def regenerate_mutfile(PredictionID):
'''I needed to write this function as I forgot to add a *.mutfile mask to the ProtocolCleaner at first so mutfiles were not kept.'''
raise Exception("We should never need to call this")
KeepHETATMLines = False
results = ddGdb.execute_select("SELECT ExperimentID, UserDataSetExperimentID FROM Prediction WHERE ID=%s", parameters = (PredictionID,))
assert(len(results) == 1)
ExperimentID = results[0]['ExperimentID']
UserDataSetExperimentID = results[0]['UserDataSetExperimentID']
results = ddGdb.execute_select("SELECT PDBFileID FROM UserDataSetExperiment WHERE ID=%s", parameters = (UserDataSetExperimentID,))
assert(len(results) == 1)
PDB_ID = results[0]['PDBFileID']
results = ddGdb.execute_select("SELECT PDBFileID, Content FROM Experiment INNER JOIN PDBFile WHERE Experiment.PDBFileID=PDBFile.ID AND Experiment.ID=%s", parameters = (ExperimentID,))
assert(len(results) == 1)
experimentPDB_ID = results[0]["PDBFileID"]
results = ddGdb.execute_select("SELECT ID, Content FROM PDBFile WHERE ID=%s", parameters=(PDB_ID))
if len(results) != 1:
raise colortext.Exception("The SQL query '%s' returned %d results where 1 result was expected." % (sql, len(results)))
predictionPDB_ID = results[0]["ID"]
# Get the related PDB ID and file
assert(len(results) == 1)
result = results[0]
pdbID = result["ID"]
contents = result["Content"]
pdb = PDB(contents.split("\n"))
# Check that the mutated positions exist and that the wild-type matches the PDB
mutations = ddGdb.call_select_proc("GetMutations", parameters = (ExperimentID,))
# todo: Hack. This should be removed when PDB homologs are dealt with properly.
for mutation in mutations:
if experimentPDB_ID == "1AJ3" and predictionPDB_ID == "1U5P":
assert(int(mutation['ResidueID']) < 1000)
mutation['ResidueID'] = str(int(mutation['ResidueID']) + 1762)
pdb.validate_mutations(mutations)
# Strip the PDB to the list of chains. This also renumbers residues in the PDB for Rosetta.
chains = [result['Chain'] for result in ddGdb.call_select_proc("GetChains", parameters = (ExperimentID,))]
pdb.stripForDDG(chains, KeepHETATMLines, numberOfModels = 1)
# - Post stripping checks -
# Get the 'Chain ResidueID' PDB-formatted identifier for each mutation mapped to Rosetta numbering
# then check again that the mutated positions exist and that the wild-type matches the PDB
remappedMutations = pdb.remapMutations(mutations, pdbID)
remappedMutations = [[m[0], PDB.ResidueID2String(m[1]), m[2], m[3]] for m in remappedMutations]
#resfile = self._createResfile(pdb, remappedMutations)
return( _createMutfile(pdb, remappedMutations))
