From 1b7f6ea2a695e1ae9d5af774b71c93a9b8180967 Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Tue, 22 Aug 2017 16:02:22 +0200
Subject: [PATCH] SCHWED-2638: fixed/cleaned-up dssp-locate-check in unit tests
---
modules/mol/alg/tests/test_accessibility.py | 17 ++++++-----------
modules/mol/alg/tests/test_sec_struct.py | 14 ++++++--------
2 files changed, 12 insertions(+), 19 deletions(-)
diff --git a/modules/mol/alg/tests/test_accessibility.py b/modules/mol/alg/tests/test_accessibility.py
index 3ff4c0fde..c3d857fd5 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 3c2d11295..207f8600c 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):
--
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