From fa7a8d57976929ffc06d8b69b20d73ab6351ebc2 Mon Sep 17 00:00:00 2001
From: Marco Biasini <marco.biasini@unibas.ch>
Date: Sun, 3 Apr 2011 18:22:32 +0200
Subject: [PATCH] added AlignmentFromChainView
---
modules/seq/alg/doc/seqalg.rst | 6 ++--
modules/seq/alg/pymod/__init__.py | 37 ++++++++++++++++++++++-
modules/seq/base/pymod/export_sequence.cc | 1 +
3 files changed, 41 insertions(+), 3 deletions(-)
diff --git a/modules/seq/alg/doc/seqalg.rst b/modules/seq/alg/doc/seqalg.rst
index ca6476b66..66cbb0f41 100644
--- a/modules/seq/alg/doc/seqalg.rst
+++ b/modules/seq/alg/doc/seqalg.rst
@@ -1,4 +1,4 @@
-:mod:`mol.alg <ost.seq.alg>` -- Algorithms for Sequences
+:mod:`seq.alg <ost.seq.alg>` -- Algorithms for Sequences
================================================================================
.. currentmodule:: ost.seq.alg
@@ -30,4 +30,6 @@
considered as aligned. There is no information in the pairwise alignment to
guide the merging, the result is undefined.
-.. autofunction:: AlignToSEQRES
\ No newline at end of file
+.. autofunction:: AlignToSEQRES
+
+.. autofunction:: AlignmentFromChainView
\ No newline at end of file
diff --git a/modules/seq/alg/pymod/__init__.py b/modules/seq/alg/pymod/__init__.py
index 1862fc812..ce80e939e 100644
--- a/modules/seq/alg/pymod/__init__.py
+++ b/modules/seq/alg/pymod/__init__.py
@@ -39,5 +39,40 @@ def AlignToSEQRES(chain, seqres):
return seq.CreateAlignment(seq.CreateSequence('SEQRES', str(seqres)),
seq.CreateSequence('atoms', aln_seq))
-
+
+def AlignmentFromChainView(chain, handle_seq_name='handle',
+ view_seq_name='view'):
+ """
+ Creates and returns the sequence alignment of the given chain view to the
+ chain handle. The alignment contains two sequences, the first containing all
+ non-ligand peptide-linking residues, the second containing all non-ligand
+ peptide-linking residues that are part of the view.
+ :param chain: A valid chain
+ :type chain: :class:`~ost.mol.ChainView`
+
+ :param handle_seq_name: Name of the handle sequence in the output alignment
+ :param view_seq_name: Name of the view sequence in the output alignment
+ :returns: The alignment
+ :rtype: :class:`~ost.seq.AlignmentHandle`
+
+ """
+ from ost import seq
+ v0=chain.handle.Select('ligand=false and peptide=true')
+ v1=chain.Select('ligand=false and peptide=true')
+ s0=seq.CreateSequence(handle_seq_name, '')
+ s1=seq.CreateSequence(view_seq_name, '')
+ s0.AttachView(v0)
+ s1.AttachView(v1)
+ res0=v0.residues
+ res1=v1.residues
+ idx0, idx1=(0, 0)
+ while idx0<len(res0):
+ s0.Append(res0[idx0].one_letter_code)
+ if idx1<len(res1) and res1[idx1].handle==res0[idx0].handle:
+ s1.Append(res1[idx1].one_letter_code)
+ idx1+=1
+ else:
+ s1.Append('-')
+ idx0+=1
+ return seq.CreateAlignment(s0, s1)
diff --git a/modules/seq/base/pymod/export_sequence.cc b/modules/seq/base/pymod/export_sequence.cc
index ca673fcba..c72fe3ae8 100644
--- a/modules/seq/base/pymod/export_sequence.cc
+++ b/modules/seq/base/pymod/export_sequence.cc
@@ -256,6 +256,7 @@ void export_sequence()
.def("SetOffset", &SequenceHandle::SetOffset)
.def("AttachView", attach_one)
.def("AttachView", attach_two)
+ .def("Append", &SequenceHandle::Append)
.def("SetString", &SequenceHandle::SetString)
.add_property("string",
make_function(&SequenceHandle::GetString,
--
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