Merge pull request #1944 from jamesmkrieger/insty_tests

better insty tests

prody/tests/datafiles/__init__.py

@@ -358,7 +358,10 @@
     },
     '2k39_disu': {
         'file': '2k39_disu.npy'
-    },    
+    },
+    '3o21_disu': {
+        'file': '3o21_disu.npy'
+    },
     '2k39_all': {
         'file': '2k39_all.npy'
     },

prody/tests/proteins/test_insty.py

@@ -1,7 +1,6 @@
 """This module contains unit tests for :mod:`~prody.proteins.interactions`."""
 
 import numpy as np
-from numpy import arange
 from prody import *
 from prody.tests import unittest
 from prody.tests.datafiles import *
@@ -20,7 +19,7 @@ def setUp(self):
         """Generating new data to compare it with the existing one"""
 
         if prody.PY3K:
-            self.ATOMS = parseDatafile('2k39_insty')
+            self.ATOMS = parseDatafile('2k39_insty') # no disulfides
             self.ALL_INTERACTIONS = parseDatafile('2k39_all')
             self.ALL_INTERACTIONS2 = parseDatafile('2k39_all2')
             self.HBS_INTERACTIONS = parseDatafile('2k39_hbs')
@@ -31,109 +30,151 @@ def setUp(self):
             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', np.array(self.data_hbs, dtype=object), allow_pickle=True)
+            self.ATOMS_3O21 = parseDatafile('3o21') # has disulfides & not traj
+            self.DISU_INTERACTIONS_3O21 = parseDatafile('3o21_disu')
 
-            self.data_sbs = calcSaltBridgesTrajectory(self.ATOMS)
-            np.save('test_2k39_sbs.npy', np.array(self.data_sbs, dtype=object), allow_pickle=True)
+    def testAllInteractionsCalc(self):
+        """Test for calculating all types of interactions."""
 
-            self.data_rib = calcRepulsiveIonicBondingTrajectory(self.ATOMS)
-            np.save('test_2k39_rib.npy', np.array(self.data_rib, dtype=object), allow_pickle=True)
-
-            self.data_PiStack = calcPiStackingTrajectory(self.ATOMS)
-            np.save('test_2k39_PiStack.npy', np.array(self.data_PiStack, dtype=object), allow_pickle=True)
-
-            self.data_PiCat = calcPiCationTrajectory(self.ATOMS)
-            np.save('test_2k39_PiCat.npy', np.array(self.data_PiCat, dtype=object), allow_pickle=True)
-
-            self.data_hph = calcHydrophobicTrajectory(self.ATOMS)
-            np.save('test_2k39_hph.npy', np.array(self.data_hph, dtype=object), allow_pickle=True)
+        if prody.PY3K:
+            self.INTERACTIONS_ALL = InteractionsTrajectory()
+            self.data_all = self.INTERACTIONS_ALL.calcProteinInteractionsTrajectory(self.ATOMS)
 
-            self.data_disu = calcDisulfideBondsTrajectory(self.ATOMS)
-            np.save('test_2k39_disu.npy', np.array(self.data_disu, dtype=object), allow_pickle=True)
+            try:
+                assert_equal(self.data_all, self.ALL_INTERACTIONS2,
+                             'failed to get correct interactions without hpb.so from calculation')
+            except AssertionError:
+                assert_equal(self.data_all, self.ALL_INTERACTIONS,
+                             'failed to get correct interactions with hpb.so from calculation')
+
+    def testAllInteractionsSave(self):
+        """Test for saving and loading all types of interactions."""
+        if prody.PY3K:
+            self.INTERACTIONS_ALL = InteractionsTrajectory()
+            self.data_all = self.INTERACTIONS_ALL.calcProteinInteractionsTrajectory(self.ATOMS)
 
-    def testAllInteractions(self):
-        """Test for all types of interactions."""
+            np.save('test_2k39_all.npy', np.array(self.data_all, dtype=object), allow_pickle=True)
 
-        if prody.PY3K:        
             data_test = np.load('test_2k39_all.npy', allow_pickle=True)
 
             try:
                 assert_equal(data_test, self.ALL_INTERACTIONS2,
-                         'failed to get correct interactions without hpb.so')
-            except:
+                             'failed to get correct interactions without hpb.so from saving and loading')
+            except AssertionError:
                 assert_equal(data_test, self.ALL_INTERACTIONS,
-                         'failed to get correct interactions with hpb.so')
+                             'failed to get correct interactions with hpb.so from saving and loading')
 
     def testHydrogenBonds(self):
         """Test for hydrogen bonds.
         Last column is compared becasue pairs of residues can be reversed and
         order can be also different in the interactions"""
 
         if prody.PY3K:                
-            data_test = np.load('test_2k39_hbs.npy', allow_pickle=True)
+            data_test = calcHydrogenBondsTrajectory(self.ATOMS)
             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."""
+    def testSaltBridgesCalc(self):
+        """Test for salt bridges without saving and loading."""
+
+        if prody.PY3K:                
+            self.data_sbs = calcSaltBridgesTrajectory(self.ATOMS)
+            assert_equal(sorted([i[-1][-1] for i in self.data_sbs]), sorted([i[-1][-1] for i in self.SBS_INTERACTIONS]),
+                         'failed to get correct salt bridges')
+
+
+    def testSaltBridgesSave(self):
+        """Test for salt bridges with saving and loading (one type with results)."""
 
         if prody.PY3K:                
+            self.data_sbs = calcSaltBridgesTrajectory(self.ATOMS)
+
+            np.save('test_2k39_sbs.npy', np.array(self.data_sbs, dtype=object), allow_pickle=True)
+
             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 self.SBS_INTERACTIONS]),
-                         'failed to get correct salt bridges')                             
+            assert_equal(sorted([i[-1][-1] for i in data_test if len(i) > 0]), sorted([i[-1][-1] for i in self.SBS_INTERACTIONS if len(i) > 0]),
+                         'failed to get correct salt bridges from saving and loading')
+
 
     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 self.RIB_INTERACTIONS if i]),
+            data_test = calcRepulsiveIonicBondingTrajectory(self.ATOMS)
+            assert_equal(sorted([i[-1][-1] for i in data_test if len(i) > 0]), sorted([i[-1][-1] for i in self.RIB_INTERACTIONS if len(i) > 0]),
                          '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 self.PISTACK_INTERACTIONS if i]),
+            data_test = calcPiStackingTrajectory(self.ATOMS)
+            assert_equal(sorted([i[-1][-1] for i in data_test if len(i) > 0]), sorted([i[-1][-1] for i in self.PISTACK_INTERACTIONS if len(i) > 0]),
                          '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 self.PICAT_INTERACTIONS if i]),
+            data_test = calcPiCationTrajectory(self.ATOMS)
+            assert_equal(sorted([i[-1][-1] for i in data_test if len(i) > 0]), sorted([i[-1][-1] for i in self.PICAT_INTERACTIONS if len(i) > 0]),
                          'failed to get correct pi-cation interactions')
 
 
     def testHydrophobicInteractions(self):
         """Test for hydrophobic interactions."""
 
         if prody.PY3K:        
-            data_test = np.load('test_2k39_hph.npy', allow_pickle=True)                                                        
+            data_test = calcHydrophobicTrajectory(self.ATOMS)
             try:
                 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:
+            except AssertionError:
                 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')
 
 
-    def testDisulfideBonds(self):
-        """Test for disulfide bonds interactions."""
+    def testDisulfideBondsCalcNone(self):
+        """Test for disulfide bonds interactions without saving and loading."""
+        if prody.PY3K:
+            data_test = calcDisulfideBondsTrajectory(self.ATOMS)
+            assert_equal(sorted([i[-1][-1] for i in data_test if len(i) > 0]), 
+                         sorted([i[-1][-1] for i in self.DISU_INTERACTIONS if len(i) > 0]),
+                         'failed to get correct disulfide bonds from 2k39 (None) from calculation')
+
+    def testDisulfideBondsSaveNone(self):
+        """Test for disulfide bonds interactions with saving and loading (one type of interactions with 0)."""
+        if prody.PY3K:
+            data_test = calcDisulfideBondsTrajectory(self.ATOMS)
+            np.save('test_2k39_disu.npy', np.array(data_test, dtype=object), 
+                    allow_pickle=True)
+
+            data_test = np.load('test_2k39_disu.npy', allow_pickle=True)
+            assert_equal(sorted([i[-1][-1] for i in data_test if len(i) > 0]), 
+                         sorted([i[-1][-1] for i in self.DISU_INTERACTIONS if len(i) > 0]),
+                         'failed to get correct disulfide bonds from 2k39 (None) from saving and loading')
+
+    def testDisulfideBondsCalcSomeNotTraj(self):
+        """Test for disulfide bonds interactions without saving and loading."""
+        if prody.PY3K:
+            data_test = calcDisulfideBonds(self.ATOMS_3O21)
+            assert_equal(sorted([i[-1] for i in data_test if len(i) > 0]), 
+                         sorted([i[-1] for i in self.DISU_INTERACTIONS_3O21 if len(i) > 0]),
+                         'failed to get correct disulfide bonds from 3o21 from calculation')
+
+    def testDisulfideBondsSaveSomeNotTraj(self):
+        """Test for disulfide bonds interactions with saving and loading (one type of interactions with 0)."""
+        if prody.PY3K:
+            data_test = calcDisulfideBonds(self.ATOMS_3O21)
+            np.save('test_3o21_disu.npy', np.array(data_test, dtype=object), 
+                    allow_pickle=True)
+
+            data_test = np.load('test_3o21_disu.npy', allow_pickle=True)
+            assert_equal(sorted([i[-1] for i in data_test if len(i) > 0]), 
+                         sorted([i[-1] for i in self.DISU_INTERACTIONS_3O21 if len(i) > 0]),
+                         'failed to get correct disulfide bonds from 3o21 from saving and loading')
 
-        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 self.DISU_INTERACTIONS if i]),
-                          'failed to get correct disulfide bonds')
-
     def testImportHpb(self):
 
         try:
@@ -155,7 +196,5 @@ def testImportHpb(self):
     def tearDownClass(cls):
         if prody.PY3K:
             import os
-            for filename in ['test_2k39_all.npy', 'test_2k39_hbs.npy', 'test_2k39_sbs.npy', 
-                            'test_2k39_rib.npy', 'test_2k39_PiStack.npy', 'test_2k39_PiCat.npy',
-                            'test_2k39_hph.npy', 'test_2k39_disu.npy']:
+            for filename in ['test_2k39_all.npy', 'test_2k39_sbs.npy', 'test_2k39_disu.npy']:
                 os.remove(filename)

prody/utilities/misctools.py

@@ -422,8 +422,12 @@ def pystr(a):
     return b
 
 def getDataPath(filename):
+    if PY3K:
+        import importlib
+        path = importlib.util.find_spec('prody.utilities.datafiles').submodule_search_locations[0]
+        return '%s/%s' %(path, filename)
     import pkg_resources
-    return pkg_resources.resource_filename('prody.utilities', 'datafiles/%s'%filename)
+    return pkg_resources.resource_filename('prody.utilities', 'datafiles/%s'%filename)      
 
 def openData(filename, mode='r'):
     return open(getDataPath(filename), mode)