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 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 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 setAlignment(self, alignment=None):
"""
Sets the alignment information (from self)
"""
if alignment == None:
pka_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)
pka_print(self.alignment)
pka_print(len(self.alignment))
else:
self.alignment = alignment