def test_Selection_contains_spin_re2(self):
"""The Selection object "#Ap4Aase:Glu | #RNA@C8" contains the spin '*C*' of the mol 'RNA'."""
# The Selection object.
obj = Selection("#Ap4Aase:Glu | #RNA@C8")
# Check if the molecule is in the selection.
self.assert_(obj.contains_spin(spin_name='*C*', mol='RNA'))
def test_Selection_contains_spin6(self):
"""The Selection object "#Ap4Aase" does contains the spin None."""
# The Selection object.
obj = Selection("#Ap4Aase")
# Check if the molecule is in the selection.
self.assert_(obj.contains_spin(mol='Ap4Aase'))
def test_Selection_contains_spin7(self):
"""The Selection object "#Ap4Aase" does not contain the spin None of the mol 'RNA'."""
# The Selection object.
obj = Selection("#Ap4Aase")
# Check if the molecule is in the selection.
self.assert_(not obj.contains_spin(mol='RNA'))
def test_Selection_contains_spin4(self):
"""The Selection object "#Ap4Aase:Glu | #RNA@C8" does not contain the spin 'N3'."""
# The Selection object.
obj = Selection("#Ap4Aase:Glu | #RNA@C8")
# Check if the molecule is in the selection.
self.assert_(not obj.contains_spin(spin_name='N3'))
def test_Selection_contains_spin5(self):
"""The Selection object "#Ap4Aase:Glu | #RNA:14@C8" does not contain the spin None."""
# The Selection object.
obj = Selection("#Ap4Aase:Glu | #RNA:14@C8")
# Check if the molecule is in the selection.
self.assert_(not obj.contains_spin())
def test_Selection_contains_spin_re2(self):
"""The Selection object "#Ap4Aase:Glu | #RNA@C8" contains the spin '*C*' of the mol 'RNA'."""
# The Selection object.
obj = Selection("#Ap4Aase:Glu | #RNA@C8")
# Check if the molecule is in the selection.
self.assert_(obj.contains_spin(spin_name='*C*', mol='RNA'))
def test_Selection_contains_spin7(self):
"""The Selection object "#Ap4Aase" does not contain the spin None of the mol 'RNA'."""
# The Selection object.
obj = Selection("#Ap4Aase")
# Check if the molecule is in the selection.
self.assert_(not obj.contains_spin(mol='RNA'))
def test_Selection_contains_spin6(self):
"""The Selection object "#Ap4Aase" does contains the spin None."""
# The Selection object.
obj = Selection("#Ap4Aase")
# Check if the molecule is in the selection.
self.assert_(obj.contains_spin(mol='Ap4Aase'))
def test_Selection_contains_spin5(self):
"""The Selection object "#Ap4Aase:Glu | #RNA:14@C8" does not contain the spin None."""
# The Selection object.
obj = Selection("#Ap4Aase:Glu | #RNA:14@C8")
# Check if the molecule is in the selection.
self.assert_(not obj.contains_spin())
def test_Selection_contains_spin4(self):
"""The Selection object "#Ap4Aase:Glu | #RNA@C8" does not contain the spin 'N3'."""
# The Selection object.
obj = Selection("#Ap4Aase:Glu | #RNA@C8")
# Check if the molecule is in the selection.
self.assert_(not obj.contains_spin(spin_name='N3'))
def sel_domain(domain_id=None, boolean='OR', change_all=False):
"""Select all spins and interatomic data containers of the given domain.
@keyword domain_id: The domain ID string.
@type domain_id: str or None
@param boolean: The boolean operator used to select the spin systems with. It can be one of 'OR', 'NOR', 'AND', 'NAND', 'XOR', or 'XNOR'. This will be ignored if the change_all flag is set.
@type boolean: str
@keyword change_all: A flag which if True will cause all spins and interatomic data containers outside of the domain to be deselected.
@type change_all: bool
"""
# Test if the current data pipe exists.
pipes.test()
# Test if the domain is defined.
if not hasattr(cdp, 'domain') or domain_id not in cdp.domain:
raise RelaxNoDomainError(domain_id)
# The domain selection object.
domain = Selection(cdp.domain[domain_id])
# Loop over the spins and select as required.
for spin, mol_name, res_num, res_name in spin_loop(full_info=True):
# Inside the domain.
if domain.contains_spin(spin_name=spin.name, spin_num=spin.num, res_name=res_name, res_num=res_num, mol=mol_name):
spin.select = boolean_select(current=spin.select, boolean=boolean)
# Deselect spins outside of the domain.
elif change_all:
spin.select = False
# Interatomic data loop.
for interatom in interatomic_loop():
# Decode the spin ids.
mol_name1, res_num1, res_name1, spin_num1, spin_name1 = spin_id_to_data_list(interatom.spin_id1)
mol_name2, res_num2, res_name2, spin_num2, spin_name2 = spin_id_to_data_list(interatom.spin_id2)
# Inside the domain.
if domain.contains_spin(spin_name=spin_name1, spin_num=spin_num1, res_name=res_name1, res_num=res_num1, mol=mol_name1) or domain.contains_spin(spin_name=spin_name2, spin_num=spin_num2, res_name=res_name2, res_num=res_num2, mol=mol_name2):
interatom.select = boolean_select(current=interatom.select, boolean=boolean)
# Deselect containers outside of the domain.
elif change_all:
interatom.select = False
def sel_domain(domain_id=None, boolean='OR', change_all=False):
"""Select all spins and interatomic data containers of the given domain.
@keyword domain_id: The domain ID string.
@type domain_id: str or None
@param boolean: The boolean operator used to select the spin systems with. It can be one of 'OR', 'NOR', 'AND', 'NAND', 'XOR', or 'XNOR'. This will be ignored if the change_all flag is set.
@type boolean: str
@keyword change_all: A flag which if True will cause all spins and interatomic data containers outside of the domain to be deselected.
@type change_all: bool
"""
# Test if the current data pipe exists.
check_pipe()
# Test if the domain is defined.
if not hasattr(cdp, 'domain') or domain_id not in cdp.domain:
raise RelaxNoDomainError(domain_id)
# The domain selection object.
domain = Selection(cdp.domain[domain_id])
# Loop over the spins and select as required.
for spin, mol_name, res_num, res_name in spin_loop(full_info=True):
# Inside the domain.
if domain.contains_spin(spin_name=spin.name, spin_num=spin.num, res_name=res_name, res_num=res_num, mol=mol_name):
spin.select = boolean_select(current=spin.select, boolean=boolean)
# Deselect spins outside of the domain.
elif change_all:
spin.select = False
# Interatomic data loop.
for interatom in interatomic_loop():
# Decode the spin ids.
mol_name1, res_num1, res_name1, spin_num1, spin_name1 = spin_id_to_data_list(interatom.spin_id1)
mol_name2, res_num2, res_name2, spin_num2, spin_name2 = spin_id_to_data_list(interatom.spin_id2)
# Inside the domain.
if domain.contains_spin(spin_name=spin_name1, spin_num=spin_num1, res_name=res_name1, res_num=res_num1, mol=mol_name1) or domain.contains_spin(spin_name=spin_name2, spin_num=spin_num2, res_name=res_name2, res_num=res_num2, mol=mol_name2):
interatom.select = boolean_select(current=interatom.select, boolean=boolean)
# Deselect containers outside of the domain.
elif change_all:
interatom.select = False