# Copyright (c) 2013-2020, SIB - Swiss Institute of Bioinformatics and
# Biozentrum - University of Basel
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""
Unit tests for modelling.
"""
import unittest
from promod3 import modelling
from ost import conop, seq, io, mol, geom
class ModellingTests(unittest.TestCase):
#######################################################################
# HELPERs
#######################################################################
def checkModel(self, mhandle):
'''
Check if model residues are properly set (peptide_linking, protein,
torsion).
'''
# check residue properties
for r in mhandle.model.residues:
# check types
self.assertTrue(r.peptide_linking)
self.assertTrue(r.is_protein)
# check links
if r.next.IsValid() and (r.next.number - r.number) == 1:
self.assertTrue(mol.InSequence(r, r.next))
# check torsions
if r.prev.IsValid() and mol.InSequence(r.prev, r):
self.assertTrue(r.phi_torsion.IsValid())
self.assertTrue(r.omega_torsion.IsValid())
if r.next.IsValid() and mol.InSequence(r, r.next):
self.assertTrue(r.psi_torsion.IsValid())
#######################################################################
def testRaiseNoAttachedView(self):
# test that BuildRawModel throws exception when no view is attached
aln = seq.CreateAlignment(seq.CreateSequence('A', 'acdef'),
seq.CreateSequence('B', 'ac-ef'))
self.assertRaises(RuntimeError, modelling.BuildRawModel, aln)
def testRaiseInvalidChainNames(self):
tpl = io.LoadPDB('data/gly.pdb')
aln = io.LoadAlignment('data/seq.fasta')
aln.AttachView(1, tpl.CreateFullView())
# perform stuff that doesn't raise, i.e. do it correctly
result = modelling.BuildRawModel(aln)
result = modelling.BuildRawModel(aln, chain_names='cheese')
self.assertEqual(result.model.chains[0].GetName(), 'cheese')
aln_lst = seq.AlignmentList()
aln_lst.append(aln)
aln_lst.append(aln)
result = modelling.BuildRawModel(aln_lst)
result = modelling.BuildRawModel(aln_lst, ['cheese', 'steak'])
self.assertEqual(result.model.chains[0].GetName(), 'cheese')
self.assertEqual(result.model.chains[1].GetName(), 'steak')
result = modelling.BuildRawModel(aln_lst, 'ch')
self.assertEqual(result.model.chains[0].GetName(), 'c')
self.assertEqual(result.model.chains[1].GetName(), 'h')
result = modelling.BuildRawModel(aln_lst, 'cheese')
self.assertEqual(result.model.chains[0].GetName(), 'c')
self.assertEqual(result.model.chains[1].GetName(), 'h')
# we only accept a string as chain_names if aln is AlignmentHandle
self.assertRaises(RuntimeError, modelling.BuildRawModel, aln, 1)
self.assertRaises(RuntimeError, modelling.BuildRawModel, aln, ['A'])
# we only accept a list or str as chain_names if aln is AlignmentList
self.assertRaises(RuntimeError, modelling.BuildRawModel, aln_lst, 1)
# size also matters...
self.assertRaises(RuntimeError, modelling.BuildRawModel, aln_lst, ['A'])
self.assertRaises(RuntimeError, modelling.BuildRawModel, aln_lst, 'A')
# increase size of aln_list => at some point we should run out of
# default chain_names
aln_lst = 100*[aln]
self.assertRaises(RuntimeError, modelling.BuildRawModel, aln_lst)
def testModeledSequence(self):
# test if the model has the sequence we want.
tpl = io.LoadPDB('data/gly.pdb')
aln = io.LoadAlignment('data/seq.fasta')
aln.AttachView(1, tpl.CreateFullView())
result = modelling.BuildRawModel(aln)
seq1 = seq.SequenceFromChain('MODEL', result.model.chains[0])
self.assertEqual(len(result.gaps), 0)
self.assertEqual(seq1.string, aln.sequences[0].string)
def testDeletion(self):
# test if the result contains a "deletion" gap at the right spot.
tpl = io.LoadPDB('data/gly.pdb')
aln = io.LoadAlignment('data/del.fasta')
aln.AttachView(1, tpl.CreateFullView())
# disable aln_preprocessing to keep the deletion in the example aln
result = modelling.BuildRawModel(aln, aln_preprocessing=False)
residues = result.model.residues
self.assertEqual(len(result.gaps), 1)
self.assertEqual(result.gaps[0].before, residues[2])
self.assertEqual(result.gaps[0].after, residues[3])
self.assertEqual(result.gaps[0].seq, '')
def testInsertion(self):
# test if the result contains an "insertion" gap at the right spot.
tpl = io.LoadPDB('data/gly.pdb')
aln = io.LoadAlignment('data/ins.fasta')
aln.AttachView(1, tpl.CreateFullView())
result = modelling.BuildRawModel(aln)
residues = result.model.residues
self.assertEqual(len(result.gaps), 1)
self.assertEqual(result.gaps[0].before, residues[1])
self.assertEqual(result.gaps[0].after, residues[2])
self.assertEqual(result.gaps[0].seq, 'AV')
def testNonFeasiblePeptideBond(self):
# test if the result contains a gap when two residues cannot be
# connected with a feasible peptide bond
tpl = io.LoadPDB('data/gly_shifted_nter.pdb')
aln = io.LoadAlignment('data/seq.fasta')
aln.AttachView(1, tpl.CreateFullView())
result = modelling.BuildRawModel(aln)
residues = result.model.residues
self.assertEqual(len(result.gaps), 1)
self.assertEqual(result.gaps[0].before, residues[1])
self.assertEqual(result.gaps[0].after, residues[2])
self.assertEqual(result.gaps[0].seq, '')
def testTer(self):
# test if the result contains two terminal gaps, one at the beginning,
# one at the end
tpl = io.LoadPDB('data/gly.pdb')
aln = io.LoadAlignment('data/ter.fasta')
aln.AttachView(1, tpl.CreateFullView())
result = modelling.BuildRawModel(aln)
residues = result.model.residues
self.assertEqual(len(result.gaps), 2)
self.assertEqual(result.gaps[0].before, mol.ResidueHandle())
self.assertEqual(result.gaps[0].after, residues[0])
self.assertEqual(result.gaps[0].seq, 'G')
self.assertEqual(result.gaps[1].before, residues[-1])
self.assertEqual(result.gaps[1].after, mol.ResidueHandle())
self.assertEqual(result.gaps[1].seq, 'G')
def testTerTrg(self):
# test if raw model ignores terminal gaps in target sequence
tpl = io.LoadPDB('data/gly.pdb')
aln = seq.CreateAlignment(
seq.CreateSequence('trg', '--GG--'),
seq.CreateSequence('tpl', 'GGGGGG'))
aln.AttachView(1, tpl.CreateFullView())
result = modelling.BuildRawModel(aln)
self.assertEqual(len(result.gaps), 0)
def testModified(self):
# test if we correctly strip off modifications
tpl = io.LoadPDB('data/sep.pdb')
aln = io.LoadAlignment('data/sep.fasta')
aln.AttachView(1, tpl.CreateFullView())
result = modelling.BuildRawModel(aln)
residues = result.model.residues
self.assertEqual(len(residues), 1)
self.assertEqual(len(residues[0].atoms), 6)
self.assertTrue(residues[0].FindAtom("N"))
self.assertTrue(residues[0].FindAtom("CA"))
self.assertTrue(residues[0].FindAtom("C"))
self.assertTrue(residues[0].FindAtom("O"))
self.assertTrue(residues[0].FindAtom("CB"))
self.assertTrue(residues[0].FindAtom("OG"))
def testModifiedMismatch(self):
# test if we allow OLC mismatch for modified AA
tpl = io.LoadPDB('data/sep.pdb')
aln = seq.CreateAlignment(
seq.CreateSequence('trg', 'S'),
seq.CreateSequence('tpl', 'X'))
aln.AttachView(1, tpl.CreateFullView())
result = modelling.BuildRawModel(aln)
residues = result.model.residues
# same as before as OLC of SEP is 'S' (i.e. matches)
self.assertEqual(len(residues), 1)
self.assertEqual(len(residues[0].atoms), 6)
self.assertTrue(residues[0].FindAtom("N"))
self.assertTrue(residues[0].FindAtom("CA"))
self.assertTrue(residues[0].FindAtom("C"))
self.assertTrue(residues[0].FindAtom("O"))
self.assertTrue(residues[0].FindAtom("CB"))
self.assertTrue(residues[0].FindAtom("OG"))
# NOTE: relevant seq-vs-str mismatch tested in testOffset
# See OST's nonstandard.cc for additional tests of handling modified
# residues. Code duplication will be removed in SCHWED-3569.
def testInsertCBeta(self):
# test if the dst residues contain cbeta, unless they are glycines
tpl = io.LoadPDB('data/cbeta.pdb')
aln = io.LoadAlignment('data/cbeta.fasta')
aln.AttachView(1, tpl.CreateFullView())
result = modelling.BuildRawModel(aln)
residues = result.model.residues
self.assertFalse(residues[0].FindAtom("CB").IsValid())
self.assertFalse(residues[1].FindAtom("CB").IsValid())
self.assertTrue(residues[2].FindAtom("CB").IsValid())
self.assertTrue(residues[3].FindAtom("CB").IsValid())
def testOffset(self):
# test if we can construct a raw model with an offset
tpl = io.LoadPDB('data/2jlp-1.pdb')
aln = io.LoadAlignment('data/2jlp-1.fasta')
aln.AttachView(1, tpl.Select("cname=A").CreateFullView())
# fail w/o offset
with self.assertRaises(RuntimeError):
mhandle = modelling.BuildRawModel(aln)
# try with hard-coded offset
aln.SetSequenceOffset(1, 55)
mhandle = modelling.BuildRawModel(aln)
self.assertEqual(len(mhandle.gaps), 4)
def testOnTop(self):
# do we clean up atoms that are on top of each other?
# ResNum 8 has CA-pos == C-pos
tpl = io.LoadPDB('data/gly_on_top.pdb')
aln = io.LoadAlignment('data/seq.fasta')
aln.AttachView(1, tpl.CreateFullView())
result = modelling.BuildRawModel(aln)
self.assertEqual(len(result.gaps), 1)
self.assertEqual(result.gaps[0].before.number.num, 7)
self.assertEqual(result.gaps[0].after.number.num, 9)
#######################################################################
def testModellingHandleOperations(self):
# handle with gap
tpl = io.LoadPDB('data/1crn_cut.pdb')
aln = io.LoadAlignment('data/1crn.fasta')
aln.AttachView(1, tpl.CreateFullView())
mhandle = modelling.BuildRawModel(aln)
# check ModellingHandle
self.assertEqual(len(mhandle.gaps), 1)
self.assertEqual(str(mhandle.gaps[0]), 'A.ALA24-(ICATYT)-A.GLY31')
self.checkModel(mhandle)
# check copy
mhandle_copy = mhandle.Copy()
self.assertEqual([str(a) for a in mhandle_copy.model.atoms],
[str(a) for a in mhandle.model.atoms])
self.assertEqual([str(g) for g in mhandle_copy.gaps],
[str(g) for g in mhandle.gaps])
self.assertEqual([str(s) for s in mhandle_copy.seqres],
[str(s) for s in mhandle.seqres])
# rest of the fields not checked...yet
# handle without gap
tpl_closed = io.LoadPDB('data/1crn_build.pdb')
seqres = str(aln.sequences[0])
aln_closed = seq.CreateAlignment(seq.CreateSequence('trg', seqres),
seq.CreateSequence('tpl', seqres))
aln_closed.AttachView(1, tpl_closed.CreateFullView())
mhandle_closed = modelling.BuildRawModel(aln_closed)
# merge with no overlap (no change)
mhandle_copy = mhandle.Copy()
modelling.MergeMHandle(mhandle_closed, mhandle_copy, 0, 0, 10, 19,
geom.Mat4())
self.assertEqual([str(a) for a in mhandle_copy.model.atoms],
[str(a) for a in mhandle.model.atoms])
self.assertEqual([str(g) for g in mhandle_copy.gaps],
[str(g) for g in mhandle.gaps])
self.assertEqual([str(s) for s in mhandle_copy.seqres],
[str(s) for s in mhandle.seqres])
self.checkModel(mhandle_copy)
# merge with overlap on N-side
mhandle_copy = mhandle.Copy()
modelling.MergeMHandle(mhandle_closed, mhandle_copy, 0, 0, 20, 29,
geom.Mat4())
self.assertEqual(len(mhandle_copy.gaps), 1)
self.assertEqual(str(mhandle_copy.gaps[0]), 'A.TYR29-(T)-A.GLY31')
self.checkModel(mhandle_copy)
# merge with overlap on C-side
mhandle_copy = mhandle.Copy()
modelling.MergeMHandle(mhandle_closed, mhandle_copy, 0, 0, 27, 35,
geom.Mat4())
self.assertEqual(len(mhandle_copy.gaps), 1)
self.assertEqual(str(mhandle_copy.gaps[0]), 'A.ALA24-(IC)-A.ALA27')
self.checkModel(mhandle_copy)
# merge with full overlap
mhandle_copy = mhandle.Copy()
modelling.MergeMHandle(mhandle_closed, mhandle_copy, 0, 0, 20, 35,
geom.Mat4())
self.assertEqual(len(mhandle_copy.gaps), 0)
self.checkModel(mhandle_copy)
#######################################################################
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')
# last gap: should throw exception
with self.assertRaises(RuntimeError):
modelling.MergeGaps(mhandle, 0)
def testMergeGapsOligo(self):
# check that merge gaps fails if on diff. chains
tpl = io.LoadPDB('data/5d52-1.pdb')
aln_A = seq.CreateAlignment(
seq.CreateSequence('trg', 'GIVEQAAACCTSICSLYQLENYCN'),
seq.CreateSequence('tpl', 'GIVEQ---CCTSICSLYQLENYCN'))
aln_B = seq.CreateAlignment(
seq.CreateSequence('trg', 'FVNQHLCG---LEALTLVCGERGFFYTPKA'),
seq.CreateSequence('tpl', 'FVNQHLCGSHLVEALYLVCGERGFFYTPKA'))
aln_A.AttachView(1, tpl.Select("cname=A").CreateFullView())
aln_B.AttachView(1, tpl.Select("cname=B").CreateFullView())
alns = seq.AlignmentList()
alns.append(aln_A)
alns.append(aln_B)
mhandle = modelling.BuildRawModel(alns)
# check
self.assertEqual(len(mhandle.gaps), 2)
with self.assertRaises(RuntimeError):
modelling.MergeGaps(mhandle, 0)
def testCountEnclosedGaps(self):
tpl = io.LoadPDB('data/2dbs.pdb')
aln = seq.CreateAlignment(
seq.CreateSequence('trg', 'GATLNGFTVPAGNTLVLN---PD--KG---ATVTMAGA'),
seq.CreateSequence('tpl', '--NGG--TL--LI--PNGTYHFLGIQMKSNVHIRVE--'))
aln.AttachView(1, tpl.CreateFullView())
mhandle = modelling.BuildRawModel(aln)
# check
self.assertEqual(len(mhandle.gaps), 8)
for g in mhandle.gaps:
self.assertEqual(modelling.CountEnclosedGaps(mhandle, g), 1)
self.assertEqual(modelling.CountEnclosedInsertions(mhandle, g),
1 if (g.length > 0) else 0)
mych = mhandle.model.chains[0]
# none
mygap = modelling.StructuralGap(mych.FindResidue(15),
mych.FindResidue(17), "L")
self.assertEqual(modelling.CountEnclosedGaps(mhandle, mygap), 0)
self.assertEqual(modelling.CountEnclosedInsertions(mhandle, mygap), 0)
# extended singles
mygap = modelling.StructuralGap(mych.FindResidue(3),
mych.FindResidue(9), "LNGFT")
self.assertEqual(modelling.CountEnclosedGaps(mhandle, mygap), 1)
self.assertEqual(modelling.CountEnclosedInsertions(mhandle, mygap), 1)
mygap = modelling.StructuralGap(mych.FindResidue(20),
mych.FindResidue(22), "K")
self.assertEqual(modelling.CountEnclosedGaps(mhandle, mygap), 1)
self.assertEqual(modelling.CountEnclosedInsertions(mhandle, mygap), 0)
# doubles
mygap = modelling.StructuralGap(mych.FindResidue(3),
mych.FindResidue(12), "LNGFTVPA")
self.assertEqual(modelling.CountEnclosedGaps(mhandle, mygap), 2)
self.assertEqual(modelling.CountEnclosedInsertions(mhandle, mygap), 2)
mygap = modelling.StructuralGap(mych.FindResidue(13),
mych.FindResidue(19), "TLVLN")
self.assertEqual(modelling.CountEnclosedGaps(mhandle, mygap), 2)
self.assertEqual(modelling.CountEnclosedInsertions(mhandle, mygap), 1)
mygap = modelling.StructuralGap(mych.FindResidue(20),
mych.FindResidue(25), "KGAT")
self.assertEqual(modelling.CountEnclosedGaps(mhandle, mygap), 2)
self.assertEqual(modelling.CountEnclosedInsertions(mhandle, mygap), 0)
#######################################################################
def testClearGapsExceptions(self):
# check that clear gaps throws exceptions when used wrongly
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())
# disable aln_preprocessing to also keep the small deletion in the end
mhandle = modelling.BuildRawModel(aln, aln_preprocessing=False)
# 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):
# check that we can clear multiple gaps at once
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):
# check that we can clear terminal gaps
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 testClearGapsOligo(self):
# check that we can clear gaps in oligomers
tpl = io.LoadPDB('data/5d52-1.pdb')
aln_A = seq.CreateAlignment(
seq.CreateSequence('trg', 'GIVEQPAYFWPPPAHCCTSICSLYQLENYCN'),
seq.CreateSequence('tpl', 'GIVEQ----------CCTSICSLYQLENYCN'))
aln_B = seq.CreateAlignment(
seq.CreateSequence('trg', 'FVNQHLCGSGHLVEALYLVCGERGFFYTPKA'),
seq.CreateSequence('tpl', 'FVNQHLCGS-HLVEALYLVCGERGFFYTPKA'))
aln_A.AttachView(1, tpl.Select("cname=A").CreateFullView())
aln_B.AttachView(1, tpl.Select("cname=B").CreateFullView())
alns = seq.AlignmentList()
alns.append(aln_A)
alns.append(aln_B)
mhandle = modelling.BuildRawModel(alns)
# 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):
# check that we can remove both terminal gaps
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):
# check that we can remove N-terminal gaps
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):
# check that we can remove C-terminal gaps
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
testutils.RunTests()