diff --git a/modules/seq/base/pymod/__init__.py b/modules/seq/base/pymod/__init__.py
index 6b92feb561d921cbf76caba2939286e5b5ca2c9f..6a742908d60a4d4c49dc5f5e0da3480679c0de75 100644
--- a/modules/seq/base/pymod/__init__.py
+++ b/modules/seq/base/pymod/__init__.py
@@ -67,8 +67,8 @@ def ViewsFromSequences(seq_a, seq_b, ent_a=None, ent_b=None,
#~ print seq_ent_a
#~ print s1
- #~ print seq_ent_a
- #~ print s1
+ #~ print seq_ent_b
+ #~ print s2
off_a = seq_ent_a.index(s1)
off_b = seq_ent_b.index(s2)
@@ -84,32 +84,34 @@ def ViewsFromSequences(seq_a, seq_b, ent_a=None, ent_b=None,
# iterate over residues
while index_a<seq_a.GetLength() and index_b<seq_b.GetLength():
# print 'index',index_a, seq_a.GetLength(), index_b, seq_b.GetLength()
- while seq_a.GetOneLetterCode(index_a)=='-':
+ while seq_a.GetOneLetterCode(index_a)=='-':
index_a+=1
if seq_a.GetLength()<index_a:
done=True
break
- while seq_b.GetOneLetterCode(index_b)=='-':
+ while seq_b.GetOneLetterCode(index_b)=='-':
index_b+=1
if seq_b.GetLength()<index_b:
done=True
break
- if done or len(res_a)<=off_a+index_b or len(res_b)<=off_b+index_a:
+ if done or len(res_a)<=off_a+index_b or len(res_b)<=off_b+index_a:
break
- ra=res_a[off_a+index_b]
- rb=res_b[off_b+index_a]
- #ra = res_a[index_b]
- #rb = res_a[index_a]
- #~ print "set align_index %d for %s %s" % (align_index, ra, rb)
- #ra.SetIntProp("align_index",align_index)
- #rb.SetIntProp("align_index",align_index)
- align_index += 1
- 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
- eda=ev_a.handle.RequestXCSEditor()
- eda.RenameChain(ent_a.chains[0].handle,ent_a.chains[0].name)
- edb=ev_b.handle.RequestXCSEditor()
- edb.RenameChain(ent_b.chains[0].handle, ent_b.chains[0].name)
+ ra=res_a[off_a+index_b]
+ rb=res_b[off_b+index_a]
+ #ra = res_a[index_b]
+ #rb = res_a[index_a]
+ #~ print "set align_index %d for %s %s" % (align_index, ra, rb)
+ #ra.SetIntProp("align_index",align_index)
+ #rb.SetIntProp("align_index",align_index)
+ align_index += 1
+ 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
+ if (ent_a.chains[0].name!=ev_a.chains[0].name):
+ eda=ev_a.handle.RequestXCSEditor()
+ eda.RenameChain(ent_a.chains[0].handle,ent_a.chains[0].name)
+ if (ent_b.chains[0].name!=ev_b.chains[0].name):
+ edb=ev_b.handle.RequestXCSEditor()
+ edb.RenameChain(ent_b.chains[0].handle, ent_b.chains[0].name)
return ev_a, ev_b
diff --git a/modules/seq/base/tests/CMakeLists.txt b/modules/seq/base/tests/CMakeLists.txt
index 62099af52d17e9f09fba08323a4e8b055f18a8be..528cb936ddae91eabe14d1b06c6aa743de7e29ac 100644
--- a/modules/seq/base/tests/CMakeLists.txt
+++ b/modules/seq/base/tests/CMakeLists.txt
@@ -1,4 +1,5 @@
set(OST_SEQ_UNIT_TESTS
+ test_seq.py
test_sequence.cc
test_aligned_column.cc
test_aligned_region.cc
diff --git a/modules/seq/base/tests/test_seq.py b/modules/seq/base/tests/test_seq.py
new file mode 100644
index 0000000000000000000000000000000000000000..db027f6d05eb6c483b905cae3e0c15f9184ea305
--- /dev/null
+++ b/modules/seq/base/tests/test_seq.py
@@ -0,0 +1,70 @@
+import unittest
+from ost import *
+from ost import settings
+from ost import seq
+
+class TestSeq(unittest.TestCase):
+
+ def setUp(self):
+ self.protein = io.LoadEntity("testfiles/testprotein.pdb")
+ c=self.protein.chains[0]
+ self.seq_a=seq.SequenceFromChain('0',c) # MRLDGKTALITGSAR
+ self.seq_a.AttachView(self.protein.Select('aname==CA'))
+ self.seq_b=seq.CreateSequence('1','---DGKTALITGSAR')
+ self.seq_b.AttachView(self.protein.Select('aname==CA'))
+ self.seq_c=seq.CreateSequence('2','MRLDG---LITGSAR')
+ self.seq_c.AttachView(self.protein.Select('aname==CA'))
+ self.seq_d=seq.CreateSequence('3','MRLDG----ITGSAR')
+ self.seq_d.AttachView(self.protein.Select('aname==CA'))
+ self.seq_e=seq.CreateSequence('4','AMRLDG----ITGSA')
+ self.seq_e.AttachView(self.protein.Select('aname==CA'))
+ self.seq_e.SetSequenceOffset(1)
+
+ def testViewsFromSequencesGapFrontSeqB(self):
+ #~ MRLDGKTALITGSAR
+ #~ ---DGKTALITGSAR
+ [a,b]=seq.ViewsFromSequences(self.seq_a,
+ self.seq_b,
+ self.seq_a.GetAttachedView(),
+ self.seq_b.GetAttachedView())
+
+
+ assert(a.atoms[0].GetResidue().GetOneLetterCode()=='D');
+ assert(b.atoms[0].GetResidue().GetOneLetterCode()=='D');
+ #~ self.seq_b.GetResidue(j.GetResidue().GetIndex()).GetOneLetterCode());
+
+ def testViewsFromSequencesGapMiddleBoth(self):
+ #~ MRLDG---LITGSAR
+ #~ MRLDG----ITGSAR
+ [a,b]=seq.ViewsFromSequences(self.seq_c,
+ self.seq_d,
+ self.seq_c.GetAttachedView(),
+ self.seq_d.GetAttachedView())
+
+ print 'aaa'+a.atoms[4].name+'aaaa'
+ assert(a.atoms[0].GetResidue().GetOneLetterCode()=='M');
+ assert(b.atoms[0].GetResidue().GetOneLetterCode()=='M');
+ assert(a.atoms[4].GetResidue().GetOneLetterCode()=='I');
+ assert(b.atoms[4].GetResidue().GetOneLetterCode()=='I');
+ #~ self.seq_b.GetResidue(j.GetResidue().GetIndex()).GetOneLetterCode());
+
+ def testViewsFromSequencesGapSeqOffset(self):
+ #~ MRLDGKTALITGSAR
+ #~ AMRLDG----ITGSA
+ [a,b]=seq.ViewsFromSequences(self.seq_a,
+ self.seq_e,
+ self.seq_a.GetAttachedView(),
+ self.seq_e.GetAttachedView())
+
+
+ assert(a.atoms[0].GetResidue().GetOneLetterCode()=='M');
+ assert(b.atoms[0].GetResidue().GetOneLetterCode()=='M');
+ assert(a.atoms[5].GetResidue().GetOneLetterCode()=='I');
+ assert(b.atoms[5].GetResidue().GetOneLetterCode()=='I');
+ #~ self.seq_b.GetResidue(j.GetResidue().GetIndex()).GetOneLetterCode());
+
+
+
+if __name__ == "__main__":
+ # test if python extension for seq module work
+ unittest.main()