def setUp(self):
self.mols1 = Read('Data/stringSel.pdb')
self.mol1 = self.mols1[0]
self.mols2 = Read('Data/protease.pdb')
self.mol2 = self.mols2[0]
self.mols = self.mols1 + self.mols2
self.stringSel = StringSelector()
def test_select_with_empty_string(self):
"""
test result with empty string returns all molecules
"""
stringSel = StringSelector()
result, msg = stringSel.select(self.molecules, "")
self.assertEquals(result, self.molecules)
self.assertEquals(result.stringRepr, self.molecules[0].name)
def test_select_with_bad_key_returns_EmptySet(self):
"""
test result with bad_key returns EmptySet
"""
selString = ":::'backbone'"
stringSel = StringSelector()
result, msg = stringSel.select(self.molecules, selString)
self.assertEquals(len(result), 0)
def test_select_with_bad_key_returns_EmptySet(self):
"""
test result with bad_key returns EmptySet
"""
selString = ":::'backbone'"
stringSel = StringSelector()
result, msg = stringSel.select(self.molecules, selString)
self.assertEquals(len(result), 0)
def test_select_with_empty_string(self):
"""
test result with empty string returns all molecules
"""
stringSel = StringSelector()
result, msg = stringSel.select(self.molecules, "")
self.assertEquals(result, self.molecules)
self.assertEquals(result.stringRepr, self.molecules[0].name)
def test_select_with_lambda_molecule_expr(self):
"""
test result with lambda x:x.name=='stringSel' returns 29 atoms
"""
selString = "lambda x:x.name=='stringSel':::"
#sanity check
stringSel = StringSelector()
result, msg = stringSel.select(self.molecules, selString)
self.assertEquals(len(result), 29)
self.assertEquals(result.stringRepr, selString)
def test_select_with_lambda_chain_expr(self):
"""
test result with lambda x:x.id=='W' returns 5 atoms
"""
selString = ":lambda x:x.id=='W'::"
#sanity check
stringSel = StringSelector()
result, msg = stringSel.select(self.molecules, selString)
self.assertEquals(len(result), 5)
self.assertEquals(result.stringRepr, selString)
def test_select_with_lambda_residue_expr(self):
"""
test result with lambda x:x.name==CA returns 9 atoms
"""
selString = "::lambda x:x.type=='GLN':"
#sanity check
stringSel = StringSelector()
result, msg = stringSel.select(self.molecules, selString)
self.assertEquals(len(result), 9)
self.assertEquals(result.stringRepr, selString)
def test_select_with_hetatm_returns_5atoms(self):
"""
test result with hetatm returns 5 atoms
"""
selString = ":::hetatm"
#sanity check
stringSel = StringSelector()
result, msg = stringSel.select(self.molecules, selString)
self.assertEquals(len(result), 5)
self.assertEquals(result.stringRepr, selString)
def test_select_with_hetatm_returns_5atoms(self):
"""
test result with hetatm returns 5 atoms
"""
selString = ":::hetatm"
#sanity check
stringSel = StringSelector()
result, msg = stringSel.select(self.molecules, selString)
self.assertEquals(len(result), 5)
self.assertEquals(result.stringRepr, selString)
def test_select_with_lambda_residue_expr(self):
"""
test result with lambda x:x.name==CA returns 9 atoms
"""
selString = "::lambda x:x.type=='GLN':"
#sanity check
stringSel = StringSelector()
result, msg = stringSel.select(self.molecules, selString)
self.assertEquals(len(result), 9)
self.assertEquals(result.stringRepr, selString)
def test_select_with_simple_Residue_full_name(self):
"""
test result with simple Residue full_name
"""
subset = self.molecules.chains.residues[:2]
selString = subset.full_name()
stringSel = StringSelector()
result, msg = stringSel.select(self.molecules, selString)
self.assertEqual(result, subset)
self.assertEquals(result.stringRepr, selString)
def test_select_with_compound_Residue_full_name(self):
"""
test result with compound Residue full_name
"""
subset = self.molecules.chains.residues[:2]
selString = subset[0].full_name() + ';' + subset[1].full_name()
stringSel = StringSelector()
result, msg = stringSel.select(self.molecules, selString)
self.assertEqual(result, subset)
self.assertEquals(result.stringRepr, selString)
def test_select_with_compound_Residue_full_name(self):
"""
test result with compound Residue full_name
"""
subset = self.molecules.chains.residues[:2]
selString = subset[0].full_name() + ';' + subset[1].full_name()
stringSel = StringSelector()
result, msg = stringSel.select(self.molecules, selString)
self.assertEqual(result, subset)
self.assertEquals(result.stringRepr, selString)
def test_select_with_simple_Residue_full_name(self):
"""
test result with simple Residue full_name
"""
subset = self.molecules.chains.residues[:2]
selString = subset.full_name()
stringSel = StringSelector()
result, msg = stringSel.select(self.molecules, selString)
self.assertEqual(result, subset)
self.assertEquals(result.stringRepr, selString)
def test_select_with_simple_Atom_full_name(self):
"""
test result with simple Atom full_name
"""
subset = self.molecules.allAtoms[:2]
selString = subset.full_name()
stringSel = StringSelector()
result, msg = stringSel.select(self.molecules, selString)
self.assertEqual(result, subset)
self.assertEquals(result.stringRepr, selString)
def test_select_with_backbone_returns_no_waters(self):
"""
test result with backbone returns no waters
"""
selString = ":::backbone"
stringSel = StringSelector()
result, msg = stringSel.select(self.molecules, selString)
self.assertEquals(len(result), 12)
self.assertEqual('HOH' not in result.parent.type, True)
self.assertEquals(result.stringRepr, selString)
def test_select_with_CA_returns_3atoms(self):
"""
test result with CA returns 3 atoms
"""
selString = ":::CA"
#sanity check
stringSel = StringSelector()
result, msg = stringSel.select(self.molecules, selString)
self.assertEquals(len(result), 3)
self.assertEquals(result.stringRepr, selString)
def test_select_with_backbone_returns_no_waters(self):
"""
test result with backbone returns no waters
"""
selString = ":::backbone"
stringSel = StringSelector()
result, msg = stringSel.select(self.molecules, selString)
self.assertEquals(len(result), 12)
self.assertEqual('HOH' not in result.parent.type, True)
self.assertEquals(result.stringRepr, selString)
def test_select_with_lambda_chain_expr(self):
"""
test result with lambda x:x.id=='W' returns 5 atoms
"""
selString = ":lambda x:x.id=='W'::"
#sanity check
stringSel = StringSelector()
result, msg = stringSel.select(self.molecules, selString)
self.assertEquals(len(result), 5)
self.assertEquals(result.stringRepr, selString)
def test_select_with_simple_Atom_full_name(self):
"""
test result with simple Atom full_name
"""
subset = self.molecules.allAtoms[:2]
selString = subset.full_name()
stringSel = StringSelector()
result, msg = stringSel.select(self.molecules, selString)
self.assertEqual(result, subset)
self.assertEquals(result.stringRepr, selString)
def test_select_with_backbone_returns_12atoms(self):
"""
test result with backbone returns 12 atoms
"""
selString = ":::backbone"
#sanity check
stringSel = StringSelector()
result, msg = stringSel.select(self.molecules, selString)
self.assertEquals(len(result), 12)
self.assertEquals(result.stringRepr, selString)
def test_select_with_backbone_returns_12atoms(self):
"""
test result with backbone returns 12 atoms
"""
selString = ":::backbone"
#sanity check
stringSel = StringSelector()
result, msg = stringSel.select(self.molecules, selString)
self.assertEquals(len(result), 12)
self.assertEquals(result.stringRepr, selString)
def test_select_with_CA_returns_3atoms(self):
"""
test result with CA returns 3 atoms
"""
selString = ":::CA"
#sanity check
stringSel = StringSelector()
result, msg = stringSel.select(self.molecules, selString)
self.assertEquals(len(result), 3)
self.assertEquals(result.stringRepr, selString)
def test_select_with_lambda_molecule_expr(self):
"""
test result with lambda x:x.name=='stringSel' returns 29 atoms
"""
selString = "lambda x:x.name=='stringSel':::"
#sanity check
stringSel = StringSelector()
result, msg = stringSel.select(self.molecules, selString)
self.assertEquals(len(result), 29)
self.assertEquals(result.stringRepr, selString)
def test_select_with_lambda_atoms_expr_with_parentheses(self):
"""
test result with lambda x:len(x.bonds)==1 returns 468 atoms for hsg1.pdb
"""
selString = ":::lambda x:len(x.bonds)==1"
stringSel = StringSelector()
from MolKit import Read
mol = Read("Data/hsg1.pdb")
mol[0].buildBondsByDistance()
result, msg = stringSel.select(mol, selString)
self.assertEquals(len(result), 468)
self.assertEquals(result.stringRepr, selString)
def test_select_with_lambda_atoms_expr_with_parentheses(self):
"""
test result with lambda x:len(x.bonds)==1 returns 468 atoms for hsg1.pdb
"""
selString = ":::lambda x:len(x.bonds)==1"
stringSel = StringSelector()
from MolKit import Read
mol = Read("Data/hsg1.pdb")
mol[0].buildBondsByDistance()
result, msg = stringSel.select(mol, selString)
self.assertEquals(len(result), 468)
self.assertEquals(result.stringRepr, selString)
def test_select_with_5_Residue_full_names(self):
"""
test result with 5 Residue full_names joined with ';'
"""
subset = self.molecules.chains.residues[:5]
selString = ''
for a in subset:
selString += a.full_name() + ';'
selString = selString[:-1]
stringSel = StringSelector()
result, msg = stringSel.select(self.molecules, selString)
self.assertEqual(result, subset)
self.assertEquals(result.stringRepr, selString)
def test_select_all_atoms_from_compound_string(self):
"""
test result using all the atoms' full_name()
"""
selString = ''
subset = self.molecules.allAtoms
for a in subset:
selString += a.full_name() + ';'
selString = selString[:-1]
stringSel = StringSelector()
result, msg = stringSel.select(self.molecules, selString)
self.assertEqual(result, subset)
self.assertEquals(result.stringRepr, selString)
def test_select_with_5_Residue_full_names(self):
"""
test result with 5 Residue full_names joined with ';'
"""
subset = self.molecules.chains.residues[:5]
selString = ''
for a in subset:
selString += a.full_name() + ';'
selString = selString[:-1]
stringSel = StringSelector()
result, msg = stringSel.select(self.molecules, selString)
self.assertEqual(result, subset)
self.assertEquals(result.stringRepr, selString)
def test_select_all_atoms_from_compound_string(self):
"""
test result using all the atoms' full_name()
"""
selString = ''
subset = self.molecules.allAtoms
for a in subset:
selString += a.full_name() + ';'
selString = selString[:-1]
stringSel = StringSelector()
result, msg = stringSel.select(self.molecules, selString)
self.assertEqual(result, subset)
self.assertEquals(result.stringRepr, selString)
def test_select_set_from_string(self):
"""
test result using string which is key in Sets dict
"""
sets = Sets()
subset = self.molecules[0].allAtoms
set_name = 'first'
sets.add(set_name, subset)
selString = ':::' + set_name
stringSel = StringSelector()
result, msg = stringSel.select(self.molecules, selString, sets=sets)
self.assertEqual(result, subset)
self.assertEquals(result.stringRepr, selString)
def test_select_set_from_string(self):
"""
test result using string which is key in Sets dict
"""
sets = Sets()
subset = self.molecules[0].allAtoms
set_name = 'first'
sets.add(set_name, subset)
selString = ':::' + set_name
stringSel = StringSelector()
result, msg = stringSel.select(self.molecules, selString, sets=sets)
self.assertEqual(result, subset)
self.assertEquals(result.stringRepr, selString)
def get(self, event=None, withMsg=False):
args = self.buildArgs()
atArg = self.atomEntry.get()
#print "atArg=", atArg, "=='' is", atArg==""
resArg = self.resEntry.get()
#print "resArg=", resArg, "=='' is", resArg==""
chainArg = self.chainEntry.get()
#print "chainArg=", chainArg, "=='' is", chainArg==""
molArg = self.molEntry.get()
#print "molArg=", molArg, "=='' is", molArg==""
if atArg != "":
args = molArg + ':' + chainArg + ':' + resArg + ':' + atArg
elif resArg != "":
args = molArg + ':' + chainArg + ':' + resArg
elif chainArg != "":
args = molArg + ':' + chainArg
else:
args = molArg
#print "calling StringSelector.select with args=", args
selitem, msgStr = StringSelector().select(self.molSet,
args,
sets=self.sets,
caseSensitive=self.userPref)
#if StringSelector starts returning msgs fix here
#selitem, msgStr = StringSelector().select(self.molSet, args, self.userPref)
#return selitem, msgStr
#if selitem and len(selitem):
# print "returning len(selitem)=", len(selitem)
if withMsg:
return selitem, msgStr
else:
return selitem
def setGeomAtomProp(self):
if not len(self.atomSets): return
from MolKit.molecule import Atom
prop = 'colors'
for actor in self.actors:
if actor.name.find(prop) > 0:
obj = actor.object
if self.atomSets.has_key(obj.fullName):
#setstr = self.atomSets[obj.fullName]['atomset']
g = obj.mol.geomContainer
aset = g.atoms[obj.name].findType(Atom)
asetstr = aset.full_name(0)
#if len(asetstr) != len(setstr):
# return
atList = []
func = g.geomPickToAtoms.get(obj.name)
if func:
atList = func(obj, range(len(obj.vertexSet.vertices)))
else:
allAtoms = g.atoms[obj.name]
if hasattr(obj, "vertexSet") and len(allAtoms) == len(
obj.vertexSet):
atList = allAtoms
if not len(atList): return
col = actor.getLastKeyFrame().getValue()
oname = None
if aset.colors.has_key(obj.name):
oname = obj.name
elif aset.colors.has_key(obj.parent.name):
oname = obj.parent.name
if not oname: return
if len(col) == 1:
for a in atList:
a.colors[oname] = tuple(col[0])
else:
for i, a in enumerate(atList):
a.colors[oname] = tuple(col[i])
from MolKit.stringSelector import StringSelector
selector = StringSelector()
#nset, msg = selector.select(atList, setstr)
nset, msg = selector.select(atList, asetstr)
def setGeomAtomProp(self):
if not len(self.atomSets) : return
from MolKit.molecule import Atom
prop = 'colors'
for actor in self.actors:
if actor.name.find(prop) > 0:
obj = actor.object
if self.atomSets.has_key(obj.fullName):
#setstr = self.atomSets[obj.fullName]['atomset']
g = obj.mol.geomContainer
aset = g.atoms[obj.name].findType(Atom)
asetstr = aset.full_name(0)
#if len(asetstr) != len(setstr):
# return
atList = []
func = g.geomPickToAtoms.get(obj.name)
if func:
atList = func(obj, range(len(obj.vertexSet.vertices)))
else:
allAtoms = g.atoms[obj.name]
if hasattr(obj, "vertexSet") and len(allAtoms) == len(obj.vertexSet):
atList = allAtoms
if not len(atList): return
col = actor.getLastKeyFrame().getValue()
oname = None
if aset.colors.has_key(obj.name):
oname = obj.name
elif aset.colors.has_key(obj.parent.name):
oname = obj.parent.name
if not oname : return
if len(col) == 1:
for a in atList:
a.colors[oname] = tuple(col[0])
else:
for i, a in enumerate(atList):
a.colors[oname] = tuple(col[i])
from MolKit.stringSelector import StringSelector
selector = StringSelector()
#nset, msg = selector.select(atList, setstr)
nset, msg = selector.select(atList, asetstr)
def setUp(self):
self.mols = Read('Data/stringSel.pdb')
self.mol = self.mols[0]
self.stringSel = StringSelector()
def test_constructor(self):
"""
instantiate a StringSelector
"""
stringSel = StringSelector()
self.assertEquals(stringSel.__class__, StringSelector)
def setUp(self):
self.mols = Read('Data/stringSel.pdb')
self.mol = self.mols[0]
self.mol.buildBondsByDistance()
self.stringSel = StringSelector()
class TwoMoleculeStringReprTests(StringReprBaseTests):
def setUp(self):
self.mols1 = Read('Data/stringSel.pdb')
self.mol1 = self.mols1[0]
self.mols2 = Read('Data/protease.pdb')
self.mol2 = self.mols2[0]
self.mols = self.mols1 + self.mols2
self.stringSel = StringSelector()
#tests for correction stringRepr initialization below sets
def test_correct_MoleculeSet_stringRepr(self):
"""
check moleculeSet stringRepr is correct
"""
self.assertEquals(self.mols.stringRepr, "stringSel/+/protease")
def test_correct_ChainSet_stringRepr(self):
"""
check ChainSet stringRepr is correct
"""
self.assertEquals(self.mols.chains.stringRepr, "stringSel:/+/protease:")
def test_correct_ResidueSet_stringRepr(self):
"""
check ResidueSet stringRepr is correct
"""
self.assertEquals(self.mols.chains.residues.stringRepr, "stringSel::/+/protease::")
def test_correct_AtomSet_stringRepr(self):
"""
check AtomSet stringRepr is correct
"""
self.assertEquals(self.mols.chains.residues.atoms.stringRepr, "stringSel:::/+/protease:::")
#tests for correction stringRepr initialization below individual
def test_correct_Molecule_ChainSet_stringRepr(self):
"""
check single Molecule's chainSet stringRepr is correct
"""
self.assertEquals(self.mol1.chains.stringRepr, "stringSel:")
def test_correct_Chain1_ResidueSet_stringRepr(self):
"""
check Chain1's residues stringRepr is correct
"""
self.assertEquals(self.mols.chains[0].residues.stringRepr, "stringSel:A:")
def test_correct_Chain2_ResidueSet_stringRepr(self):
"""
check two chain's residues stringRepr is correct
"""
self.assertEquals(self.mols.chains[1].residues.stringRepr, "stringSel:W:")
def Qtest_correct_2Chain_ResidueSet_stringRepr(self):
"""
check two Chains residues stringRepr is correct
"""
self.assertEquals(self.mols.chains[0-2].residues.stringRepr, "stringSel::")
def test_correct_last_Chain_ResidueSet_stringRepr(self):
"""
check last Chain's residues stringRepr is correct
"""
self.assertEquals(self.mols.chains[-1].residues.stringRepr, "protease:B:")
def test_correct_Mol0_Chain0_ResidueSet_stringRepr(self):
"""
check single Mol's single Chain's residues stringRepr
"""
self.assertEquals(self.mols[0].chains[0].residues.stringRepr, "stringSel:A:")
def Xtest_correct_Mol0_Chains1_2_ResidueSet_stringRepr(self):
"""
check single Mol's two Chain's residues stringRepr
"""
self.assertEquals(self.mols[0].chains[0:].residues.stringRepr, "stringSel::")
def test_correct_Mols_Chains1_residues_atoms_stringRepr(self):
"""
check single Chain's residues's atoms stringRepr
"""
self.assertEquals(self.mols.chains[0].residues.atoms.stringRepr, "stringSel:A::")
def test_select_with_empty_string(self):
"""
test result with empty string returns all mols
"""
result, msg = self.stringSel.select(self.mols, "")
self.assertEqual(self.mols.stringRepr, "stringSel/+/protease")
def test_setLevel_protein_protein(self):
"""
test setting protein level to protein
"""
mols = self.mols.setLevel(Protein)
self.assertEqual(mols.stringRepr, "stringSel/+/protease")
def test_setLevel_protein_chain(self):
"""
test setting protein level to chain
"""
chains = self.mols.setLevel(Chain)
self.assertEqual(chains.stringRepr, "stringSel:/+/protease:")
def test_setLevel_protein_residue(self):
"""
test setting protein level to residue
"""
res = self.mols.setLevel(Residue)
self.assertEqual(res.stringRepr, "stringSel::/+/protease::")
def test_setLevel_protein_residue(self):
"""
test setting protein level to Atom
"""
ats = self.mols.setLevel(Atom)
self.assertEqual(ats.stringRepr, "stringSel:::/+/protease:::")
def test_setLevel_chain_protein(self):
"""
test setting chain level to protein
"""
mols = self.mols.chains.setLevel(Protein)
self.assertEqual(mols.stringRepr, "stringSel/+/protease")
def test_setLevel_chain_chain(self):
"""
test setting chain level to chain
"""
chains = self.mols.chains.setLevel(Chain)
self.assertEqual(chains.stringRepr, "stringSel:/+/protease:")
def test_setLevel_chain_residue(self):
"""
test setting chain level to residue
"""
res = self.mols.chains.setLevel(Residue)
self.assertEqual(res.stringRepr, "stringSel::/+/protease::")
def test_setLevel_chain_atom(self):
"""
test setting chain level to Atom
"""
ats = self.mols.chains.setLevel(Atom)
self.assertEqual(ats.stringRepr, "stringSel:::/+/protease:::")
def test_setLevel_residues_protein(self):
"""
test setting residue level to protein
"""
mols = self.mols.chains.residues.setLevel(Protein)
self.assertEqual(mols.stringRepr, "stringSel/+/protease")
def test_setLevel_residues_chain(self):
"""
test setting residues level to chain
"""
chains = self.mols.chains.residues.setLevel(Chain)
self.assertEqual(chains.stringRepr, "stringSel:/+/protease:")
def test_setLevel_residues_residue(self):
"""
test setting residues level to residue
"""
res = self.mols.chains.residues.setLevel(Residue)
self.assertEqual(res.stringRepr, "stringSel::/+/protease::")
def test_setLevel_residues_atom(self):
"""
test setting residue level to Atom
"""
ats = self.mols.chains.residues.setLevel(Atom)
self.assertEqual(ats.stringRepr, "stringSel:::/+/protease:::")
class StringSelectorTests(StringSelectorBaseTests):
def setUp(self):
self.mols = Read('Data/stringSel.pdb')
self.mol = self.mols[0]
self.mol.buildBondsByDistance()
self.stringSel = StringSelector()
def tearDown(self):
"""
clean-up
"""
del(self.mol)
#tests with 1 change of level
def test_1level_select_with_empty_string(self):
"""
test result with empty string ":" returns all chains
"""
#stringSel = MVProteinSetSelector(self.mols, self.selString)
#result, msg = stringSel.go()
result, msg = self.stringSel.select(self.mols, ":")
self.assertEquals(result, self.mols.chains)
self.assertEquals(result.__class__, self.mols.chains.__class__)
def test_1level_select_end(self):
"""
test select with '$' returns last molecule.chains
"""
new_mols = Read("Data/1crn.pdb")
self.mols +=new_mols
result, msg = self.stringSel.select(self.mols, "$:")
self.assertEquals(result, self.mols[-1:].chains)
def test_1level_select_end_2(self):
"""
test select with ':$' returns molecule's last chain
"""
new_mols = Read("Data/1crn.pdb")
self.mols +=new_mols
result, msg = self.stringSel.select(self.mols, ":$")
self.assertEquals(result[0], self.mols[-1:].chains[-1])
def test_1level_select_with_valid_index(self):
"""
test string with valid_index returns set with 1 item
"""
selString = "0:"
#selString = "1:"
result, msg = self.stringSel.select(self.mols, selString)
self.assertEquals(len(result), len(self.mols[0].chains))
self.assertEquals(result.__class__, self.mols.chains.__class__)
def test_1level_select_with_invalid_index_returns_empty_set(self):
"""
test string with invalid_index returns empty ChainSet
FIX THIS: should it be an empty ChainSet?
"""
selString = "2:"
result, msg = self.stringSel.select(self.mols, selString)
self.assertEqual(result.__class__, ChainSet)
#self.assertEqual(result.__class__, self.mols.chains.__class__)
self.assertEqual(len(result), 0)
self.assertEqual(msg[0], selString[0])
def test_1level_select_with_valid_range(self):
"""
test string with valid_range returns ChainSet with 2 items
"""
new_mols = Read("Data/1crn.pdb")
self.mols +=new_mols
selString = "0-1:"
#selString = "1-2:"
result, msg = self.stringSel.select(self.mols, selString)
self.assertEquals(len(result), len(self.mols.chains))
def test_1level_select_with_invalid_range(self):
"""
test string with invalid_range returns set with 0 items
FIX THIS: should it be an empty ChainSet?
"""
new_mols = Read("Data/1crn.pdb")
self.mols +=new_mols
selString = "4-6:"
result, msg = self.stringSel.select(self.mols, selString)
self.assertEquals(len(result), 0)
self.assertEquals(result.__class__, ChainSet)
#self.assertEquals(result.__class__, self.mols.chains.__class__)
def test_1level_select_with_valid_regex(self):
"""
test string with valid_regex returns set with 1 items
<this regex is intended to match 1, 2,or 3 followed by anything>
"""
new_mols = Read("Data/1crn.pdb")
self.mols +=new_mols
selString = "[1-3]*:"
result, msg = self.stringSel.select(self.mols, selString)
#print "result=", result
#1crn has 1 chain
self.assertEquals(len(result), 1)
self.assertEquals(result.__class__, self.mols.chains.__class__)
def test_1level_select_with_valid_regex_2(self):
"""
test string with valid_regex returns set with 1 items
<this regex is intended to match anything in range s-z
followed by anything>
"""
new_mols = Read("Data/1crn.pdb")
self.mols +=new_mols
selString = "[s-z]*:"
result, msg = self.stringSel.select(self.mols, selString)
#print "result=", result
self.assertEquals(len(result), len(self.mols[0].chains))
self.assertEquals(result.__class__, self.mols.chains.__class__)
#tests with 2 changes of level
def test_2level_select_with_empty_string(self):
"""
test result with empty string "::" returns all residues
"""
#stringSel = MVProteinSetSelector(self.mols, self.selString)
#result, msg = stringSel.go()
result, msg = self.stringSel.select(self.mols, "::")
self.assertEquals(result, self.mols.chains.residues)
self.assertEquals(result.__class__, self.mols.chains.residues.__class__)
def test_2level_select_end(self):
"""
test select with '$' returns last molecule.residues
"""
new_mols = Read("Data/1crn.pdb")
self.mols +=new_mols
result, msg = self.stringSel.select(self.mols, "$::")
self.assertEquals(result, self.mols[-1:].chains.residues)
def test_2level_select_end_2(self):
"""
test select with ':$' returns molecule's last residue
"""
new_mols = Read("Data/1crn.pdb")
self.mols +=new_mols
result, msg = self.stringSel.select(self.mols, "::$")
self.assertEquals(result[0], self.mols[-1:].chains.residues[-1])
def test_2level_select_with_valid_index(self):
"""
test string with valid_index:: returns residue set of 54
"""
selString = "0::"
#selString = "1::"
result, msg = self.stringSel.select(self.mols, selString)
self.assertEquals(len(result), len(self.mols.chains.residues))
self.assertEquals(result.__class__, self.mols.chains.residues.__class__)
def test_2level_select_with_invalid_index_returns_empty_set(self):
"""
test string with invalid_index:: returns empty ResidueSet
FIX THIS: should it be an empty residueSet?
"""
selString = "2::"
result, msg = self.stringSel.select(self.mols, selString)
self.assertEqual(result.__class__, ResidueSet)
#self.assertEqual(result.__class__, self.mols.chains.residues.__class__)
self.assertEqual(len(result), 0)
self.assertEqual(msg[0], selString[0])
def test_2level_select_with_valid_range(self):
"""
test string with valid_range returns all residues
"""
new_mols = Read("Data/1crn.pdb")
self.mols +=new_mols
selString = "0-1::"
#selString = "1-2::"
result, msg = self.stringSel.select(self.mols, selString)
self.assertEquals(len(result), len(self.mols.chains.residues))
def test_2level_select_with_invalid_range(self):
"""
test string with invalid_range returns set with 0 items
FIX THIS: should it be an empty ResidueSet?
"""
new_mols = Read("Data/1crn.pdb")
self.mols +=new_mols
selString = "4-6::"
result, msg = self.stringSel.select(self.mols, selString)
self.assertEquals(len(result), 0)
self.assertEquals(result.__class__, ResidueSet)
#self.assertEquals(result.__class__, self.mols.chains.residues.__class__)
def test_2level_select_with_valid_regex(self):
"""
test string with valid_regex:: returns set with 46 residues
<this regex is intended to match 1, 2,or 3 followed by anything>
"""
new_mols = Read("Data/1crn.pdb")
self.mols +=new_mols
selString = "[1-3]*::"
result, msg = self.stringSel.select(self.mols, selString)
#print "result=", result
#result matches 1crn only
self.assertEquals(len(result), len(self.mols[1].chains.residues))
self.assertEquals(result.__class__, self.mols.chains.residues.__class__)
def test_2level_select_with_valid_regex_2(self):
"""
test string with valid_regex:: returns residueSet of 8
<this regex is intended to match anything in range s-z
followed by anything>
"""
new_mols = Read("Data/1crn.pdb")
self.mols +=new_mols
selString = "[s-z]*::"
result, msg = self.stringSel.select(self.mols, selString)
#print "result=", result
#result matches mols[0] only
self.assertEquals(len(result), len(self.mols[0].chains.residues))
self.assertEquals(result.__class__, self.mols.chains.residues.__class__)
#tests with 3 changes of level
def test_3level_select_with_empty_string(self):
"""
test result with empty string ":::" returns all atoms
"""
#stringSel = MVProteinSetSelector(self.mols, self.selString)
#result, msg = stringSel.go()
result, msg = self.stringSel.select(self.mols, ":::")
self.assertEquals(result, self.mols.allAtoms)
self.assertEquals(result.__class__, self.mols.allAtoms.__class__)
def test_3level_select_end(self):
"""
test select with '$' returns last molecule.atoms
"""
new_mols = Read("Data/1crn.pdb")
self.mols +=new_mols
result, msg = self.stringSel.select(self.mols, "$:::")
self.assertEquals(result, self.mols[-1:].allAtoms)
def test_3level_select_end_2(self):
"""
test select with ':$' returns molecule's last atom
"""
new_mols = Read("Data/1crn.pdb")
self.mols +=new_mols
result, msg = self.stringSel.select(self.mols, ":::$")
self.assertEquals(result[0], self.mols[-1:].allAtoms[-1])
def test_3level_select_with_valid_index(self):
"""
test string with valid_index returns set of atoms
"""
selString = "0:::"
#selString = "1:::"
result, msg = self.stringSel.select(self.mols, selString)
#print "result=", result
self.assertEquals(len(result), len(self.mols[0].allAtoms))
self.assertEquals(result.__class__, self.mols.allAtoms.__class__)
def test_3level_select_with_invalid_index_returns_empty_set(self):
"""
test string with invalid_index returns empty AtomSet
FIX THIS: should it be an empty AtomSet?
"""
selString = "2:::"
result, msg = self.stringSel.select(self.mols, selString)
self.assertEqual(result.__class__, AtomSet)
self.assertEqual(len(result), 0)
self.assertEqual(msg[0], selString[0])
def test_3level_select_with_valid_range(self):
"""
test string with valid_range returns 1crn.allAtoms
"""
new_mols = Read("Data/1crn.pdb")
self.mols +=new_mols
selString = "0-1:::"
#selString = "1-2:::"
result, msg = self.stringSel.select(self.mols, selString)
self.assertEquals(len(result), len(self.mols.allAtoms))
def test_3level_select_with_invalid_range(self):
"""
test string with invalid_range returns set with 0 items
FIX THIS: should it be an empty AtomSet?
"""
new_mols = Read("Data/1crn.pdb")
self.mols +=new_mols
selString = "4-6:::"
result, msg = self.stringSel.select(self.mols, selString)
self.assertEquals(len(result), 0)
self.assertEquals(result.__class__, AtomSet)
#self.assertEquals(result.__class__, self.mols.allAtoms.__class__)
def test_3level_select_with_valid_regex(self):
"""
test string with valid_regex returns AtomSet 1crn.allAtoms
<this regex is intended to match 1, 2,or 3 followed by anything>
"""
new_mols = Read("Data/1crn.pdb")
self.mols +=new_mols
selString = "[1-3]*:::"
result, msg = self.stringSel.select(self.mols, selString)
#print "result=", result
#result matches 1crn only
self.assertEquals(len(result), len(self.mols[1].allAtoms))
self.assertEquals(result.__class__, self.mols.allAtoms.__class__)
def test_3level_select_with_valid_regex_2(self):
"""
test string with valid_regex returns set with 1 items
<this regex is intended to match anything in range s-z
followed by anything>
"""
new_mols = Read("Data/1crn.pdb")
self.mols +=new_mols
selString = "[s-z]*:::"
result, msg = self.stringSel.select(self.mols, selString)
#print "result=", result
#result matches mols[0] only
self.assertEquals(len(result), len(self.mols[0].allAtoms))
self.assertEquals(result.__class__, self.mols.allAtoms.__class__)