def __getitem__(self, index):
acsi = self._acsi
if isinstance(index, int):
n_atoms = self._n_atoms
if index >= n_atoms or index < -n_atoms:
raise IndexError('index out of bounds')
return Atom(self, index if index >= 0 else n_atoms + index, acsi)
elif isinstance(index, slice):
start, stop, step = index.indices(self._n_atoms)
start = start or 0
index = np.arange(start, stop, step)
if len(index):
if start > stop:
index = index[::-1]
selstr = 'index {0}:{1}:{2}'.format(start, stop, step)
return Selection(self, index, selstr, acsi, unique=True)
elif isinstance(index, (list, np.ndarray)):
unique = np.unique(index)
if unique[0] < 0 or unique[-1] >= self._n_atoms:
raise IndexError('index out of range')
return Selection(self, unique, 'index ' + rangeString(index),
acsi, unique=True)
elif isinstance(index, (str, tuple)):
return self.getHierView()[index]
else:
raise TypeError('invalid index')
def iterFragments(atoms):
"""Yield fragments, connected subsets in *atoms*, as :class:`Selection`
instances."""
if not isinstance(atoms, Atomic):
raise TypeError('atoms must be an Atomic instance')
if isinstance(atoms, AtomGroup):
ag = atoms
atoms.iterFragments().next()
fragments = atoms._fragments
else:
ag = atoms.getAtomGroup()
bonds = atoms._iterBonds()
fids = zeros((len(ag)), int)
fdict = {}
c = 0
for a, b in bonds:
af = fids[a]
bf = fids[b]
if af and bf:
if af != bf:
frag = fdict[af]
temp = fdict[bf]
fids[temp] = af
frag.extend(temp)
fdict.pop(bf)
elif af:
fdict[af].append(b)
fids[b] = af
elif bf:
fdict[bf].append(a)
fids[a] = bf
else:
c += 1
fdict[c] = [a, b]
fids[a] = fids[b] = c
fragments = []
append = fragments.append
fidset = set()
indices = atoms._getIndices()
for i, fid in zip(indices, fids[indices]):
if fid in fidset:
continue
elif fid:
fidset.add(fid)
indices = fdict[fid]
indices.sort()
append(indices)
else:
# these are non-bonded atoms, e.g. ions
append([i])
acsi = atoms.getACSIndex()
for indices in fragments:
yield Selection(ag, indices, 'index ' + rangeString(indices), acsi,
unique=True)
def _iterFragments(atoms, ag, bonds):
fids = zeros((len(ag)), int)
fdict = {}
c = 0
for a, b in bonds:
af = fids[a]
bf = fids[b]
if af and bf:
if af != bf:
frag = fdict[af]
temp = fdict[bf]
fids[temp] = af
frag.extend(temp)
fdict.pop(bf)
elif af:
fdict[af].append(b)
fids[b] = af
elif bf:
fdict[bf].append(a)
fids[a] = bf
else:
c += 1
fdict[c] = [a, b]
fids[a] = fids[b] = c
fragments = []
append = fragments.append
fidset = set()
indices = atoms._getIndices()
for i, fid in zip(indices, fids[indices]):
if fid in fidset:
continue
elif fid:
fidset.add(fid)
indices = fdict[fid]
indices.sort()
append(indices)
else:
# these are non-bonded atoms, e.g. ions
append([i])
acsi = atoms.getACSIndex()
for indices in fragments:
yield Selection(ag,
indices,
'index ' + rangeString(indices),
acsi,
unique=True)
def __call__(self, radius, center):
"""Select atoms radius *radius* (Å) of *center*, which can be point(s)
in 3-d space (:class:`numpy.ndarray` with shape ``(n_atoms, 3)``) or a
set of atoms, e.g. :class:`.Selection`."""
try:
center = center._getCoords()
except AttributeError:
try:
ndim, shape = center.ndim, center.shape
except AttributeError:
raise TypeError('center must be an Atomic instance or a'
'coordinate array')
else:
if shape == (3, ):
center = [center]
elif not ndim == 2 and shape[1] == 3:
raise ValueError('center.shape must be (n_atoms, 3) or'
'(3,)')
else:
if center is None:
raise ValueError('center does not have coordinate data')
search = self._kdtree.search
get_indices = self._kdtree.getIndices
get_count = self._kdtree.getCount
indices = set()
update = indices.update
radius = float(radius)
for xyz in center:
search(radius, xyz)
if get_count():
update(get_indices())
indices = list(indices)
if indices:
indices.sort()
if self._ag is None:
return array(indices)
else:
if self._indices is not None:
indices = self._indices[indices]
return Selection(self._ag,
array(indices),
'index ' + rangeString(indices),
acsi=self._acsi,
unique=True)
def _iterFragments(atoms, ag, bonds):
fids = zeros((len(ag)), int)
fdict = {}
c = 0
for a, b in bonds:
af = fids[a]
bf = fids[b]
if af and bf:
if af != bf:
frag = fdict[af]
temp = fdict[bf]
fids[temp] = af
frag.extend(temp)
fdict.pop(bf)
elif af:
fdict[af].append(b)
fids[b] = af
elif bf:
fdict[bf].append(a)
fids[a] = bf
else:
c += 1
fdict[c] = [a, b]
fids[a] = fids[b] = c
fragments = []
append = fragments.append
fidset = set()
indices = atoms._getIndices()
for i, fid in zip(indices, fids[indices]):
if fid in fidset:
continue
elif fid:
fidset.add(fid)
indices = fdict[fid]
indices.sort()
append(indices)
else:
# these are non-bonded atoms, e.g. ions
append([i])
acsi = atoms.getACSIndex()
for indices in fragments:
yield Selection(ag, indices, 'index ' + rangeString(indices), acsi,
unique=True)
def __call__(self, radius, center):
"""Select atoms radius *radius* (Å) of *center*, which can be point(s)
in 3-d space (:class:`numpy.ndarray` with shape ``(n_atoms, 3)``) or a
set of atoms, e.g. :class:`.Selection`."""
try:
center = center._getCoords()
except AttributeError:
try:
ndim, shape = center.ndim, center.shape
except AttributeError:
raise TypeError('center must be an Atomic instance or a'
'coordinate array')
else:
if shape == (3,):
center = [center]
elif not ndim == 2 and shape[1] == 3:
raise ValueError('center.shape must be (n_atoms, 3) or'
'(3,)')
else:
if center is None:
raise ValueError('center does not have coordinate data')
search = self._kdtree.search
get_indices = self._kdtree.getIndices
get_count = self._kdtree.getCount
indices = set()
update = indices.update
radius = float(radius)
for xyz in center:
search(radius, xyz)
if get_count():
update(get_indices())
indices = list(indices)
if indices:
indices.sort()
if self._ag is None:
return array(indices)
else:
if self._indices is not None:
indices = self._indices[indices]
return Selection(self._ag, array(indices), 'index ' +
rangeString(indices), acsi=self._acsi,
unique=True)
def select(self, within, what):
"""Select atoms *within* of *what*. *within* is distance in Å and
*what* can be point(s) in 3-d space (:class:`~numpy.ndarray` with
shape N,3) or a set of atoms, i.e. :class:`~atomic.bases.Atomic`
instances."""
if isinstance(what, np.ndarray):
if what.ndim == 1 and len(what) == 3:
what = [what]
elif not (what.ndim == 2 and what.shape[1] == 3):
raise ValueError('*what* must be a coordinate array, '
'shape (N, 3) or (3,).')
else:
try:
what = what._getCoords()
except:
raise TypeError('*what* must have a getCoords() method.')
if not isinstance(what, np.ndarray):
raise ValueError('what.getCoords() method must '
'return a numpy.ndarray instance.')
search = self._kdtree.search
get_indices = self._kdtree.getIndices
get_count = self._kdtree.getCount
indices = set()
update = indices.update
within = float(within)
for xyz in what:
search(within, xyz)
if get_count():
update(get_indices())
indices = list(indices)
indices.sort()
if indices:
if self._indices is not None:
indices = self._indices[indices]
return Selection(self._ag, np.array(indices), 'index ' +
rangeString(indices), acsi=self._acsi, unique=True)
def testContinuous(self):
self.assertEqual(rangeString(list(range(10))), '0 to 9')
def getSelstr(self):
"""Return selection string that selects mapped atoms."""
return 'index ' + rangeString(self._indices)
def getSelstr(self):
"""Returns selection string that selects mapped atoms."""
return 'index ' + rangeString(self._indices)
def testRepeated(self):
self.assertEqual(
rangeString(
list(range(10, 20)) + list(range(15, 20)) + list(range(30))),
'0 to 29')
def testGapped(self):
self.assertEqual(
rangeString(list(range(-5, 10)) + list(range(15, 20)) +
list(range(25, 30)),
pos=False), '-5 to 9 15 to 19 25 to 29')
def testNegative(self):
self.assertEqual(rangeString(list(range(-5, 10)), pos=False),
'-5 to 9')
def testRepeated(self):
self.assertEqual(rangeString(list(range(10, 20)) +
list(range(15, 20)) +
list(range(30))), '0 to 29')
def testGapped(self):
self.assertEqual(rangeString(list(range(-5, 10)) +
list(range(15, 20)) +
list(range(25, 30)), pos=False),
'-5 to 9 15 to 19 25 to 29')
def testNegative(self):
self.assertEqual(rangeString(list(range(-5, 10)), pos=False),
'-5 to 9')
def testContinuous(self):
self.assertEqual(rangeString(list(range(10))), '0 to 9')
