def test_example4(self):
'''
Single chain with two multiple-chain domains
'''
argstring = \
'--chain '+self.dimer1+':A '+self.linker+' '+self.dimer2+':B '+\
'--fixed '+self.dimer1
args = C.parsing(argstring.split())
CHAINS = C.create_chains(args)
build = bu.Builder(CHAINS, args.debug, args.number, args.destination)
model = build.run()
self.assertTrue(model.lenChains() == 3)
def test_example1(self):
'''
Single chain example
'''
# testdir = tempfile.mkdtemp('', self.__class__.__name__.lower() + \
# '_example1_')
argstring = '--chain ' + self.mono1 + ' ' + self.linker + ' ' + self.mono2 # +\
# ' --destination '+testdir ... to write the models to disk
args = C.parsing(argstring.split())
CHAINS = C.create_chains(args)
build = bu.Builder(CHAINS, args.debug, args.number, args.destination)
model = build.run()
self.assertTrue(model.lenChains() == 1)
def test_symp3(self):
'''
Test with symmetry
'''
# There is no need to specify chain for the symmetric core
argstring = \
'--chain '+self.trimer+' '+self.linker+' '+self.mono1+\
' --symmetry p3 --symtemplate '+self.trimer+\
' --poolsym s'
args = C.parsing(argstring.split())
CHAINS = C.create_chains(args)
build = bu.Builder(CHAINS, args.debug, args.number, args.destination)
model = build.run()
self.assertTrue(model.lenChains() == 3)
def test_3ch2(self):
'''
Example 2 with three chains
'''
argstring = \
'--chain '+self.mono1+' '+self.linker+' '+self.dimer1+':A '+\
self.linker+' '+self.mono2+\
' --chain '+self.dimer1+':B '+self.linker+' '+self.dimer2+':A'+\
' --chain '+self.mono1+' '+self.linker+' '+self.dimer2+':B '+\
self.linker+' '+self.mono2
args = C.parsing(argstring.split())
CHAINS = C.create_chains(args)
build = bu.Builder(CHAINS, args.debug, args.number, args.destination)
model = build.run()
self.assertTrue(model.lenChains() == 3)
def setUp(self):
self.testpath = self.testpath or \
os.path.join(os.path.abspath(os.path.dirname(__file__)), 'testdata')
self.mono1 = self.mono1 or os.path.join(self.testpath, '2z6o.pdb')
self.mono2 = self.mono2 or os.path.join(self.testpath, 'histone.pdb')
self.mono3 = self.mono3 or os.path.join(self.testpath, '2h5q.pdb')
self.dimer1 = self.dimer1 or os.path.join(self.testpath, 'domAB1.pdb')
self.dimer2 = self.dimer2 or os.path.join(self.testpath, 'domAB2.pdb')
self.dimer3 = self.dimer3 or os.path.join(self.testpath, '2qud.pdb')
self.trimer = self.trimer or os.path.join(self.testpath, '2ei4.pdb')
self.linker = self.linker or 'TG' * 15
#### SINGLE CHAIN EXAMPLES
# Assemble argument strings
self.argstring1 = self.argstring1 or \
'--chain '+self.mono1+' '+self.linker+' '+self.mono2
# Careful with the names of fixed domains... cannot be repeated in the chain
# for repeating pdbs that are not fixed or are not symtemplates there
# should be no problem
self.argstring4 = self.argstring4 or \
'--chain '+self.dimer1+':A '+self.linker+' '+\
self.dimer2+':B --fixed '+self.dimer1
#### SYMMETRY EXAMPLE
# Careful with symtemplate name... cannot be repeated in the chain
self.argstring5 = self.argstring5 or '--chain '+self.dimer1+' '+\
self.linker+' '+self.dimer2+':A --symmetry p2 --symtemplate '\
+self.dimer1+' --poolsym s'
#### DOUBLE CHAIN
# Not fixed
self.argstring2ch = self.argstring2ch or '--chain '+self.dimer1+':A '+\
self.linker+' '+self.dimer3+':A '+self.linker+' '+self.dimer2+':A '+\
'--chain '+self.dimer1+':B '+self.linker+' '+self.dimer3+':B '+\
self.linker+' '+self.dimer2+':B'
# Fixed
# The model is the same as the previous one, but the coordinates of the
# dimers will be fixed
self.argstring2chfixed = self.argstring2chfixed or '--chain '+self.dimer1+\
':A '+self.linker+' '+self.dimer3+':A '+self.linker+' '+\
self.dimer2+':A '+'--chain '+self.dimer1+':B '+self.linker+' '+\
self.dimer3+':B '+self.linker+' '+self.dimer2+':B --fixed '+\
self.dimer1+' '+self.dimer2+' '+self.dimer3
#### TRIPLE CHAIN
self.argstring3ch = self.argstring3ch or '--chain '+self.trimer+':A '+\
self.linker+' '+self.mono1+' --chain '+self.trimer+':B '+\
self.linker+' '+self.mono2+' --chain '+self.trimer+':C '+\
self.linker+' '+self.mono3
# Create Chain objects and Builder instance
args1 = C.parsing(self.argstring1.split())
CHAINS1 = C.create_chains(args1)
self.builder1 = Builder(CHAINS1, args1.debug, args1.number,
args1.destination)
args4 = C.parsing(self.argstring4.split())
CHAINS4 = C.create_chains(args4)
self.builder4 = Builder(CHAINS4, args4.debug, args4.number,
args4.destination)
args5 = C.parsing(self.argstring5.split())
CHAINS5 = C.create_chains(args5)
self.builder5 = Builder(CHAINS5, args5.debug, args5.number,
args5.destination)
args2ch = C.parsing(self.argstring2ch.split())
CHAINS2ch = C.create_chains(args2ch)
self.builder2ch = Builder(CHAINS2ch, args2ch.debug, args2ch.number,
args2ch.destination)
args2chfixed = C.parsing(self.argstring2chfixed.split())
CHAINS2chfixed = C.create_chains(args2chfixed)
self.builder2chfixed = Builder(CHAINS2chfixed, args2chfixed.debug,
args2chfixed.number,
args2chfixed.destination)
args3ch = C.parsing(self.argstring3ch.split())
CHAINS3ch = C.create_chains(args3ch)
self.builder3ch = Builder(CHAINS3ch, args3ch.debug, args3ch.number,
args3ch.destination)