diff --git a/modules/base/src/CMakeLists.txt b/modules/base/src/CMakeLists.txt
index 30660f6d5cdb4511271e8fb771b3ad4d11bcbb6f..386e9d920a5f23f59dd187bc0d25e6db7d3faac2 100644
--- a/modules/base/src/CMakeLists.txt
+++ b/modules/base/src/CMakeLists.txt
@@ -30,8 +30,13 @@ fixed_string.hh
tri_matrix.hh
)
+set(OST_EXPORT_HELPERS
+generic_property_def.hh
+pair_to_tuple_conv.hh
+)
module(NAME base SOURCES ${OST_BASE_SOURCES}
- HEADERS generic_property_def.hh IN_DIR export_helper compare_files.hh IN_DIR test_utils ${OST_BASE_HEADERS}
+ HEADERS ${OST_EXPORT_HELPERS} IN_DIR export_helper
+ compare_files.hh IN_DIR test_utils ${OST_BASE_HEADERS}
DEPENDS_ON geom
HEADER_OUTPUT_DIR ost)
diff --git a/modules/base/src/export_helper/pair_to_tuple_conv.hh b/modules/base/src/export_helper/pair_to_tuple_conv.hh
new file mode 100644
index 0000000000000000000000000000000000000000..eba6ebd9b1ebbdbd7723d6ebaee656d0121e02d8
--- /dev/null
+++ b/modules/base/src/export_helper/pair_to_tuple_conv.hh
@@ -0,0 +1,37 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2010 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+#include <boost/python.hpp>
+
+namespace ost {
+
+/// \brief helper to convert between python tuple and std::pair
+///
+/// Usage:
+///
+/// register_to_python_converter<PairToTupleConverter<T1, T2>,
+/// std::pair<T1, T2>>()
+template<class T1, class T2>
+struct PairToTupleConverter {
+ static PyObject* convert(const std::pair<T1, T2>& pair) {
+ boost::python::tuple t=boost::python::make_tuple<T1,T2>(pair.first,
+ pair.second);
+ return boost::python::incref(t.ptr());
+ }
+};
+}
\ No newline at end of file
diff --git a/modules/gfx/pymod/export_entity.cc b/modules/gfx/pymod/export_entity.cc
index 23e341b04754d0d960e78747277459dba023d54c..a81f8299ea0cdc549b1fb34b0255cdb66f4938d7 100644
--- a/modules/gfx/pymod/export_entity.cc
+++ b/modules/gfx/pymod/export_entity.cc
@@ -23,7 +23,7 @@ using namespace boost::python;
#include <ost/gfx/entity.hh>
using namespace ost;
using namespace ost::gfx;
-
+#include <ost/export_helper/pair_to_tuple_conv.hh>
#include "color_by_def.hh"
namespace {
@@ -177,14 +177,6 @@ void ent_apply_62(Entity* e, MapHandleColorOp& mhco){
}
#endif //OST_IMG_ENABLED
-template<class T1, class T2>
-struct PairToTupleConverter {
- static PyObject* convert(const std::pair<T1, T2>& pair) {
- tuple t=boost::python::make_tuple<T1,T2>(pair.first,pair.second);
- return incref(t.ptr());
- }
-};
-
RenderOptionsPtr ent_sline_opts(Entity* ent)
{
diff --git a/modules/seq/base/pymod/__init__.py b/modules/seq/base/pymod/__init__.py
index 27e186b7565ace6021f3cff5e274d9181c23b291..0bc8f1b300e952bbf5ce5ae9bd52cbf9735c3420 100644
--- a/modules/seq/base/pymod/__init__.py
+++ b/modules/seq/base/pymod/__init__.py
@@ -16,67 +16,4 @@
# along with this library; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
#------------------------------------------------------------------------------
-from _seq import *
-from ost import mol
-
-## \brief Create two views from sequence alignment such that the matching
-# residues occur at the same index within the chain.
-#
-# The first sequence in the sequence alignment belongs to ent_a, the second to
-# ent_b.
-#
-# Requires that each of the entities/views only contains one chain and that
-# the sequence offset of the sequences in the alignment is set appropriately.
-def ViewsFromAlignment(multi_seq_ali, ent_a, ent_b, include_atoms=True):
- seq_a=multi_seq_ali.GetSequence(0)
- seq_b=multi_seq_ali.GetSequence(1)
- return ViewsFromSequences(seq_a, seq_b, ent_a, ent_b, include_atoms)
-
-def ViewsFromSequences(seq_a, seq_b, ent_a=None, ent_b=None,
- include_atoms=True):
- ent_a=ent_a or seq_a.attached_view
- ent_b=ent_b or seq_b.attached_view
- if ent_a.chain_count>1:
- raise RuntimeError("first entity contains more than one chain")
- if ent_b.chain_count>1:
- raise RuntimeError("second entity contains more than one chain")
- is_ha=isinstance(ent_a, mol.EntityHandle)
- is_hb=isinstance(ent_b, mol.EntityHandle)
-
- ev_a= is_ha and ent_a.CreateEmptyView() or ent_a.handle.CreateEmptyView()
- ev_b= is_hb and ent_b.CreateEmptyView() or ent_b.handle.CreateEmptyView()
-
- flags=include_atoms and mol.ViewAddFlag.INCLUDE_ATOMS or 0
- res_a=ent_a.residues
- res_b=ent_b.residues
- off_a=seq_a.GetSequenceOffset()
- off_b=seq_b.GetSequenceOffset()
-
- index_a, index_b=(0, 0)
- done=False
- #~ for i,j in zip(ent_a.residues,ent_b.residues): print i,i.index,j,j.index
- #~ print
- while index_a<seq_a.GetLength() and index_b<seq_b.GetLength():
- while seq_a.GetOneLetterCode(index_a+off_b)=='-':
- index_a+=1
- print 'gap a'
- if seq_a.GetLength()<=index_a+off_b:
- done=True
- break
- while seq_b.GetOneLetterCode(index_b+off_a)=='-':
- index_b+=1
- print 'gap b'
- if seq_b.GetLength()<=index_b+off_a:
- done=True
- break
- if done or len(res_a)<=index_b+off_a or len(res_b)<=index_a+off_b:
- break
- ra=res_a[off_a+index_b]
- rb=res_b[off_b+index_a]
- print 'index_a',index_a, seq_a.GetLength(),seq_a.GetOneLetterCode(index_a+off_a),ra
- print 'index_b',index_b, seq_b.GetLength(),seq_b.GetOneLetterCode(index_b+off_b),rb
- ev_a.AddResidue(is_ha and ra or ra.handle, flags)
- ev_b.AddResidue(is_hb and rb or rb.handle, flags)
- index_a+=1
- index_b+=1
- return ev_a, ev_b
+from _seq import *
\ No newline at end of file
diff --git a/modules/seq/base/pymod/export_sequence.cc b/modules/seq/base/pymod/export_sequence.cc
index 87f9d3a6f9dde794a00586cb7aecba81541f8cf1..ce0e19864e6e6d4ee182b4f74391f31c32a078bf 100644
--- a/modules/seq/base/pymod/export_sequence.cc
+++ b/modules/seq/base/pymod/export_sequence.cc
@@ -20,8 +20,9 @@
#include <boost/python/slice.hpp>
#include <boost/python/register_ptr_to_python.hpp>
#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
-using namespace boost::python;
+
+#include <ost/export_helper/pair_to_tuple_conv.hh>
#include <ost/generic_property.hh>
#include <ost/export_helper/generic_property_def.hh>
#include <ost/info/info.hh>
@@ -31,10 +32,12 @@ using namespace boost::python;
#include <ost/seq/sequence_op.hh>
#include <ost/seq/sequence_list.hh>
#include <ost/seq/aligned_region.hh>
+#include <ost/seq/views_from_sequences.hh>
#include "const_seq_list_export_def.hh"
using namespace ost;
using namespace ost::seq;
+using namespace boost::python;
namespace {
@@ -292,10 +295,15 @@ void export_sequence()
.def("__getitem__", &do_slice_b)
;
implicitly_convertible<SequenceList, ConstSequenceList>();
+ to_python_converter<std::pair<mol::EntityView, mol::EntityView>,
+ PairToTupleConverter<mol::EntityView, mol::EntityView> >();
def("CreateSequenceList", &CreateSequenceList);
def("SequenceFromChain", seq_from_chain_a);
def("SequenceFromChain", seq_from_chain_b);
def("SequenceToInfo", &SequenceToInfo);
+ def("ViewsFromSequences", &ViewsFromSequences, (arg("seq1"), arg("seq2")));
+ def("ViewsFromAlignment", &ViewsFromAlignment,
+ (arg("aln"), arg("index1")=0, arg("index2")=1));
def("SequenceListToInfo", &SequenceListToInfo);
def("SequenceFromInfo", &SequenceFromInfo);
def("CreateAlignment", &CreateAlignment);
diff --git a/modules/seq/base/src/CMakeLists.txt b/modules/seq/base/src/CMakeLists.txt
index 3cd12d19a6af292471fde3dbb6d85c32e5eaaef5..9a7015bdae3e8162ab76c711893a70e874fea101 100644
--- a/modules/seq/base/src/CMakeLists.txt
+++ b/modules/seq/base/src/CMakeLists.txt
@@ -15,6 +15,7 @@ aligned_region.hh
aligned_column.hh
aligned_column_iterator.hh
invalid_sequence.hh
+views_from_sequences.hh
)
set(OST_SEQ_SOURCES
@@ -26,6 +27,7 @@ aligned_column.cc
sequence_list.cc
alignment_handle.cc
sequence_op.cc
+views_from_sequences.cc
)
module(NAME seq SOURCES ${OST_SEQ_SOURCES}
HEADERS ${OST_SEQ_IMPL_HEADERS} IN_DIR impl
diff --git a/modules/seq/base/src/sequence_handle.cc b/modules/seq/base/src/sequence_handle.cc
index eeb3d1acb8f363c750c3327e7e4a648d36f88a9c..a7f5347e1f36521635b28d4ef6076b0c876ef8a0 100644
--- a/modules/seq/base/src/sequence_handle.cc
+++ b/modules/seq/base/src/sequence_handle.cc
@@ -51,6 +51,11 @@ bool ConstSequenceHandle::operator!=(const ConstSequenceHandle& rhs) const
return impl_!=rhs.impl_;
}
+char ConstSequenceHandle::operator[](int index) const
+{
+ this->CheckValidity();
+ return this->GetOneLetterCode(index);
+}
void ConstSequenceHandle::CheckValidity() const
{
diff --git a/modules/seq/base/src/sequence_handle.hh b/modules/seq/base/src/sequence_handle.hh
index ad4d294e33f518cc6575ff1aed82df63db3397c3..de03a505be77b43ad87b9c5d97edf2a9a681a01b 100644
--- a/modules/seq/base/src/sequence_handle.hh
+++ b/modules/seq/base/src/sequence_handle.hh
@@ -116,6 +116,8 @@ public:
bool operator==(const ConstSequenceHandle& rhs) const;
bool operator!=(const ConstSequenceHandle& rhs) const;
+ char operator[](int index) const;
+
/// \brief whether the sequence is valid
bool IsValid() const;
/// \internal
diff --git a/modules/seq/base/src/views_from_sequences.cc b/modules/seq/base/src/views_from_sequences.cc
new file mode 100644
index 0000000000000000000000000000000000000000..7ab0ff1f6806c1d303baac5e0689f12d06d91f89
--- /dev/null
+++ b/modules/seq/base/src/views_from_sequences.cc
@@ -0,0 +1,87 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2010 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+#include <ost/integrity_error.hh>
+#include <ost/seq/views_from_sequences.hh>
+
+namespace ost { namespace seq {
+
+namespace {
+
+bool skip_gaps(const ConstSequenceHandle& seq1,
+ const ConstSequenceHandle& seq2, int& pos,
+ int& index_a, int& index_b)
+{
+ while (seq1.GetLength()>pos) {
+ if (seq1[pos]=='-') {
+ if (seq2[pos]!='-') {
+ index_b+=1;
+ }
+ } else if (seq2[pos]=='-') {
+ index_a+=1;
+ } else {
+ return true;
+ }
+ pos+=1;
+ }
+ return false;
+}
+
+}
+
+std::pair<mol::EntityView, mol::EntityView>
+ViewsFromSequences(const ConstSequenceHandle& seq1,
+ const ConstSequenceHandle& seq2)
+{
+ if (seq1.GetLength()!=seq2.GetLength()) {
+ throw IntegrityError("Sequence lengths do not match");
+ }
+ if (!seq1.HasAttachedView()) {
+ throw IntegrityError("First sequence does not have an attached view");
+ }
+ if (!seq2.HasAttachedView()) {
+ throw IntegrityError("Second sequence does not have an attached view");
+ }
+ mol::EntityView src_a=seq1.GetAttachedView();
+ mol::EntityView src_b=seq2.GetAttachedView();
+
+ mol::EntityView dst_a=src_a.CreateEmptyView();
+ mol::EntityView dst_b=src_b.CreateEmptyView();
+ mol::ResidueViewList res_a=src_a.GetResidueList();
+ mol::ResidueViewList res_b=src_b.GetResidueList();
+ int pos=0, index_a=0, index_b=0;
+ while (skip_gaps(seq1, seq2, pos, index_a, index_b)) {
+ dst_a.AddResidue(res_a.at(seq1.GetSequenceOffset()+index_a),
+ mol::ViewAddFlag::INCLUDE_ATOMS);
+ dst_b.AddResidue(res_b.at(seq2.GetSequenceOffset()+index_b),
+ mol::ViewAddFlag::INCLUDE_ATOMS);
+ pos+=1;
+ index_a+=1;
+ index_b+=1;
+ }
+ return std::make_pair(dst_a, dst_b);
+}
+
+
+std::pair<mol::EntityView, mol::EntityView>
+ViewsFromAlignment(const AlignmentHandle& aln, int index1, int index2)
+{
+ return ViewsFromSequences(aln.GetSequence(index1), aln.GetSequence(index2));
+}
+
+}}
diff --git a/modules/seq/base/src/views_from_sequences.hh b/modules/seq/base/src/views_from_sequences.hh
new file mode 100644
index 0000000000000000000000000000000000000000..1a46965b1a7078038bc868090a1b9d590d3c5376
--- /dev/null
+++ b/modules/seq/base/src/views_from_sequences.hh
@@ -0,0 +1,36 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2010 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+#ifndef OST_SEQ_VIEWS_FROM_SEQUENCES_HH
+#define OST_SEQ_VIEWS_FROM_SEQUENCES_HH
+
+#include <ost/seq/module_config.hh>
+#include <ost/seq/alignment_handle.hh>
+
+namespace ost { namespace seq {
+
+std::pair<mol::EntityView, mol::EntityView> DLLEXPORT_OST_SEQ
+ViewsFromSequences(const ConstSequenceHandle& seq1,
+ const ConstSequenceHandle& seq2);
+
+std::pair<mol::EntityView, mol::EntityView> DLLEXPORT_OST_SEQ
+ViewsFromAlignment(const AlignmentHandle& aln, int index1=0, int index2=1);
+
+}}
+
+#endif
diff --git a/modules/seq/base/tests/test_seq.py b/modules/seq/base/tests/test_seq.py
index 69644ffc80e707c2bb8282b23b58fb0586277082..4eed73b1132f82109cc0250807561cb0675db3c0 100644
--- a/modules/seq/base/tests/test_seq.py
+++ b/modules/seq/base/tests/test_seq.py
@@ -4,174 +4,124 @@ from ost import settings
from ost import seq
-def fixture(seq_str='MRLDGKTALITGSAR'):
+def fixture():
e=mol.CreateEntity()
ede=e.RequestXCSEditor()
chain=ede.InsertChain('A')
- res_str='MET ARG LEU ASP GLY LYS THR ALA LEU ILE THR GLY SER ALA ARG'
- res=res_str.split()
- olc={}
- counter=0
- for i in 'MRLDGKTALITGSAR':
- olc[i]=res[counter]
- counter+=1
-
- for i in seq_str:
- if i!='-':
- r=ede.AppendResidue(chain,olc[i])
- r.SetOneLetterCode(i)
- a=ede.InsertAtom(r,'CA',geom.Vec3())
- #~ for i in e.atoms: print i,i.index
- return e.Copy()
+ for res in 'ABCDEFGH':
+ r=ede.AppendResidue(chain, res)
+ r.SetOneLetterCode(res)
+ ede.InsertAtom(r, "XXX", geom.Vec3())
+
+ return e
class TestSeq(unittest.TestCase):
def setUp(self):
- #sequence and entity must correspond
- print 'initialising'
- ent=fixture()
- self.protein=ent.Select('')
- c=self.protein.chains[0]
- self.seq_a=seq.SequenceFromChain('0',c) # MRLDGKTALITGSAR
- self.seq_a.AttachView(self.protein)
- self.seq_b=seq.CreateSequence('1','---DGKTALITGSAR')
- self.seq_b.AttachView(fixture('---DGKTALITGSAR').Select(''))
- #~ self.seq_c=seq.CreateSequence('2','MRLDG---LITGSAR')
- #~ self.seq_c.AttachView(self.protein)
- #~ self.seq_d=seq.CreateSequence('3','MRLDG----ITGSAR')
- #~ self.seq_d.AttachView(self.protein)
- self.seq_e=seq.CreateSequence('4','AMRLDG----ITGSA')
- self.seq_e.AttachView(fixture('AMRLDG----ITGSA').Select(''))
- ##self.seq_e.AttachView(self.protein)
- self.seq_e.SetSequenceOffset(1)
- self.seq_f=seq.CreateSequence('5','MRLDGKTA-ITGSAR')
- self.seq_f.AttachView(fixture('MRLDGKTA-ITGSAR').Select(''))
- self.seq_g=seq.CreateSequence('6','MRLDGKTALITG---')
- self.seq_g.AttachView(fixture('MRLDGKTALITG---').Select(''))
-
-#~ MRLDGKTALITGSAR
-#~ ---DGKTALITGSAR
- def testViewsFromSequences1(self):
+ self.ent=fixture()
+
+ def testViewsFromSequences_01(self):
+ seq_a=seq.CreateSequence("A", "ABCD-FGH")
+ seq_a.AttachView(self.ent.Select('rname=A,B,C,D,F,G,H'))
+ seq_b=seq.CreateSequence("B", "ABCDEFGH")
+ seq_b.AttachView(self.ent.Select(''))
+ a, b=seq.ViewsFromSequences(seq_a, seq_b)
+ string_a=''.join([r.one_letter_code for r in a.residues])
+ string_b=''.join([r.one_letter_code for r in b.residues])
+ self.assertEqual(string_a, 'ABCDFGH')
+ self.assertEqual(string_b, 'ABCDFGH')
+
+ def testViewsFromSequences_02(self):
+ seq_a=seq.CreateSequence("A", "ABCD-FGH")
+ seq_a.AttachView(self.ent.Select('rname=A,B,C,D,F,G,H'))
+ seq_b=seq.CreateSequence("B", "ABCD-FGH")
+ seq_b.AttachView(self.ent.Select('rname=A,B,C,D,F,G,H'))
+ a, b=seq.ViewsFromSequences(seq_a, seq_b)
+ string_a=''.join([r.one_letter_code for r in a.residues])
+ string_b=''.join([r.one_letter_code for r in b.residues])
+ self.assertEqual(string_a, 'ABCDFGH')
+ self.assertEqual(string_b, 'ABCDFGH')
- [a,b]=seq.ViewsFromSequences(self.seq_a,
- self.seq_b,
- self.seq_a.GetAttachedView(),
- self.seq_b.GetAttachedView())
-
- #~ for i,j in zip(a.atoms,b.atoms):
- #~ print i,i.residue.one_letter_code,j,j.residue.one_letter_code
+ def testViewsFromSequences_03(self):
+ seq_a=seq.CreateSequence("A", "ABCD--GH")
+ seq_a.AttachView(self.ent.Select('rname=A,B,C,D,G,H'))
+ seq_b=seq.CreateSequence("B", "ABCD-FGH")
+ seq_b.AttachView(self.ent.Select('rname=A,B,C,D,F,G,H'))
+ a, b=seq.ViewsFromSequences(seq_a, seq_b)
+ string_a=''.join([r.one_letter_code for r in a.residues])
+ string_b=''.join([r.one_letter_code for r in b.residues])
+ self.assertEqual(string_a, 'ABCDGH')
+ self.assertEqual(string_b, 'ABCDGH')
+
+ def testViewsFromSequences_04(self):
+ seq_a=seq.CreateSequence("A", "ABCD-FGH")
+ seq_a.AttachView(self.ent.Select('rname=A,B,C,D,F,G,H'))
+ seq_b=seq.CreateSequence("B", "ABCD--GH")
+ seq_b.AttachView(self.ent.Select('rname=A,B,C,D,G,H'))
+ a, b=seq.ViewsFromSequences(seq_a, seq_b)
+ string_a=''.join([r.one_letter_code for r in a.residues])
+ string_b=''.join([r.one_letter_code for r in b.residues])
+ self.assertEqual(string_a, 'ABCDGH')
+ self.assertEqual(string_b, 'ABCDGH')
- self.assertEqual(a.atoms[0].GetResidue().GetOneLetterCode(),'D');
- self.assertEqual(b.atoms[0].GetResidue().GetOneLetterCode(),'D');
- self.assertEqual(a.atoms[11].GetResidue().GetOneLetterCode(),'R');
- self.assertEqual(b.atoms[11].GetResidue().GetOneLetterCode(),'R');
-
-#~ ---DGKTALITGSAR
-#~ MRLDGKTALITGSAR
- def testViewsFromSequences2(self):
- [a,b]=seq.ViewsFromSequences(self.seq_b,
- self.seq_a,
- self.seq_b.GetAttachedView(),
- self.seq_a.GetAttachedView())
-
- self.assertEqual(a.atoms[0].GetResidue().GetOneLetterCode(),'D');
- self.assertEqual(b.atoms[0].GetResidue().GetOneLetterCode(),'D');
- self.assertEqual(a.atoms[11].GetResidue().GetOneLetterCode(),'R');
- self.assertEqual(b.atoms[11].GetResidue().GetOneLetterCode(),'R');
-
-
-##~ MRLDGKTALITGSAR
-##~ MRLDGKTALITG---
- def testViewsFromSequences3(self):
- [a,b]=seq.ViewsFromSequences(self.seq_a,
- self.seq_g,
- self.seq_a.GetAttachedView(),
- self.seq_g.GetAttachedView())
-
- self.assertEqual(a.atoms[0].GetResidue().GetOneLetterCode(),'M');
- self.assertEqual(b.atoms[0].GetResidue().GetOneLetterCode(),'M');
- self.assertEqual(a.atoms[-1].GetResidue().GetOneLetterCode(),'G');
- self.assertEqual(b.atoms[-1].GetResidue().GetOneLetterCode(),'G');
+ def testViewsFromSequences_05(self):
+ seq_a=seq.CreateSequence("A", "ABCD-F--")
+ seq_a.AttachView(self.ent.Select('rname=A,B,C,D,F'))
+ seq_b=seq.CreateSequence("B", "ABCDEFGH")
+ seq_b.AttachView(self.ent.Select('rname=A,B,C,D,E,F,G,H'))
+ a, b=seq.ViewsFromSequences(seq_a, seq_b)
+ string_a=''.join([r.one_letter_code for r in a.residues])
+ string_b=''.join([r.one_letter_code for r in b.residues])
+ self.assertEqual(string_a, 'ABCDF')
+ self.assertEqual(string_b, 'ABCDF')
-
-##~ MRLDGKTALITG---
-##~ MRLDGKTALITGSAR
- def testViewsFromSequences4(self):
- [a,b]=seq.ViewsFromSequences(self.seq_g,
- self.seq_a,
- self.seq_g.GetAttachedView(),
- self.seq_a.GetAttachedView())
-
- self.assertEqual(a.atoms[0].GetResidue().GetOneLetterCode(),'M');
- self.assertEqual(b.atoms[0].GetResidue().GetOneLetterCode(),'M');
- self.assertEqual(a.atoms[-1].GetResidue().GetOneLetterCode(),'G');
- self.assertEqual(b.atoms[-1].GetResidue().GetOneLetterCode(),'G');
-
-
-
-##~ MRLDGKTALITGSAR
-##~ MRLDGKTA-ITGSAR
- def testViewsFromSequences5(self):
- [a,b]=seq.ViewsFromSequences(self.seq_a,
- self.seq_f,
- self.seq_a.GetAttachedView(),
- self.seq_f.GetAttachedView())
- print 'result'
- for i,j in zip(a.residues,b.residues): print i,i.index,j,j.index
-
- self.assertEqual(a.atoms[0].GetResidue().GetOneLetterCode(),'M');
- self.assertEqual(b.atoms[0].GetResidue().GetOneLetterCode(),'M');
- #~ for i,j in zip(a.atoms,b.atoms): print i,j
- self.assertEqual(a.atoms[8].GetResidue().GetOneLetterCode(),'I');
- self.assertEqual(b.atoms[8].GetResidue().GetOneLetterCode(),'I');
-
-##~ MRLDGKTA-ITGSAR
-##~ MRLDGKTALITGSAR
- #def testViewsFromSequences6(self):
- #[a,b]=seq.ViewsFromSequences(self.seq_f,
- #self.seq_a,
- #self.seq_f.GetAttachedView(),
- #self.seq_a.GetAttachedView())
-
- #self.assertEqual(a.atoms[0].GetResidue().GetOneLetterCode(),'M');
- #self.assertEqual(b.atoms[0].GetResidue().GetOneLetterCode(),'M');
- #self.assertEqual(a.atoms[8].GetResidue().GetOneLetterCode(),'I');
- #self.assertEqual(b.atoms[8].GetResidue().GetOneLetterCode(),'I');
-
-##~ MRLDG---LITGSAR
-##~ MRLDG----ITGSAR
- #~ def testViewsFromSequences7(self):
- #~ [a,b]=seq.ViewsFromSequences(self.seq_c,
- #~ self.seq_d,
- #~ self.seq_c.GetAttachedView(),
- #~ self.seq_d.GetAttachedView())
-#~
- #~ self.assertEqual(a.atoms[0].GetResidue().GetOneLetterCode(),'M');
- #~ self.assertEqual(b.atoms[0].GetResidue().GetOneLetterCode(),'M');
- #~ self.assertEqual(a.atoms[5].GetResidue().GetOneLetterCode(),'I');
- #~ self.assertEqual(b.atoms[5].GetResidue().GetOneLetterCode(),'I');
-
-#~ MRLDGKTALITGSAR
-#~ AMRLDG----ITGSA
- def testViewsFromSequences8(self):
- [a,b]=seq.ViewsFromSequences(self.seq_a,
- self.seq_e,
- self.seq_a.GetAttachedView(),
- self.seq_e.GetAttachedView())
- print 'result'
- for i,j in zip(a.residues,b.residues): print i,i.index,j,j.index
- self.assertEqual(a.atoms[0].GetResidue().GetOneLetterCode(),'M');
- self.assertEqual(b.atoms[0].GetResidue().GetOneLetterCode(),'M');
- self.assertEqual(a.atoms[6].GetResidue().GetOneLetterCode(),'I');
- self.assertEqual(b.atoms[6].GetResidue().GetOneLetterCode(),'I');
-
-
-
-
-if __name__ == "__main__":
- # test if python extension for seq module work
- suite = unittest.TestLoader().loadTestsFromTestCase(TestSeq)
- unittest.TextTestRunner(verbosity=3).run(suite)
-
- #~ unittest.main()
+ def testViewsFromSequences_06(self):
+ seq_a=seq.CreateSequence("A", "--CD-FGH")
+ seq_a.AttachView(self.ent.Select('rname=C,D,F,G,H'))
+ seq_b=seq.CreateSequence("B", "ABCDEFGH")
+ seq_b.AttachView(self.ent.Select('rname=A,B,C,D,E,F,G,H'))
+ a, b=seq.ViewsFromSequences(seq_a, seq_b)
+ string_a=''.join([r.one_letter_code for r in a.residues])
+ string_b=''.join([r.one_letter_code for r in b.residues])
+ self.assertEqual(string_a, 'CDFGH')
+ self.assertEqual(string_b, 'CDFGH')
+
+
+ def testViewsFromSequences_07(self):
+ seq_a=seq.CreateSequence("A", "AB-D-FGH")
+ seq_a.AttachView(self.ent.Select('rname=A,B,D,F,G,H'))
+ seq_b=seq.CreateSequence("B", "AB-DEF-H")
+ seq_b.AttachView(self.ent.Select('rname=A,B,D,E,F,H'))
+ a, b=seq.ViewsFromSequences(seq_a, seq_b)
+ string_a=''.join([r.one_letter_code for r in a.residues])
+ string_b=''.join([r.one_letter_code for r in b.residues])
+ self.assertEqual(string_a, 'ABDFH')
+ self.assertEqual(string_b, 'ABDFH')
+
+
+ def testViewsFromSequences_08(self):
+ seq_a=seq.CreateSequence("A", "A-C-E-G")
+ seq_a.AttachView(self.ent.Select('rname=A,C,E,G'))
+ seq_b=seq.CreateSequence("B", "-B-D-H-")
+ seq_b.AttachView(self.ent.Select('rname=B,D,H'))
+ a, b=seq.ViewsFromSequences(seq_a, seq_b)
+ string_a=''.join([r.one_letter_code for r in a.residues])
+ string_b=''.join([r.one_letter_code for r in b.residues])
+ self.assertEqual(string_a, '')
+ self.assertEqual(string_b, '')
+
+ def testViewsFromSequences_09(self):
+ seq_a=seq.CreateSequence("A", "B-D-FGH")
+ seq_a.AttachView(self.ent.Select('rname=A,B,D,F,G,H'))
+ seq_a.SetSequenceOffset(1)
+ seq_b=seq.CreateSequence("B", "B-DEF-H")
+ seq_b.SetSequenceOffset(1)
+ seq_b.AttachView(self.ent.Select('rname=A,B,D,E,F,H'))
+ a, b=seq.ViewsFromSequences(seq_a, seq_b)
+ string_a=''.join([r.one_letter_code for r in a.residues])
+ string_b=''.join([r.one_letter_code for r in b.residues])
+ self.assertEqual(string_a, 'BDFH')
+ self.assertEqual(string_b, 'BDFH')
+suite = unittest.TestLoader().loadTestsFromTestCase(TestSeq)
+unittest.TextTestRunner().run(suite)