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Interactions tests fixes #1762

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merged 3 commits into from
Oct 8, 2023
Merged

Interactions tests fixes #1762

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cb0afcd
fixing py2.7 issue in InSty tests
karolamik13 Oct 7, 2023
fa83dcb
fixes in InSty tests
karolamik13 Oct 8, 2023
9502b60
fixes in InSty tests - missing self
karolamik13 Oct 8, 2023
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99 changes: 51 additions & 48 deletions prody/tests/proteins/test_insty.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,57 +12,60 @@
from prody.proteins.interactions import calcPiCationTrajectory, calcHydrophobicTrajectory
from prody.proteins.interactions import calcDisulfideBondsTrajectory, calcProteinInteractions

ATOMS = parseDatafile('2k39_insty')
ALL_INTERACTIONS = parseDatafile('2k39_all')
ALL_INTERACTIONS2 = parseDatafile('2k39_all2')
HBS_INTERACTIONS = parseDatafile('2k39_hbs')
SBS_INTERACTIONS = parseDatafile('2k39_sbs')
RIB_INTERACTIONS = parseDatafile('2k39_rib')
PISTACK_INTERACTIONS = parseDatafile('2k39_PiStack')
PICAT_INTERACTIONS = parseDatafile('2k39_PiCat')
HPH_INTERACTIONS = parseDatafile('2k39_hph')
HPH_INTERACTIONS2 = parseDatafile('2k39_hph2')
DISU_INTERACTIONS = parseDatafile('2k39_disu')

# Generating new data to compare it with the existing one:
INTERACTIONS_ALL = InteractionsTrajectory()
data_all = INTERACTIONS_ALL.calcProteinInteractionsTrajectory(ATOMS)
np.save('test_2k39_all.npy', data_all, allow_pickle=True)

data_hbs = calcHydrogenBondsTrajectory(ATOMS)
np.save('test_2k39_hbs.npy', data_hbs, allow_pickle=True)

data_sbs = calcSaltBridgesTrajectory(ATOMS)
np.save('test_2k39_sbs.npy', data_sbs, allow_pickle=True)

data_rib = calcRepulsiveIonicBondingTrajectory(ATOMS)
np.save('test_2k39_rib.npy', data_rib, allow_pickle=True)

data_PiStack = calcPiStackingTrajectory(ATOMS)
np.save('test_2k39_PiStack.npy', data_PiStack, allow_pickle=True)

data_PiCat = calcPiCationTrajectory(ATOMS)
np.save('test_2k39_PiCat.npy', data_PiCat, allow_pickle=True)

data_hph = calcHydrophobicTrajectory(ATOMS)
np.save('test_2k39_hph.npy', data_hph, allow_pickle=True)
class TestInteractions(unittest.TestCase):

data_disu = calcDisulfideBondsTrajectory(ATOMS)
np.save('test_2k39_disu.npy', data_disu, allow_pickle=True)
def setUp(self):
"""Generating new data to compare it with the existing one"""

if prody.PY3K:
self.ATOMS = parseDatafile('2k39_insty')
self.ALL_INTERACTIONS = parseDatafile('2k39_all')
self.ALL_INTERACTIONS2 = parseDatafile('2k39_all2')
self.HBS_INTERACTIONS = parseDatafile('2k39_hbs')
self.SBS_INTERACTIONS = parseDatafile('2k39_sbs')
self.RIB_INTERACTIONS = parseDatafile('2k39_rib')
self.PISTACK_INTERACTIONS = parseDatafile('2k39_PiStack')
self.PICAT_INTERACTIONS = parseDatafile('2k39_PiCat')
self.HPH_INTERACTIONS = parseDatafile('2k39_hph')
self.HPH_INTERACTIONS2 = parseDatafile('2k39_hph2')
self.DISU_INTERACTIONS = parseDatafile('2k39_disu')

self.INTERACTIONS_ALL = InteractionsTrajectory()
self.data_all = self.INTERACTIONS_ALL.calcProteinInteractionsTrajectory(self.ATOMS)
np.save('test_2k39_all.npy', self.data_all, allow_pickle=True)

self.data_hbs = calcHydrogenBondsTrajectory(self.ATOMS)
np.save('test_2k39_hbs.npy', self.data_hbs, allow_pickle=True)

self.data_sbs = calcSaltBridgesTrajectory(self.ATOMS)
np.save('test_2k39_sbs.npy', self.data_sbs, allow_pickle=True)

self.data_rib = calcRepulsiveIonicBondingTrajectory(self.ATOMS)
np.save('test_2k39_rib.npy', self.data_rib, allow_pickle=True)

self.data_PiStack = calcPiStackingTrajectory(self.ATOMS)
np.save('test_2k39_PiStack.npy', self.data_PiStack, allow_pickle=True)

self.data_PiCat = calcPiCationTrajectory(self.ATOMS)
np.save('test_2k39_PiCat.npy', self.data_PiCat, allow_pickle=True)

self.data_hph = calcHydrophobicTrajectory(self.ATOMS)
np.save('test_2k39_hph.npy', self.data_hph, allow_pickle=True)

self.data_disu = calcDisulfideBondsTrajectory(self.ATOMS)
np.save('test_2k39_disu.npy', self.data_disu, allow_pickle=True)

class TestInteractions(unittest.TestCase):

def testAllInsteractions(self):
"""Test for all types of interactions."""

if prody.PY3K:
data_test = np.load('test_2k39_all.npy', allow_pickle=True)

try:
assert_equal(data_test, ALL_INTERACTIONS2,
assert_equal(data_test, self.ALL_INTERACTIONS2,
'failed to get correct interactions without hpb.so')
except:
assert_equal(data_test, ALL_INTERACTIONS,
assert_equal(data_test, self.ALL_INTERACTIONS,
'failed to get correct interactions with hpb.so')

def testHydrogenBonds(self):
Expand All @@ -72,39 +75,39 @@ def testHydrogenBonds(self):

if prody.PY3K:
data_test = np.load('test_2k39_hbs.npy', allow_pickle=True)
assert_equal(sorted([i[-1][-1] for i in data_test]), sorted([i[-1][-1] for i in HBS_INTERACTIONS]),
assert_equal(sorted([i[-1][-1] for i in data_test]), sorted([i[-1][-1] for i in self.HBS_INTERACTIONS]),
'failed to get correct hydrogen bonds')

def testSaltBridges(self):
"""Test for salt bridges."""

if prody.PY3K:
data_test = np.load('test_2k39_sbs.npy', allow_pickle=True)
assert_equal(sorted([i[-1][-1] for i in data_test]), sorted([i[-1][-1] for i in SBS_INTERACTIONS]),
assert_equal(sorted([i[-1][-1] for i in data_test]), sorted([i[-1][-1] for i in self.SBS_INTERACTIONS]),
'failed to get correct salt bridges')

def testRepulsiveIonicBonding(self):
"""Test for repulsive ionic bonding."""

if prody.PY3K:
data_test = np.load('test_2k39_rib.npy', allow_pickle=True)
assert_equal(sorted([i[-1][-1] for i in data_test if i]), sorted([i[-1][-1] for i in RIB_INTERACTIONS if i]),
assert_equal(sorted([i[-1][-1] for i in data_test if i]), sorted([i[-1][-1] for i in self.RIB_INTERACTIONS if i]),
'failed to get correct repulsive ionic bonding')

def testPiStacking(self):
"""Test for pi-stacking interactions."""

if prody.PY3K:
data_test = np.load('test_2k39_PiStack.npy', allow_pickle=True)
assert_equal(sorted([i[-1][-1] for i in data_test if i]), sorted([i[-1][-1] for i in PISTACK_INTERACTIONS if i]),
assert_equal(sorted([i[-1][-1] for i in data_test if i]), sorted([i[-1][-1] for i in self.PISTACK_INTERACTIONS if i]),
'failed to get correct pi-stacking interactions')

def testPiCation(self):
"""Test for pi-stacking interactions."""

if prody.PY3K:
data_test = np.load('test_2k39_PiCat.npy', allow_pickle=True)
assert_equal(sorted([i[-1][-1] for i in data_test if i]), sorted([i[-1][-1] for i in PICAT_INTERACTIONS if i]),
assert_equal(sorted([i[-1][-1] for i in data_test if i]), sorted([i[-1][-1] for i in self.PICAT_INTERACTIONS if i]),
'failed to get correct pi-cation interactions')


Expand All @@ -114,10 +117,10 @@ def testHydrophobicInteractions(self):
if prody.PY3K:
data_test = np.load('test_2k39_hph.npy', allow_pickle=True)
try:
assert_equal(sorted([i[-1][-1] for i in data_test]), sorted([i[-1][-1] for i in HPH_INTERACTIONS2]),
assert_equal(sorted([i[-1][-1] for i in data_test]), sorted([i[-1][-1] for i in self.HPH_INTERACTIONS2]),
'failed to get correct hydrophobic interactions without hpb.so')
except:
assert_equal(sorted([i[-1][-1] for i in data_test]), sorted([i[-1][-1] for i in HPH_INTERACTIONS]),
assert_equal(sorted([i[-1][-1] for i in data_test]), sorted([i[-1][-1] for i in self.HPH_INTERACTIONS]),
'failed to get correct hydrophobic interactions with hpb.so')


Expand All @@ -126,7 +129,7 @@ def testDisulfideBonds(self):

if prody.PY3K:
data_test = np.load('test_2k39_disu.npy', allow_pickle=True)
assert_equal(sorted([i[-1][-1] for i in data_test if i]), sorted([i[-1][-1] for i in DISU_INTERACTIONS if i]),
assert_equal(sorted([i[-1][-1] for i in data_test if i]), sorted([i[-1][-1] for i in self.DISU_INTERACTIONS if i]),
'failed to get correct disulfide bonds')


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