def test_select_add_mols_allAtoms(self):
"""
test selecting with stringRepr of atoms of added mols
"""
stringSel = CompoundStringSelector()
selString = self.mols.allAtoms.stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
self.assertEquals(selected, self.mols.allAtoms)
self.assertEquals(selString, "stringSel:::/+/protease:::")
def test_select_subtract_allAtoms(self):
"""
test selecting with stringRepr of subtracted allAtoms
"""
stringSel = CompoundStringSelector()
diff_atoms = self.mols.allAtoms - self.mols1.allAtoms
selString = diff_atoms.stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
self.assertEquals(selected, diff_atoms)
self.assertEquals(selString, "stringSel:::/+/protease:::/-/stringSel:::")
def test_select_subtract_chains(self):
"""
test selecting with stringRepr of subtracted chains
"""
stringSel = CompoundStringSelector()
diff_chains = self.mols.chains - self.mols1.chains
selString = diff_chains.stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
self.assertEquals(selected, diff_chains)
self.assertEquals(selString, "stringSel:/+/protease:/-/stringSel:")
def test_select_subtract_residues(self):
"""
test selecting with stringRepr of subtracted residues
"""
stringSel = CompoundStringSelector()
diff_residues = self.mols.chains.residues - self.mols1.chains.residues
selString = diff_residues.stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
self.assertEquals(selected, diff_residues)
self.assertEquals(selString, "stringSel::/+/protease::/-/stringSel::")
def test_select_add_mols_atoms(self):
"""
test selecting with stringRepr of atoms of added mols
"""
stringSel = CompoundStringSelector()
selString = self.mols.chains.residues.atoms.stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
self.assertEquals(selected, self.mols.chains.residues.atoms)
#print "selString=", selString
self.assertEquals(selString, "stringSel:::/+/protease:::")
def test_select_subtract_mols(self):
"""
test selecting with stringRepr of subtracted mols
"""
stringSel = CompoundStringSelector()
diff_mols = self.mols - self.mols1
selString = diff_mols.stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
self.assertEquals(selected, diff_mols)
self.assertEquals(selString, "stringSel/+/protease/-/stringSel")
def test_select_subtract_mols(self):
"""
test selecting with stringRepr of subtracted mols
"""
stringSel = CompoundStringSelector()
diff_mols = self.mols - self.mols1
selString = diff_mols.stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
self.assertEquals(selected, diff_mols)
self.assertEquals(selString, "stringSel/+/protease/-/stringSel")
def test_select_xor_mols_all(self):
"""
test selecting with stringRepr of xor mols returning all
"""
stringSel = CompoundStringSelector()
diff_mols = self.mols1 ^ self.mols2
selString = diff_mols.stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
self.assertEquals(selected, diff_mols)
self.assertEquals(selected, self.mols)
self.assertEquals(selString, "stringSel/^/protease")
def test_select_intersect_allAtoms(self):
"""
test selecting with stringRepr of intersected allAtoms
"""
stringSel = CompoundStringSelector()
diff_atoms = self.mols1.allAtoms & self.mols2.allAtoms
selString = diff_atoms.stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
self.assertEquals(selected, diff_atoms)
self.assertEquals(selected, AtomSet())
self.assertEquals(selString, "stringSel:::/&/protease:::")
def test_select_intersect_residues_empty(self):
"""
test selecting with stringRepr of empty intersected residues
"""
stringSel = CompoundStringSelector()
diff_residues = self.mols1.chains.residues & self.mols2.chains.residues
selString = diff_residues.stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
self.assertEquals(selected, diff_residues)
self.assertEquals(selected, ResidueSet())
self.assertEquals(selString, "stringSel::/&/protease::")
def test_select_intersect_allAtoms(self):
"""
test selecting with stringRepr of intersected allAtoms
"""
stringSel = CompoundStringSelector()
diff_atoms = self.mols1.allAtoms & self.mols2.allAtoms
selString = diff_atoms.stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
self.assertEquals(selected, diff_atoms)
self.assertEquals(selected, AtomSet())
self.assertEquals(selString, "stringSel:::/&/protease:::")
def test_select_union_atoms_all(self):
"""
test selecting with stringRepr of union 2X atoms returning single copy
"""
stringSel = CompoundStringSelector()
diff_atoms = self.mols1.chains.residues.atoms | self.mols1.chains.residues.atoms
selString = diff_atoms.stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
self.assertEquals(selected, diff_atoms)
self.assertEquals(selected, self.mols1.chains.residues.atoms)
self.assertEquals(selString, "stringSel:::")
def test_select_union_mols_single(self):
"""
test selecting with stringRepr of union 2X same mols returning single
"""
stringSel = CompoundStringSelector()
diff_mols = self.mols1 | self.mols1
selString = diff_mols.stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
self.assertEquals(selected, diff_mols)
self.assertEquals(selected, self.mols1)
self.assertEquals(selString, "stringSel")
def test_select_union_residues(self):
"""
test selecting with stringRepr of union residues
"""
stringSel = CompoundStringSelector()
diff_residues = self.mols.chains.residues | self.mols1.chains.residues
selString = diff_residues.stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
self.assertEquals(selected, diff_residues)
self.assertEquals(selected, self.mols.chains.residues)
self.assertEquals(selString, "stringSel::/+/protease::/|/stringSel::")
def test_select_xor_residues_all(self):
"""
test selecting with stringRepr of xor residues returning all
"""
stringSel = CompoundStringSelector()
diff_residues = self.mols1.chains.residues ^ self.mols2.chains.residues
selString = diff_residues.stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
self.assertEquals(selected, diff_residues)
self.assertEquals(selected, self.mols.chains.residues)
self.assertEquals(selString, "stringSel::/^/protease::")
def test_select_xor_allAtoms_all(self):
"""
test selecting with stringRepr of xor allAtoms returning all
"""
stringSel = CompoundStringSelector()
diff_atoms = self.mols1.allAtoms ^ self.mols2.allAtoms
selString = diff_atoms.stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
self.assertEquals(selected, diff_atoms)
self.assertEquals(selected, self.mols.allAtoms)
self.assertEquals(selString, "stringSel:::/^/protease:::")
def test_select_subtract_allAtoms(self):
"""
test selecting with stringRepr of subtracted allAtoms
"""
stringSel = CompoundStringSelector()
diff_atoms = self.mols.allAtoms - self.mols1.allAtoms
selString = diff_atoms.stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
self.assertEquals(selected, diff_atoms)
self.assertEquals(selString,
"stringSel:::/+/protease:::/-/stringSel:::")
def test_select_intersect_chains_empty(self):
"""
test selecting with stringRepr of empty intersected chains
"""
stringSel = CompoundStringSelector()
diff_chains = self.mols1.chains & self.mols2.chains
selString = diff_chains.stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
self.assertEquals(selected, diff_chains)
self.assertEquals(selected, ChainSet())
self.assertEquals(selString, "stringSel:/&/protease:")
def test_select_intersect_mols_empty(self):
"""
test selecting with stringRepr of empty intersect mols
"""
stringSel = CompoundStringSelector()
diff_mols = self.mols1 & self.mols2
selString = diff_mols.stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
self.assertEquals(selected, diff_mols)
self.assertEquals(selString, "stringSel/&/protease")
self.assertEquals(selected, ProteinSet())
def test_select_intersect_chains_empty(self):
"""
test selecting with stringRepr of empty intersected chains
"""
stringSel = CompoundStringSelector()
diff_chains = self.mols1.chains & self.mols2.chains
selString = diff_chains.stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
self.assertEquals(selected, diff_chains)
self.assertEquals(selected, ChainSet())
self.assertEquals(selString, "stringSel:/&/protease:")
def test_select_intersect_mols_empty(self):
"""
test selecting with stringRepr of empty intersect mols
"""
stringSel = CompoundStringSelector()
diff_mols = self.mols1 & self.mols2
selString = diff_mols.stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
self.assertEquals(selected, diff_mols)
self.assertEquals(selString, "stringSel/&/protease")
self.assertEquals(selected, ProteinSet())
def test_select_intersect_residues_empty(self):
"""
test selecting with stringRepr of empty intersected residues
"""
stringSel = CompoundStringSelector()
diff_residues = self.mols1.chains.residues & self.mols2.chains.residues
selString = diff_residues.stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
self.assertEquals(selected, diff_residues)
self.assertEquals(selected, ResidueSet())
self.assertEquals(selString, "stringSel::/&/protease::")
def test_select_union_atoms_all(self):
"""
test selecting with stringRepr of union 2X atoms returning single copy
"""
stringSel = CompoundStringSelector()
diff_atoms = self.mols1.chains.residues.atoms | self.mols1.chains.residues.atoms
selString = diff_atoms.stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
self.assertEquals(selected, diff_atoms)
self.assertEquals(selected, self.mols1.chains.residues.atoms)
self.assertEquals(selString, "stringSel:::")
def test_select_xor_atoms(self):
"""
test selecting with stringRepr of xor atoms
"""
stringSel = CompoundStringSelector()
diff_atoms = self.mols.chains.residues.atoms ^ self.mols1.chains.residues.atoms
selString = diff_atoms.stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
self.assertEquals(selected, diff_atoms)
self.assertEquals(selected, self.mols2.chains.residues.atoms)
self.assertEquals(selString, "stringSel:::/+/protease:::/^/stringSel:::")
def test_select_union_mols_single(self):
"""
test selecting with stringRepr of union 2X same mols returning single
"""
stringSel = CompoundStringSelector()
diff_mols = self.mols1 | self.mols1
selString = diff_mols.stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
self.assertEquals(selected, diff_mols)
self.assertEquals(selected, self.mols1)
self.assertEquals(selString, "stringSel")
def test_select_xor_chains(self):
"""
test selecting with stringRepr of xor chains
"""
stringSel = CompoundStringSelector()
diff_chains = self.mols.chains ^ self.mols1.chains
selString = diff_chains.stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
self.assertEquals(selected, diff_chains)
self.assertEquals(selected, self.mols2.chains)
self.assertEquals(selString, "stringSel:/+/protease:/^/stringSel:")
def test_select_xor_mols_all(self):
"""
test selecting with stringRepr of xor mols returning all
"""
stringSel = CompoundStringSelector()
diff_mols = self.mols1 ^ self.mols2
selString = diff_mols.stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
self.assertEquals(selected, diff_mols)
self.assertEquals(selected, self.mols)
self.assertEquals(selString, "stringSel/^/protease")
def test_select_xor_residues_all(self):
"""
test selecting with stringRepr of xor residues returning all
"""
stringSel = CompoundStringSelector()
diff_residues = self.mols1.chains.residues ^ self.mols2.chains.residues
selString = diff_residues.stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
self.assertEquals(selected, diff_residues)
self.assertEquals(selected, self.mols.chains.residues)
self.assertEquals(selString, "stringSel::/^/protease::")
def test_select_xor_allAtoms_all(self):
"""
test selecting with stringRepr of xor allAtoms returning all
"""
stringSel = CompoundStringSelector()
diff_atoms = self.mols1.allAtoms ^ self.mols2.allAtoms
selString = diff_atoms.stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
self.assertEquals(selected, diff_atoms)
self.assertEquals(selected, self.mols.allAtoms)
self.assertEquals(selString, "stringSel:::/^/protease:::")
def test_select_subset_chains(self):
"""
test selecting with stringRepr of subset of chains
"""
stringSel = CompoundStringSelector()
diff_chains = self.mols.chains.get('B')
selString = "(stringSel:/+/protease:\\s\\B)"
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
#selected, msg = stringSel.select(self.mols, selString)
self.assertEquals(selected, diff_chains)
self.assertEquals(selected, self.mols.chains[-1:])
self.assertEquals(selected.stringRepr, selString)
def test_select_xor_atoms(self):
"""
test selecting with stringRepr of xor atoms
"""
stringSel = CompoundStringSelector()
diff_atoms = self.mols.chains.residues.atoms ^ self.mols1.chains.residues.atoms
selString = diff_atoms.stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
self.assertEquals(selected, diff_atoms)
self.assertEquals(selected, self.mols2.chains.residues.atoms)
self.assertEquals(selString,
"stringSel:::/+/protease:::/^/stringSel:::")
def test_select_subset_mols(self):
"""
test selecting with stringRepr for subset
"""
stringSel = CompoundStringSelector()
diff_mols = self.mols[-1:]
selString = "(stringSel/+/protease\\s\\protease)"
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
#selected, msg = stringSel.select(self.mols, selString)
self.assertEquals(selected, diff_mols)
self.assertEquals(selected, self.mols[-1:])
self.assertEquals(selected.stringRepr, selString)
def test_select_subset_chains(self):
"""
test selecting with stringRepr of subset of chains
"""
stringSel = CompoundStringSelector()
diff_chains = self.mols.chains.get('B')
selString = "(stringSel:/+/protease:\\s\\B)"
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
#selected, msg = stringSel.select(self.mols, selString)
self.assertEquals(selected, diff_chains)
self.assertEquals(selected, self.mols.chains[-1:])
self.assertEquals(selected.stringRepr, selString)
def test_select_subset_mols(self):
"""
test selecting with stringRepr for subset
"""
stringSel = CompoundStringSelector()
diff_mols = self.mols[-1:]
selString = "(stringSel/+/protease\\s\\protease)"
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
#selected, msg = stringSel.select(self.mols, selString)
self.assertEquals(selected, diff_mols)
self.assertEquals(selected, self.mols[-1:])
self.assertEquals(selected.stringRepr, selString)
def test_select_subset_allAtoms(self):
"""
test selecting with stringRepr of subset allAtoms
select the first atom in protease from mols.allAtoms
"""
stringSel = CompoundStringSelector()
diff_atoms = self.mols.allAtoms.get('0')
selString = "(stringSel:::/+/protease:::\\s\\0)"
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
#selected, msg = stringSel.select(self.mols, selString)
self.assertEquals(selected, diff_atoms)
self.assertEquals(selected, self.mols.allAtoms[0:1])
self.assertEquals(selected.stringRepr, selString)
def test_select_set_from_string(self):
"""
test result using key into Sets
"""
sets = Sets()
subset = self.mols.allAtoms[:3]
set_name = 'first_three_atoms'
sets.add(set_name, subset)
selString = ':::' + set_name
css = CompoundStringSelector()
result, msg = css.select(self.mols, selString, sets=sets)
self.assertEqual(result, subset)
self.assertEquals(result.stringRepr, selString)
def test_select_subset_residues(self):
"""
test selecting with stringRepr of subset residues
"""
stringSel = CompoundStringSelector()
#this is the name of the 7th residue in the first molecule
diff_residues = self.mols.chains.residues.get("HOH617")
selString = "(stringSel::/+/protease::\\s\\HOH617)"
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
#selected, msg = stringSel.select(self.mols, selString)
self.assertEquals(selected, diff_residues)
self.assertEquals(selected, self.mols.chains.residues[7:8])
self.assertEquals(selected.stringRepr, selString)
def test_select_set_from_string(self):
"""
test result using key into Sets
"""
sets = Sets()
subset = self.mols.allAtoms[:3]
set_name = 'first_three_atoms'
sets.add(set_name, subset)
selString = ':::' + set_name
css = CompoundStringSelector()
result, msg = css.select(self.mols, selString, sets=sets)
self.assertEqual(result, subset)
self.assertEquals(result.stringRepr, selString)
def test_select_subset_allAtoms(self):
"""
test selecting with stringRepr of subset allAtoms
select the first atom in protease from mols.allAtoms
"""
stringSel = CompoundStringSelector()
diff_atoms = self.mols.allAtoms.get('0')
selString = "(stringSel:::/+/protease:::\\s\\0)"
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
#selected, msg = stringSel.select(self.mols, selString)
self.assertEquals(selected, diff_atoms)
self.assertEquals(selected, self.mols.allAtoms[0:1])
self.assertEquals(selected.stringRepr, selString)
def test_select_subset_residues(self):
"""
test selecting with stringRepr of subset residues
"""
stringSel = CompoundStringSelector()
#this is the name of the 7th residue in the first molecule
diff_residues = self.mols.chains.residues.get("HOH617")
selString = "(stringSel::/+/protease::\\s\\HOH617)"
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
#selected, msg = stringSel.select(self.mols, selString)
self.assertEquals(selected, diff_residues)
self.assertEquals(selected, self.mols.chains.residues[7:8])
self.assertEquals(selected.stringRepr, selString)
def test_select_complicated_sidechain_atoms2(self):
"""
test selecting w/stringRepr of complicated sidechain atoms(bug 673)
"""
stringSel = CompoundStringSelector()
#arg is ARG8 in chain A
arg = self.mols2.chains.residues[7]
sidechain = arg.atoms.get('sidechain') - arg.atoms.get('CB')
#diff_atoms = self.mols1.allAtoms | self.mols1.allAtoms
selString = sidechain.stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
self.assertEquals(selected, sidechain)
self.assertEquals(selected, self.mols2.allAtoms[67:73])
self.assertEquals(selString, selected.stringRepr)
def test_select_complicated_sidechain_atoms2(self):
"""
test selecting w/stringRepr of complicated sidechain atoms(bug 673)
"""
stringSel = CompoundStringSelector()
#arg is ARG8 in chain A
arg = self.mols2.chains.residues[7]
sidechain = arg.atoms.get('sidechain')-arg.atoms.get('CB')
#diff_atoms = self.mols1.allAtoms | self.mols1.allAtoms
selString = sidechain.stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
self.assertEquals(selected, sidechain)
self.assertEquals(selected, self.mols2.allAtoms[67:73])
self.assertEquals(selString, selected.stringRepr)
def test_select_get_from_get_result(self):
"""
test selecting w/stringRepr of get from the result of a get
"""
stringSel = CompoundStringSelector()
m = self.mols2
cats = m.allAtoms.get('C.?')
cbats = cats.get('CB')
expectedString = "((protease:::\\s\\C.?)\\s\\CB)"
selString = cbats.stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
#selected, msg = stringSel.select(self.mols, selString)
self.assertEquals(selected, cbats)
self.assertEquals(selString, expectedString)
self.assertEquals(selected.stringRepr, expectedString)
def test_select_get_from_get_result(self):
"""
test selecting w/stringRepr of get from the result of a get
"""
stringSel = CompoundStringSelector()
m = self.mols2
cats = m.allAtoms.get('C.?')
cbats = cats.get('CB')
expectedString = "((protease:::\\s\\C.?)\\s\\CB)"
selString = cbats.stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
#selected, msg = stringSel.select(self.mols, selString)
self.assertEquals(selected, cbats)
self.assertEquals(selString, expectedString)
self.assertEquals(selected.stringRepr, expectedString)
def test_select_complicated_sidechain_atoms(self):
"""
test selecting w/stringRepr of complicated sidechain atoms(bug 672)
ARG8 atoms excluding backbone atoms and CB atoms
"""
stringSel = CompoundStringSelector()
#arg is ARG8 in chain A
arg = self.mols2.chains.residues[7]
sidechain = arg.atoms-arg.atoms.get('backbone')-arg.atoms.get('CB')
#diff_atoms = self.mols1.allAtoms | self.mols1.allAtoms
selString = sidechain.stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
self.assertEquals(selected, sidechain)
self.assertEquals(selected, self.mols2.allAtoms[67:73])
self.assertEquals(selString, 'protease:A:ARG8:/-/(protease:A:ARG8:\\s\\backbone)/-/(protease:A:ARG8:\\s\\CB)')
self.assertEquals(selString, selected.stringRepr)
def expandNodes(self, nodes):
"""Takes nodes as string or TreeNode or TreeNodeSet and returns
a TreeNodeSet
If nodes is a string it can contain a series of set descriptors with operators
separated by / characters. There is always a first set, followed by pairs of
operators and sets. All sets ahve to describe nodes of the same level.
example:
'1crn:::CA*/+/1crn:::O*' describes the union of all CA ans all O in 1crn
'1crn:::CA*/+/1crn:::O*/-/1crn::TYR29:'
"""
if isinstance(nodes,TreeNode):
result = nodes.setClass([nodes])
result.setStringRepr(nodes.full_name())
elif type(nodes)==StringType:
stringRepr = nodes
css = CompoundStringSelector()
result = css.select(self.Mols, stringRepr)[0]
## setsStrings = stringRepr.split('/')
## getSet = self.Mols.NodesFromName
## result = getSet(setsStrings[0])
## for i in range(1, len(setsStrings), 2):
## op = setsStrings[i]
## arg = setsStrings[i+1]
## if op=='|': # or
## result += getSet(arg)
## elif op=='-': # subtract
## result -= getSet(arg)
## elif op=='&': # intersection
## result &= getSet(arg)
## elif op=='^': # xor
## result ^= getSet(arg)
## elif op=='s': # sub select (i.e. select from previous result)
## result = result.get(arg)
## else:
## raise ValueError, '%s bad operation in selection string'%op
## result.setStringRepr(stringRepr)
elif isinstance(nodes,TreeNodeSet):
result = nodes
else:
raise ValueError, 'Could not expand nodes %s\n'%str(nodes)
return result
def test_select_complicated_sidechain_atoms(self):
"""
test selecting w/stringRepr of complicated sidechain atoms(bug 672)
ARG8 atoms excluding backbone atoms and CB atoms
"""
stringSel = CompoundStringSelector()
#arg is ARG8 in chain A
arg = self.mols2.chains.residues[7]
sidechain = arg.atoms - arg.atoms.get('backbone') - arg.atoms.get('CB')
#diff_atoms = self.mols1.allAtoms | self.mols1.allAtoms
selString = sidechain.stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
self.assertEquals(selected, sidechain)
self.assertEquals(selected, self.mols2.allAtoms[67:73])
self.assertEquals(
selString,
'protease:A:ARG8:/-/(protease:A:ARG8:\\s\\backbone)/-/(protease:A:ARG8:\\s\\CB)'
)
self.assertEquals(selString, selected.stringRepr)
def test_select_complicated_sidechain_atoms3(self):
"""
test selecting w/stringRepr of complicated sidechain atoms
-> carbon atoms in sidechains of ARG residues in protease except CB atoms
"""
stringSel = CompoundStringSelector()
#arg is ARG8 in chain A
args = self.mols2.chains.residues.get('ARG*')
sidechains = args.atoms.get('sidechain')
sc_carbons = sidechains.get('C*')
#sc_carbons = sidechains.get('C.?')
target = sc_carbons - args.atoms.get('CB')
selString = target.stringRepr
#check that built set has expected stringRepr
targetStr = '(((protease::\\s\\ARG*):\\s\\sidechain)\\s\\C*)/-/((protease::\\s\\ARG*):\\s\\CB)'
self.assertEquals(selString, targetStr)
# try to get same atoms by selecting using built set's stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
#sanity check that 24 atoms are found
self.assertEquals(len(selected), 24)
#check that the same atoms are found
self.assertEquals(selected, target)
#check that selected set has expected stringRepr
self.assertEquals(targetStr, selected.stringRepr)
def test_select_complicated_sidechain_atoms3(self):
"""
test selecting w/stringRepr of complicated sidechain atoms
-> carbon atoms in sidechains of ARG residues in protease except CB atoms
"""
stringSel = CompoundStringSelector()
#arg is ARG8 in chain A
args = self.mols2.chains.residues.get('ARG*')
sidechains = args.atoms.get('sidechain')
sc_carbons = sidechains.get('C*')
#sc_carbons = sidechains.get('C.?')
target = sc_carbons - args.atoms.get('CB')
selString = target.stringRepr
#check that built set has expected stringRepr
targetStr = '(((protease::\\s\\ARG*):\\s\\sidechain)\\s\\C*)/-/((protease::\\s\\ARG*):\\s\\CB)'
self.assertEquals(selString, targetStr)
# try to get same atoms by selecting using built set's stringRepr
selected, msg = stringSel.select(self.mols, selString, returnMsg=True)
#sanity check that 24 atoms are found
self.assertEquals(len(selected), 24)
#check that the same atoms are found
self.assertEquals(selected, target)
#check that selected set has expected stringRepr
self.assertEquals(targetStr, selected.stringRepr)
class TreeViewWithCheckbuttons(TreeView, KeySelectable):
"""Tree Widget class
A TreeWiget contains tree nodes (object of Class Node).
Each node can have children. Nodes that do have children can be expanded
and collapsed using the + - icon placed before de nodes' icon. Each no has an
icon and a name. It is possible to associate an arbitrary Python object to each
node. The node in the tree is the graphical representation of the object.
"""
def __init__(self, master=None, name='Tree', multi_choice=False,
width=800, height=200, treeWidth=140, treeHeight=100,
historyWidth=100, historyHeight=100, mode='Extended',
historyVisible=False,nohistory=False,
mouseBinding=None,obj2Node=True, displayValue=False,
offx=0, offy=0):
TreeView. __init__(self, master=master, name=name,
multi_choice=multi_choice,
width=width, height=height,
treeWidth=treeWidth, treeHeight=treeHeight,
historyWidth=historyWidth,
historyHeight=historyHeight,
mode=mode, historyVisible=historyVisible,
nohistory=nohistory,
mouseBinding=mouseBinding, obj2Node=obj2Node,
displayValue=displayValue,
offx=offx, offy=offy, canvasHeaderCol=True)
KeySelectable.__init__(self, self.canvas)
# assign method that need to be overriden
self.match = self.findFirstMatchNodeFromName
self.selectItem = self.showNode
self.ctrlModCallback = self.handleControlKey
self.sets = None # used to save pmv.sets so that the selector can
# use it to allow selecting sets
self.balloons = Pmw.Balloon(master, yoffset=0)
self.inChain = False # true when calling chained commands.
# used to prevent calling chained or chained
nbcol = self.nbColumns = 15
#nbcol += 10
self.callbacks = [None]*nbcol
# will be the list of call backs associated with
# columns of checkbuttons
self.names = [None]*nbcol
# will be the list of names associated with
# columns of checkbuttons
self.colHeaderButtons = [None]*nbcol
self.colHeaderTkVars = [None]*nbcol
self.colOptionPanels = [None]*nbcol
self.pmvcmd = [None]*nbcol
self.chainWith = [None]*nbcol
for i in range(nbcol):
self.chainWith[i] = [None]*nbcol
self.balloonText = ['No Help']*nbcol
self.buttonValFunc = [None]*nbcol # function for getting the current values
# force molecule visible when selecting, displaying or labeling
# parts of molecules
for i in range(1,9): # chains command 0 after command 1 through 9
# 'Checked': call 0 when command 1 is checked
# 'True': always check the button of the chained command
# 'All': apply to the whole moelcular fragment
self.chainWith[i][0] = ('Checked', 'True', 'All')
# make display lines, S&B and CPK mutually exclusive
for i in range(2,5):
for j in range(2,5):
if i==j: continue
self.chainWith[i][j] = ('Checked','False','All')
# make color commands (9-14) radio
for i in range(9,15):
for j in range(9,15):
if i==j: continue
self.chainWith[i][j] = ('Checked','False','All')
self.bbmode = ['All']*nbcol
self.colHeaderTkVars = [None]*nbcol # list of button in the header
from mglutil.util.packageFilePath import findFilePath
self.ICONPATH = os.path.abspath(findFilePath('Icons', 'Pmv'))
self.ICONDIR = os.path.join(self.ICONPATH, '32x32')
self.iconList = [None]*nbcol # save references to icon images to
# prevent them from being garbage collected
# add the backbone menu option
self.bbmodevar = Tkinter.StringVar()
self.bbmodevar.set("Cmd setting")
self.bbmode_menu = Pmw.OptionMenu(
self.master, labelpos = 'w', label_text = 'Protein:',
menubutton_textvariable = self.bbmodevar,
items = ['Cmd setting', 'Backbone', 'Sidechain',
'Sidechains+CA', 'All'],
menubutton_width = 8
)
cid = self.canvasHeaderCol.create_window(
10, 15, window=self.bbmode_menu, anchor='w')
self.proteinHelp = """This option menu allows to specify for peptidic molecular fragments
whether the command should be applied to the backbone atoms only,
the side chain atoms only, the sidechain atoms and CA atoms or the
full molecular frament."""
self.balloons.bind(self.bbmode_menu, self.proteinHelp)
# add a compound selector entry
self.selectorEntry = Pmw.EntryField(
self.master, labelpos = 'w', label_text = 'Select: ',
entry_width=12, validate = None, command=self.selectFromString)
cid = self.canvasHeaderCol.create_window(
10, 40, window=self.selectorEntry, anchor='w')
self.selectorHelp = """This entry allows selecting enties in the Tree using a Pmv compound selector.
Only expanded nodes will be selected. Selected nodes are outlined with a
yellow selection box. When a button is checked for a selected node, the
command is applied to all selecte nodes.
The syntax for a compound selector is a ; separated list of expressions.
Each expression is a : separated list of selectors applying at the various
levels of the tree.
for instance:
:::CA selects all carbon alpha atoms
:A::CA selects all CA in chain A
::CYS* selects all cysteins"""
self.balloons.bind(self.selectorEntry, self.selectorHelp)
from MolKit.stringSelector import CompoundStringSelector
self.selector = CompoundStringSelector()
def handleControlKey(self, event):
if event.keysym in ['z', 'Z']:
self.undoSelect()
def colHasButtton(self, column, klass):
"""returns True if a given column has check buttons for a given klass
"""
if column==0:
if klass not in [Molecule, Protein, MoleculeSet, ProteinSet]:
return False
return True
def findFirstMatchNodeFromName(self, name):
"""walks the tree and find the first node whose fullname
matches name"""
pat = re.compile('.*'+name.lower()+'.*')
for root in self.roots:
n = root._matchName(pat)
if n:
return n
return None
def selectFromString(self):
value = self.selectorEntry.getvalue()
allMols = self.roots[0].objectKey
molFrag = self.selector.select(allMols, value, self.sets)
self.selectNodes(molFrag[0])
def setCallback(self, column, pmvcmd, iconName=None, balloonText=None,
name='command', function=None, bValFunc=None):
"""define a callback for the checkbuttons in a given column.
pmvcmd is the Pmv command to run in the callback associated with the
checkbuttons and used to get default values using the 'default form.
name is a string describing the command in that column, defaults to cmd.name
iconName is the name of the icon to be used for the button
balloonText is the tooltip, defaults to name.
function is an option callback to override the default callback.
It gets called with (node, column, pmvcmd)
"""
assert column<1000
def callback(node, column):
# default call back
# search for button because some commands do not have
# buttons at all levels
while node and not node.chkbt[column]:
node = node.parent
if node is None: return
# get Pmv's command default arguments
pmvcmd = node.tree.pmvcmd[column]
defaultValues = pmvcmd.getLastUsedValues()
# handle negate key to reflect state of checkbutton
val = node.chkbtVar[column].get()
if defaultValues.has_key('negate'):
defaultValues['negate'] = not val
defaultValues['callListener'] = False
# apply the command at each level of the current selection
for obj in node.getObjects(column):
apply( pmvcmd, (obj,), defaultValues)
if pmvcmd.lastUsedValues['default'].has_key('callListener'):
del pmvcmd.lastUsedValues['default']['callListener']
if function is None:
function = callback
self.callbacks[column] = function
self.buttonValFunc[column] = bValFunc
if name is None:
if hasattr(function, 'name'):
name = function.name
self.names[column] = name
self.pmvcmd[column] = pmvcmd
if balloonText is None:
balloonText = name
self.balloonText[column] = balloonText
if iconName:
iconfile = os.path.join(self.ICONDIR, iconName)
image = Image.open(iconfile)
im = ImageTk.PhotoImage(image=image, master=self.master)
self.iconList[column] = im
v = Tkinter.IntVar()
cb = CallbackFunction(self.editColumn, column)
button = Tkinter.Checkbutton(
self.master, variable=v, command=cb, height=32, width=32,
indicatoron=0, image=im)
self.colHeaderButtons[column] = button
self.colHeaderTkVars[column] = v
cid = self.canvasHeaderCol.create_window(
20 + self.offx + 175 + column*35, 32, window=button,
width=40, height=40, anchor='center')
self.balloons.bind(button, self.balloonText[column])
else:
cid = self.canvasHeaderCol.create_text(
20 + self.offx + 175 + column*35, 5, text=name, anchor='n')
def editColumn(self, column):
if self.colHeaderTkVars[column].get()==0: # editor is shown
self.colOptionPanels[column].hide()
else:
if self.colOptionPanels[column]:
self.colOptionPanels[column].show()
else:
self.colOptionPanels[column] = CPCommandEditor(column, self)
def initCallback(self, node, column):
self.manageChildren(node, column)
def manageChildren(self, node, column):
# sets the checkbutton of all children to value of parent
if len(node.children)==0:
return
val = node.chkbtVar[column].get()
for c in node.children:
c.chkbtVar[column].set(val)
self.manageChildren(c, column)
def chainCommands(self, node, column):
if self.inChain is True:
return
self.inChain = True
buttonValue = node.chkbtVar[column].get()
chainWith = self.chainWith[column]
for col in range(self.nbColumns):
# find out with what argument this col's command should be called
val = chainWith[col]
if val is None: continue
run, arg, prot = val
if run=='Checked' and not buttonValue: continue
if run=='Unchecked' and buttonValue: continue
if arg=='Same': value = buttonValue
elif arg=='Opposite': value= not buttonValue
elif arg=='True': value= 1
elif arg=='False': value= 0
# temporarly overwrite protin mode
bbmode = self.bbmodevar
oldbbmode = bbmode.get()
bbmode.set(prot)
#print 'col', col, 'run', run, 'arg', arg, 'prot', prot
if node.selected:
for n in self.list_selected:
while n and not n.chkbt[col]:
n = n.parent
if n:
n.chkbtVar[col].set(value)
if n:
self.callbacks[col](n, col)
self.manageChildren(n, col)
else:
n = node
while n and not n.chkbt[col]:
n = n.parent
if n:
n.chkbtVar[col].set(value)
self.callbacks[col](n, col)
self.manageChildren(n, col)
# restore bbmode
bbmode.set(oldbbmode)
def addNodeTree(self, obj):
"""recursively add a nodes for a hierarchy of objects rooted at obj
"""
node = self.addNode(obj.name, object=obj, parent=obj.parent,
hasChildren=len(obj.children),
nodeClass=NodeWithCheckbuttons)
node.createTkVar(self.nbColumns)
for child in obj.children:
self.addNodeTree(child)
def test_constructor(self):
"""
instantiate a StringSelector
"""
stringSel = CompoundStringSelector()
self.assertEquals(stringSel.__class__, CompoundStringSelector)
for residue in res:
all_res += res
if verbose: print(" added ", res.name, " to ", all_res)
else:
print("WARNING: no residue named " + n)
else:
# '1JFF_protein:A:THR179_GLU183,1JFF_protein:B:TRP21_ARG64_LEU275'
chainStart = res_names_by_chain.index(':') + 1
molName = res_names_by_chain[:chainStart - 1]
#if verbose: print "molName = ", molName, " chainStart=", chainStart
n = res_names_by_chain[chainStart:].replace("_", ",")
#if verbose: print "after comma replaced '_', n is ", n, '\n'
selStr = molName + ":" + n
#if verbose: print "now selStr", selStr
#eg: 'hsg1:A:ARG8,ILE82'
result, msg = CompoundStringSelector().select(
ProteinSet([rec]), selStr)
if verbose:
print("prepare_flexreceptor4 line 157: result=", result)
if result.__class__ != ResidueSet:
print(residues_to_move,
" is not a ResidueSet instead it is a ",
result.__class__)
#if verbose: print selStr, " selection =", res, " msg=", msg, '\n'
resS = ResidueSet()
if result.__class__ == AtomSet:
resS = result.parent.uniq()
else:
resS = result
if len(resS):
all_res += resS
else:
l = Read(ligand_filename)[0]
l.buildBondsByDistance()
if verbose: print 'read ', ligand_filename
r = Read(receptor_filename)[0]
r.buildBondsByDistance()
if verbose: print 'read ', receptor_filename
all_res = ResidueSet()
res_names = residues_to_move.split('_')
for n in res_names:
if n.find(':') == -1:
res = r.chains.residues.get(lambda x: x.name == n)
all_res += res
if verbose: print "get: adding ", res.name, " to ", all_res
else:
res, msg = CompoundStringSelector().select(ProteinSet([r]), n)
all_res += res
if verbose: print "css: adding ", res.name, " to ", all_res
if verbose:
print "all_res=", all_res.full_name(
), 'all_res.__class__=', all_res.__class__
#?check for duplicates
d = {}
for res in all_res:
d[res] = 1
all_res = d.keys()
all_res = ResidueSet(all_res)
#inactivate specified bonds
#disallowed_Pairs "CA_CB:CB_CG:C_CA"
all_bnds = BondSet()
msg = 'invalid vina_result filename: ' + vina_result + " not found"
assert os.path.exists(vina_result), msg
ligs = Read(vina_result, "conformations")
msg = vina_result + " contains no valid molecules"
assert len(ligs), msg
lig = ligs[0]
#determine the receptor molecule to read in
rec_file = ratom_name.split(":")[0] + ".pdbqt"
msg = rec_file + " file not found"
assert os.path.exists(rec_file), msg
recs = Read(rec_file)
msg = rec_file + " contains no valid molecules"
assert len(recs), msg
rec = recs[0]
# locate the receptor atom
css = CompoundStringSelector()
rec_ats = css.select(recs, ratom_name)[0]
msg = ratom_name + " did not match exactly 1 atom in " + rec_file
assert len(rec_ats)==1, msg
rec_at = rec_ats[0]
rec_at_coords = rec_at.coords
if verbose:
print("found rec_at = ", rec_at.full_name(), end=' ')
print("with initial coords = ", rec_at.coords)
# locate the ligand atom
lig_ats = css.select(ligs, latom_name)[0]
msg = latom_name + " did not match exactly 1 atom in " + ligs[0].name
assert len(lig_ats)==1, msg
lig_at = lig_ats[0]
if verbose:
print("found lig_at =>", lig_at.full_name())
def __init__(self, master=None, name='Tree', multi_choice=False,
width=800, height=200, treeWidth=140, treeHeight=100,
historyWidth=100, historyHeight=100, mode='Extended',
historyVisible=False,nohistory=False,
mouseBinding=None,obj2Node=True, displayValue=False,
offx=0, offy=0):
TreeView. __init__(self, master=master, name=name,
multi_choice=multi_choice,
width=width, height=height,
treeWidth=treeWidth, treeHeight=treeHeight,
historyWidth=historyWidth,
historyHeight=historyHeight,
mode=mode, historyVisible=historyVisible,
nohistory=nohistory,
mouseBinding=mouseBinding, obj2Node=obj2Node,
displayValue=displayValue,
offx=offx, offy=offy, canvasHeaderCol=True)
KeySelectable.__init__(self, self.canvas)
# assign method that need to be overriden
self.match = self.findFirstMatchNodeFromName
self.selectItem = self.showNode
self.ctrlModCallback = self.handleControlKey
self.sets = None # used to save pmv.sets so that the selector can
# use it to allow selecting sets
self.balloons = Pmw.Balloon(master, yoffset=0)
self.inChain = False # true when calling chained commands.
# used to prevent calling chained or chained
nbcol = self.nbColumns = 15
#nbcol += 10
self.callbacks = [None]*nbcol
# will be the list of call backs associated with
# columns of checkbuttons
self.names = [None]*nbcol
# will be the list of names associated with
# columns of checkbuttons
self.colHeaderButtons = [None]*nbcol
self.colHeaderTkVars = [None]*nbcol
self.colOptionPanels = [None]*nbcol
self.pmvcmd = [None]*nbcol
self.chainWith = [None]*nbcol
for i in range(nbcol):
self.chainWith[i] = [None]*nbcol
self.balloonText = ['No Help']*nbcol
self.buttonValFunc = [None]*nbcol # function for getting the current values
# force molecule visible when selecting, displaying or labeling
# parts of molecules
for i in range(1,9): # chains command 0 after command 1 through 9
# 'Checked': call 0 when command 1 is checked
# 'True': always check the button of the chained command
# 'All': apply to the whole moelcular fragment
self.chainWith[i][0] = ('Checked', 'True', 'All')
# make display lines, S&B and CPK mutually exclusive
for i in range(2,5):
for j in range(2,5):
if i==j: continue
self.chainWith[i][j] = ('Checked','False','All')
# make color commands (9-14) radio
for i in range(9,15):
for j in range(9,15):
if i==j: continue
self.chainWith[i][j] = ('Checked','False','All')
self.bbmode = ['All']*nbcol
self.colHeaderTkVars = [None]*nbcol # list of button in the header
from mglutil.util.packageFilePath import findFilePath
self.ICONPATH = os.path.abspath(findFilePath('Icons', 'Pmv'))
self.ICONDIR = os.path.join(self.ICONPATH, '32x32')
self.iconList = [None]*nbcol # save references to icon images to
# prevent them from being garbage collected
# add the backbone menu option
self.bbmodevar = Tkinter.StringVar()
self.bbmodevar.set("Cmd setting")
self.bbmode_menu = Pmw.OptionMenu(
self.master, labelpos = 'w', label_text = 'Protein:',
menubutton_textvariable = self.bbmodevar,
items = ['Cmd setting', 'Backbone', 'Sidechain',
'Sidechains+CA', 'All'],
menubutton_width = 8
)
cid = self.canvasHeaderCol.create_window(
10, 15, window=self.bbmode_menu, anchor='w')
self.proteinHelp = """This option menu allows to specify for peptidic molecular fragments
whether the command should be applied to the backbone atoms only,
the side chain atoms only, the sidechain atoms and CA atoms or the
full molecular frament."""
self.balloons.bind(self.bbmode_menu, self.proteinHelp)
# add a compound selector entry
self.selectorEntry = Pmw.EntryField(
self.master, labelpos = 'w', label_text = 'Select: ',
entry_width=12, validate = None, command=self.selectFromString)
cid = self.canvasHeaderCol.create_window(
10, 40, window=self.selectorEntry, anchor='w')
self.selectorHelp = """This entry allows selecting enties in the Tree using a Pmv compound selector.
Only expanded nodes will be selected. Selected nodes are outlined with a
yellow selection box. When a button is checked for a selected node, the
command is applied to all selecte nodes.
The syntax for a compound selector is a ; separated list of expressions.
Each expression is a : separated list of selectors applying at the various
levels of the tree.
for instance:
:::CA selects all carbon alpha atoms
:A::CA selects all CA in chain A
::CYS* selects all cysteins"""
self.balloons.bind(self.selectorEntry, self.selectorHelp)
from MolKit.stringSelector import CompoundStringSelector
self.selector = CompoundStringSelector()