Utilities test case added

packman/__init__.py

@@ -13,4 +13,4 @@
 
 
 #VERSION CHANGE HERE CHANGES IT IN docs AND setup.py
-__version__='1.4.10'
+__version__='1.4.11'

packman/tests/anm/test_anm.py

@@ -5,7 +5,7 @@
 import logging
 from os import remove as rm
 
-class TestMolecule(unittest.TestCase):
+class Test_ANM(unittest.TestCase):
 
     def setUp(self):
         self.mol = molecule.load_structure('packman/tests/data/4hla.cif',ftype='cif')

packman/tests/dci/test_dci.py

@@ -5,7 +5,7 @@
 import logging
 from os import remove as rm
 
-class TestMolecule(unittest.TestCase):
+class Test_DCI(unittest.TestCase):
 
     def setUp(self):
         self.mol = molecule.load_structure('packman/tests/data/4hla.cif',ftype='cif')

packman/tests/entropy/test_entropy.py

@@ -5,7 +5,7 @@
 import logging
 from os import remove as rm
 
-class TestMolecule(unittest.TestCase):
+class Test_Entropy(unittest.TestCase):
 
     def setUp(self):
         self.mol = molecule.load_structure('packman/tests/data/4hla.cif',ftype='cif')

packman/tests/geometry/test_geometry.py

@@ -6,7 +6,7 @@
 import logging
 from os import remove as rm
 
-class TestGeometry(unittest.TestCase):
+class Test_Geometry(unittest.TestCase):
 
     def setUp(self):
         self.mol = molecule.load_structure('packman/tests/data/4hla.cif',ftype='cif')
@@ -25,7 +25,7 @@ def test_AlphaShape(self):
             self.assertIsInstance( geometry.AlphaShape( [j for i in self.mol[0].get_backbone() for j in i], 4 )[0][0][0], molecule.Atom )
 
     def tearDown(self):
-        logging.info('Molecule Test Done.')
+        logging.info('Geometry Test Done.')
 
 if(__name__=='__main__'):
     unittest.main()

packman/tests/gnm/test_gnm.py

@@ -5,7 +5,7 @@
 import logging
 from os import remove as rm
 
-class TestMolecule(unittest.TestCase):
+class Test_GNM(unittest.TestCase):
 
     def setUp(self):
         self.mol = molecule.load_structure('packman/tests/data/4hla.cif',ftype='cif')

packman/tests/molecule/test_molecule.py

@@ -5,7 +5,7 @@
 import logging
 from os import remove as rm
 
-class TestMolecule(unittest.TestCase):
+class Test_Molecule(unittest.TestCase):
 
     def setUp(self):
         self.mol = molecule.load_structure('packman/tests/data/4hla.cif',ftype='cif')

packman/tests/utilities/test_utilities.py

@@ -0,0 +1,43 @@
+from ... import molecule, utilities, geometry
+import unittest
+import numpy
+
+import logging
+from os import remove as rm
+
+class Test_Utilities(unittest.TestCase):
+
+    def setUp(self):
+        self.mol = molecule.load_structure('packman/tests/data/4hla.cif',ftype='cif')
+
+    def test_superimpose(self):
+        # Double check later.
+        expected_a1 = [[-4.99437660e-01, -8.66349433e-01, -8.26228195e-04], [-8.66349792e-01,  4.99437142e-01, 7.60871525e-04], [-2.46531567e-04,  1.09581052e-03, -9.99999369e-01]]
+        expected_b1 = [[-0.02974615, -0.02141248,  0.65529778]]
+
+        expected_a2 = [[ 9.99999994e-01,  6.44035795e-05,  8.82404191e-05], [-6.44835190e-05,  9.99999587e-01,  9.06225051e-04], [-8.81820186e-05, -9.06230736e-04,  9.99999585e-01]]
+        expected_b2 = [[ 6.31828525e-03,  9.14265397e-05, -4.94164731e-03]]
+
+        a1, b1 = utilities.superimporse(self.mol[0]['A'], self.mol[0]['B'], use='calpha')
+        self.assertTrue( numpy.allclose( a1, expected_a1, rtol=1e-14 ) )
+        self.assertTrue( numpy.allclose( b1, expected_b1, rtol=1e-14 ) )
+
+        # since superimpose change the coordinates, keep it mind for future debugging in case that is changed.
+        a2, b2 = utilities.superimporse(self.mol[0]['A'], self.mol[0]['B'], use='backbone')
+        self.assertTrue( numpy.allclose( a2, expected_a2, rtol=1e-14 ) )
+        self.assertTrue( numpy.allclose( b2, expected_b2, rtol=1e-14 ) )
+
+    def test_RMSD(self):
+        self.assertTrue( (utilities.RMSD(self.mol[0]['A'], self.mol[0]['B'], use='calpha') - 0.10400695339185048) < 0.001 )
+        self.assertTrue( (utilities.RMSD(self.mol[0]['A'], self.mol[0]['B'], use='backbone')- 0.11195505579911495) < 0.001  )
+
+    def test_WriteOBJ(self):
+        AS = geometry.AlphaShape([i for i in self.mol[0].get_atoms()], float('inf'))
+        utilities.WriteOBJ( self.mol[0].get_atoms(), AS[0], open('test.obj','wb') )
+
+    def tearDown(self):
+        logging.info('Utilities Test Done.')
+
+if(__name__=='__main__'):
+    unittest.main()
+

packman/utilities/utilities.py

@@ -6,10 +6,10 @@
 import logging
 import numpy
 
-from typing import TYPE_CHECKING, List, Tuple, Dict
+from typing import TYPE_CHECKING, List, Tuple, Dict, IO
 
 if(TYPE_CHECKING):
-    from ..molecule import Chain
+    from ..molecule import Chain, Atom
 
 def superimporse(reference: 'Chain', target: 'Chain', use: str='calpha', ids: List[int]=[], change_target: bool=True) -> Tuple[numpy.matrix, numpy.ndarray]:
     """This function is used to superimpose the Target Chain(coordinates will be changed) on the Reference Chain(coordinates will change).
@@ -172,21 +172,24 @@ def load_hinge(filename: str) -> Dict[str, List[float]]:
 ##################################################################################################
 '''
 
-def WriteOBJ(atoms, faces, fh):
+def WriteOBJ(atoms: List['Atom'], faces: List['Atom'], fh: IO):
     """Write the .obj file to visualize the obtain alpha shape tesselations.
+
+    Note:
+        * One chain at a time.
     
     Args:
         atoms (packman.molecule.Atom): Atoms (Just for the node records)
-        faces ([float])              : SelectedTesselations (See the packman.apps.predict_hinge)
+        faces ([Atom])              : SelectedTesselations (See the packman.apps.predict_hinge)
         fh (file)                    : Output file with .obj extension
-    
     """
+    atoms = [i for i in atoms]
     NewIDs = {i.get_id():numi+1 for numi,i in enumerate(atoms)}
     fh.write('mtllib master.mtl\ng\n'.encode())
     fh.write('usemtl atoms\n'.encode())
     for i in atoms:
         x, y, z = i.get_location()
-        fh.write("v %f %f %f\n".encode()%(x,y,z))
+        fh.write("v %f %f %f\n".encode()%(x, y, z))
 
     line='usemtl bonds\nl'
     for i in atoms:
@@ -196,8 +199,8 @@ def WriteOBJ(atoms, faces, fh):
 
     fh.write('usemtl faces\n'.encode())
     for i in faces:
-        faces = [NewIDs[j.get_id()] for j in i]
-        fh.write("f %i %i %i %i\n".encode()%(faces[0],faces[1],faces[2],faces[3]))
+        local_faces = [NewIDs[j.get_id()] for j in i]
+        fh.write("f %i %i %i %i\n".encode()%(local_faces[0], local_faces[1], local_faces[2], local_faces[3]))
         #fh.write("l %i %i %i %i\n"%(faces[0],faces[1],faces[2],faces[3]))
     return True