def extractMutationLabel(generic_mutation):
"""
extracts a mutation-label string from a mutation, e.g. ["2vuj::A:N25R/A:S27T/A:N181D"] -> "N25R/S27T/N181D"
"""
if isinstance(generic_mutation, str):
mutations = [generic_mutation]
elif isinstance(generic_mutation, list):
mutations = generic_mutation
elif isinstance(generic_mutation, dict):
""" do nothing """
label = ""
if isinstance(generic_mutation, dict):
for key in generic_mutation.keys():
code1, resName = lib.convertResidueCode(resName=key[:3])
code2, resName = lib.convertResidueCode(resName=generic_mutation[key]['label'][:3])
label += "/%s%d%s" % (code1, int(key[3:7]), code2)
else:
for mutation in mutations:
pdbcode, mutation_string = splitStringMutationInTwo(mutation)
single_mutations = splitIntoSingleMutations(mutation_string)
for single_mutation in single_mutations:
chainID1, chainID2, gotcha = splitSingleMutation(single_mutation)
label += "/%s" % (gotcha)
return label[1:]
def splitIntoMutationData(generic_mutation):
"""
split 'mutation' into multiple mutation data, e.g. 'A:N25R/A:N181D' -> [[A, N, 25, R], [A, N, 181, D]]
"""
# making sure mutation is used properly
mutation_data = []
if isinstance(generic_mutation, str):
mutation_list = [generic_mutation]
elif isinstance(generic_mutation, list):
mutation_list = generic_mutation
elif isinstance(generic_mutation, dict):
for key in generic_mutation.keys():
chainID1 = generic_mutation[key]['target'][-1]
code1, resName = lib.convertResidueCode(resName=generic_mutation[key]['target'][:3])
resNumb = int(generic_mutation[key]['target'][3:7])
code2, resName = lib.convertResidueCode(resName=generic_mutation[key]['label'][:3])
mutation_data.append([chainID1, code1, resNumb, code2])
if len(mutation_data) > 0:
return mutation_data
else:
for mutation in mutation_list:
thermophile, mutation_string = splitStringMutationInTwo(mutation)
for single_mutation in splitIntoSingleMutations(mutation_string):
chainID1, chainID2, mutation_label = splitSingleMutation(single_mutation)
code1, resNumb, code2 = extractSingleMutationInformation(mutation_label)
mutation_data.append([chainID1, code1, resNumb, code2])
return mutation_data
def makeMutationAddendum(target=None, template=None, options=None):
"""
converting two residue labels to a mutation tag
"""
if target == " gap " or template == " gap ":
return None
else:
code1, resName = convertResidueCode(resName=target[:3])
code2, resName = convertResidueCode(resName=template[:3])
resNumb = int(target[3:7])
return "%s%d%s" % (code1, resNumb, code2)
def makeSequence(self, mutation=None):
"""
creates a sequence from the chain object to be used in Scwrl-mutations
"""
sequence = ""
for residue in self.residues:
if residue.resName in lib.residueList("standard"):
if mutation == None:
code, resName = lib.convertResidueCode(resName=residue.resName)
sequence += code.lower()
elif residue.label in mutation:
new_label = mutation[residue.label]['label']
code, resName = lib.convertResidueCode(resName=new_label[:3])
sequence += code.upper()
else:
code, resName = lib.convertResidueCode(resName=residue.resName)
sequence += code.lower()
return sequence
def setAlignment(self, alignment=None):
"""
Sets the alignment information (from self)
"""
if alignment == None:
print("setting alignment according to protein")
self.alignment = ""
for residue in self.residues:
if residue.resName != "N+ " and residue.resName != "C- ":
code, resName = lib.convertResidueCode(resName=residue.resName)
if code in "ARNDCQEGHILKMFPSTWYV":
self.alignment += (code)
print(self.alignment)
print( len(self.alignment) )
else:
self.alignment = alignment
def recastIntoDictionary(input_mutation=None, alignment=None, protein=None, chains=None):
"""
recasting the mutation from string or list format into dictionary format; needed for more complicated mutations
"""
if protein == None:
mesophile = None
else:
mesophile = protein.name
# making sure mutation is used properly
if isinstance(input_mutation, str):
mutation_list = [input_mutation]
elif isinstance(input_mutation, list):
mutation_list = input_mutation
elif isinstance(input_mutation, dict):
return input_mutation
dictionary_mutation = {}
for mutation in mutation_list:
thermophile, mutation_string = splitStringMutationInTwo(mutation)
for single_mutation in splitIntoSingleMutations(mutation_string):
chainID1, chainID2, mutation_label = splitSingleMutation(single_mutation)
code1, resNumb, code2 = extractSingleMutationInformation(mutation_label)
code, resName_mesophile = lib.convertResidueCode(code=code1)
code, resName_thermophile = lib.convertResidueCode(code=code2)
if alignment == None or mesophile == None:
# No alignment mutation as far as I can judge, just reformatting
thermophile = None
template = None
# repeat for all chains
if chainID1 == None:
chainIDs = chains
else:
chainIDs = [[chainID1, None]]
for chainID, chainID2 in chainIDs:
key = "%s%4d%2s" % (resName_mesophile, resNumb, chainID)
new_label = "%s%4d%2s" % (resName_thermophile, resNumb, chainID)
dictionary_mutation[key] = {'pdb': thermophile, 'target': key, 'template': template, 'label': new_label}
else:
# preparing for alignment or overlap mutation
# thermophile
resNumb_mesophile = alignment[thermophile][mesophile]["resNumb"]
resNumb_thermophile = alignment[thermophile][thermophile]["resNumb"]
for i in range(len(alignment[thermophile][mesophile]["sequence"])):
if alignment[thermophile][mesophile]["sequence"][i] in "ARNDCQEGHILKMFPSTWYV":
resNumb_mesophile += 1
if alignment[thermophile][thermophile]["sequence"][i] in "ARNDCQEGHILKMFPSTWYV":
resNumb_thermophile += 1
if resNumb_mesophile == resNumb:
if chainID1 == None and chainID2 == None:
chainIDs = chains
else:
chainIDs = [[chainID1, chainID2]]
for chainID1, chainID2 in chainIDs:
key = "%s%4d%2s" % (resName_mesophile, resNumb, chainID1)
template = "%s%4d%2s" % (resName_thermophile, resNumb_thermophile, chainID2)
new_label = "%s%4d%2s" % (resName_thermophile, resNumb_mesophile, chainID1)
dictionary_mutation[key] = {'pdb': thermophile, 'target': key, 'template': template, 'label': new_label}
return dictionary_mutation