diff --git a/modules/mol/alg/doc/molalg.rst b/modules/mol/alg/doc/molalg.rst
index e64bdcfd798f882b6e70ae12432d37f1ed0b9699..9d128af1e1823abfb7da4e2f384b60543a31102c 100644
--- a/modules/mol/alg/doc/molalg.rst
+++ b/modules/mol/alg/doc/molalg.rst
@@ -46,6 +46,8 @@
.. autofunction:: MatchResidueByNum
+.. autofunction:: MatchResidueByIdx
+
.. autofunction:: Superpose
diff --git a/modules/mol/alg/pymod/superpose.py b/modules/mol/alg/pymod/superpose.py
index 44c337d8788d91e9daf33c32b6b14dd976addfe3..5e842b8f1150618371049645adbcf152ec52de5b 100644
--- a/modules/mol/alg/pymod/superpose.py
+++ b/modules/mol/alg/pymod/superpose.py
@@ -27,6 +27,7 @@ def ParseAtomNames(atoms):
:param atoms: Identifier or list of atoms
:type atoms: :class:`str`, :class:`list`, :class:`set`
"""
+ ## get a set of atoms or None
if atoms==None:
return None
if isinstance(atoms, str):
@@ -62,6 +63,16 @@ def _fetch_atoms(r_a, r_b, result_a, result_b, atmset):
return result_a, result_b
+def _no_of_chains(ent_a, ent_b):
+ """
+ for internal use, only
+ """
+ ## get lower no. of chains
+ if ent_a.chain_count < ent_b.chain_count:
+ return ent_a.chain_count
+ return ent_b.chain_count
+
+
def MatchResidueByNum(ent_a, ent_b, atoms='all'):
"""
Returns a tuple of views containing exactly the same number of atoms.
@@ -82,20 +93,15 @@ def MatchResidueByNum(ent_a, ent_b, atoms='all'):
## init. final views
result_a=_EmptyView(ent_a)
result_b=_EmptyView(ent_b)
- ## get lower no. of chains
- if ent_a.chain_count < ent_b.chain_count:
- n_chains=ent_a.chain_count
- else:
- n_chains=ent_b.chain_count
- ## get a set of atoms or None
+ n_chains=_no_of_chains(ent_a, ent_b)
atmset=ParseAtomNames(atoms)
## iterate chains
for i in range(0, n_chains):
chain_a=ent_a.chains[i]
chain_b=ent_b.chains[i]
- ## residues of chains need to be consecutively numbered (sorted)
+ residues_a=iter(chain_a.residues)
+ ## decide on order of residues
if chain_a.InSequence() and chain_b.InSequence():
- residues_a=iter(chain_a.residues)
residues_b=iter(chain_b.residues)
## check residues & copy to views
try:
@@ -112,7 +118,6 @@ def MatchResidueByNum(ent_a, ent_b, atoms='all'):
pass
else:
## iterate one list of residues, search in other list
- residues_a=iter(chain_a.residues)
try:
while True:
r_a=residues_a.next()
@@ -126,6 +131,46 @@ def MatchResidueByNum(ent_a, ent_b, atoms='all'):
return result_a, result_b
+def MatchResidueByIdx(ent_a, ent_b, atoms='all'):
+ """
+ Returns a tuple of views containing exactly the same number of atoms.
+ Residues are matched by position in the chains of an entity. A subset of
+ atoms to be included in the views can be specified in the **atoms** argument.
+ Regardless of what the list of **atoms** says, only those present in two
+ matched residues will be 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. The number of residues per
+ chain is supposed to be the same.
+
+ :param ent_a: The first entity
+ :type ent_a: :class:`~ost.mol.EntityView` or :class:`~ost.mol.EntityHandle`
+ :param ent_b: The second entity
+ :type ent_b: :class:`~ost.mol.EntityView` or :class:`~ost.mol.EntityHandle`
+ :param atoms: The subset of atoms to be included in the two views.
+ :type atoms: :class:`str`, :class:`list`, :class:`set`
+ """
+ not_supported="MatchResidueByIdx has no support for chains of different "\
+ +"lengths"
+ ## init. final views
+ result_a=_EmptyView(ent_a)
+ result_b=_EmptyView(ent_b)
+ n_chains=_no_of_chains(ent_a, ent_b)
+ atmset=ParseAtomNames(atoms)
+ ## iterate chains
+ for i in range(0, n_chains):
+ chain_a=ent_a.chains[i]
+ chain_b=ent_b.chains[i]
+ ## check equal no. of residues
+ if chain_a.residue_count!=chain_b.residue_count:
+ raise RuntimeError(not_supported)
+ ## iterate residues & copy to views
+ for r_a,r_b in zip(chain_a.residues, chain_b.residues):
+ result_a,result_b=_fetch_atoms(r_a, r_b, result_a, result_b, atmset)
+ result_a.AddAllInclusiveBonds()
+ result_b.AddAllInclusiveBonds()
+ return result_a, result_b
+
+
def Superpose(ent_a, ent_b, match='number', atoms='all'):
"""
Superposes the first entity onto the second. To do so, two views are created,
@@ -137,6 +182,9 @@ def Superpose(ent_a, ent_b, match='number', atoms='all'):
* ``number`` - select residues by residue number, includes **atoms**, calls
:func:`~ost.mol.alg.MatchResidueByNum`
+ * ``index`` - select residues by index in chain, includes **atoms**, calls
+ :func:`~ost.mol.alg.MatchResidueByIdx`
+
:param ent_a: The first entity
:type ent_a: :class:`~ost.mol.EntityView` or :class:`~ost.mol.EntityHandle`
:param ent_b: The second entity
@@ -150,6 +198,8 @@ def Superpose(ent_a, ent_b, match='number', atoms='all'):
## create views to superpose
if match.upper()=='NUMBER':
view_a, view_b=MatchResidueByNum(ent_a, ent_b, atoms)
+ elif match.upper()=='INDEX':
+ view_a, view_b=MatchResidueByIdx(ent_a, ent_b, atoms)
else:
raise ValueError(not_supported)
## action
diff --git a/modules/mol/alg/tests/test_convenient_superpose.py b/modules/mol/alg/tests/test_convenient_superpose.py
index 0b8e5bc4f0613f03f3af27fb92866c35c22a7e90..e247b68b2de26b8b5ee0cbf3b66b4a5c3219e8cf 100644
--- a/modules/mol/alg/tests/test_convenient_superpose.py
+++ b/modules/mol/alg/tests/test_convenient_superpose.py
@@ -7,11 +7,6 @@ class TestConvenientSuperpose(unittest.TestCase):
def setUp(self):
pass
- def runAtomOrdering(self, view1, view2):
- # call atom ordering function here
- view1, view2 = ost.mol.alg.MatchResidueByNum(view1, view2)
- return view1, view2
-
def assertEqualAtomOrder(self, view1, view2):
self.assertEquals(len(view1.atoms),len(view2.atoms))
for a1, a2 in zip(view1.atoms, view2.atoms):
@@ -30,45 +25,74 @@ class TestConvenientSuperpose(unittest.TestCase):
def testCorrectlyOrdered(self):
ent1_ent = io.LoadEntity(os.path.join("testfiles","1aho.pdb"))
ent1_view = ent1_ent.Select("")
- view1, view2 = self.runAtomOrdering(ent1_ent, ent1_ent)
+ ## test MatchResidueByNum
+ view1, view2 = mol.alg.MatchResidueByNum(ent1_ent, ent1_ent)
+ 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)
+ self.assertEqualAtomOrder(view1, view2)
+ view1, view2 = mol.alg.MatchResidueByNum(ent1_view, ent1_view)
+ self.assertEqualAtomOrder(view1, view2)
+ ## test MatchResidueByIdx
+ view1, view2 = mol.alg.MatchResidueByIdx(ent1_ent, ent1_ent)
self.assertEqualAtomOrder(view1, view2)
- view1, view2 = self.runAtomOrdering(ent1_view, ent1_ent)
+ view1, view2 = mol.alg.MatchResidueByIdx(ent1_view, ent1_ent)
self.assertEqualAtomOrder(view1, view2)
- view1, view2 = self.runAtomOrdering(ent1_ent, ent1_view)
+ view1, view2 = mol.alg.MatchResidueByIdx(ent1_ent, ent1_view)
self.assertEqualAtomOrder(view1, view2)
- view1, view2 = self.runAtomOrdering(ent1_view, ent1_view)
+ view1, view2 = mol.alg.MatchResidueByIdx(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)")
- view1, view2 = self.runAtomOrdering(ent_view, ent_view_missing)
+ ## test MatchResidueByNum
+ view1, view2 = mol.alg.MatchResidueByNum(ent_view, ent_view_missing)
+ self.assertEqualAtomOrder(view1, view2)
+ view1, view2 = mol.alg.MatchResidueByNum(ent_view_missing, ent_view)
self.assertEqualAtomOrder(view1, view2)
- view1, view2 = self.runAtomOrdering(ent_view_missing, ent_view)
+ ## test MatchResidueByIdx
+ view1, view2 = mol.alg.MatchResidueByIdx(ent_view, ent_view_missing)
+ self.assertEqualAtomOrder(view1, view2)
+ view1, view2 = mol.alg.MatchResidueByIdx(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)")
- view1, view2 = self.runAtomOrdering(ent_view, ent_view_missing)
+ ## test MatchResidueByNum
+ view1, view2 = mol.alg.MatchResidueByNum(ent_view, ent_view_missing)
+ self.assertEqualAtomOrder(view1, view2)
+ view1, view2 = mol.alg.MatchResidueByNum(ent_view_missing, ent_view)
self.assertEqualAtomOrder(view1, view2)
- view1, view2 = self.runAtomOrdering(ent_view_missing, ent_view)
+ ## test MatchResidueByIdx
+ view1, view2 = mol.alg.MatchResidueByIdx(ent_view, ent_view_missing)
+ self.assertEqualAtomOrder(view1, view2)
+ view1, view2 = mol.alg.MatchResidueByIdx(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)")
- view1, view2 = self.runAtomOrdering(ent_view, ent_view_missing)
+ ## test MatchResidueByNum
+ view1, view2 = mol.alg.MatchResidueByNum(ent_view, ent_view_missing)
self.assertEqualAtomOrder(view1, view2)
- view1, view2 = self.runAtomOrdering(ent_view_missing, ent_view)
+ view1, view2 = mol.alg.MatchResidueByNum(ent_view_missing, ent_view)
self.assertEqualAtomOrder(view1, view2)
-
+
def testMissingHydrogens(self):
ent_view = io.LoadEntity(os.path.join("testfiles","1aho.pdb")).Select("")
ent_view_missing = ent_view.Select("ele!=H")
- view1, view2 = self.runAtomOrdering(ent_view, ent_view_missing)
+ ## test MatchResidueByNum
+ view1, view2 = mol.alg.MatchResidueByNum(ent_view, ent_view_missing)
+ self.assertEqualAtomOrder(view1, view2)
+ view1, view2 = mol.alg.MatchResidueByNum(ent_view_missing, ent_view)
self.assertEqualAtomOrder(view1, view2)
- view1, view2 = self.runAtomOrdering(ent_view_missing, ent_view)
+ ## test MatchResidueByIdx
+ view1, view2 = mol.alg.MatchResidueByIdx(ent_view, ent_view_missing)
+ self.assertEqualAtomOrder(view1, view2)
+ view1, view2 = mol.alg.MatchResidueByIdx(ent_view_missing, ent_view)
self.assertEqualAtomOrder(view1, view2)
def testWrongAtomOrder(self):
@@ -82,9 +106,15 @@ class TestConvenientSuperpose(unittest.TestCase):
random.shuffle(atoms)
for a in atoms:
ent_view_wrong.AddAtom(a)
- view1, view2 = self.runAtomOrdering(ent_view, ent_view_wrong)
+ ## test MatchResidueByNum
+ view1, view2 = mol.alg.MatchResidueByNum(ent_view, ent_view_wrong)
+ self.assertEqualAtomOrder(view1, view2)
+ view1, view2 = mol.alg.MatchResidueByNum(ent_view_wrong, ent_view)
+ self.assertEqualAtomOrder(view1, view2)
+ ## test MatchResidueByIdx
+ view1, view2 = mol.alg.MatchResidueByIdx(ent_view, ent_view_wrong)
self.assertEqualAtomOrder(view1, view2)
- view1, view2 = self.runAtomOrdering(ent_view_wrong, ent_view)
+ view1, view2 = mol.alg.MatchResidueByIdx(ent_view_wrong, ent_view)
self.assertEqualAtomOrder(view1, view2)
def testWrongResidueOrder(self):
@@ -98,9 +128,10 @@ class TestConvenientSuperpose(unittest.TestCase):
ent_view_wrong.AddResidue(r)
for a in r.atoms:
av=ent_view_wrong.AddAtom(a)
- view1, view2 = self.runAtomOrdering(ent_view, ent_view_wrong)
+ ## test MatchResidueByNum
+ view1, view2 = mol.alg.MatchResidueByNum(ent_view, ent_view_wrong)
self.assertEqualAtomOrder(view1, view2)
- view1, view2 = self.runAtomOrdering(ent_view_wrong, ent_view)
+ view1, view2 = mol.alg.MatchResidueByNum(ent_view_wrong, ent_view)
self.assertEqualAtomOrder(view1, view2)
if __name__ == "__main__":