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Commit dd465a80 authored by Bienchen's avatar Bienchen
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SCHWED-372: Implemented, tested, documented

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rawmodel/pymod/_closegaps.py
+ 62
− 7
View file @ dd465a80
......@@ -160,9 +160,34 @@ def _MergeGapsByDistance(self, distance):
Check if two neighbouring gaps are at max. *distance* residues apart from
each other. Then delete the residues and store a new gap spanning the whole
stretch of original gaps and the deleted region. Original gaps will be
removed.
removed. Stem residues count to the gap, so **A-A-A** has a distance of 0.
EXAMPLE!
.. testcode:: mergegapsbydist
:hide:
from promod3 import rawmodel
tpl = ost.io.LoadPDB('../tests/rawmodel/data/raw-modeling/1mcg.pdb')
aln = ost.seq.CreateAlignment(ost.seq.CreateSequence('trg',
'DDFAGDTKNLGHN'),
ost.seq.CreateSequence('tpl',
'NN----A----LF'))
aln.AttachView(1, tpl.CreateFullView())
rmodel = rawmodel.BuildRawModel(aln)
assert len(rmodel.gaps) == 2
rmodel.MergeGapsByDistance(0)
assert len(rmodel.gaps) == 1
.. doctest:: mergegapsbydist
import ost
from promod3 import rawmodel
tpl = ost.io.LoadPDB('1mcg.pdb')
aln = ost.io.LoadAlignment('1mcg_aln.fasta')
aln.AttachView(1, tpl.CreateFullView())
rmodel = rawmodel.BuildRawModel(aln)
rmodel.MergeGapsByDistance(0)
:param distance: The max. no. of residues between two gaps up to which
merge happens.
......@@ -170,10 +195,40 @@ def _MergeGapsByDistance(self, distance):
:return: Nothing.
'''
ost.LogVerbose(self)
ost.LogVerbose(distance)
__all__ = ['_CloseSmallDeletions']
# IMPORTANT: the assumption is that RawModelingResult stores gaps
# sequentially
# indicate if we merged gaps and should check for more
try_again = True
# The number of gaps changes on merge, so we cannot just iterate them.
# If we merged gaps, we do not know if this was the last one so try_again
# is set to True. If no more gaps were merged, we stop by leaving try_again
# as False.
while try_again:
try_again = False
# iterate all but the last gap, since we are always looking ahead
for i in range(len(self.gaps) - 1):
current_gap = self.gaps[i]
next_gap = self.gaps[i+1]
# check that we are on the same chain
if current_gap.GetChain() != next_gap.GetChain():
continue
# no merging of gaps at the end AND the start :)
if current_gap.IsNTerminal() and next_gap.IsCTerminal():
continue
# get the distance between the gaps
dist = next_gap.before.GetNumber().GetNum() \
- current_gap.after.GetNumber().GetNum()
if dist <= distance:
# gaps are close enough, combine! combine!
self.MergeGaps(i)
ost.LogVerbose("Merged gap %s and %s into %s" % \
(current_gap, next_gap, self.gaps[i]))
try_again = True
break
__all__ = ['_CloseSmallDeletions', '_MergeGapsByDistance']
# LocalWords: modeling stereochemically param
rawmodel/tests/CMakeLists.txt
+ 2
− 1
View file @ dd465a80
set(RAWMODEL_UNIT_TESTS
test_raw_modeling.py
test_gap_extension.py
test_closesgaps.py
test_close_gaps.py
)
set(RAWMODEL_TEST_DATA
......@@ -16,6 +16,7 @@ set(RAWMODEL_TEST_DATA
data/raw-modeling/del.fasta
data/raw-modeling/cbeta.pdb
data/raw-modeling/cbeta.fasta
data/raw-modeling/1mcg.pdb
)
promod3_unittest(MODULE rawmodel
......
rawmodel/tests/data/raw-modeling/1mcg.pdb 0 → 100644
+ 78
− 0
View file @ dd465a80
HELIX 1 1 ASN A 41 ARG A 52 1 12
HELIX 2 2 LEU A 223 TYR A 228 1 6
HELIX 3 3 ARG A 295 VAL A 302 1 8
HELIX 4 4 ASP A 332 TYR A 342 1 11
HELIX 5 5 GLN A 369 PHE A 375 1 7
SHEET 1 1 1 GLY A 57 ILE A 61 0
SHEET 2 2 1 GLY A 64 PHE A 68 0
SHEET 3 3 1 VAL A 77 VAL A 81 0
SHEET 4 4 1 VAL A 85 PRO A 89 0
SHEET 5 5 1 PHE A 101 VAL A 103 0
SHEET 6 6 1 PHE A 112 GLY A 116 0
SHEET 7 7 1 PHE A 121 ASP A 124 0
SHEET 8 8 1 PHE A 136 LEU A 138 0
SHEET 9 9 1 TYR A 144 SER A 147 0
SHEET 10 10 1 PHE A 149 ASP A 152 0
SHEET 11 11 1 ILE A 161 VAL A 163 0
SHEET 12 12 1 THR A 166 ARG A 168 0
SHEET 13 13 1 ARG A 171 HIS A 173 0
SHEET 14 14 1 GLY A 178 GLU A 181 0
SHEET 15 15 1 ILE A 183 ASN A 186 0
SHEET 16 16 1 ILE A 195 THR A 197 0
SHEET 17 17 1 GLY A 199 ASP A 201 0
SHEET 18 18 1 ILE A 203 ARG A 206 0
SHEET 19 19 1 LEU A 208 GLU A 211 0
SHEET 20 20 1 LEU A 216 GLU A 219 0
SHEET 21 21 1 GLY A 232 ARG A 234 0
SHEET 22 22 1 ILE A 236 ASP A 239 0
SHEET 23 23 1 ILE A 241 SER A 244 0
SHEET 24 24 1 VAL A 250 GLY A 253 0
SHEET 25 25 1 VAL A 262 THR A 265 0
SHEET 26 26 1 VAL A 267 VAL A 270 0
SHEET 27 27 1 VAL A 276 SER A 278 0
SHEET 28 28 1 VAL A 352 PHE A 355 0
SHEET 29 29 1 VAL A 357 ARG A 360 0
SHEET 30 30 1 ALA A 365 LEU A 367 0
SHEET 31 31 1 TYR A 400 GLY A 402 0
SHEET 32 32 1 VAL A 408 ASP A 410 0
ATOM 1170 N ASN A 186 4.019 30.959 20.793 1.00 11.38 N
ATOM 1171 CA ASN A 186 3.429 31.085 19.456 1.00 11.67 C
ATOM 1172 C ASN A 186 3.017 32.515 19.097 1.00 11.36 C
ATOM 1173 O ASN A 186 2.635 33.316 19.975 1.00 9.55 O
ATOM 1174 CB ASN A 186 2.310 30.087 19.262 1.00 11.85 C
ATOM 1175 CG ASN A 186 2.649 28.733 19.852 1.00 14.79 C
ATOM 1176 OD1 ASN A 186 1.924 28.219 20.686 1.00 17.92 O
ATOM 1177 ND2 ASN A 186 3.784 28.161 19.443 1.00 19.24 N
ATOM 1178 N ASN A 187 3.222 32.838 17.819 1.00 12.09 N
ATOM 1179 CA ASN A 187 2.676 34.038 17.169 1.00 13.35 C
ATOM 1180 C ASN A 187 3.048 35.377 17.837 1.00 13.30 C
ATOM 1181 O ASN A 187 2.182 36.129 18.305 1.00 13.67 O
ATOM 1182 CB ASN A 187 1.156 33.861 17.052 1.00 13.63 C
ATOM 1183 CG ASN A 187 0.496 34.969 16.298 1.00 15.82 C
ATOM 1184 OD1 ASN A 187 1.061 35.533 15.353 1.00 17.79 O
ATOM 1185 ND2 ASN A 187 -0.723 35.304 16.715 1.00 17.94 N
ATOM 1186 N ALA A 188 4.347 35.638 17.899 1.00 13.36 N
ATOM 1187 CA ALA A 188 4.919 36.848 18.497 1.00 13.12 C
ATOM 1188 C ALA A 188 4.983 37.951 17.450 1.00 13.42 C
ATOM 1189 O ALA A 188 4.986 37.656 16.241 1.00 13.21 O
ATOM 1190 CB ALA A 188 6.361 36.560 19.037 1.00 12.49 C
ATOM 1191 N LEU A 189 5.089 39.207 17.904 1.00 13.18 N
ATOM 1192 CA LEU A 189 5.305 40.332 16.986 1.00 13.51 C
ATOM 1193 C LEU A 189 6.774 40.408 16.615 1.00 14.04 C
ATOM 1194 O LEU A 189 7.617 40.263 17.469 1.00 13.93 O
ATOM 1195 CB LEU A 189 4.842 41.649 17.627 1.00 13.73 C
ATOM 1196 CG LEU A 189 4.810 43.000 16.889 1.00 12.27 C
ATOM 1197 CD1 LEU A 189 4.011 42.955 15.599 1.00 10.44 C
ATOM 1198 CD2 LEU A 189 4.259 44.029 17.846 1.00 9.81 C
ATOM 1199 N PHE A 190 7.081 40.622 15.340 1.00 15.37 N
ATOM 1200 CA PHE A 190 8.475 40.714 14.893 1.00 16.40 C
ATOM 1201 C PHE A 190 9.443 41.387 15.872 1.00 17.11 C
ATOM 1202 O PHE A 190 10.514 40.836 16.173 1.00 18.24 O
ATOM 1203 CB PHE A 190 8.587 41.340 13.499 1.00 16.62 C
ATOM 1204 CG PHE A 190 8.259 42.798 13.451 1.00 16.71 C
ATOM 1205 CD1 PHE A 190 6.946 43.216 13.309 1.00 14.70 C
ATOM 1206 CD2 PHE A 190 9.271 43.754 13.517 1.00 15.08 C
ATOM 1207 CE1 PHE A 190 6.638 44.580 13.244 1.00 16.59 C
ATOM 1208 CE2 PHE A 190 8.975 45.127 13.463 1.00 15.55 C
ATOM 1209 CZ PHE A 190 7.664 45.544 13.337 1.00 16.66 C
END
rawmodel/tests/test_closesgaps.py → rawmodel/tests/test_close_gaps.py
+ 94
− 0
View file @ dd465a80
......@@ -18,10 +18,13 @@ class _FetchLog(ost.LogSink):
self.messages[level].append(message.strip())
class CloseGapsTests(unittest.TestCase):
def testClosesmalldel(self):
log = _FetchLog()
def setUp(self):
self.log = _FetchLog()
ost.PushLogSink(self.log)
ost.PushVerbosityLevel(4)
ost.PushLogSink(log)
def testClosesmalldel(self):
# check that very small gaps are closed
# create a rawmodel to work with (which actually is a bit dangerous:
# the PDB file has nothing to do with the alignment...)
tpl = io.LoadPDB('data/raw-modeling/gly.pdb')
......@@ -35,13 +38,57 @@ class CloseGapsTests(unittest.TestCase):
scorer = loop.SetupBackboneScorer(rmodel)
rmodel.CloseSmallDeletions(scorer)
self.assertEqual(len(rmodel.gaps), 0)
self.assertEqual(log.messages['VERBOSE'],
self.assertEqual(self.log.messages['VERBOSE'],
['Assigning MOL_IDs',
'selected 1 chain(s), 20 residue(s), 80 atom(s) 79 '+
'bond(s)',
'Closed: A.GLY3-()-A.GLY4 by relaxing '+
'A.GLY3-(GG)-A.GLY6'])
def testMergeGapsByDistance(self):
# test that merging two close gaps works
tpl = io.LoadPDB('data/raw-modeling/1mcg.pdb')
aln = seq.CreateAlignment(seq.CreateSequence('trg', 'DDFAGDTKNLGHN'),
seq.CreateSequence('tpl', 'NN----A----LF'))
aln.AttachView(1, tpl.CreateFullView())
rmodel = rawmodel.BuildRawModel(aln)
self.assertEqual(len(rmodel.gaps), 2)
self.assertEqual(str(rmodel.gaps[0]), 'A.ASP2-(FAGD)-A.THR7')
self.assertEqual(str(rmodel.gaps[1]), 'A.THR7-(KNLG)-A.HIS12')
rmodel.MergeGapsByDistance(0)
self.assertEqual(len(rmodel.gaps), 1)
self.assertEqual(str(rmodel.gaps[0]), 'A.ASP2-(FAGDTKNLG)-A.HIS12')
self.assertEqual(self.log.messages['VERBOSE'],
['Assigning MOL_IDs',
'selected 1 chain(s), 5 residue(s), 40 atom(s) 40 '+
'bond(s)',
'Merged gap A.ASP2-(FAGD)-A.THR7 and '+
'A.THR7-(KNLG)-A.HIS12 into '+
'A.ASP2-(FAGDTKNLG)-A.HIS12'])
def testMergeGapsByDistanceBothTerminals(self):
# test that we do not delete the whole thing for gaps at terminals
tpl = io.LoadPDB('data/raw-modeling/1mcg.pdb')
aln = seq.CreateAlignment(seq.CreateSequence('trg', 'DDFAGDTKNLGHN'),
seq.CreateSequence('tpl', '----NNALF----'))
aln.AttachView(1, tpl.CreateFullView())
rmodel = rawmodel.BuildRawModel(aln)
self.assertEqual(len(rmodel.gaps), 2)
rmodel.MergeGapsByDistance(4)
self.assertEqual(len(rmodel.gaps), 2)
def testMergeGapsByDistanceOneTerminal(self):
# test that we do not delete the whole thing for gaps at terminals
tpl = io.LoadPDB('data/raw-modeling/1mcg.pdb')
aln = seq.CreateAlignment(seq.CreateSequence('trg', 'DDFAGDTKNLGHN'),
seq.CreateSequence('tpl', 'NN----ALF----'))
aln.AttachView(1, tpl.CreateFullView())
rmodel = rawmodel.BuildRawModel(aln)
self.assertEqual(len(rmodel.gaps), 2)
rmodel.MergeGapsByDistance(2)
self.assertEqual(len(rmodel.gaps), 1)
if __name__ == "__main__":
from ost import testutils
testutils.RunTests()
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