def compress(self, clustering, workspace_handler, trajectory_handler,
matrix_handler):
representatives = []
compression_type = self.parameters.get_value("type",
default_value="KMEDOIDS")
pdb_name = self.parameters.get_value("file",
default_value="compressed")
if compression_type == "RANDOM":
representatives = self.__naive_compression(clustering,
matrix_handler)
elif compression_type == "KMEDOIDS":
representatives = self.__kmedoids_compression(
clustering, matrix_handler)
else:
print "[ERROR Compressor::compress] The compression type does not exist (%s)" % (
self.type)
return save_representatives(
representatives,
pdb_name,
workspace_handler,
trajectory_handler,
do_merged_files_have_correlative_models=True,
write_frame_number_instead_of_correlative_model_number=False,
keep_remarks=(lambda params: params['keep_remarks']
if 'keep_remarks' in params else False)(
self.parameters))
def test_save_representatives(self):
representatives = [1,5]
pdbs = ["data/pdb1.pdb", "data/pdb2.pdb", "data/pdb3.pdb"]
file_path = save_representatives(representatives,
"representatives.pdb",
{"results":"data/","tmp":"data/"},
pdbs,
do_merged_files_have_correlative_models = False,
write_frame_number_instead_of_correlative_model_number = False)
self.assertEqual("".join(open(file_path,"r").readlines()), merged_1_5_correlative)
file_path = save_representatives(representatives,
"representatives.pdb",
{"results":"data/","tmp":"data/"},
pdbs,
do_merged_files_have_correlative_models = False,
write_frame_number_instead_of_correlative_model_number = True)
self.assertEqual("".join(open(file_path,"r").readlines()), merged_1_5)
def test_extract_prototypes(self):
self.fail("TODO: Update Test")
prototypes = [2,26,48,56,100]
open("data/prototypes.pdb","w").write(proto_pdb)
file_path = save_representatives([prototypes[3]],
"prototype.pdb",
{"results":"data/","tmp":"data/"},
["data/prototypes.pdb"],
do_merged_files_have_correlative_models = False,
write_frame_number_instead_of_correlative_model_number = True)
print "".join(open(file_path,"r").readlines())
