diff --git a/modules/mol/alg/pymod/superpose.py b/modules/mol/alg/pymod/superpose.py
index e50a814bc9d2bcac7c56a89a71722761f4ff960d..4cf8de56d57c97e2dc7a46352cff3e3ab30d259c 100644
--- a/modules/mol/alg/pymod/superpose.py
+++ b/modules/mol/alg/pymod/superpose.py
@@ -203,8 +203,8 @@ def _MatchResidueByAln(ent_a, ent_b, atoms, alnmethod):
## evaluate alignment
for aln in aln_a_b:
## bind chain to alignment
- aln.AttachView(0, chain_a.Select(""))
- aln.AttachView(1, chain_b.Select(""))
+ aln.AttachView(0, chain_a.Select('protein=True'))
+ aln.AttachView(1, chain_b.Select('protein=True'))
## select residues (only replacement edges)
for i in range(0, aln.GetLength()):
if aln.sequences[0][i]!='-' and aln.sequences[1][i]!='-':
@@ -218,13 +218,12 @@ def _MatchResidueByAln(ent_a, ent_b, atoms, alnmethod):
def MatchResidueByLocalAln(ent_a, ent_b, atoms='all'):
"""
Match residues by local alignment. Takes **ent_a** and **ent_b**, extracts
- the sequences chain-wise and aligns them in Smith/Waterman manner. For
- scoring, the BLOSUM62 matrix is used. The local alignment is used to gather
- residues from both entities, only touching atoms as defined by **atoms**.
- Regardless of what the list of **atoms** says, only those present in two
- matched residues will be included in the returned views. Chains are processed
- in order of appearance. If **ent_a** and **ent_b** contain a different number
- of chains, processing stops with the lower count.
+ the sequences chain-wise and aligns them in Smith/Waterman manner using the
+ BLOSUM62 matrix for scoring. The residues of the entities are then matched
+ based on this alignment. Only atoms present in both residues are included in
+ the views. Chains are processed in order of appearance. If **ent_a** and
+ **ent_b** contain a different number of chains, processing stops with
+ the lower count.
:param ent_a: The first entity
:type ent_a: :class:`~ost.mol.EntityView` or :class:`~ost.mol.EntityHandle`
@@ -240,13 +239,12 @@ def MatchResidueByLocalAln(ent_a, ent_b, atoms='all'):
def MatchResidueByGlobalAln(ent_a, ent_b, atoms='all'):
"""
Match residues by global alignment. Takes **ent_a** and **ent_b**, extracts
- the sequences chain-wise and aligns them in Needleman/Wunsch manner. For
- scoring, the BLOSUM62 matrix is used. The global alignment is used to gather
- residues from both entities, only touching atoms as defined by **atoms**.
- Regardless of what the list of **atoms** says, only those present in two
- matched residues will be included in the returned views. Chains are processed
- in order of appearance. If **ent_a** and **ent_b** contain a different number
- of chains, processing stops with the lower count.
+ the sequences chain-wise and aligns them in Needleman/Wunsch manner using the
+ BLOSUM62 matrix for scoring. The residues of the entities are then matched
+ based on this alignment. Only atoms present in both residues are included in
+ the views. Chains are processed in order of appearance. If **ent_a** and
+ **ent_b** contain a different number of chains, processing stops with
+ the lower count.
:param ent_a: The first entity
:type ent_a: :class:`~ost.mol.EntityView` or :class:`~ost.mol.EntityHandle`
@@ -274,10 +272,10 @@ def Superpose(ent_a, ent_b, match='number', atoms='all'):
* ``index`` - select residues by index in chain, includes **atoms**, calls
:func:`~ost.mol.alg.MatchResidueByIdx`
- * ``local`` - select residues from a Smith/Waterman alignment, includes
+ * ``local-aln`` - select residues from a Smith/Waterman alignment, includes
**atoms**, calls :func:`~ost.mol.alg.MatchResidueByLocalAln`
- * ``global`` - select residues from a Needleman/Wunsch alignment, includes
+ * ``global-aln`` - select residues from a Needleman/Wunsch alignment, includes
**atoms**, calls :func:`~ost.mol.alg.MatchResidueByGlobalAln`
:param ent_a: The first entity
@@ -290,7 +288,7 @@ def Superpose(ent_a, ent_b, match='number', atoms='all'):
:type atoms: :class:`str`, :class:`list`, :class:`set`
:returns: An instance of :class:`SuperpositionResult`, containing members
- * ``rmsd`` - Rmsd of the superposed entities
+ * ``rmsd`` - RMSD of the superposed entities
* ``view1`` - First :class:`~ost.mol.EntityView` used
@@ -302,10 +300,10 @@ def Superpose(ent_a, ent_b, match='number', atoms='all'):
view_a, view_b = MatchResidueByNum(ent_a, ent_b, atoms)
elif match.upper() == 'INDEX':
view_a, view_b=MatchResidueByIdx(ent_a, ent_b, atoms)
- elif match.upper() == 'LOCAL':
+ elif match.upper() == 'LOCAL-ALN':
view_a, view_b=_MatchResidueByAln(ent_a, ent_b, atoms,
ost.seq.alg.LocalAlign)
- elif match.upper() == 'GLOBAL':
+ elif match.upper() == 'GLOBAL-ALN':
view_a, view_b=_MatchResidueByAln(ent_a, ent_b, atoms,
ost.seq.alg.GlobalAlign)
else:
diff --git a/modules/mol/alg/tests/test_convenient_superpose.py b/modules/mol/alg/tests/test_convenient_superpose.py
index e247b68b2de26b8b5ee0cbf3b66b4a5c3219e8cf..7e03558c06647705589200688fb313df909e5c5b 100644
--- a/modules/mol/alg/tests/test_convenient_superpose.py
+++ b/modules/mol/alg/tests/test_convenient_superpose.py
@@ -27,7 +27,7 @@ class TestConvenientSuperpose(unittest.TestCase):
ent1_view = ent1_ent.Select("")
## test MatchResidueByNum
view1, view2 = mol.alg.MatchResidueByNum(ent1_ent, ent1_ent)
- self.assertEqualAtomOrder(view1, view2)
+ self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByNum(ent1_view, ent1_ent)
self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByNum(ent1_ent, ent1_view)
@@ -36,14 +36,32 @@ class TestConvenientSuperpose(unittest.TestCase):
self.assertEqualAtomOrder(view1, view2)
## test MatchResidueByIdx
view1, view2 = mol.alg.MatchResidueByIdx(ent1_ent, ent1_ent)
- self.assertEqualAtomOrder(view1, view2)
+ self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByIdx(ent1_view, ent1_ent)
self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByIdx(ent1_ent, ent1_view)
self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByIdx(ent1_view, ent1_view)
self.assertEqualAtomOrder(view1, view2)
-
+ ## test MatchResidueByGlobalAln
+ view1, view2 = mol.alg.MatchResidueByGlobalAln(ent1_ent, ent1_ent)
+ self.assertEqualAtomOrder(view1, view2)
+ view1, view2 = mol.alg.MatchResidueByGlobalAln(ent1_view, ent1_ent)
+ self.assertEqualAtomOrder(view1, view2)
+ view1, view2 = mol.alg.MatchResidueByGlobalAln(ent1_ent, ent1_view)
+ self.assertEqualAtomOrder(view1, view2)
+ view1, view2 = mol.alg.MatchResidueByGlobalAln(ent1_view, ent1_view)
+ self.assertEqualAtomOrder(view1, view2)
+ ## test MatchResidueByLocalAln
+ view1, view2 = mol.alg.MatchResidueByLocalAln(ent1_ent, ent1_ent)
+ self.assertEqualAtomOrder(view1, view2)
+ view1, view2 = mol.alg.MatchResidueByLocalAln(ent1_view, ent1_ent)
+ self.assertEqualAtomOrder(view1, view2)
+ view1, view2 = mol.alg.MatchResidueByLocalAln(ent1_ent, ent1_view)
+ self.assertEqualAtomOrder(view1, view2)
+ view1, view2 = mol.alg.MatchResidueByLocalAln(ent1_view, ent1_view)
+ self.assertEqualAtomOrder(view1, view2)
+
def testMissingFirstAtom(self):
ent_view = io.LoadEntity(os.path.join("testfiles","1aho.pdb")).Select("")
ent_view_missing = ent_view.Select("not (cname=A and rnum=1 and aname=N)")
@@ -57,7 +75,17 @@ class TestConvenientSuperpose(unittest.TestCase):
self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByIdx(ent_view_missing, ent_view)
self.assertEqualAtomOrder(view1, view2)
-
+ ## test MatchResidueByGlobalAln
+ view1, view2 = mol.alg.MatchResidueByGlobalAln(ent_view, ent_view_missing)
+ self.assertEqualAtomOrder(view1, view2)
+ view1, view2 = mol.alg.MatchResidueByGlobalAln(ent_view_missing, ent_view)
+ self.assertEqualAtomOrder(view1, view2)
+ ## test MatchResidueByLocalAln
+ view1, view2 = mol.alg.MatchResidueByLocalAln(ent_view, ent_view_missing)
+ self.assertEqualAtomOrder(view1, view2)
+ view1, view2 = mol.alg.MatchResidueByLocalAln(ent_view_missing, ent_view)
+ self.assertEqualAtomOrder(view1, view2)
+
def testMissingManyAtoms(self):
ent_view = io.LoadEntity(os.path.join("testfiles","1aho.pdb")).Select("")
ent_view_missing = ent_view.Select("not (cname=A and rnum=3,19,32 and aname=CB,CA,CD)")
@@ -71,7 +99,17 @@ class TestConvenientSuperpose(unittest.TestCase):
self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByIdx(ent_view_missing, ent_view)
self.assertEqualAtomOrder(view1, view2)
-
+ ## test MatchResidueByGlobalAln
+ view1, view2 = mol.alg.MatchResidueByGlobalAln(ent_view, ent_view_missing)
+ self.assertEqualAtomOrder(view1, view2)
+ view1, view2 = mol.alg.MatchResidueByGlobalAln(ent_view_missing, ent_view)
+ self.assertEqualAtomOrder(view1, view2)
+ ## test MatchResidueByLocalAln
+ view1, view2 = mol.alg.MatchResidueByLocalAln(ent_view, ent_view_missing)
+ self.assertEqualAtomOrder(view1, view2)
+ view1, view2 = mol.alg.MatchResidueByLocalAln(ent_view_missing, ent_view)
+ self.assertEqualAtomOrder(view1, view2)
+
def testMissingFirstResidue(self):
ent_view = io.LoadEntity(os.path.join("testfiles","1aho.pdb")).Select("")
ent_view_missing = ent_view.Select("not (cname=A and rnum=1)")
@@ -80,6 +118,16 @@ class TestConvenientSuperpose(unittest.TestCase):
self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByNum(ent_view_missing, ent_view)
self.assertEqualAtomOrder(view1, view2)
+ ## test MatchResidueByGlobalAln
+ view1, view2 = mol.alg.MatchResidueByGlobalAln(ent_view, ent_view_missing)
+ self.assertEqualAtomOrder(view1, view2)
+ view1, view2 = mol.alg.MatchResidueByGlobalAln(ent_view_missing, ent_view)
+ self.assertEqualAtomOrder(view1, view2)
+ ## test MatchResidueByLocalAln
+ view1, view2 = mol.alg.MatchResidueByLocalAln(ent_view, ent_view_missing)
+ self.assertEqualAtomOrder(view1, view2)
+ view1, view2 = mol.alg.MatchResidueByLocalAln(ent_view_missing, ent_view)
+ self.assertEqualAtomOrder(view1, view2)
def testMissingHydrogens(self):
ent_view = io.LoadEntity(os.path.join("testfiles","1aho.pdb")).Select("")
@@ -116,7 +164,17 @@ class TestConvenientSuperpose(unittest.TestCase):
self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByIdx(ent_view_wrong, ent_view)
self.assertEqualAtomOrder(view1, view2)
-
+ ## test MatchResidueByGlobalAln
+ view1, view2 = mol.alg.MatchResidueByGlobalAln(ent_view, ent_view_wrong)
+ self.assertEqualAtomOrder(view1, view2)
+ view1, view2 = mol.alg.MatchResidueByGlobalAln(ent_view_wrong, ent_view)
+ self.assertEqualAtomOrder(view1, view2)
+ ## test MatchResidueByLocalAln
+ view1, view2 = mol.alg.MatchResidueByLocalAln(ent_view, ent_view_wrong)
+ self.assertEqualAtomOrder(view1, view2)
+ view1, view2 = mol.alg.MatchResidueByLocalAln(ent_view_wrong, ent_view)
+ self.assertEqualAtomOrder(view1, view2)
+
def testWrongResidueOrder(self):
ent_view = io.LoadEntity(os.path.join("testfiles","1aho.pdb")).Select("")
ent_view_wrong = ent_view.CreateEmptyView()
@@ -133,6 +191,6 @@ class TestConvenientSuperpose(unittest.TestCase):
self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByNum(ent_view_wrong, ent_view)
self.assertEqualAtomOrder(view1, view2)
-
+
if __name__ == "__main__":
unittest.main()