def mutateToAla(self):
"""
mutating residue to 'ALA'
Note, if you mutate a ionizable residue to Ala it will remain in 'ionizable_residues list'
and propka will try to calcualte the pKa of it !!!
"""
keep_atoms = lib.atomList("ALA")
self.printLabel()
self.resName = "ALA"
self.setResidueLabel()
self.printLabel()
new_atoms = []
for atom in self.atoms:
if atom.name in keep_atoms:
new_atoms.append(atom)
print(self.atoms)
print(new_atoms)
self.cleanupResidue
self.pKa_mod = pKa_mod(self.resName)
self.pKa_pro = self.pKa_mod
self.atoms = new_atoms
def mutateToAla(self):
"""
mutating residue to 'ALA'
Note, if you mutate a ionizable residue to Ala it will remain in 'ionizable_residues list'
and propka will try to calcualte the pKa of it !!!
"""
keep_atoms = lib.atomList("ALA")
self.printLabel()
self.resName = "ALA"
self.setResidueLabel()
self.printLabel()
new_atoms = []
for atom in self.atoms:
if atom.name in keep_atoms:
new_atoms.append(atom)
pka_print(self.atoms)
pka_print(new_atoms)
self.cleanupResidue
self.pKa_mod = pKa_mod(self.resName)
self.pKa_pro = self.pKa_mod
self.atoms = new_atoms
def checkAtoms(self, options=None):
"""
Checks that all heavy atoms are there
"""
outstr = "%s%4d - " % (self.resName, self.resNumb)
atom_list = lib.atomList(self.resName)
OK = True
for name in atom_list:
FOUND = False
for atom in self.atoms:
if atom.name == name:
FOUND = True
if FOUND == False:
outstr += " %s" % (name)
OK = False
if OK == True:
self.checkConfigurations(verbose=False)
outstr += " OK (%2d: %2d)" % (len(self.atoms), len(self.configurations))
if options.verbose == True:
print(outstr)
else:
outstr += " missing"
print(outstr)
def makeCorrespondingAtomNames():
"""
setting up a dictionary to define 'corresponding atoms' between two residues for 'overlap'
"""
# getting list of all atoms
resNames = residueList("standard")
names = {}
# ----- back-bone & 'CB' section -----
# simplifying the setup by including back-bone and 'CB' with this loop
for resName1 in resNames:
names[resName1] = {}
for resName2 in resNames:
names[resName1][resName2] = [['N', 'N'],
['CA', 'CA'],
['C', 'C'],
['O', 'O']]
if resName1 != "GLY" and resName2 != "GLY":
names[resName1][resName2].append(['CB', 'CB'])
# ----- self-overlap section -----
# setting up all atoms for self-comparison
for resName in resNames:
atmNames = atomList(resName)
for atmName in atmNames:
if atmName not in ['N', 'CA', 'CB', 'C', 'O']:
names[resName][resName].append([atmName, atmName])
# ----- side-chain section -----
# side-chains left to consider (sorted alphabetically):
# ['ARG', 'ASN', 'ASP', 'CYS', 'GLN', 'GLU', 'HIS', 'ILE', 'LEU', 'LYS', 'MET', 'PHE', 'PRO', 'SER', 'THR', 'TRP', 'TYR', 'VAL']
# ARG
# None
# ASN
str1 = "ASN CG"
str2 = "ARG CG"
extendCorrespondingAtomsDictionary(names, str1, str2)
# ASP
str1 = "ASP CG"
str2 = "ARG CG"
extendCorrespondingAtomsDictionary(names, str1, str2)
str1 = "ASP OD1 OD2"
str2 = "ASN OD1 ND2"
extendCorrespondingAtomsDictionary(names, str1, str2)
# CYS
# None
# GLN
str1 = "GLN CG CD"
str2 = "ARG CG CD"
extendCorrespondingAtomsDictionary(names, str1, str2)
str1 = "GLN CG"
str2 = "ASN CG"
extendCorrespondingAtomsDictionary(names, str1, str2)
str1 = "GLN CG"
str2 = "ASP CG"
extendCorrespondingAtomsDictionary(names, str1, str2)
# GLU
# HIS
# ILE
# LEU
# LYS
# MET
# PHE
# PRO
# SER
# THR
# TRP
# TYR
str1 = "TYR CG"
str2 = "LYS CG"
extendCorrespondingAtomsDictionary(names, str1, str2)
# VAL
return names
def makeCorrespondingAtomNames():
"""
setting up a dictionary to define 'corresponding atoms' between two residues for 'overlap'
"""
# getting list of all atoms
resNames = residueList("standard")
names = {}
# ----- back-bone & 'CB' section -----
# simplifying the setup by including back-bone and 'CB' with this loop
for resName1 in resNames:
names[resName1] = {}
for resName2 in resNames:
names[resName1][resName2] = [['N', 'N'], ['CA', 'CA'], ['C', 'C'],
['O', 'O']]
if resName1 != "GLY" and resName2 != "GLY":
names[resName1][resName2].append(['CB', 'CB'])
# ----- self-overlap section -----
# setting up all atoms for self-comparison
for resName in resNames:
atmNames = atomList(resName)
for atmName in atmNames:
if atmName not in ['N', 'CA', 'CB', 'C', 'O']:
names[resName][resName].append([atmName, atmName])
# ----- side-chain section -----
# side-chains left to consider (sorted alphabetically):
# ['ARG', 'ASN', 'ASP', 'CYS', 'GLN', 'GLU', 'HIS', 'ILE', 'LEU', 'LYS', 'MET', 'PHE', 'PRO', 'SER', 'THR', 'TRP', 'TYR', 'VAL']
# ARG
# None
# ASN
str1 = "ASN CG"
str2 = "ARG CG"
extendCorrespondingAtomsDictionary(names, str1, str2)
# ASP
str1 = "ASP CG"
str2 = "ARG CG"
extendCorrespondingAtomsDictionary(names, str1, str2)
str1 = "ASP OD1 OD2"
str2 = "ASN OD1 ND2"
extendCorrespondingAtomsDictionary(names, str1, str2)
# CYS
# None
# GLN
str1 = "GLN CG CD"
str2 = "ARG CG CD"
extendCorrespondingAtomsDictionary(names, str1, str2)
str1 = "GLN CG"
str2 = "ASN CG"
extendCorrespondingAtomsDictionary(names, str1, str2)
str1 = "GLN CG"
str2 = "ASP CG"
extendCorrespondingAtomsDictionary(names, str1, str2)
# GLU
# HIS
# ILE
# LEU
# LYS
# MET
# PHE
# PRO
# SER
# THR
# TRP
# TYR
str1 = "TYR CG"
str2 = "LYS CG"
extendCorrespondingAtomsDictionary(names, str1, str2)
# VAL
return names
