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 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 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_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_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_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_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_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_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_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_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_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 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()
