def test_08_removeHydrogens(self):
mol2file = os.path.join(self.dataDir, 'benzamidine.mol2')
sm = SmallMol(mol2file)
sm_c = sm.copy()
b = Builder(sm_c)
b.removeHydrogens()
sm_b = b.getSmallMol()
sm_b_element = sm_b.element.tolist()
self.assertListEqual(sm_b_element, BENZAMIDINE_ELEMENTS_NOHS)
sm_c = sm.copy()
b = Builder(sm_c)
b.removeHydrogens(removeNonPolars=False)
sm_b = b.getSmallMol()
sm_b_element = sm_b.element.tolist()
self.assertListEqual(sm_b_element, BENZAMIDINE_ELEMENTS_NO_POLARHS)
sm_c = sm.copy()
b = Builder(sm_c)
b.removeHydrogens(removePolars=False)
sm_b = b.getSmallMol()
sm_b_element = sm_b.element.tolist()
self.assertListEqual(sm_b_element, BENZAMIDINE_ELEMENTS_NO_NONPOLARHS)
def test_08_removeHydrogens(self):
mol2file = os.path.join(self.dataDir, 'benzamidine.mol2')
sm = SmallMol(mol2file)
sm_c = sm.copy()
b = Builder(sm_c)
b.removeHydrogens()
sm_b = b.getSmallMol()
sm_b_element = sm_b.element.tolist()
self.assertListEqual(sm_b_element, BENZAMIDINE_ELEMENTS_NOHS)
sm_c = sm.copy()
b = Builder(sm_c)
b.removeHydrogens(removeNonPolars=False)
sm_b = b.getSmallMol()
sm_b_element = sm_b.element.tolist()
self.assertListEqual(sm_b_element, BENZAMIDINE_ELEMENTS_NO_POLARHS)
sm_c = sm.copy()
b = Builder(sm_c)
b.removeHydrogens(removePolars=False)
sm_b = b.getSmallMol()
sm_b_element = sm_b.element.tolist()
self.assertListEqual(sm_b_element, BENZAMIDINE_ELEMENTS_NO_NONPOLARHS)
def test_06_getSmallMol(self):
sm = SmallMol(ETANOLAMMINE_SMILE, removeHs=True, fixHs=False)
sm_c = sm.copy()
b = Builder(sm_c)
sm_b = b.getSmallMol()
self.assertIsInstance(sm_b, SmallMol, msg="The molecule was not loaded correctly")
def test_06_getSmallMol(self):
sm = SmallMol(ETANOLAMMINE_SMILE, removeHs=True, fixHs=False)
sm_c = sm.copy()
b = Builder(sm_c)
sm_b = b.getSmallMol()
self.assertIsInstance(sm_b,
SmallMol,
msg="The molecule was not loaded correctly")
def test_07_addHydrogens(self):
sm = SmallMol(ETANOLAMMINE_SMILE, removeHs=True, fixHs=False)
sm_c = sm.copy()
b = Builder(sm_c)
b.addHydrogens()
sm_b = b.getSmallMol()
sm_b_elements = sm_b.element.tolist()
self.assertListEqual(sm_b_elements, ETANOLAMMINE_ELEMENTS_ALL)
sm_c = sm.copy()
b = Builder(sm_c)
b.addHydrogens(onlyExplicit=True)
sm_b = b.getSmallMol()
sm_b_elements = sm_b.element.tolist()
self.assertListEqual(sm_b_elements, ETANOLAMMINE_ELEMENTS_POLARHS)
def test_07_addHydrogens(self):
sm = SmallMol(ETANOLAMMINE_SMILE, removeHs=True, fixHs=False)
sm_c = sm.copy()
b = Builder(sm_c)
b.addHydrogens()
sm_b = b.getSmallMol()
sm_b_elements = sm_b.element.tolist()
self.assertListEqual(sm_b_elements, ETANOLAMMINE_ELEMENTS_ALL)
sm_c = sm.copy()
b = Builder(sm_c)
b.addHydrogens(onlyExplicit=True)
sm_b = b.getSmallMol()
sm_b_elements = sm_b.element.tolist()
self.assertListEqual(sm_b_elements, ETANOLAMMINE_ELEMENTS_POLARHS)
def test_05_Builder_load(self):
sm = SmallMol(ETANOLAMMINE_SMILE, removeHs=True, fixHs=False)
sm_c = sm.copy()
b = Builder()
b.loadMol(sm_c)
sm_b = b.getSmallMol()
expectedFalse = np.array_equal(sm_b.coords, sm.coords)
self.assertIsInstance(b, Builder, msg="The molecule was not creted in the Builder")
self.assertFalse(expectedFalse, msg="A initial conformation was not created")
def test_05_Builder_load(self):
sm = SmallMol(ETANOLAMMINE_SMILE, removeHs=True, fixHs=False)
sm_c = sm.copy()
b = Builder()
b.loadMol(sm_c)
sm_b = b.getSmallMol()
expectedFalse = np.array_equal(sm_b.coords, sm.coords)
self.assertIsInstance(b,
Builder,
msg="The molecule was not creted in the Builder")
self.assertFalse(expectedFalse,
msg="A initial conformation was not created")