mols, conf.list_num_query_mols)
# loop over data-set sources
for dataset in conf.set_data.keys():
print dataset
# loop over targets
for target in conf.set_data[dataset]['ids']:
print target
# read in actives and calculate fps
actives = []
for line in gzip.open(
inpath_cmp + dataset + '/cmp_list_' + dataset + '_' +
str(target) + '_actives.dat.gz', 'r'):
if line[0] != '#':
# structure of line: [external ID, internal ID, SMILES]]