Merge branch 'develop' into dockerize

modules/conop/doc/cleanup.rst

 :mod:`conop.cleanup <ost.conop.cleanup>` -- Sanitize structures
 ================================================================================
 
-.. module:: ost.conop.ceanup
+.. module:: ost.conop.cleanup
    :synopsis: Contains functions to sanitize (cleanup) structures by using 
         information from the compound library.
 

modules/io/src/mol/chemdict_parser.cc

@@ -195,17 +195,18 @@ void ChemdictParser::InitTypeMap()
   tm_["DNA LINKING"]=mol::ChemClass(mol::ChemClass::DNA_LINKING);
   tm_["RNA LINKING"]=mol::ChemClass(mol::ChemClass::RNA_LINKING);
   tm_["L-DNA LINKING"]=mol::ChemClass(mol::ChemClass::DNA_LINKING);
-  tm_["L-RNA LINKING"]=mol::ChemClass(mol::ChemClass::RNA_LINKING);  
+  tm_["L-RNA LINKING"]=mol::ChemClass(mol::ChemClass::RNA_LINKING);
   tm_["R-DNA LINKING"]=mol::ChemClass(mol::ChemClass::DNA_LINKING);
-  tm_["R-RNA LINKING"]=mol::ChemClass(mol::ChemClass::RNA_LINKING);  
+  tm_["R-RNA LINKING"]=mol::ChemClass(mol::ChemClass::RNA_LINKING);
   tm_["DNA OH 3 PRIME TERMINUS"]=mol::ChemClass(mol::ChemClass::DNA_LINKING);
+  tm_["DNA OH 5 PRIME TERMINUS"]=mol::ChemClass(mol::ChemClass::DNA_LINKING);
   tm_["PEPTIDE-LIKE"]=mol::ChemClass(mol::ChemClass::PEPTIDE_LINKING);
   tm_["PEPTIDE LINKING"]=mol::ChemClass(mol::ChemClass::PEPTIDE_LINKING);
-  tm_["PEPTIDE-LINKING"]=mol::ChemClass(mol::ChemClass::PEPTIDE_LINKING);  
+  tm_["PEPTIDE-LINKING"]=mol::ChemClass(mol::ChemClass::PEPTIDE_LINKING);
   tm_["NON-POLYMER"]=mol::ChemClass(mol::ChemClass::NON_POLYMER);
   tm_["RNA OH 3 PRIME TERMINUS"]=mol::ChemClass(mol::ChemClass::RNA_LINKING);
   tm_["RNA OH 5 PRIME TERMINUS"]=mol::ChemClass(mol::ChemClass::RNA_LINKING);
-  tm_["?"]=mol::ChemClass(mol::ChemClass::UNKNOWN);  
+  tm_["?"]=mol::ChemClass(mol::ChemClass::UNKNOWN);
   tm_["WATER"]=mol::ChemClass(mol::ChemClass::WATER);
 }
 

modules/mol/alg/pymod/qsscoring.py

@@ -56,6 +56,8 @@ class QSscorer:
       qs_scorer = qsscoring.QSscorer(ent_1, ent_2)
       ost.LogScript('QSscore:', str(qs_scorer.global_score))
       ost.LogScript('Chain mapping used:', str(qs_scorer.chain_mapping))
+      # commonly you want the QS global score as output
+      qs_score = qs_scorer.global_score
     except qsscoring.QSscoreError as ex:
       # default handling: report failure and set score to 0
       ost.LogError('QSscore failed:', str(ex))

modules/mol/base/tests/CMakeLists.txt

@@ -17,7 +17,7 @@ set(OST_MOL_BASE_UNIT_TESTS
 )
 
 if (USE_NUMPY)
-   set(OST_MOST_BASE_UNIT_TESTS "${OST_MOST_BASE_UNIT_TESTS}" test_numpy.py)
+  list(APPEND OST_MOL_BASE_UNIT_TESTS test_numpy.py)
 endif (USE_NUMPY)
 
 ost_unittest(MODULE mol SOURCES "${OST_MOL_BASE_UNIT_TESTS}")

modules/mol/base/tests/test_numpy.py

@@ -5,6 +5,7 @@ if __name__== '__main__':
   sys.path.insert(0,"../../../../stage/lib/openstructure/")
   
 import ost
+from ost import geom, mol
 
 if ost.WITH_NUMPY:
   has_numpy=True
@@ -16,10 +17,10 @@ else:
   has_numpy=False
 
 def v2v(v):
-  return ost.geom.Vec3(float(v[0]),float(v[1]),float(v[2]))
+  return geom.Vec3(float(v[0]),float(v[1]),float(v[2]))
 
 def dd(v1,v2):
-  return ost.geom.Distance(v1,v2)<1e-8
+  return geom.Distance(v1,v2)<1e-8
 
 class TestNumpy(unittest.TestCase):
   def setUp(self):
@@ -28,46 +29,46 @@ class TestNumpy(unittest.TestCase):
   def test_(self):
     if not has_numpy:
       return
-    entity=ost.mol.CreateEntity()
+    entity=mol.CreateEntity()
     ed=entity.EditXCS()
     ch=ed.InsertChain("X")
     re=ed.AppendResidue(ch,"ALA")
-    a0=ed.InsertAtom(re,"A",ost.geom.Vec3(0,0,0))
+    a0=ed.InsertAtom(re,"A",geom.Vec3(0,0,0))
     self.assertEqual(a0.GetIndex(),0)
-    a1=ed.InsertAtom(re,"B",ost.geom.Vec3(1,0,0))
+    a1=ed.InsertAtom(re,"B",geom.Vec3(1,0,0))
     self.assertEqual(a1.GetIndex(),1)
-    a2=ed.InsertAtom(re,"C",ost.geom.Vec3(2,0,0))
+    a2=ed.InsertAtom(re,"C",geom.Vec3(2,0,0))
     self.assertEqual(a2.GetIndex(),2)
-    a3=ed.InsertAtom(re,"D",ost.geom.Vec3(3,0,0))
+    a3=ed.InsertAtom(re,"D",geom.Vec3(3,0,0))
     self.assertEqual(a3.GetIndex(),3)
 
-    self.assertTrue(dd(a0.pos,ost.geom.Vec3(0,0,0)))
-    self.assertTrue(dd(a1.pos,ost.geom.Vec3(1,0,0)))
-    self.assertTrue(dd(a2.pos,ost.geom.Vec3(2,0,0)))
-    self.assertTrue(dd(a3.pos,ost.geom.Vec3(3,0,0)))
+    self.assertTrue(dd(a0.pos,geom.Vec3(0,0,0)))
+    self.assertTrue(dd(a1.pos,geom.Vec3(1,0,0)))
+    self.assertTrue(dd(a2.pos,geom.Vec3(2,0,0)))
+    self.assertTrue(dd(a3.pos,geom.Vec3(3,0,0)))
 
     ed.SetAtomTransformedPos(entity.GetAtomList(),
                              numpy.array([[0,1,0],[0,2,0],[0,3,0],[0,4,0]], dtype=numpy.float32))
 
-    self.assertTrue(dd(a0.pos,ost.geom.Vec3(0,1,0)))
-    self.assertTrue(dd(a1.pos,ost.geom.Vec3(0,2,0)))
-    self.assertTrue(dd(a2.pos,ost.geom.Vec3(0,3,0)))
-    self.assertTrue(dd(a3.pos,ost.geom.Vec3(0,4,0)))
+    self.assertTrue(dd(a0.pos,geom.Vec3(0,1,0)))
+    self.assertTrue(dd(a1.pos,geom.Vec3(0,2,0)))
+    self.assertTrue(dd(a2.pos,geom.Vec3(0,3,0)))
+    self.assertTrue(dd(a3.pos,geom.Vec3(0,4,0)))
 
     na=entity.positions
 
-    self.assertTrue(dd(v2v(na[0]),ost.geom.Vec3(0,1,0)))
-    self.assertTrue(dd(v2v(na[1]),ost.geom.Vec3(0,2,0)))
-    self.assertTrue(dd(v2v(na[2]),ost.geom.Vec3(0,3,0)))
-    self.assertTrue(dd(v2v(na[3]),ost.geom.Vec3(0,4,0)))
+    self.assertTrue(dd(v2v(na[0]),geom.Vec3(0,1,0)))
+    self.assertTrue(dd(v2v(na[1]),geom.Vec3(0,2,0)))
+    self.assertTrue(dd(v2v(na[2]),geom.Vec3(0,3,0)))
+    self.assertTrue(dd(v2v(na[3]),geom.Vec3(0,4,0)))
 
     ed.SetAtomTransformedPos([3,99,2],
                              numpy.array([[0,0,-3],[-1,-1,-1],[0,0,-2]], dtype=numpy.float32))
 
-    self.assertTrue(dd(a0.pos,ost.geom.Vec3(0,1,0)))
-    self.assertTrue(dd(a1.pos,ost.geom.Vec3(0,2,0)))
-    self.assertTrue(dd(a2.pos,ost.geom.Vec3(0,0,-2)))
-    self.assertTrue(dd(a3.pos,ost.geom.Vec3(0,0,-3)))
+    self.assertTrue(dd(a0.pos,geom.Vec3(0,1,0)))
+    self.assertTrue(dd(a1.pos,geom.Vec3(0,2,0)))
+    self.assertTrue(dd(a2.pos,geom.Vec3(0,0,-2)))
+    self.assertTrue(dd(a3.pos,geom.Vec3(0,0,-3)))
 
 if __name__== '__main__':
     unittest.main()