def gen_dist_matrix(plane_type, atg_or_atb, res_or_tri):
data_dir = os.path.join(data237_fp175_padded_root, "%s-%s-%s" % (plane_type, atg_or_atb, res_or_tri))
dataloader = make_dataloader(data_dir, make_single_line_converter(None))
c_id_list = complex_ids(data_dir)
complex_pairwise_calc(c_id_list, dataloader, corr_coef, callback=callback)
def gen_pairwise_dist(res_or_tri):
data_dir = os.path.join(data480_root, "fp_aaindex_if_padded" if res_or_tri == "res" else "fp_aaindex_if_padded_tri")
dataloader = make_dataloader(data_dir, make_single_line_converter(None))
c_id_list = complex_ids(data_dir)
complex_pairwise_calc(c_id_list, dataloader, corr_coef, callback=callback)
def main_480():
import os
from ve.util.load_pdb import complex_ids
from ve.config import data480_root
from data480 import fp370_atg_dataloader, fp370_atb_dataloader
fp_dir = os.path.join(data480_root, "fp_370_atg")
cids = complex_ids(fp_dir)
cids = map(lambda x: x.split(",")[0], cids)
complex_pairwise_calc(cids, fp370_atb_dataloader, corr_coef, callback = callback)
def test_exception_list_empty(self):
"""test for the case no error are encountered,that is to say the exception list is empty"""
complex_id_list = range(1,4) #1~3
dataloader = lambda d: d
calc_func = lambda d1,d2: d1 + d2
_, actual = complex_pairwise_calc(complex_id_list, dataloader, calc_func, symmetry=False)
expected = []
self.assertEqual(actual, expected)
def test_silly_asymmetrical_case(self):
"""very silly and asymmetrical test case"""
complex_id_list = ["a", "b", "c"]
dataloader = lambda s: s
calc_func = lambda c1,c2: c1 + c2
actual,_ = complex_pairwise_calc(complex_id_list, dataloader, calc_func, callback = None, symmetry=False)
expected = [("a", "b", "ab"), ('a', 'c', 'ac'), ('b', 'a', 'ba'), ('b', 'c', 'bc'), ('c', 'a', 'ca'), ('c', 'b', 'cb'),
('a','a','aa'), ('b','b','bb'), ('c','c','cc')]
self.assertEqual(actual, expected)
def test_exception_list_nonempty(self):
"""test for the case errors are encountered,that is to say the exception list is NOT empty"""
complex_id_list = map(float, range(0,3)) #0.0 ~ 2.0
dataloader = lambda d: d
calc_func = lambda d1,d2: d1 / d2 #DivisionByZeroError
actual_result, actual_exception = complex_pairwise_calc(complex_id_list, dataloader, calc_func, symmetry=False)
expected_exception = [(1,0),(2,0),(0,0)]
expected_result = [(0.0, 1.0, 0.0), (0.0, 2.0, 0.0), (1.0, 2.0, 0.5), (2.0, 1.0, 2.0), (1.0, 1.0, 1.0), (2.0, 2.0, 1.0)]
self.assertEqual(actual_result, expected_result)
self.assertEqual(actual_exception, expected_exception)
def test_silly_symmetrical_case(self):
"""very silly and symmetrical test case"""
complex_id_list = range(1,4) #1~3
dataloader = lambda d: d
calc_func = lambda d1,d2: d1 + d2
actual,_ = complex_pairwise_calc(complex_id_list, dataloader, calc_func, callback = None, symmetry=True)
expected = [(1, 2, 3), (1, 3, 4), (2, 3, 5),
(1, 1, 2), (2, 2, 4), (3, 3, 6)]
self.assertEqual(actual, expected)
def test_callback_with_return_values(self):
"""similar to silly and symmetrical test case,
but with calback
"""
complex_id_list = range(1,4) #1~3
dataloader = lambda d: d
calc_func = lambda d1,d2: d1 + d2
callback = lambda c1,c2,v: (c1,c2,v+1)
actual,_ = complex_pairwise_calc(complex_id_list, dataloader, calc_func, callback = callback, symmetry=True)
expected = [(1, 2, 4), (1, 3, 5), (2, 3, 6),
(1, 1, 3), (2, 2, 5), (3, 3, 7)]
self.assertEqual(actual, expected)
def main_237():
filter_list = set(["1UWX_AP"])
c_id_list = set(complex_ids()) - filter_list
# complex_pairwise_calc(c_id_list, src.fp370_atg_dataloader, corr_coef, callback = callback)
complex_pairwise_calc(c_id_list, src.fp370_atb_dataloader, corr_coef, callback = callback)
