diff --git a/modules/mol/alg/tests/test_accessibility.py b/modules/mol/alg/tests/test_accessibility.py index 3ff4c0fde1431336b798f21c2545527baed62fd1..c3d857fd52f43dc5c30c58ebab47b763fa28da45 100644 --- a/modules/mol/alg/tests/test_accessibility.py +++ b/modules/mol/alg/tests/test_accessibility.py @@ -111,19 +111,14 @@ class TestAccessibility(unittest.TestCase): def testAccDSSP(self): - dssp_path = None - + # only relevant if dssp there try: - dssp_path = settings.Locate("dssp") + # same check used in dssp binding + dssp_path = settings.Locate(['dsspcmbi', 'dssp', 'mkdssp'], + env_name='DSSP_EXECUTABLE') except: - try: - dssp_path = settings.locate("mkdssp") - except: - pass - pass - - if dssp_path == None: print "Could not find DSSP, could not compare Accessibility function..." + return # we assume oligo mode to be working as it is tested in # testAccNACCESS. So we only test the single residue @@ -133,7 +128,7 @@ class TestAccessibility(unittest.TestCase): ent_one = ent_one.Select("peptide=true") ent_two = ent_two.Select("peptide=true") - dssp.AssignDSSP(ent_one, extract_burial_status=True, dssp_bin = dssp_path) + dssp.AssignDSSP(ent_one, extract_burial_status=True, dssp_bin=dssp_path) mol.alg.Accessibility(ent_two, algorithm=mol.alg.AccessibilityAlgorithm.DSSP) for a,b in zip(ent_one.residues, ent_two.residues): diff --git a/modules/mol/alg/tests/test_sec_struct.py b/modules/mol/alg/tests/test_sec_struct.py index 3c2d11295a39ac866abb286390c356d60a700591..207f8600c8f14589577fd1fabddd6ee0ebf72598 100644 --- a/modules/mol/alg/tests/test_sec_struct.py +++ b/modules/mol/alg/tests/test_sec_struct.py @@ -9,20 +9,18 @@ class TestSecStruct(unittest.TestCase): def testSecStruct(self): # unit test only makes sense, when a dssp binary is around - dssp_path = None try: - dssp_path = settings.Locate("dssp") + # same check used in dssp binding + dssp_path = settings.Locate(['dsspcmbi', 'dssp', 'mkdssp'], + env_name='DSSP_EXECUTABLE') except: - try: - dssp_path = settings.Locate("mkdssp") - except: - print "Could not find dssp, could not compare sec struct assignment..." - return + print "Could not find DSSP, could not compare sec struct assignment..." + return dssp_ent = io.LoadPDB(os.path.join("testfiles", "1a0s.pdb")) ost_ent = io.LoadPDB(os.path.join("testfiles", "1a0s.pdb")) - dssp.AssignDSSP(dssp_ent, dssp_bin = dssp_path) + dssp.AssignDSSP(dssp_ent, dssp_bin=dssp_path) mol.alg.AssignSecStruct(ost_ent) for a, b in zip(dssp_ent.residues, ost_ent.residues):