From 27f67ebc9388028e53d5d5b3e3c09a178d26b8a9 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Fri, 27 May 2011 18:41:14 +0200
Subject: [PATCH] Added MatchResidueByGlobalAln, implemented as shared function
with MatchResidueByLocalAln
---
modules/mol/alg/doc/molalg.rst | 2 +
modules/mol/alg/pymod/superpose.py | 76 ++++++++++++++++++++++--------
2 files changed, 58 insertions(+), 20 deletions(-)
diff --git a/modules/mol/alg/doc/molalg.rst b/modules/mol/alg/doc/molalg.rst
index 2ccd72b6a..578d9d1d1 100644
--- a/modules/mol/alg/doc/molalg.rst
+++ b/modules/mol/alg/doc/molalg.rst
@@ -53,6 +53,8 @@
.. autofunction:: MatchResidueByLocalAln
+.. autofunction:: MatchResidueByGlobalAln
+
.. autofunction:: Superpose
diff --git a/modules/mol/alg/pymod/superpose.py b/modules/mol/alg/pymod/superpose.py
index d17194c46..e50a814bc 100644
--- a/modules/mol/alg/pymod/superpose.py
+++ b/modules/mol/alg/pymod/superpose.py
@@ -178,25 +178,9 @@ def MatchResidueByIdx(ent_a, ent_b, atoms='all'):
return result_a, result_b
-def MatchResidueByLocalAln(ent_a, ent_b, atoms='all'):
+def _MatchResidueByAln(ent_a, ent_b, atoms, alnmethod):
"""
- 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.
+ For internal use, only
"""
## init. final views
result_a = _EmptyView(ent_a)
@@ -215,7 +199,7 @@ def MatchResidueByLocalAln(ent_a, ent_b, atoms='all'):
## 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)
+ aln_a_b = alnmethod(seq_a, seq_b, ost.seq.alg.BLOSUM62)
## evaluate alignment
for aln in aln_a_b:
## bind chain to alignment
@@ -231,6 +215,51 @@ def MatchResidueByLocalAln(ent_a, ent_b, atoms='all'):
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. 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.
+
+ :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.
+ """
+ return _MatchResidueByAln(ent_a, ent_b, atoms, ost.seq.alg.LocalAlign)
+
+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.
+
+ :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.
+ """
+ return _MatchResidueByAln(ent_a, ent_b, atoms, ost.seq.alg.GlobalAlign)
+
+
def Superpose(ent_a, ent_b, match='number', atoms='all'):
"""
Superposes the first entity onto the second. To do so, two views are created,
@@ -248,6 +277,9 @@ def Superpose(ent_a, ent_b, match='number', atoms='all'):
* ``local`` - select residues from a Smith/Waterman alignment, includes
**atoms**, calls :func:`~ost.mol.alg.MatchResidueByLocalAln`
+ * ``global`` - select residues from a Needleman/Wunsch alignment, includes
+ **atoms**, calls :func:`~ost.mol.alg.MatchResidueByGlobalAln`
+
:param ent_a: The first entity
:type ent_a: :class:`~ost.mol.EntityView` or :class:`~ost.mol.EntityHandle`
:param ent_b: The second entity
@@ -271,7 +303,11 @@ def Superpose(ent_a, ent_b, match='number', atoms='all'):
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)
+ view_a, view_b=_MatchResidueByAln(ent_a, ent_b, atoms,
+ ost.seq.alg.LocalAlign)
+ elif match.upper() == 'GLOBAL':
+ view_a, view_b=_MatchResidueByAln(ent_a, ent_b, atoms,
+ ost.seq.alg.GlobalAlign)
else:
raise ValueError(not_supported)
## action
--
GitLab