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import unittest,os
from ost.db import LinearIndexer
from ost.db import LinearCharacterContainer
from ost.db import LinearPositionContainer
from ost import geom
def ComparePosList(l1, l2):
if len(l1)!= len(l2):
return False
eps = 0.0001
for i in range(len(l1)):
if geom.Distance(l1[i],l2[i]) > eps:
return False
return True
class TestLinearDB(unittest.TestCase):
def testLinearIndexer(self):
indexer = LinearIndexer()
self.assertEqual(indexer.GetNumResidues(), 0)
# check whether error is thrown when list parameters do not have
# same length
self.assertRaises(Exception, indexer.AddAssembly, "HELLOU",
["AA", "B"], [20, 33, 1])
# correct it and add first assembly
indexer.AddAssembly("HELLOU", ["AA", "B", "CCC"], [20, 33, 1])
# check whether according entry has been added
self.assertEqual(indexer.GetAssemblies(), ["HELLOU"])
self.assertEqual(indexer.GetNumResidues(), 54)
# check whether error get thrown when the same assembly is added again
# and directly add another assembly
self.assertRaises(Exception, indexer.AddAssembly, "HELLOU",
["AA", "B", "CCC"], [20, 33, 1])
indexer.AddAssembly("HELLOUYOU", ["X", "Y", "ZZZ"], [10, 26, 20])
# check whether according entry has been added. we need to sort the
# output since the GetAssemblies function gives no guarantee about ordering
entries = indexer.GetAssemblies()
entries.sort()
self.assertEqual(entries, ["HELLOU", "HELLOUYOU"])
self.assertEqual(indexer.GetNumResidues(), 110)
# check the GetDataRange functions and all their errors when
# inexistent data is accessed
self.assertRaises(Exception, indexer.GetDataRange, "HELL", "CCC")
self.assertRaises(Exception, indexer.GetDataRange, "HELLOU", "CC")
self.assertEqual(indexer.GetDataRange("HELLOU", "CCC"), (53,54))
self.assertRaises(Exception, indexer.GetDataRange, "HELL")
self.assertEqual(indexer.GetDataRange("HELLOU"), (0,54))
# add some more assemblies to test proper removal
indexer.AddAssembly("THIRDENTRY", ["X"], [5])
indexer.AddAssembly("FOURTHENTRY", ["R","asdf"],[22, 10])
# check the errors to be thrown when the RemoveAssembly function is called
self.assertRaises(Exception, indexer.RemoveAssembly, "HELLOUYO")
# before removing anything we check tons of ranges, we expect
# them to be ordered as they have been added to the indexer
self.assertEqual(indexer.GetDataRange("HELLOU"), (0, 54))
self.assertEqual(indexer.GetDataRange("HELLOU", "B"), (20, 53))
self.assertEqual(indexer.GetDataRange("HELLOUYOU"), (54, 110))
self.assertEqual(indexer.GetDataRange("HELLOUYOU", "Y"), (64, 90))
self.assertEqual(indexer.GetDataRange("THIRDENTRY"), (110, 115))
self.assertEqual(indexer.GetDataRange("THIRDENTRY", "X"), (110, 115))
self.assertEqual(indexer.GetDataRange("FOURTHENTRY"), (115, 147))
self.assertEqual(indexer.GetDataRange("FOURTHENTRY", "asdf"), (137, 147))
self.assertEqual(indexer.GetNumResidues(), 147)
# remove an assembly
indexer.RemoveAssembly("HELLOUYOU")
# we expect, that the data ranges for assembly HELLOU stays the same,
# but for all others there should be a decrease of 10+26+20=56
self.assertEqual(indexer.GetDataRange("HELLOU"), (0, 54))
self.assertEqual(indexer.GetDataRange("HELLOU", "B"), (20, 53))
self.assertEqual(indexer.GetDataRange("THIRDENTRY"), (110 - 56, 115 - 56))
self.assertEqual(indexer.GetDataRange("THIRDENTRY", "X"), (110 - 56, 115 - 56))
self.assertEqual(indexer.GetDataRange("FOURTHENTRY"), (115 - 56, 147 - 56))
self.assertEqual(indexer.GetDataRange("FOURTHENTRY", "asdf"), (137 - 56, 147 - 56))
self.assertEqual(indexer.GetNumResidues(), 147 - 56)
# We additionally check, whether the thing is really gone
current_entries = indexer.GetAssemblies()
current_entries.sort()
self.assertEqual(current_entries, ["FOURTHENTRY", "HELLOU", "THIRDENTRY"])
# Let's finally test saving and loading
indexer.Save("test_indexer.dat")
loaded_indexer = LinearIndexer.Load("test_indexer.dat")
self.assertEqual(indexer, loaded_indexer)
if os.path.exists("test_indexer.dat"):
os.remove("test_indexer.dat")
def testCharacterContainer(self):
container = LinearCharacterContainer()
self.assertEqual(container.GetNumElements(), 0)
# define a few sequences to play with
s1 = "AAAAAAA"
s2 = "BBB"
s3 = "CCCCCCCCCC"
# add some stuff
container.AddCharacters(s1)
container.AddCharacters(s2)
container.AddCharacters(s3)
# check whether stuff has properly been added
self.assertEqual(container.GetNumElements(), len(s1) + len(s2) + len(s3))
self.assertEqual(container.GetCharacters((0, container.GetNumElements())),
s1 + s2 + s3)
self.assertEqual(container.GetCharacters((0, len(s1))), "AAAAAAA")
self.assertEqual(container.GetCharacters((len(s1), len(s1) + len(s2))), "BBB")
self.assertEqual(container.GetCharacters((len(s1) + len(s2),
len(s1) + len(s2) + len(s3))),
"CCCCCCCCCC")
# check whether errors get thrown for invalid ranges
self.assertRaises(Exception, container.GetCharacters, (5,5))
self.assertRaises(Exception, container.GetCharacters, (5,4))
self.assertRaises(Exception, container.GetCharacters, (5,100))
self.assertRaises(Exception, container.GetCharacters, (100,120))
self.assertRaises(Exception, container.ClearRange, (5,5))
self.assertRaises(Exception, container.ClearRange, (5,4))
self.assertRaises(Exception, container.ClearRange, (5,100))
self.assertRaises(Exception, container.ClearRange, (100,120))
# let's remove s2 and then check whether the content is as expected
container.ClearRange((len(s1),len(s1) + len(s2)))
self.assertEqual(container.GetNumElements(), len(s1) + len(s3))
self.assertEqual(container.GetCharacters((0, len(s1))), "AAAAAAA")
self.assertEqual(container.GetCharacters((len(s1), len(s1) + len(s3))), "CCCCCCCCCC")
# let's check the single character extraction function
full_expected_string = s1 + s3
for i in range(container.GetNumElements()):
self.assertEqual(full_expected_string[i], container.GetCharacter(i))
# save / load and check for equality
container.Save("test_character_container.dat")
loaded_container = LinearCharacterContainer.Load("test_character_container.dat")
self.assertEqual(container, loaded_container)
if os.path.exists("test_character_container.dat"):
os.remove("test_character_container.dat")
def testPositionContainer(self):
container = LinearPositionContainer()
self.assertEqual(container.GetNumElements(), 0)
# define a few position lists to play with
pos_1 = geom.Vec3List()
pos_2 = geom.Vec3List()
pos_3 = geom.Vec3List()
pos_1.append(geom.Vec3(-10.234, -45.333, -45.338))
pos_1.append(geom.Vec3(10.234, 45.333, 45.338))
pos_1.append(geom.Vec3(10.234, 45.333, 45.338))
pos_1.append(geom.Vec3(10.234, 45.333, 45.338))
pos_1.append(geom.Vec3(10.234, 45.333, 45.338))
pos_1.append(geom.Vec3(10.234, 45.333, 45.338))
pos_2.append(geom.Vec3(50000.34, 32.43, 33.2222))
pos_2.append(geom.Vec3(-50000.34, -32.43, -33.2222))
pos_2.append(geom.Vec3(50000.34, 32.43, 33.2222))
pos_3.append(geom.Vec3(87.909, 65.222, 1000.556))
pos_3.append(geom.Vec3(87.909, 65.222, 1000.556))
# get the rounded target values (the accuracy with which they)
# are stored in the container)
pos_1_target = geom.Vec3(10.23, 45.33, 45.34)
pos_2_target = geom.Vec3(50000.3, 32.4, 33.2) # reduced accuracy!
pos_3_target = geom.Vec3(87.91, 65.22, 1000.56)
pos_1_target_list = geom.Vec3List()
pos_2_target_list = geom.Vec3List()
pos_3_target_list = geom.Vec3List()
for i in range(6):
pos_1_target_list.append(pos_1_target)
pos_1_target_list[0] = -pos_1_target_list[0]
for i in range(3):
pos_2_target_list.append(pos_2_target)
pos_2_target_list[1] = -pos_2_target_list[1]
pos_3_target_list.append(pos_3_target)
pos_3_target_list.append(pos_3_target)
# add it
container.AddPositions(pos_1)
container.AddPositions(pos_2)
container.AddPositions(pos_3)
extracted_pos_list = geom.Vec3List()
extracted_pos = geom.Vec3()
# check whether stuff has properly been added
self.assertEqual(container.GetNumElements(),
len(pos_1) + len(pos_2) + len(pos_3))
container.GetPositions((0,len(pos_1)), extracted_pos_list)
self.assertTrue(ComparePosList(pos_1_target_list, extracted_pos_list))
container.GetPositions((len(pos_1),len(pos_1)+len(pos_2)), extracted_pos_list)
self.assertTrue(ComparePosList(pos_2_target_list, extracted_pos_list))
container.GetPositions((len(pos_1)+len(pos_2),
len(pos_1)+len(pos_2)+len(pos_3)), extracted_pos_list)
self.assertTrue(ComparePosList(pos_3_target_list, extracted_pos_list))
# check whether errors get thrown for invalid ranges
dummy_list = geom.Vec3List()
dummy_pos = geom.Vec3()
self.assertRaises(Exception, container.GetPositions, (5,5), dummy_list)
self.assertRaises(Exception, container.GetPositions, (5,4), dummy_list)
self.assertRaises(Exception, container.GetPositions, (5,100), dummy_list)
self.assertRaises(Exception, container.GetPositions, (100,120), dummy_list)
self.assertRaises(Exception, container.GetPosition, 100, dummy_pos)
self.assertRaises(Exception, container.ClearRange, (5,5))
self.assertRaises(Exception, container.ClearRange, (5,4))
self.assertRaises(Exception, container.ClearRange, (5,100))
self.assertRaises(Exception, container.ClearRange, (100,120))
# lets remove pos_2_list and check, whether the result is as expected
container.ClearRange((len(pos_1), len(pos_1)+len(pos_2)))
self.assertEqual(container.GetNumElements(), len(pos_1) + len(pos_3))
container.GetPositions((0,len(pos_1)), extracted_pos_list)
self.assertTrue(ComparePosList(pos_1_target_list, extracted_pos_list))
container.GetPositions((len(pos_1), len(pos_1) + len(pos_3)), extracted_pos_list)
self.assertTrue(ComparePosList(pos_3_target_list, extracted_pos_list))
# check the single position getter
pos_13_target_list = geom.Vec3List()
for item in pos_1_target_list:
pos_13_target_list.append(item)
for item in pos_3_target_list:
pos_13_target_list.append(item)
eps = 0.00001
for i in range(len(pos_13_target_list)):
container.GetPosition(i, extracted_pos)
self.assertTrue(geom.Distance(extracted_pos, pos_13_target_list[i]) < eps)
# save / load and check for equality
container.Save("test_position_container.dat")
loaded_container = LinearPositionContainer.Load("test_position_container.dat")
self.assertEqual(container, loaded_container)
if os.path.exists("test_position_container.dat"):
os.remove("test_position_container.dat")
if __name__ == "__main__":
from ost import testutils
testutils.RunTests()
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