From 4e4e86165764aa6879a212be91f32e8c20912b29 Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Wed, 3 Feb 2016 17:58:05 +0100
Subject: [PATCH] Modelling update: tests, ClearGaps rewrite, doc
---
modelling/doc/index.rst | 6 +-
modelling/pymod/_closegaps.py | 16 ++-
modelling/pymod/_pipeline.py | 5 +-
modelling/src/gap.cc | 8 +-
modelling/src/model.cc | 179 +++++---------------------
modelling/src/model.hh | 17 +--
modelling/tests/test_gap_extension.py | 32 +++++
modelling/tests/test_modelling.py | 151 ++++++++++++++++++++++
8 files changed, 243 insertions(+), 171 deletions(-)
diff --git a/modelling/doc/index.rst b/modelling/doc/index.rst
index 60b99d64..a0e0a7b5 100644
--- a/modelling/doc/index.rst
+++ b/modelling/doc/index.rst
@@ -116,7 +116,7 @@ Closing Gaps
:type gap: :class:`StructuralGap`
:return: Index of next gap in mhandle.gaps after removal.
- Returns -1 if last gap was removed.
+ Returns -1 if last gap was removed or no gaps in *mhandle*.
:rtype: :class:`int`
:raises: A :exc:`RuntimeError` if any gap in mhandle.gaps is only partially
@@ -124,7 +124,9 @@ Closing Gaps
.. function:: MergeGaps(mhandle, index)
- Merges two gaps mhandle.gaps[index] and mhandle.gaps[index+1].
+ Merges two gaps `mhandle.gaps[index]` and `mhandle.gaps[index+1]`.
+ The residues in between the gaps are removed from `mhandle.model` and added
+ to the new `mhandle.gaps[index]`.
:param mhandle: Modelling handle on which to apply change.
:type mhandle: :class:`ModellingHandle`
diff --git a/modelling/pymod/_closegaps.py b/modelling/pymod/_closegaps.py
index 2ef87d52..c46c126b 100644
--- a/modelling/pymod/_closegaps.py
+++ b/modelling/pymod/_closegaps.py
@@ -13,7 +13,8 @@ import sys
# helper functions
def _InitGapExtenders(mhandle, use_scoring_extender):
# adds field extender_penalties to mhandle
- if use_scoring_extender and not hasattr(mhandle, 'extender_penalties'):
+ # recomputed at each call (as old behavior)
+ if use_scoring_extender: # and not hasattr(mhandle, 'extender_penalties'):
mhandle.extender_penalties = list()
for i in range(len(mhandle.model.chains)):
mhandle.extender_penalties.append([0.0] * len(mhandle.seqres[i]))
@@ -25,6 +26,11 @@ def _InitGapExtenders(mhandle, use_scoring_extender):
def _GetGapExtender(mhandle, actual_gap, actual_chain_idx,
use_scoring_extender, max_length=-1):
+
+ # TODO (GT): try removing _InitGapExtenders and recomputing
+ # extender_penalties (changes as gaps filled!!)
+ # -> or only once and for all? (see commented hasattr above)
+
# return appropriate gap extender
if use_scoring_extender:
return modelling.ScoringGapExtender(actual_gap, 0.8,
@@ -774,6 +780,12 @@ def CloseLargeDeletions(mhandle, scorer, structure_db, linker_length = 8,
if not actual_extender.Extend():
break
+ # FAIL (Fragger needs at least 3 residues)
+ if len(actual_gap.full_seq) < 3:
+ ost.LogInfo("Failed in CloseLargeDeletions (%s)" % str(gap_orig))
+ gap_idx += 1
+ continue
+
# extract gap info
n_res = actual_gap.before
c_res = actual_gap.after
@@ -869,7 +881,7 @@ def CloseLargeDeletions(mhandle, scorer, structure_db, linker_length = 8,
# update scorer
scorer.SetEnvironment(bb_list, first_num, actual_chain_idx)
# will return -1 if last gap removed
- gap_idx = modelling.ClearGaps(mhandle, gap_orig)
+ gap_idx = modelling.ClearGaps(mhandle, actual_gap)
ost.LogInfo("Resolved %s by sampling %s as linker" % \
(str(gap_orig), str(actual_gap)))
diff --git a/modelling/pymod/_pipeline.py b/modelling/pymod/_pipeline.py
index f6d3dbcd..1f493b8e 100644
--- a/modelling/pymod/_pipeline.py
+++ b/modelling/pymod/_pipeline.py
@@ -180,9 +180,8 @@ def BuildFromRawModel(mhandle):
_closegaps.FillLoopsByMonteCarlo(mhandle, scorer, torsion_sampler)
if len(mhandle.gaps) > 0:
- msg = "There are still unsolved gaps, possibly large deletions. "
- msg += "Try to resolve them by sampling a linker region."
- ost.LogInfo(msg)
+ ost.LogInfo("There are still unsolved gaps, possibly large deletions. "
+ "Try to resolve them by sampling a linker region.")
_closegaps.CloseLargeDeletions(mhandle, scorer, structure_db)
# check if we succeeded
diff --git a/modelling/src/gap.cc b/modelling/src/gap.cc
index 5a7016ee..9e7022af 100644
--- a/modelling/src/gap.cc
+++ b/modelling/src/gap.cc
@@ -11,22 +11,18 @@ String StructuralGap::GetChainName() const
{
if (this->IsCTerminal()) {
return before.GetChain().GetName();
- }
- if (this->IsNTerminal()) {
+ } else {
return after.GetChain().GetName();
}
- return before.GetChain().GetName();
}
ost::mol::ChainHandle StructuralGap::GetChain() const
{
if (this->IsCTerminal()) {
return before.GetChain();
- }
- if (this->IsNTerminal()) {
+ } else {
return after.GetChain();
}
- return before.GetChain();
}
uint StructuralGap::GetChainIndex() const
diff --git a/modelling/src/model.cc b/modelling/src/model.cc
index 52900d8e..c0965445 100644
--- a/modelling/src/model.cc
+++ b/modelling/src/model.cc
@@ -49,160 +49,51 @@ bool CheckBackboneAtoms(ResidueView res)
}
int ClearGaps(ModellingHandle& mhandle, const StructuralGap& gap) {
-
- String chain_name = gap.GetChainName();
+
+ // return -1 if no more gaps
int next_gap = -1;
-
- if(gap.IsNTerminal()){
- for(StructuralGapList::iterator i = mhandle.gaps.begin(); i != mhandle.gaps.end();){
- if(i->GetChainName() != chain_name){
- ++i;
- continue;
- }
- if(i->IsCTerminal()){
- if(gap.after.GetNumber() > i->before.GetNumber()){
- if(gap.after.GetNumber() < i->before.GetNumber() + i->GetLength()){
- std::stringstream ss;
- ss << "Tried to clear gap "<<*i<<" but"<<gap;
- ss << " is only overlapping not fully enclosing!";
- throw promod3::Error(ss.str());
- }
- i = mhandle.gaps.erase(i);
- next_gap = i-mhandle.gaps.begin();
- continue;
- }
- }else if(i->IsNTerminal()){
- if(i->after.GetNumber() <= gap.after.GetNumber()){
- i = mhandle.gaps.erase(i);
- next_gap = i-mhandle.gaps.begin();
- continue;
- }
- }else{
- if(gap.after.GetNumber() > i->before.GetNumber()){
- if(gap.after.GetNumber() < i->after.GetNumber()){
- std::stringstream ss;
- ss << "Tried to clear gap "<<*i<<" but"<<gap;
- ss << " is only overlapping not fully enclosing!";
- throw promod3::Error(ss.str());
- }
- }
- i = mhandle.gaps.erase(i);
- next_gap = i-mhandle.gaps.begin();
- continue;
- }
+
+ // extract info for this gap
+ String my_chain_name = gap.GetChainName();
+ ResNum my_b_res(0);
+ if (!gap.IsNTerminal()) my_b_res = gap.before.GetNumber();
+ ResNum my_a_res = my_b_res + gap.GetLength() + 1;
+
+ for (StructuralGapList::iterator i = mhandle.gaps.begin();
+ i != mhandle.gaps.end(); ) {
+
+ // skip different chains
+ if (i->GetChainName() != my_chain_name) {
++i;
+ continue;
}
- return next_gap;
- }
- if(gap.IsCTerminal()){
- for(StructuralGapList::iterator i = mhandle.gaps.begin(); i != mhandle.gaps.end();){
- if(i->GetChainName() != chain_name){
- ++i;
- continue;
- }
- if(i->IsNTerminal()){
- if(gap.before.GetNumber() < i->after.GetNumber()){
- if(gap.before.GetNumber() > i->after.GetNumber() - i->GetLength()){
- std::stringstream ss;
- ss << "Tried to clear gap "<<*i<<" but"<<gap;
- ss << " is only overlapping not fully enclosing!";
- throw promod3::Error(ss.str());
- }
- i = mhandle.gaps.erase(i);
- next_gap = i-mhandle.gaps.begin();
- continue;
- }
- }else if(i->IsCTerminal()){
- if(i->before.GetNumber() >= gap.before.GetNumber()){
- i = mhandle.gaps.erase(i);
- next_gap = i-mhandle.gaps.begin();
- continue;
- }
- }else{
- if(gap.before.GetNumber() < i->after.GetNumber()){
- if(gap.before.GetNumber() > i->before.GetNumber()){
- std::stringstream ss;
- ss << "Tried to clear gap "<<*i<<" but"<<gap;
- ss << " is only overlapping not fully enclosing!";
- throw promod3::Error(ss.str());
- }
- }
- i = mhandle.gaps.erase(i);
- next_gap = i-mhandle.gaps.begin();
- continue;
- }
- ++i;
- }
- return next_gap;
- }
+ // get res_nums
+ ResNum b_res(0);
+ if (!i->IsNTerminal()) b_res = i->before.GetNumber();
+ ResNum a_res = b_res + i->GetLength() + 1;
- for(StructuralGapList::iterator i = mhandle.gaps.begin(); i != mhandle.gaps.end();){
- if(i->GetChainName() != chain_name){
- ++i;
- continue;
- }
- if(i->IsNTerminal()){
- if(gap.before.GetNumber() < i->after.GetNumber()){
- if(gap.after.GetNumber() < i->after.GetNumber()){
- std::stringstream ss;
- ss << "Tried to clear gap "<<*i<<" but"<<gap;
- ss << " is only overlapping not fully enclosing!";
- throw promod3::Error(ss.str());
- }
- if(gap.before.GetNumber() > i->after.GetNumber()-i->GetLength()){
- std::stringstream ss;
- ss << "Tried to clear gap "<<*i<<" but"<<gap;
- ss << " is only overlapping not fully enclosing!";
- throw promod3::Error(ss.str());
- }
- i = mhandle.gaps.erase(i);
- next_gap = i-mhandle.gaps.begin();
- continue;
- }
- }
- else if(i->IsCTerminal()){
- if(gap.after.GetNumber() > i->before.GetNumber()){
- if(gap.before.GetNumber() > i->before.GetNumber()){
- std::stringstream ss;
- ss << "Tried to clear gap "<<*i<<" but"<<gap;
- ss << " is only overlapping not fully enclosing!";
- }
- if(gap.after.GetNumber() < i->before.GetNumber() + i->GetLength()){
- std::stringstream ss;
- ss << "Tried to clear gap "<<*i<<" but"<<gap;
- ss << " is only overlapping not fully enclosing!";
- throw promod3::Error(ss.str());
- }
- i = mhandle.gaps.erase(i);
- next_gap = i-mhandle.gaps.begin();
- continue;
- }
- }else{
- if(i->before.GetNumber() >= gap.before.GetNumber() &&
- i->after.GetNumber() <= gap.after.GetNumber()){
- i = mhandle.gaps.erase(i);
- next_gap = i-mhandle.gaps.begin();
- continue;
- }
- if(i->before.GetNumber() > gap.before.GetNumber() &&
- i->before.GetNumber() < gap.after.GetNumber()){
- std::stringstream ss;
- ss << "Tried to clear gap "<<*i<<" but"<<gap;
- ss << " is only overlapping not fully enclosing!";
- throw promod3::Error(ss.str());
+ // check full overlap
+ if (b_res >= my_b_res && a_res <= my_a_res) {
+ i = mhandle.gaps.erase(i);
+ if (i == mhandle.gaps.end()) {
+ next_gap = -1;
+ } else {
+ next_gap = i - mhandle.gaps.begin();
}
- if(i->after.GetNumber() > gap.before.GetNumber() &&
- i->after.GetNumber() < gap.after.GetNumber()){
+ } else {
+ // check partial overlaps
+ if ( (my_b_res > b_res && my_b_res < a_res)
+ || (my_a_res > b_res && my_a_res < a_res)) {
std::stringstream ss;
- ss << "Tried to clear gap "<<*i<<" but"<<gap;
- ss << " is only overlapping not fully enclosing!";
- throw promod3::Error(ss.str());
+ ss << "Tried to clear gap " << *i << " but " << gap
+ << " is only overlapping not fully enclosing!";
+ throw promod3::Error(ss.str());
}
+ // moving on
+ ++i;
}
- ++i;
}
-
return next_gap;
}
diff --git a/modelling/src/model.hh b/modelling/src/model.hh
index 26f792b0..8e7be7d2 100644
--- a/modelling/src/model.hh
+++ b/modelling/src/model.hh
@@ -32,24 +32,13 @@ struct ModellingHandle {
ost::seq::SequenceList seqres;
};
-/// \brief Removes all gaps from mhandle which are fully enclosed by given gap.
-///
-/// \returns Index of next gap in mhandle.gaps after removal.
-/// Returns -1 if last gap was removed.
-///
-/// \throws promod3::Error if any gap in mhandle.gaps is only partially
-/// enclosed by given gap.
+// see Python doc
int ClearGaps(ModellingHandle& mhandle, const StructuralGap& gap);
-/// \brief Merges two gaps mhandle.gaps[index] and mhandle.gaps[index+1].
-///
-/// \throws promod3::Error if indices out of range or if trying to merge
-/// N-terminal gap with a C-terminal gap.
+// see Python doc
void MergeGaps(ModellingHandle& mhandle, uint index);
-/// \brief Removes all gaps in mhandle which are at N-terminal or C-terminal.
-///
-/// \returns Number of gaps which were removed.
+// see Python doc
int RemoveTerminalGaps(ModellingHandle& mhandle);
/// \brief copies all atom of src_res to dst_res
diff --git a/modelling/tests/test_gap_extension.py b/modelling/tests/test_gap_extension.py
index 49595437..3281293a 100644
--- a/modelling/tests/test_gap_extension.py
+++ b/modelling/tests/test_gap_extension.py
@@ -82,6 +82,38 @@ class GapExtension(unittest.TestCase):
self.assertFalse(ext.Extend())
self.checkGap(gap, 4, 8, 'TLN')
+ def testFullGapExtenderMerge(self):
+ mhandle = self.getRawModel()
+ modelling.MergeGaps(mhandle, 1)
+ # use first gap
+ gap = mhandle.gaps[0].Copy()
+ self.checkGap(gap, 4, 8, 'TLN')
+ # setup extender
+ ext = modelling.FullGapExtender(gap, mhandle.seqres[0])
+ self.assertTrue(ext.Extend())
+ self.checkGap(gap, 3, 8, 'ATLN')
+ self.assertTrue(ext.Extend())
+ self.checkGap(gap, 4, 9, 'TLNG')
+ self.assertTrue(ext.Extend())
+ self.checkGap(gap, 2, 8, 'AATLN')
+ self.assertTrue(ext.Extend())
+ self.checkGap(gap, 3, 9, 'ATLNG')
+ self.assertTrue(ext.Extend())
+ self.checkGap(gap, 1, 8, 'AAATLN')
+ self.assertTrue(ext.Extend())
+ self.checkGap(gap, 2, 9, 'AATLNG')
+ self.assertTrue(ext.Extend())
+ self.checkGap(gap, 1, 9, 'AAATLNG')
+ self.assertTrue(ext.Extend())
+ self.checkGap(gap, 4, 19, 'TLNGFTVPAGNTLV')
+ self.assertTrue(ext.Extend())
+ self.checkGap(gap, 3, 19, 'ATLNGFTVPAGNTLV')
+ # check rest
+ exp_max_length = mhandle.seqres[0].GetLength()-3
+ while ext.Extend():
+ self.assertLessEqual(gap.length, exp_max_length)
+ self.assertEqual(gap.length, exp_max_length)
+
def testScoringGapExtender(self):
mhandle = self.getRawModel()
seq_length = mhandle.seqres[0].GetLength()
diff --git a/modelling/tests/test_modelling.py b/modelling/tests/test_modelling.py
index 2e6eff48..909fc2db 100644
--- a/modelling/tests/test_modelling.py
+++ b/modelling/tests/test_modelling.py
@@ -106,6 +106,157 @@ class ModellingTests(unittest.TestCase):
self.assertTrue(residues[2].FindAtom("CB").IsValid())
self.assertTrue(residues[3].FindAtom("CB").IsValid())
+ def testMergeGaps(self):
+ tpl = io.LoadPDB('data/1mcg.pdb')
+ aln = seq.CreateAlignment(seq.CreateSequence('trg', 'DDFAGTHN'),
+ seq.CreateSequence('tpl', 'N-N-A-LF'))
+ aln.AttachView(1, tpl.CreateFullView())
+ mhandle = modelling.BuildRawModel(aln)
+ # check
+ seqres = ''.join([r.one_letter_code for r in mhandle.model.residues])
+ self.assertEqual(seqres, 'DFGHN')
+ self.assertEqual(len(mhandle.gaps), 3)
+ modelling.MergeGaps(mhandle, 0)
+ seqres = ''.join([r.one_letter_code for r in mhandle.model.residues])
+ self.assertEqual(seqres, 'DGHN')
+ self.assertEqual(len(mhandle.gaps), 2)
+ self.assertEqual(str(mhandle.gaps[0]), 'A.ASP1-(DFA)-A.GLY5')
+ modelling.MergeGaps(mhandle, 0)
+ seqres = ''.join([r.one_letter_code for r in mhandle.model.residues])
+ self.assertEqual(seqres, 'DHN')
+ self.assertEqual(len(mhandle.gaps), 1)
+ self.assertEqual(str(mhandle.gaps[0]), 'A.ASP1-(DFAGT)-A.HIS7')
+ with self.assertRaises(RuntimeError):
+ modelling.MergeGaps(mhandle, 0)
+
+ def testClearGapsExceptions(self):
+ tpl = io.LoadPDB('data/1mcg.pdb')
+ aln = seq.CreateAlignment(seq.CreateSequence('trg', 'DDFAGTHN'),
+ seq.CreateSequence('tpl', 'N-N-A-LF'))
+ aln.AttachView(1, tpl.CreateFullView())
+ mhandle = modelling.BuildRawModel(aln)
+ # get gaps before we remove residues in MergeGaps
+ mych = mhandle.model.chains[0]
+ mygap = modelling.StructuralGap(mych.FindResidue(0),
+ mych.FindResidue(3), "DD")
+ mygap2 = modelling.StructuralGap(mych.FindResidue(3),
+ mych.FindResidue(9), "AGTHN")
+ mygap3 = modelling.StructuralGap(mych.FindResidue(3),
+ mych.FindResidue(5), "A")
+ # check
+ modelling.MergeGaps(mhandle, 0)
+ modelling.MergeGaps(mhandle, 0)
+ self.assertEqual(len(mhandle.gaps), 1)
+ with self.assertRaises(RuntimeError):
+ modelling.ClearGaps(mhandle, mygap)
+ with self.assertRaises(RuntimeError):
+ modelling.ClearGaps(mhandle, mygap2)
+ with self.assertRaises(RuntimeError):
+ modelling.ClearGaps(mhandle, mygap3)
+ self.assertEqual(len(mhandle.gaps), 1)
+
+ def testClearGaps(self):
+ tpl = io.LoadPDB('data/2dbs.pdb')
+ aln = seq.CreateAlignment(
+ seq.CreateSequence('trg', 'TLNGFTVPAGNTLVLN---PDKG--ATVTM-A'),
+ seq.CreateSequence('tpl', 'N-GG-TLLI--PNGTYHFLGIQMKSNVHIRVE'))
+ aln.AttachView(1, tpl.CreateFullView())
+ mhandle = modelling.BuildRawModel(aln)
+ # check
+ self.assertEqual(len(mhandle.gaps), 6)
+ self.assertEqual(modelling.ClearGaps(mhandle, mhandle.gaps[1]), 1)
+ self.assertEqual(len(mhandle.gaps), 5)
+ self.assertEqual(modelling.ClearGaps(mhandle, mhandle.gaps[2]), 2)
+ self.assertEqual(len(mhandle.gaps), 4)
+ # special gaps
+ mych = mhandle.model.chains[0]
+ mygap = modelling.StructuralGap(mych.FindResidue(8),
+ mych.FindResidue(13), "AGNT")
+ self.assertEqual(modelling.ClearGaps(mhandle, mygap), 1)
+ self.assertEqual(len(mhandle.gaps), 3)
+ mygap = modelling.StructuralGap(mych.FindResidue(19),
+ mych.FindResidue(22), "GA")
+ self.assertEqual(modelling.ClearGaps(mhandle, mygap), 1)
+ self.assertEqual(len(mhandle.gaps), 2)
+ mygap = modelling.StructuralGap(mych.FindResidue(25),
+ mych.FindResidue(27), "A")
+ self.assertEqual(modelling.ClearGaps(mhandle, mygap), -1)
+ self.assertEqual(len(mhandle.gaps), 1)
+ mygap = modelling.StructuralGap(mych.FindResidue(0),
+ mych.FindResidue(3), "TL")
+ self.assertEqual(modelling.ClearGaps(mhandle, mygap), -1)
+ self.assertEqual(len(mhandle.gaps), 0)
+ self.assertEqual(modelling.ClearGaps(mhandle, mygap), -1)
+
+ def testClearMultipleGaps(self):
+ tpl = io.LoadPDB('data/2dbs.pdb')
+ aln = seq.CreateAlignment(
+ seq.CreateSequence('trg', 'TLNGFTVPAGNTLVLN---PD--KG---ATVTMA'),
+ seq.CreateSequence('tpl', 'NGG--TL--LI--PNGTYHFLGIQMKSNVHIRVE'))
+ aln.AttachView(1, tpl.CreateFullView())
+ mhandle = modelling.BuildRawModel(aln)
+ # check
+ self.assertEqual(len(mhandle.gaps), 6)
+ mych = mhandle.model.chains[0]
+ mygap = modelling.StructuralGap(mych.FindResidue(1),
+ mych.FindResidue(10), "LNGFTVPA")
+ self.assertEqual(modelling.ClearGaps(mhandle, mygap), 0)
+ self.assertEqual(len(mhandle.gaps), 4)
+ mygap = modelling.StructuralGap(mych.FindResidue(11),
+ mych.FindResidue(17), "TLVLN")
+ self.assertEqual(modelling.ClearGaps(mhandle, mygap), 0)
+ self.assertEqual(len(mhandle.gaps), 2)
+ mygap = modelling.StructuralGap(mych.FindResidue(18),
+ mych.FindResidue(23), "KGAT")
+ self.assertEqual(modelling.ClearGaps(mhandle, mygap), -1)
+ self.assertEqual(len(mhandle.gaps), 0)
+
+ def testClearGapsTermnini(self):
+ tpl = io.LoadPDB('data/1mcg.pdb')
+ aln = seq.CreateAlignment(seq.CreateSequence('trg', 'DDFAGTHN'),
+ seq.CreateSequence('tpl', '--NNALF-'))
+ aln.AttachView(1, tpl.CreateFullView())
+ mhandle = modelling.BuildRawModel(aln)
+ # check
+ self.assertEqual(len(mhandle.gaps), 2)
+ self.assertEqual(modelling.ClearGaps(mhandle, mhandle.gaps[0]), 0)
+ self.assertEqual(len(mhandle.gaps), 1)
+ self.assertEqual(modelling.ClearGaps(mhandle, mhandle.gaps[0]), -1)
+ self.assertEqual(len(mhandle.gaps), 0)
+
+ def testRemoveTerminalGaps(self):
+ tpl = io.LoadPDB('data/1mcg.pdb')
+ aln = seq.CreateAlignment(seq.CreateSequence('trg', 'DDFAGTHN'),
+ seq.CreateSequence('tpl', '--NNALF-'))
+ aln.AttachView(1, tpl.CreateFullView())
+ mhandle = modelling.BuildRawModel(aln)
+ # check
+ self.assertEqual(len(mhandle.gaps), 2)
+ self.assertEqual(modelling.RemoveTerminalGaps(mhandle), 2)
+ self.assertEqual(len(mhandle.gaps), 0)
+
+ def testRemoveTerminalGapsN(self):
+ tpl = io.LoadPDB('data/1mcg.pdb')
+ aln = seq.CreateAlignment(seq.CreateSequence('trg', 'DDFAGTH'),
+ seq.CreateSequence('tpl', '--NNALF'))
+ aln.AttachView(1, tpl.CreateFullView())
+ mhandle = modelling.BuildRawModel(aln)
+ # check
+ self.assertEqual(len(mhandle.gaps), 1)
+ self.assertEqual(modelling.RemoveTerminalGaps(mhandle), 1)
+ self.assertEqual(len(mhandle.gaps), 0)
+
+ def testRemoveTerminalGapsC(self):
+ tpl = io.LoadPDB('data/1mcg.pdb')
+ aln = seq.CreateAlignment(seq.CreateSequence('trg', 'FAGTHN'),
+ seq.CreateSequence('tpl', 'NNALF-'))
+ aln.AttachView(1, tpl.CreateFullView())
+ mhandle = modelling.BuildRawModel(aln)
+ # check
+ self.assertEqual(len(mhandle.gaps), 1)
+ self.assertEqual(modelling.RemoveTerminalGaps(mhandle), 1)
+ self.assertEqual(len(mhandle.gaps), 0)
+
if __name__ == "__main__":
from ost import testutils
--
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