()
| 5278 | |
| 5279 | @report |
| 5280 | def testModificationsDB(): |
| 5281 | mdb = pyopenms.ModificationsDB() |
| 5282 | del mdb |
| 5283 | |
| 5284 | # create a second instance of ModificationsDB without anything bad happening |
| 5285 | mdb = pyopenms.ModificationsDB() |
| 5286 | |
| 5287 | assert mdb.getNumberOfModifications() > 1 |
| 5288 | m = mdb.getModification(1) |
| 5289 | |
| 5290 | assert mdb.getNumberOfModifications() > 1 |
| 5291 | m = mdb.getModification(1) |
| 5292 | assert m is not None |
| 5293 | |
| 5294 | mods = set([]) |
| 5295 | mdb.searchModifications(mods, s("Phosphorylation"), s("T"), pyopenms.ResidueModification.TermSpecificity.ANYWHERE) |
| 5296 | assert len(mods) == 1 |
| 5297 | |
| 5298 | mods = set([]) |
| 5299 | mdb.searchModifications(mods, s("NIC"), s("T"), pyopenms.ResidueModification.TermSpecificity.N_TERM) |
| 5300 | assert len(mods) == 1 |
| 5301 | |
| 5302 | mods = set([]) |
| 5303 | mdb.searchModifications(mods, s("NIC"), s("T"), pyopenms.ResidueModification.TermSpecificity.N_TERM) |
| 5304 | assert len(mods) == 1 |
| 5305 | |
| 5306 | mods = set([]) |
| 5307 | mdb.searchModifications(mods, s("Acetyl"), s("T"), pyopenms.ResidueModification.TermSpecificity.N_TERM) |
| 5308 | assert len(mods) == 1 |
| 5309 | assert list(mods)[0].getFullId() == "Acetyl (N-term)" |
| 5310 | |
| 5311 | m = mdb.getModification(s("Carboxymethyl (C)"), "", pyopenms.ResidueModification.TermSpecificity.NUMBER_OF_TERM_SPECIFICITY) |
| 5312 | assert m.getFullId() == "Carboxymethyl (C)" |
| 5313 | |
| 5314 | m = mdb.getModification( s("Phosphorylation"), s("S"), pyopenms.ResidueModification.TermSpecificity.ANYWHERE) |
| 5315 | assert m.getId() == "Phospho" |
| 5316 | |
| 5317 | # get out all mods (there should be many, some known ones as well!) |
| 5318 | mods = [] |
| 5319 | m = mdb.getAllSearchModifications(mods) |
| 5320 | assert len(mods) > 100 |
| 5321 | |
| 5322 | assert b"Phospho (S)" in mods |
| 5323 | assert b"Sulfo (S)" in mods |
| 5324 | assert not (b"Phospho" in mods) |
| 5325 | |
| 5326 | # search for specific modifications by mass |
| 5327 | m = mdb.getBestModificationByDiffMonoMass( 80.0, 1.0, "T", pyopenms.ResidueModification.TermSpecificity.ANYWHERE) |
| 5328 | assert m is not None |
| 5329 | assert m.getId() == "Phospho" |
| 5330 | assert m.getFullName() == "Phosphorylation" |
| 5331 | assert m.getUniModAccession() == "UniMod:21" |
| 5332 | |
| 5333 | m = mdb.getBestModificationByDiffMonoMass(80, 100, "T", pyopenms.ResidueModification.TermSpecificity.ANYWHERE) |
| 5334 | assert m is not None |
| 5335 | assert m.getId() == "Phospho" |
| 5336 | assert m.getFullName() == "Phosphorylation" |
| 5337 | assert m.getUniModAccession() == "UniMod:21" |
nothing calls this directly
no test coverage detected