def test_bool():
sp = parse_selection("protein or water")
eq(sp.source, "(atom.residue.is_protein or atom.residue.is_water)\n")
sp = parse_selection("protein or water or all\n")
eq(sp.source,
"(atom.residue.is_protein or atom.residue.is_water or True)\n")
def test_bool():
sp = parse_selection("protein or water")
eq(sp.source, "(atom.residue.is_protein or atom.residue.is_water)")
sp = parse_selection("protein or water or all")
eq(sp.source,
"(atom.residue.is_protein or atom.residue.is_water or True)")
def test_unary_2():
sp = parse_selection('all')
for a in tt.atoms:
assert sp.expr(a)
sp = parse_selection('none')
for a in tt.atoms:
assert not sp.expr(a)
def test_unary_2():
sp = parse_selection('all')
for a in tt.atoms:
assert sp.expr(a)
sp = parse_selection('none')
for a in tt.atoms:
assert not sp.expr(a)
def test_nested_bool():
sp = parse_selection("nothing and water or all")
eq(sp.source,
"((False and atom.residue.is_water) or True)")
sp = parse_selection("nothing and (water or all)")
eq(sp.source,
"(False and (atom.residue.is_water or True))")
def test_nested_bool():
sp = parse_selection("nothing and water or all")
eq(sp.source,
"((False and atom.residue.is_water) or True)")
sp = parse_selection("nothing and (water or all)")
eq(sp.source,
"(False and (atom.residue.is_water or True))")
def test_not():
sp = parse_selection("not protein")
eq(sp.source, "(not atom.residue.is_protein)")
sp = parse_selection("not not protein")
eq(sp.source, "(not (not atom.residue.is_protein))")
sp = parse_selection('!protein')
eq(sp.source, "(not atom.residue.is_protein)")
def test_range():
eq(parse_selection('resSeq 1 to 10').astnode, pnode('1 <= atom.residue.resSeq <= 10'))
sp = parse_selection('resSeq 5 to 6')
for a in tt.atoms:
assert sp.expr(a)
sp = parse_selection('resSeq 7 to 8')
for a in tt.atoms:
assert not sp.expr(a)
def test_not():
sp = parse_selection("not protein")
eq(sp.source, "(not atom.residue.is_protein)\n")
sp = parse_selection("not not protein")
eq(sp.source, "(not (not atom.residue.is_protein))\n")
sp = parse_selection('!protein')
eq(sp.source, "(not atom.residue.is_protein)\n")
def test_range():
eq(parse_selection('resSeq 1 to 10').astnode, pnode('1 <= atom.residue.resSeq <= 10'))
sp = parse_selection('resSeq 5 to 6')
for a in tt.atoms:
assert sp.expr(a)
sp = parse_selection('resSeq 7 to 8')
for a in tt.atoms:
assert not sp.expr(a)
def test_values():
sp = parse_selection("resid 4")
eq(sp.source, "(atom.residue.index == 4)")
sp = parse_selection("resid > 4")
eq(sp.source, "(atom.residue.index > 4)")
sp = parse_selection("resid gt 4")
eq(sp.source, "(atom.residue.index > 4)")
sp = parse_selection("resid 5 to 8")
eq(sp.source, "(5 <= atom.residue.index <= 8)")
def test_binary_1():
sp = parse_selection('resname "ALA"')
assert sp.expr(tt.atom(0))
assert sp.expr(tt.atom(1))
sp = parse_selection('mass > 2')
assert sp.expr(tt.atom(0))
assert not sp.expr(tt.atom(1))
assert sp.expr(tt.atom(2))
sp = parse_selection('name ne O')
assert sp.expr(tt.atom(0))
assert not sp.expr(tt.atom(2))
def test_binary_1():
sp = parse_selection('resname "ALA"')
assert sp.expr(tt.atom(0))
assert sp.expr(tt.atom(1))
sp = parse_selection('mass > 2')
assert sp.expr(tt.atom(0))
assert not sp.expr(tt.atom(1))
assert sp.expr(tt.atom(2))
sp = parse_selection('name ne O')
assert sp.expr(tt.atom(0))
assert not sp.expr(tt.atom(2))
def test_quotes():
should_be = "((atom.name == 'CA') and (atom.residue.name == 'ALA'))\n"
sp = parse_selection("name CA and resname ALA")
eq(sp.source, should_be)
assert sp.expr(tt.atom(0))
sp = parse_selection('name "CA" and resname ALA')
eq(sp.source, should_be)
assert sp.expr(tt.atom(0))
sp = parse_selection("name 'CA' and resname ALA")
eq(sp.source, should_be)
assert sp.expr(tt.atom(0))
def test_quotes():
should_be = "((atom.name == 'CA') and (atom.residue.name == 'ALA'))"
sp = parse_selection("name CA and resname ALA")
eq(sp.source, should_be)
assert sp.expr(tt.atom(0))
sp = parse_selection('name "CA" and resname ALA')
eq(sp.source, should_be)
assert sp.expr(tt.atom(0))
sp = parse_selection("name 'CA' and resname ALA")
eq(sp.source, should_be)
assert sp.expr(tt.atom(0))
def test_values():
sp = parse_selection("resid 4")
eq(sp.source, "(atom.residue.index == 4)\n")
sp = parse_selection("chainid 4")
eq(sp.source, "(atom.residue.chain.index == 4)\n")
sp = parse_selection("resid > 4")
eq(sp.source, "(atom.residue.index > 4)\n")
sp = parse_selection("resid gt 4")
eq(sp.source, "(atom.residue.index > 4)\n")
sp = parse_selection("resid 5 to 8")
eq(sp.source, "(5 <= atom.residue.index <= 8)\n")
def test_unary_1():
eq(parse_selection('all').astnode, pnode('True'))
eq(parse_selection('everything').astnode, pnode('True'))
eq(parse_selection('none').astnode, pnode('False'))
eq(parse_selection('nothing').astnode, pnode('False'))
# eq(parse_selection('nucleic').astnode, pnode('atom.residue.is_nucleic'))
# eq(parse_selection('is_nucleic').astnode, pnode('atom.residue.is_nucleic'))
eq(parse_selection('protein').astnode, pnode('atom.residue.is_protein'))
eq(parse_selection('is_protein').astnode, pnode('atom.residue.is_protein'))
eq(parse_selection('water').astnode, pnode('atom.residue.is_water'))
eq(parse_selection('is_water').astnode, pnode('atom.residue.is_water'))
eq(parse_selection('waters').astnode, pnode('atom.residue.is_water'))
def test_unary_1():
eq(parse_selection('all').astnode, pnode('True'))
eq(parse_selection('everything').astnode, pnode('True'))
eq(parse_selection('none').astnode, pnode('False'))
eq(parse_selection('nothing').astnode, pnode('False'))
# eq(parse_selection('nucleic').astnode, pnode('atom.residue.is_nucleic'))
# eq(parse_selection('is_nucleic').astnode, pnode('atom.residue.is_nucleic'))
eq(parse_selection('protein').astnode, pnode('atom.residue.is_protein'))
eq(parse_selection('is_protein').astnode, pnode('atom.residue.is_protein'))
eq(parse_selection('water').astnode, pnode('atom.residue.is_water'))
eq(parse_selection('is_water').astnode, pnode('atom.residue.is_water'))
eq(parse_selection('waters').astnode, pnode('atom.residue.is_water'))
def select(self, selection_string):
"""Execute a selection against the topology
Parameters
----------
selection_string : str
An expression in the MDTraj atom selection DSL
Examples
--------
>>> topology.select('name O and water')
array([1, 3, 5, 10, ...])
Returns
-------
indices : np.ndarray, dtype=int, ndim=1
Array of the indices of the atoms matching the selection expression.
See Also
--------
select_expression, mdtraj.core.selection.parse_selection
"""
filter_func = parse_selection(selection_string).expr
indices = np.array([a.index for a in self.atoms if filter_func(a)])
return indices
def select(self, selection_string):
"""Execute a selection against the topology
Parameters
----------
selection_string : str
An expression in the MDTraj atom selection DSL
Examples
--------
>>> topology.select('name O and water')
array([1, 3, 5, 10, ...])
Returns
-------
indices : np.ndarray, dtype=int, ndim=1
Array of the indices of the atoms matching the selection expression.
See Also
--------
select_expression, mdtraj.core.selection.parse_selection
"""
filter_func = parse_selection(selection_string).expr
indices = np.array([a.index for a in self.atoms if filter_func(a)])
return indices
def test_unary_3():
sp = parse_selection('protein or water')
for a in tt.atoms:
assert sp.expr(a)
sp = parse_selection('protein and water')
for a in tt.atoms:
assert not sp.expr(a)
sp = parse_selection('not (protein and water)')
for a in tt.atoms:
assert sp.expr(a)
sp = parse_selection('not not (protein and water)')
for a in tt.atoms:
assert not sp.expr(a)
def test_unary_3():
sp = parse_selection('protein or water')
for a in tt.atoms:
assert sp.expr(a)
sp = parse_selection('protein and water')
for a in tt.atoms:
assert not sp.expr(a)
sp = parse_selection('not (protein and water)')
for a in tt.atoms:
assert sp.expr(a)
sp = parse_selection('not not (protein and water)')
for a in tt.atoms:
assert not sp.expr(a)
def test_raises2():
pytest.raises(ValueError, lambda: parse_selection('dog 5'))
pytest.raises(ValueError, lambda: parse_selection('dog == 5'))
pytest.raises(ValueError, lambda: parse_selection('dog frog'))
pytest.raises(ValueError, lambda: parse_selection('not dog'))
pytest.raises(ValueError, lambda: parse_selection('protein or dog'))
pytest.raises(ValueError, lambda: parse_selection('dog 1 to 5'))
pytest.raises(ValueError, lambda: parse_selection('dog'))
def test_raises2():
pytest.raises(ValueError, lambda: parse_selection('dog 5'))
pytest.raises(ValueError, lambda: parse_selection('dog == 5'))
pytest.raises(ValueError, lambda: parse_selection('dog frog'))
pytest.raises(ValueError, lambda: parse_selection('not dog'))
pytest.raises(ValueError, lambda: parse_selection('protein or dog'))
pytest.raises(ValueError, lambda: parse_selection('dog 1 to 5'))
pytest.raises(ValueError, lambda: parse_selection('dog'))
def select_expression(self, selection_string):
"""Translate a atom selection expression into a pure python expression.
Parameters
----------
selection_string : str
An expression in the MDTraj atom selection DSL
Examples
--------
>>> topology.select_expression('name O and water')
"[atom.index for atom in topology.atoms if ((atom.name == 'O') and atom.residue.is_water)]")
Returns
-------
python_string : str
A string containing a pure python expression, equivalent to the
selection expression.
"""
condition = parse_selection(selection_string).source
fmt_string = "[atom.index for atom in topology.atoms if {condition}]"
return fmt_string.format(condition=condition)
def select_expression(self, selection_string):
"""Translate a atom selection expression into a pure python expression.
Parameters
----------
selection_string : str
An expression in the MDTraj atom selection DSL
Examples
--------
>>> topology.select_expression('name O and water')
"[atom.index for atom in topology.atoms if ((atom.name == 'O') and atom.residue.is_water)]")
Returns
-------
python_string : str
A string containing a pure python expression, equivalent to the
selection expression.
"""
condition = parse_selection(selection_string).source
fmt_string = "[atom.index for atom in topology.atoms if {condition}]"
return fmt_string.format(condition=condition)
def test_binary_2():
sp = parse_selection('name O and mass > 2')
assert sp.expr(tt.atom(2))
assert not sp.expr(tt.atom(3))
def test_alias():
sp = parse_selection("waters")
eq(sp.source, "atom.residue.is_water\n")
assert sp.expr(tt.atom(3))
assert sp.expr(tt.atom(4))
assert not sp.expr(tt.atom(0))
def test_simple():
sp = parse_selection("protein")
eq(sp.source, "atom.residue.is_protein\n")
assert sp.expr(tt.atom(0))
assert sp.expr(tt.atom(1))
assert not sp.expr(tt.atom(2))
def test_binary_selection_operator():
eq(parse_selection('name < 1').astnode, pnode('atom.name < 1'))
eq(parse_selection('name lt 1').astnode, pnode('atom.name < 1'))
eq(parse_selection('name > 1').astnode, pnode('atom.name > 1'))
eq(parse_selection('name gt 1').astnode, pnode('atom.name > 1'))
eq(parse_selection('name == 1').astnode, pnode('atom.name == 1'))
eq(parse_selection('name eq 1').astnode, pnode('atom.name == 1'))
eq(parse_selection('name != 1').astnode, pnode('atom.name != 1'))
eq(parse_selection('name ne 1').astnode, pnode('atom.name != 1'))
eq(parse_selection('name >= 1').astnode, pnode('atom.name >= 1'))
eq(parse_selection('name ge 1').astnode, pnode('atom.name >= 1'))
eq(parse_selection('name <= 1').astnode, pnode('atom.name <= 1'))
eq(parse_selection('name le 1').astnode, pnode('atom.name <= 1'))
eq(parse_selection('1 == name').astnode, pnode('1 == atom.name'))
eq(parse_selection('1 eq name').astnode, pnode('1 == atom.name'))
def test_re():
sp = parse_selection("name =~ 'C.*'")
eq(sp.source, "(re.match('C.*', atom.name) is not None)")
sp = parse_selection("(name =~ 'C.*') and all")
eq(sp.source, "((re.match('C.*', atom.name) is not None) and True)")
def test_raises():
pytest.raises(ValueError, lambda: parse_selection('or'))
pytest.raises(ValueError, lambda: parse_selection('a <'))
def test_element():
sp = parse_selection("element 'O'")
eq(sp.source, "(atom.element.symbol == 'O')")
sp = parse_selection("mass 5.5 to 12.3")
eq(sp.astnode, pnode("(5.5 <= atom.element.mass <= 12.3)"))
def test_in():
sp = parse_selection("resname ALA ASP GLU")
eq(sp.source, "(atom.residue.name in ['ALA', 'ASP', 'GLU'])\n")
sp = parse_selection("resid 100 101 102")
eq(sp.source, "(atom.residue.index in [100, 101, 102])\n")
def test_in():
sp = parse_selection("resname ALA ASP GLU")
eq(sp.source, "(atom.residue.name in ['ALA', 'ASP', 'GLU'])")
sp = parse_selection("resid 100 101 102")
eq(sp.source, "(atom.residue.index in [100, 101, 102])")
def test_binary_2():
sp = parse_selection('name O and mass > 2')
assert sp.expr(tt.atom(2))
assert not sp.expr(tt.atom(3))
def test_binary_selection_operator():
eq(parse_selection('name < 1').astnode, pnode('atom.name < 1'))
eq(parse_selection('name lt 1').astnode, pnode('atom.name < 1'))
eq(parse_selection('name > 1').astnode, pnode('atom.name > 1'))
eq(parse_selection('name gt 1').astnode, pnode('atom.name > 1'))
eq(parse_selection('name == 1').astnode, pnode('atom.name == 1'))
eq(parse_selection('name eq 1').astnode, pnode('atom.name == 1'))
eq(parse_selection('name != 1').astnode, pnode('atom.name != 1'))
eq(parse_selection('name ne 1').astnode, pnode('atom.name != 1'))
eq(parse_selection('name >= 1').astnode, pnode('atom.name >= 1'))
eq(parse_selection('name ge 1').astnode, pnode('atom.name >= 1'))
eq(parse_selection('name <= 1').astnode, pnode('atom.name <= 1'))
eq(parse_selection('name le 1').astnode, pnode('atom.name <= 1'))
eq(parse_selection('1 == name').astnode, pnode('1 == atom.name'))
eq(parse_selection('1 eq name').astnode, pnode('1 == atom.name'))
def test_re():
sp = parse_selection("name =~ 'C.*'")
eq(sp.source, "(re.match('C.*', atom.name) is not None)\n")
sp = parse_selection("(name =~ 'C.*') and all")
eq(sp.source, "((re.match('C.*', atom.name) is not None) and True)\n")
def test_alias():
sp = parse_selection("waters")
eq(sp.source, "atom.residue.is_water")
assert sp.expr(tt.atom(3))
assert sp.expr(tt.atom(4))
assert not sp.expr(tt.atom(0))
def test_simple():
sp = parse_selection("protein")
eq(sp.source, "atom.residue.is_protein")
assert sp.expr(tt.atom(0))
assert sp.expr(tt.atom(1))
assert not sp.expr(tt.atom(2))
def test_raises():
assert_raises(ValueError, lambda: parse_selection('or'))
assert_raises(ValueError, lambda: parse_selection('a <'))
def test_element():
sp = parse_selection("element 'O'")
eq(sp.source, "(atom.element.symbol == 'O')\n")
sp = parse_selection("mass 5.5 to 12.3")
eq(sp.astnode, pnode("(5.5 <= atom.element.mass <= 12.3)"))
def test_raises():
pytest.raises(ValueError, lambda: parse_selection('or'))
pytest.raises(ValueError, lambda: parse_selection('a <'))
def test_raises():
assert_raises(ValueError, lambda: parse_selection('or'))
assert_raises(ValueError, lambda: parse_selection('a <'))
