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Commit 571e47d1 authored by Gerardo Tauriello's avatar Gerardo Tauriello
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fixed tests and doc

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modelling/pymod/_closegaps.py
+ 17
− 0
View file @ 571e47d1
......@@ -309,6 +309,23 @@ def FillLoopsByDatabase(mhandle, scorer, fragment_db, structure_db,
evaluated per loop.
:type max_loops_to_search: :class:`int`
:param extended_search: True = more loop candidates are considered.
The candidate search is done less precisely (see
:meth:`~promod3.loop.LoopCandidates.FillFromDatabase`).
The candidates are still scored and evaluated the
same though (only more of them considered).
:type extended_search: :class:`bool`
:param use_scoring_extender: True = use :class:`ScoringGapExtender` instead
of :class:`GapExtender`.
The gap is penalized according as
0.8*length + sum(helices) + sum(sheets).
For the scondary-structure-penalty to work,
the model-template must have the appropriate
information before :func:`BuildRawModel` is
called (e.g. with :mod:`ost.bindings.dssp`).
:type use_scoring_extender: :class:`bool`
:param max_db_loop_len: Max. len of loops for which a database search makes
sense. Should correspond to the biggest loop stored
in the database.
......
modelling/tests/data/1crn_build.pdb
+ 327
− 327
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modelling/tests/data/1crn_final.pdb
+ 327
− 327
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modelling/tests/data/1crn_rec.pdb
+ 158
− 152
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modelling/tests/data/1crn_sc.pdb
+ 76
− 76
View file @ 571e47d1
......@@ -151,82 +151,82 @@ ATOM 150 O THR A 21 5.947 10.757 -2.523 1.00 5.82 O
ATOM 151 CB THR A 21 2.992 10.188 -2.225 1.00 4.13 C
ATOM 152 OG1 THR A 21 2.051 9.144 -2.623 1.00 5.45 O
ATOM 153 CG2 THR A 21 2.260 11.349 -1.551 1.00 5.41 C
ATOM 154 N PRO A 22 4.995 12.718 -3.161 1.00 5.04 N
ATOM 155 CA PRO A 22 6.125 13.499 -2.698 1.00 4.69 C
ATOM 156 C PRO A 22 6.393 13.232 -1.238 1.00 4.19 C
ATOM 157 O PRO A 22 5.479 13.059 -0.431 1.00 4.47 O
ATOM 158 CB PRO A 22 5.842 14.958 -2.898 1.00 7.12 C
ATOM 159 CG PRO A 22 4.828 14.995 -4.046 1.00 0.00 C
ATOM 160 CD PRO A 22 3.965 13.756 -3.791 1.00 0.00 C
ATOM 161 N GLU A 23 7.659 13.237 -0.852 1.00 0.00 N
ATOM 162 CA GLU A 23 7.981 12.921 0.510 1.00 0.00 C
ATOM 163 C GLU A 23 7.304 13.857 1.511 1.00 0.00 C
ATOM 164 O GLU A 23 7.052 13.494 2.646 1.00 0.00 O
ATOM 165 CB GLU A 23 9.467 13.004 0.692 1.00 0.00 C
ATOM 166 CG GLU A 23 10.297 11.898 -0.021 1.00 0.00 C
ATOM 167 CD GLU A 23 11.816 12.011 0.122 1.00 0.00 C
ATOM 168 OE1 GLU A 23 12.221 13.057 0.694 1.00 0.00 O
ATOM 169 OE2 GLU A 23 12.558 11.100 -0.315 1.00 0.00 O
ATOM 170 N ALA A 24 7.051 15.110 1.093 1.00 0.00 N
ATOM 171 CA ALA A 24 6.502 16.036 2.035 1.00 0.00 C
ATOM 172 C ALA A 24 5.061 15.672 2.409 1.00 0.00 C
ATOM 173 O ALA A 24 4.651 15.824 3.552 1.00 0.00 O
ATOM 174 CB ALA A 24 6.528 17.415 1.446 1.00 0.00 C
ATOM 175 N ILE A 25 4.278 15.191 1.441 1.00 0.00 N
ATOM 176 CA ILE A 25 2.933 14.772 1.782 1.00 0.00 C
ATOM 177 C ILE A 25 2.979 13.577 2.729 1.00 0.00 C
ATOM 178 O ILE A 25 2.263 13.547 3.729 1.00 0.00 O
ATOM 179 CB ILE A 25 2.190 14.398 0.534 1.00 0.00 C
ATOM 180 CG1 ILE A 25 1.909 15.599 -0.405 1.00 0.00 C
ATOM 181 CG2 ILE A 25 0.924 13.550 0.789 1.00 0.00 C
ATOM 182 CD1 ILE A 25 1.405 15.198 -1.802 1.00 0.00 C
ATOM 183 N CYS A 26 3.796 12.600 2.436 1.00 0.00 N
ATOM 184 CA CYS A 26 3.902 11.454 3.296 1.00 0.00 C
ATOM 185 C CYS A 26 4.378 11.792 4.694 1.00 0.00 C
ATOM 186 O CYS A 26 3.914 11.207 5.676 1.00 0.00 O
ATOM 187 CB CYS A 26 4.858 10.475 2.683 1.00 0.00 C
ATOM 188 SG CYS A 26 4.242 9.705 1.134 1.00 0.00 S
ATOM 189 N ALA A 27 5.306 12.737 4.789 1.00 0.00 N
ATOM 190 CA ALA A 27 5.714 13.193 6.113 1.00 0.00 C
ATOM 191 C ALA A 27 4.495 13.506 6.968 1.00 0.00 C
ATOM 192 O ALA A 27 4.442 13.067 8.116 1.00 0.00 O
ATOM 193 CB ALA A 27 6.564 14.422 5.980 1.00 0.00 C
ATOM 194 N THR A 28 3.550 14.258 6.443 1.00 0.00 N
ATOM 195 CA THR A 28 2.347 14.540 7.202 1.00 0.00 C
ATOM 196 C THR A 28 1.555 13.313 7.553 1.00 0.00 C
ATOM 197 O THR A 28 1.107 13.181 8.698 1.00 0.00 O
ATOM 198 CB THR A 28 1.477 15.463 6.401 1.00 0.00 C
ATOM 199 OG1 THR A 28 2.113 16.712 6.143 1.00 0.00 O
ATOM 200 CG2 THR A 28 0.094 15.760 6.991 1.00 0.00 C
ATOM 201 N TYR A 29 1.353 12.434 6.586 1.00 0.00 N
ATOM 202 CA TYR A 29 0.582 11.206 6.825 1.00 0.00 C
ATOM 203 C TYR A 29 1.248 10.213 7.722 1.00 0.00 C
ATOM 204 O TYR A 29 0.606 9.295 8.239 1.00 0.00 O
ATOM 205 CB TYR A 29 0.316 10.548 5.504 1.00 0.00 C
ATOM 206 CG TYR A 29 -0.686 11.303 4.661 1.00 0.00 C
ATOM 207 CD1 TYR A 29 -1.640 12.095 5.267 1.00 0.00 C
ATOM 208 CD2 TYR A 29 -0.647 11.200 3.286 1.00 0.00 C
ATOM 209 CE1 TYR A 29 -2.568 12.794 4.486 1.00 0.00 C
ATOM 210 CE2 TYR A 29 -1.576 11.899 2.505 1.00 0.00 C
ATOM 211 CZ TYR A 29 -2.529 12.689 3.091 1.00 0.00 C
ATOM 212 OH TYR A 29 -3.457 13.388 2.310 1.00 0.00 O
ATOM 213 N THR A 30 2.564 10.347 7.911 1.00 0.00 N
ATOM 214 CA THR A 30 3.365 9.322 8.604 1.00 0.00 C
ATOM 215 C THR A 30 3.916 9.808 9.928 1.00 0.00 C
ATOM 216 O THR A 30 4.324 8.972 10.710 1.00 0.00 O
ATOM 217 CB THR A 30 4.506 8.915 7.720 1.00 0.00 C
ATOM 218 OG1 THR A 30 5.373 10.007 7.424 1.00 0.00 O
ATOM 219 CG2 THR A 30 4.121 8.255 6.392 1.00 0.00 C
ATOM 220 N GLY A 31 3.995 11.118 10.162 1.00 0.00 N
ATOM 221 CA GLY A 31 4.730 11.637 11.306 1.00 0.00 C
ATOM 222 C GLY A 31 6.208 11.784 11.116 1.00 0.00 C
ATOM 223 O GLY A 31 6.940 12.074 12.076 1.00 0.00 O
ATOM 224 N CYS A 32 6.712 11.563 9.959 1.00 4.30 N
ATOM 225 CA CYS A 32 8.139 11.683 9.606 1.00 4.89 C
ATOM 226 C CYS A 32 8.450 13.152 9.215 1.00 5.50 C
ATOM 227 O CYS A 32 7.585 13.992 8.970 1.00 5.82 O
ATOM 228 CB CYS A 32 8.417 10.765 8.469 1.00 4.66 C
ATOM 229 SG CYS A 32 8.145 8.992 8.862 1.00 0.00 S
ATOM 154 N PRO A 22 4.971 12.703 -3.176 1.00 5.04 N
ATOM 155 CA PRO A 22 6.143 13.513 -2.696 1.00 4.69 C
ATOM 156 C PRO A 22 6.400 13.233 -1.225 1.00 4.19 C
ATOM 157 O PRO A 22 5.485 13.061 -0.382 1.00 4.47 O
ATOM 158 CB PRO A 22 5.703 14.969 -2.920 1.00 7.12 C
ATOM 159 CG PRO A 22 4.676 14.893 -3.996 1.00 7.03 C
ATOM 160 CD PRO A 22 3.964 13.567 -3.811 1.00 4.90 C
ATOM 161 N GLU A 23 7.728 13.297 -0.921 1.00 5.16 N
ATOM 162 CA GLU A 23 8.114 13.103 0.500 1.00 5.31 C
ATOM 163 C GLU A 23 7.427 14.073 1.410 1.00 4.11 C
ATOM 164 O GLU A 23 7.036 13.682 2.540 1.00 5.11 O
ATOM 165 CB GLU A 23 9.648 13.285 0.660 1.00 6.16 C
ATOM 166 CG GLU A 23 10.440 12.093 0.063 1.00 7.48 C
ATOM 167 CD GLU A 23 11.941 12.170 0.391 1.00 9.40 C
ATOM 168 OE1 GLU A 23 12.416 13.225 0.681 1.00 10.40 O
ATOM 169 OE2 GLU A 23 12.539 11.070 0.292 1.00 13.32 O
ATOM 170 N ALA A 24 7.206 15.339 0.972 1.00 4.56 N
ATOM 171 CA ALA A 24 6.625 16.316 1.907 1.00 4.49 C
ATOM 172 C ALA A 24 5.206 15.933 2.351 1.00 4.10 C
ATOM 173 O ALA A 24 4.867 16.052 3.523 1.00 5.64 O
ATOM 174 CB ALA A 24 6.585 17.662 1.246 1.00 5.80 C
ATOM 175 N ILE A 25 4.400 15.462 1.405 1.00 0.00 N
ATOM 176 CA ILE A 25 3.013 15.077 1.697 1.00 0.00 C
ATOM 177 C ILE A 25 2.949 13.799 2.532 1.00 0.00 C
ATOM 178 O ILE A 25 2.149 13.704 3.465 1.00 0.00 O
ATOM 179 CB ILE A 25 2.276 14.865 0.408 1.00 0.00 C
ATOM 180 CG1 ILE A 25 2.083 16.162 -0.418 1.00 0.00 C
ATOM 181 CG2 ILE A 25 0.958 14.073 0.562 1.00 0.00 C
ATOM 182 CD1 ILE A 25 1.575 15.925 -1.850 1.00 0.00 C
ATOM 183 N CYS A 26 3.801 12.828 2.191 1.00 0.00 N
ATOM 184 CA CYS A 26 3.820 11.519 2.858 1.00 0.00 C
ATOM 185 C CYS A 26 4.443 11.568 4.247 1.00 0.00 C
ATOM 186 O CYS A 26 3.895 10.981 5.191 1.00 0.00 O
ATOM 187 CB CYS A 26 4.593 10.553 2.011 1.00 0.00 C
ATOM 188 SG CYS A 26 3.768 10.129 0.427 1.00 0.00 S
ATOM 189 N ALA A 27 5.577 12.255 4.371 1.00 0.00 N
ATOM 190 CA ALA A 27 6.381 12.218 5.600 1.00 0.00 C
ATOM 191 C ALA A 27 5.720 12.806 6.859 1.00 0.00 C
ATOM 192 O ALA A 27 5.714 12.148 7.900 1.00 0.00 O
ATOM 193 CB ALA A 27 7.654 12.970 5.347 1.00 0.00 C
ATOM 194 N THR A 28 5.158 14.043 6.781 1.00 0.00 N
ATOM 195 CA THR A 28 4.495 14.590 7.965 1.00 0.00 C
ATOM 196 C THR A 28 3.288 13.781 8.406 1.00 0.00 C
ATOM 197 O THR A 28 3.207 13.408 9.584 1.00 0.00 O
ATOM 198 CB THR A 28 4.056 15.994 7.669 1.00 0.00 C
ATOM 199 OG1 THR A 28 5.156 16.850 7.373 1.00 0.00 O
ATOM 200 CG2 THR A 28 3.217 16.676 8.755 1.00 0.00 C
ATOM 201 N TYR A 29 2.381 13.481 7.483 1.00 0.00 N
ATOM 202 CA TYR A 29 1.150 12.736 7.809 1.00 0.00 C
ATOM 203 C TYR A 29 1.442 11.314 8.293 1.00 0.00 C
ATOM 204 O TYR A 29 0.559 10.652 8.849 1.00 0.00 O
ATOM 205 CB TYR A 29 0.279 12.671 6.590 1.00 0.00 C
ATOM 206 CG TYR A 29 -0.340 14.004 6.236 1.00 0.00 C
ATOM 207 CD1 TYR A 29 0.250 14.806 5.281 1.00 0.00 C
ATOM 208 CD2 TYR A 29 -1.494 14.418 6.869 1.00 0.00 C
ATOM 209 CE1 TYR A 29 -0.323 16.041 4.953 1.00 0.00 C
ATOM 210 CE2 TYR A 29 -2.067 15.653 6.541 1.00 0.00 C
ATOM 211 CZ TYR A 29 -1.494 16.461 5.595 1.00 0.00 C
ATOM 212 OH TYR A 29 -2.067 17.696 5.267 1.00 0.00 O
ATOM 213 N THR A 30 2.676 10.862 8.093 1.00 0.00 N
ATOM 214 CA THR A 30 3.102 9.534 8.547 1.00 0.00 C
ATOM 215 C THR A 30 3.922 9.620 9.845 1.00 0.00 C
ATOM 216 O THR A 30 4.406 8.609 10.339 1.00 0.00 O
ATOM 217 CB THR A 30 3.931 8.885 7.478 1.00 0.00 C
ATOM 218 OG1 THR A 30 5.105 9.636 7.178 1.00 0.00 O
ATOM 219 CG2 THR A 30 3.213 8.599 6.155 1.00 0.00 C
ATOM 220 N GLY A 31 4.092 10.832 10.363 1.00 0.00 N
ATOM 221 CA GLY A 31 4.903 11.062 11.544 1.00 0.00 C
ATOM 222 C GLY A 31 6.393 11.105 11.251 1.00 0.00 C
ATOM 223 O GLY A 31 7.221 10.693 12.071 1.00 0.00 O
ATOM 224 N CYS A 32 6.755 11.608 10.078 1.00 4.30 N
ATOM 225 CA CYS A 32 8.167 11.695 9.659 1.00 4.89 C
ATOM 226 C CYS A 32 8.465 13.129 9.146 1.00 5.50 C
ATOM 227 O CYS A 32 7.601 13.916 8.762 1.00 5.82 O
ATOM 228 CB CYS A 32 8.411 10.688 8.583 1.00 4.66 C
ATOM 229 SG CYS A 32 8.094 8.955 9.101 1.00 0.00 S
ATOM 230 N ILE A 33 9.793 13.410 9.173 1.00 6.02 N
ATOM 231 CA ILE A 33 10.280 14.760 8.823 1.00 5.24 C
ATOM 232 C ILE A 33 11.346 14.658 7.743 1.00 5.16 C
......
modelling/tests/test_close_gaps.py
+ 97
− 58
View file @ 571e47d1
......@@ -97,8 +97,11 @@ class CloseGapsTests(unittest.TestCase):
modelling.MergeGapsByDistance(mhandle, 2)
self.assertEqual(len(mhandle.gaps), 1)
def testFillGapsByDatabase(self):
'''Get rid of 2 gaps by db.'''
#######################################################################
# HELPERs - same test cases for all fill-loop-routines
#######################################################################
def getGapTest(self):
'''Helper to get test with 2 gaps.'''
tpl = io.LoadPDB('data/2dbs.pdb')
aln = seq.CreateAlignment(
seq.CreateSequence('trg', 'TLNGFTVPAGNTLV--LNPDKGATVTMAAAA'),
......@@ -107,15 +110,10 @@ class CloseGapsTests(unittest.TestCase):
aln.AttachView(1, tpl.CreateFullView())
mhandle = modelling.BuildRawModel(aln)
self.assertEqual(len(mhandle.gaps), 2)
scorer = modelling.SetupBackboneScorer(mhandle)
modelling.FillLoopsByDatabase(mhandle, scorer, self.frag_db,
self.structure_db,
self.torsion_sampler)
self.assertEqual(len(mhandle.gaps), 0)
# no log-check as this can easily change whenever we change DB
return mhandle
def testFillGapsByDatabaseDeletion(self):
'''Get rid of deletion by db.'''
def getGapTestDeletion(self):
'''Helper to get test with deletion.'''
tpl = io.LoadPDB('data/2dbs.pdb')
aln = seq.CreateAlignment(
seq.CreateSequence('trg', 'TLNGFTVPAGNTLV--LNPDKGATVTMA'),
......@@ -124,15 +122,10 @@ class CloseGapsTests(unittest.TestCase):
aln.AttachView(1, tpl.CreateFullView())
mhandle = modelling.BuildRawModel(aln)
self.assertEqual(len(mhandle.gaps), 1)
scorer = modelling.SetupBackboneScorer(mhandle)
modelling.FillLoopsByDatabase(mhandle, scorer, self.frag_db,
self.structure_db,
self.torsion_sampler)
self.assertEqual(len(mhandle.gaps), 0)
# no log-check as this can easily change whenever we change DB
return mhandle
def testFillGapsByDatabaseInsertion(self):
'''Get rid of insertion by db.'''
def getGapTestInsertion(self):
'''Helper to get test with insertion.'''
tpl = io.LoadPDB('data/2dbs.pdb')
aln = seq.CreateAlignment(
seq.CreateSequence('trg', 'TLNGFTVPAGNTLVAALNPDKGGAGATVTMA'),
......@@ -141,15 +134,10 @@ class CloseGapsTests(unittest.TestCase):
aln.AttachView(1, tpl.CreateFullView())
mhandle = modelling.BuildRawModel(aln)
self.assertEqual(len(mhandle.gaps), 1)
scorer = modelling.SetupBackboneScorer(mhandle)
modelling.FillLoopsByDatabase(mhandle, scorer, self.frag_db,
self.structure_db,
self.torsion_sampler)
self.assertEqual(len(mhandle.gaps), 0)
# no log-check as this can easily change whenever we change DB
return mhandle
def testFillGapsByDatabaseTerminal(self):
'''Terminal loops are not altered.'''
def getGapTestTerminal(self):
'''Helper to get test with terminal gaps.'''
tpl = io.LoadPDB('data/2dbs.pdb')
aln = seq.CreateAlignment(
seq.CreateSequence('trg', 'TLNGFTVPAGNTLVAALNPDKGGAGATVTMA'),
......@@ -158,22 +146,94 @@ class CloseGapsTests(unittest.TestCase):
aln.AttachView(1, tpl.CreateFullView())
mhandle = modelling.BuildRawModel(aln)
self.assertEqual(len(mhandle.gaps), 2)
return mhandle
#######################################################################
def testFillGapsByDatabase(self):
'''Get rid of 2 gaps by db.'''
mhandle = self.getGapTest()
scorer = modelling.SetupBackboneScorer(mhandle)
modelling.FillLoopsByDatabase(mhandle, scorer, self.frag_db,
self.structure_db,
self.torsion_sampler)
self.assertEqual(len(mhandle.gaps), 0)
# no log-check as this can easily change whenever we change DB
def testFillGapsByDatabaseDeletion(self):
'''Get rid of deletion by db.'''
mhandle = self.getGapTestDeletion()
scorer = modelling.SetupBackboneScorer(mhandle)
modelling.FillLoopsByDatabase(mhandle, scorer, self.frag_db,
self.structure_db,
self.torsion_sampler)
self.assertEqual(len(mhandle.gaps), 0)
# no log-check as this can easily change whenever we change DB
def testFillGapsByDatabaseInsertion(self):
'''Get rid of insertion by db.'''
mhandle = self.getGapTestInsertion()
scorer = modelling.SetupBackboneScorer(mhandle)
modelling.FillLoopsByDatabase(mhandle, scorer, self.frag_db,
self.structure_db,
self.torsion_sampler)
self.assertEqual(len(mhandle.gaps), 0)
# no log-check as this can easily change whenever we change DB
def testFillGapsByDatabaseTerminal(self):
'''Terminal loops are not altered.'''
mhandle = self.getGapTestTerminal()
scorer = modelling.SetupBackboneScorer(mhandle)
modelling.FillLoopsByDatabase(mhandle, scorer, self.frag_db,
self.structure_db,
self.torsion_sampler)
self.assertEqual(len(mhandle.gaps), 2)
def testFillGapsByMonteCarlo(self):
'''Get rid of 2 gaps by MC.'''
tpl = io.LoadPDB('data/2dbs.pdb')
aln = seq.CreateAlignment(
seq.CreateSequence('trg', 'TLNGFTVPAGNTLVA-LNPDKGATVTMAA'),
seq.CreateSequence('tpl', 'NGGTLLIPNGTYHFLGIQMKSN-VHIRVE'))
def testFillGapsByDatabaseNoSE(self):
'''Get rid of 2 gaps by db (without scoring extender).'''
mhandle = self.getGapTest()
scorer = modelling.SetupBackboneScorer(mhandle)
modelling.FillLoopsByDatabase(mhandle, scorer, self.frag_db,
self.structure_db,
self.torsion_sampler,
use_scoring_extender=False)
self.assertEqual(len(mhandle.gaps), 0)
# no log-check as this can easily change whenever we change DB
aln.AttachView(1, tpl.CreateFullView())
mhandle = modelling.BuildRawModel(aln)
def testFillGapsByDatabaseDeletionNoSE(self):
'''Get rid of deletion by db (without scoring extender).'''
mhandle = self.getGapTestDeletion()
scorer = modelling.SetupBackboneScorer(mhandle)
modelling.FillLoopsByDatabase(mhandle, scorer, self.frag_db,
self.structure_db,
self.torsion_sampler,
use_scoring_extender=False)
self.assertEqual(len(mhandle.gaps), 0)
# no log-check as this can easily change whenever we change DB
def testFillGapsByDatabaseInsertionNoSE(self):
'''Get rid of insertion by db (without scoring extender).'''
mhandle = self.getGapTestInsertion()
scorer = modelling.SetupBackboneScorer(mhandle)
modelling.FillLoopsByDatabase(mhandle, scorer, self.frag_db,
self.structure_db,
self.torsion_sampler,
use_scoring_extender=False)
self.assertEqual(len(mhandle.gaps), 0)
# no log-check as this can easily change whenever we change DB
def testFillGapsByDatabaseTerminalNoSE(self):
'''Terminal loops are not altered (without scoring extender).'''
mhandle = self.getGapTestTerminal()
scorer = modelling.SetupBackboneScorer(mhandle)
modelling.FillLoopsByDatabase(mhandle, scorer, self.frag_db,
self.structure_db,
self.torsion_sampler,
use_scoring_extender=False)
self.assertEqual(len(mhandle.gaps), 2)
def testFillGapsByMonteCarlo(self):
'''Get rid of 2 gaps by MC.'''
mhandle = self.getGapTest()
scorer = modelling.SetupBackboneScorer(mhandle)
modelling.FillLoopsByMonteCarlo(mhandle, scorer,
self.torsion_sampler,
......@@ -183,14 +243,7 @@ class CloseGapsTests(unittest.TestCase):
def testFillGapsByMonteCarloDeletion(self):
'''Get rid of deletion by MC.'''
tpl = io.LoadPDB('data/2dbs.pdb')
aln = seq.CreateAlignment(
seq.CreateSequence('trg', 'TLNGFTVPAGNTLVA-LNPDKGATVTMA'),
seq.CreateSequence('tpl', 'NGGTLLIPNGTYHFLGIQMKSNVHIRVE'))
aln.AttachView(1, tpl.CreateFullView())
mhandle = modelling.BuildRawModel(aln)
self.assertEqual(len(mhandle.gaps), 1)
mhandle = self.getGapTestDeletion()
scorer = modelling.SetupBackboneScorer(mhandle)
modelling.FillLoopsByMonteCarlo(mhandle, scorer,
self.torsion_sampler,
......@@ -200,14 +253,7 @@ class CloseGapsTests(unittest.TestCase):
def testFillGapsByMonteCarloInsertion(self):
'''Get rid of insertion by MC.'''
tpl = io.LoadPDB('data/2dbs.pdb')
aln = seq.CreateAlignment(
seq.CreateSequence('trg', 'TLNGFTVPAGNTLVAALNPDKGAGTVTMA'),
seq.CreateSequence('tpl', 'NGGTLLIPNGTYHFLGIQMKSN-VHIRVE'))
aln.AttachView(1, tpl.CreateFullView())
mhandle = modelling.BuildRawModel(aln)
self.assertEqual(len(mhandle.gaps), 1)
mhandle = self.getGapTestInsertion()
scorer = modelling.SetupBackboneScorer(mhandle)
modelling.FillLoopsByMonteCarlo(mhandle, scorer,
self.torsion_sampler,
......@@ -217,14 +263,7 @@ class CloseGapsTests(unittest.TestCase):
def testFillGapsByMonteCarloTerminal(self):
'''Terminal loops are not altered.'''
tpl = io.LoadPDB('data/2dbs.pdb')
aln = seq.CreateAlignment(
seq.CreateSequence('trg', 'TLNGFTVPAGNTLVAALNPDKGGAGATVTMA'),
seq.CreateSequence('tpl', '-NGGTLLIPNGTYHFLGIQMKSNVHIRVE--'))
aln.AttachView(1, tpl.CreateFullView())
mhandle = modelling.BuildRawModel(aln)
self.assertEqual(len(mhandle.gaps), 2)
mhandle = self.getGapTestTerminal()
scorer = modelling.SetupBackboneScorer(mhandle)
modelling.FillLoopsByMonteCarlo(mhandle, scorer,
self.torsion_sampler,
......
modelling/tests/test_pipeline.py
+ 31
− 0
View file @ 571e47d1
......@@ -26,6 +26,37 @@ from ost import io, mol
# seq.CreateSequence('tpl', seqres_cut))
# io.SaveAlignment(aln, "data/1crn.fasta")
################################################################
# Code to generate reference solutions:
################################################################
# from ost import io
# from promod3 import loop,modelling
# # create raw model
# tpl = io.LoadPDB('data/1crn_cut.pdb')
# aln = io.LoadAlignment('data/1crn.fasta')
# aln.AttachView(1, tpl.CreateFullView())
# mhandle = modelling.BuildRawModel(aln)
# # do it all
# final_model = modelling.BuildFromRawModel(mhandle)
# io.SavePDB(final_model, 'data/1crn_build.pdb')
# # step-by-step - loop
# mhandle = modelling.BuildRawModel(aln)
# scorer = modelling.SetupBackboneScorer(mhandle)
# frag_db = loop.LoadFragDB()
# structure_db = loop.LoadStructureDB()
# torsion_sampler = loop.LoadTorsionSamplerCoil()
# modelling.FillLoopsByDatabase(mhandle, scorer, frag_db,
# structure_db,
# torsion_sampler)
# io.SavePDB(mhandle.model, 'data/1crn_rec.pdb')
# # step-by-step - sidechains
# mhandle.model = io.LoadPDB('data/1crn_rec.pdb')
# modelling.BuildSidechains(mhandle)
# io.SavePDB(mhandle.model, 'data/1crn_sc.pdb')
# # step-by-step - energy minimization
# mhandle.model = io.LoadPDB('data/1crn_sc.pdb')
# modelling.MinimizeModelEnergy(mhandle)
# io.SavePDB(mhandle.model, 'data/1crn_final.pdb')
################################################################
class PipelineTests(unittest.TestCase):
@classmethod
......
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