diff --git a/modules/mol/alg/doc/molalg.rst b/modules/mol/alg/doc/molalg.rst
index 32bd3dd54897266ccff8b3f4d9b5192288c49a93..2ccd72b6a78f84887938be38ac17a781ea9f4acc 100644
--- a/modules/mol/alg/doc/molalg.rst
+++ b/modules/mol/alg/doc/molalg.rst
@@ -51,6 +51,8 @@
.. autofunction:: MatchResidueByIdx
+.. autofunction:: MatchResidueByLocalAln
+
.. autofunction:: Superpose
diff --git a/modules/mol/alg/pymod/superpose.py b/modules/mol/alg/pymod/superpose.py
index 5e842b8f1150618371049645adbcf152ec52de5b..d17194c46d49842f2226e854f22c48946df42478 100644
--- a/modules/mol/alg/pymod/superpose.py
+++ b/modules/mol/alg/pymod/superpose.py
@@ -6,7 +6,7 @@ Authors: Stefan Bienert
import math
import ost.mol.alg
-
+import ost.seq.alg
def ParseAtomNames(atoms):
"""
@@ -26,6 +26,7 @@ def ParseAtomNames(atoms):
:param atoms: Identifier or list of atoms
:type atoms: :class:`str`, :class:`list`, :class:`set`
+ :returns: A :class:`set` of atoms.
"""
## get a set of atoms or None
if atoms==None:
@@ -89,6 +90,9 @@ def MatchResidueByNum(ent_a, ent_b, atoms='all'):
: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`
+ :returns: Two :class:`~ost.mol.EntityView` instances with the same amount of
+ residues matched by number. Each residue will have the same number
+ & type of atoms.
"""
## init. final views
result_a=_EmptyView(ent_a)
@@ -148,6 +152,9 @@ def MatchResidueByIdx(ent_a, ent_b, atoms='all'):
: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`
+ :returns: Two :class:`~ost.mol.EntityView` instances with the same amount of
+ residues matched by position. Each residue will have the same number
+ & type of atoms.
"""
not_supported="MatchResidueByIdx has no support for chains of different "\
+"lengths"
@@ -164,13 +171,66 @@ def MatchResidueByIdx(ent_a, ent_b, atoms='all'):
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):
+ 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 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. This local
+ alignment is then 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.
+
+ :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`
+ :returns: Two :class:`~ost.mol.EntityView` instances with the same number of
+ residues. Each residue will have the same number & type of atoms.
+ """
+ ## 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]
+ ## fetch residues
+ s_a = ''.join([r.one_letter_code
+ for r in chain_a.Select('protein=True').residues])
+ s_b = ''.join([r.one_letter_code
+ for r in chain_b.Select('protein=True').residues])
+ ## create sequence from residue lists & alignment
+ seq_a = ost.seq.CreateSequence(chain_a.name, s_a)
+ seq_b = ost.seq.CreateSequence(chain_b.name, s_b)
+ aln_a_b = ost.seq.alg.LocalAlign(seq_a, seq_b, ost.seq.alg.BLOSUM62)
+ ## evaluate alignment
+ for aln in aln_a_b:
+ ## bind chain to alignment
+ aln.AttachView(0, chain_a.Select(""))
+ aln.AttachView(1, chain_b.Select(""))
+ ## select residues (only replacement edges)
+ for i in range(0, aln.GetLength()):
+ if aln.sequences[0][i]!='-' and aln.sequences[1][i]!='-':
+ r_a = aln.GetResidue(0,i)
+ r_b = aln.GetResidue(1,i)
+ 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,
@@ -185,6 +245,9 @@ 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
+ **atoms**, calls :func:`~ost.mol.alg.MatchResidueByLocalAln`
+
:param ent_a: The first entity
:type ent_a: :class:`~ost.mol.EntityView` or :class:`~ost.mol.EntityHandle`
:param ent_b: The second entity
@@ -193,13 +256,22 @@ def Superpose(ent_a, ent_b, match='number', atoms='all'):
:type match: :class:`str`
:param atoms: The subset of atoms to be used in the superposition.
:type atoms: :class:`str`, :class:`list`, :class:`set`
+ :returns: An instance of :class:`SuperpositionResult`, containing members
+
+ * ``rmsd`` - Rmsd of the superposed entities
+
+ * ``view1`` - First :class:`~ost.mol.EntityView` used
+
+ * ``view2`` - Second :class:`~ost.mol.EntityView` used
"""
not_supported="Superpose called with unsupported matching request."
## create views to superpose
- if match.upper()=='NUMBER':
- view_a, view_b=MatchResidueByNum(ent_a, ent_b, atoms)
- elif match.upper()=='INDEX':
+ 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)
+ elif match.upper() == 'LOCAL':
+ view_a, view_b=MatchResidueByLocalAln(ent_a, ent_b, atoms)
else:
raise ValueError(not_supported)
## action