def update(self, **kwargs):
"""Rebuild hierarchical view of atoms. This method is called at
instantiation, but can be used to rebuild the hierarchical view
when attributes of atoms change."""
array = np.array
atoms = self._atoms
if isinstance(atoms, AtomGroup):
ag = atoms
_indices = np.arange(ag._n_atoms)
selstr = False
else:
ag = atoms.getAtomGroup()
_indices = atoms._indices
selstr = atoms.getSelstr()
acsi = self._atoms.getACSIndex()
n_atoms = len(ag)
self._dict = _dict = dict()
self._chains = _chains = list()
self._residues = _residues = list()
self._segments = _segments = list()
segindex = -1
segindices = np.zeros(n_atoms, int)
chindex = -1
chindices = np.zeros(n_atoms, int)
resindex = -1
resindices = np.zeros(n_atoms, int)
sgnms = ag._getSegnames()
if sgnms is None:
_segments = None
else:
if selstr:
sgnms = sgnms[_indices]
unique = np.unique(sgnms)
s = sgnms[0]
if len(unique) == 1:
if s != '':
segment = Segment(ag, _indices, acsi=acsi, unique=True,
selstr=selstr)
_dict[s] = segment
_segments.append(segment)
LOGGER.info('Hierarchical view contains segments.')
else:
_segments = None
else:
ps = None
for i, s in enumerate(sgnms):
if s == ps or s in _dict:
continue
ps = s
segindex += 1
idx = _indices[i:][sgnms[i:] == s]
segment = Segment(ag, idx, acsi=acsi, unique=True,
selstr=selstr)
segindices[idx] = segindex
_dict[s] = segment
_segments.append(segment)
LOGGER.info('Hierarchical view contains segments.')
chids = ag._getChids()
if chids is None:
_chains = None
else:
if selstr:
chids = chids[_indices]
if _segments is None:
if len(np.unique(chids)) == 1:
chain = Chain(ag, _indices, acsi=acsi, unique=True)
_dict[(None, chids[0] or None)] = chain
_chains.append(chain)
else:
pc = None
for i, c in enumerate(chids):
if c == pc or (None, c) in _dict:
continue
pc = c
chindex += 1
idx = _indices[i:][chids[i:] == c]
chain = Chain(ag, idx, acsi=acsi, unique=True)
chindices[idx] = chindex
_dict[(None, c)] = chain
_chains.append(chain)
else:
pc = chids[0]
ps = sgnms[0]
_i = 0
for i, c in enumerate(chids):
s = sgnms[i]
if c == pc and s == ps:
continue
s_c = (ps, pc or None)
chain = _dict.get(s_c)
if chain is None:
segment = _dict[ps]
chindex += 1
idx = _indices[_i:i]
chain = Chain(ag, idx, acsi=acsi, segment=segment,
unique=True)
chindices[idx] = chindex
_dict[s_c] = chain
segment._dict[pc] = len(segment._list)
segment._list.append(chain)
_chains.append(chain)
else:
idx = _indices[_i:i]
chindices[idx] = chain._indices[0]
chain._indices = np.concatenate((chain._indices, idx))
pc = c
ps = s
_i = i
s_c = (ps, pc or None)
chain = _dict.get(s_c)
idx = _indices[_i:]
if chain is None:
segment = _dict[ps]
chindex += 1
chindices[idx] = chindex
chain = Chain(ag, idx, acsi=acsi, segment=segment,
unique=True)
_dict[s_c] = chain
segment._dict[pc] = len(segment._list)
segment._list.append(chain)
_chains.append(chain)
else:
chindices[idx] = chain._indices[0]
chain._indices = np.concatenate((chain._indices, idx))
if kwargs.get('chain') == True:
return
rnums = ag._getResnums()
if rnums is None:
raise ValueError('resnums are not set')
if selstr:
rnums = rnums[_indices]
nones = None
if _segments is None:
if nones is None:
nones = [None] * len(rnums)
sgnms = nones
if _chains is None:
if nones is None:
nones = [None] * len(rnums)
chids = nones
icods = ag._getIcodes()
if icods is None:
if nones is None:
nones = [None] * len(rnums)
icods = nones
elif selstr:
icods = icods[_indices]
pr = rnums[0]
pi = icods[0] or None
pc = chids[0]
ps = sgnms[0] or None
_j = 0
for j, r in enumerate(rnums):
i = icods[j] or None
c = chids[j] or None
s = sgnms[j]
if r != pr or i != pi or c != pc or s != ps:
s_c_r_i = (ps, pc, pr, pi)
res = _dict.get(s_c_r_i)
if res is None:
chain = _dict.get((ps, pc))
resindex += 1
idx = _indices[_j:j]
res = Residue(ag, idx, acsi=acsi, chain=chain,
unique=True, selstr=selstr)
resindices[idx] = resindex
if chain is not None:
chain._dict[(pr, pi)] = len(chain._list)
chain._list.append(res)
_residues.append(res)
_dict[s_c_r_i] = res
else:
res._indices = np.concatenate((res._indices,
_indices[_j:j]))
ps = s
pc = c
pr = r
pi = i
_j = j
s_c_r_i = (ps, pc, pr, pi)
res = _dict.get(s_c_r_i)
idx = _indices[_j:]
if res is None:
chain = _dict.get((ps, pc))
resindex += 1
res = Residue(ag, idx, acsi=acsi, chain=chain, unique=True,
selstr=selstr)
resindices[idx] = resindex
if chain is not None:
chain._dict[(pr, pi)] = len(chain._list)
chain._list.append(res)
_residues.append(res)
_dict[s_c_r_i] = res
else:
resindices[idx] = res._indices[0]
res._indices = np.concatenate((res._indices, idx))
ag._data['segindices'] = segindices
ag._data['chindices'] = chindices
ag._data['resindices'] = resindices
def update(self, **kwargs):
"""Update (or build) hierarchical view of atoms. This method is called
at instantiation, but can be used to rebuild the hierarchical view when
attributes of atoms change."""
atoms = self._atoms
if isinstance(atoms, AtomGroup):
ag = atoms
selstr = False
_indices = arange(atoms._n_atoms)
else:
ag = atoms.getAtomGroup()
_indices = atoms._getIndices()
selstr = atoms.getSelstr()
set_indices = False
if atoms == ag:
set_indices = True
_dict = dict()
_residues = list()
_segments = list()
_chains = list()
# also set the attributes, so that when no segments or chains
# are available, num/iter methods won't raise exceptions
self._dict = _dict
self._residues = _residues
self._segments = _segments
self._chains = _chains
acsi = atoms.getACSIndex()
n_atoms = len(ag)
# identify segments
if set_indices:
segindex = -1
segindices = zeros(n_atoms, int)
sgnms = ag._getSegnames()
if sgnms is None:
_segments = None
else:
if selstr:
sgnms = sgnms[_indices]
s = sgnms[0]
if len(unique(sgnms)) == 1:
if s != '':
segment = Segment(ag, _indices, acsi=acsi, unique=True,
selstr=selstr)
_dict[s] = segment
_segments.append(segment)
LOGGER.info('Hierarchical view contains segments.')
else:
_segments = None
else:
ps = None # previous segment name
for i, s in enumerate(sgnms):
if s == ps or s in _dict:
continue
ps = s
idx = _indices[i:][sgnms[i:] == s]
segment = Segment(ag, idx, acsi=acsi, unique=True,
selstr=selstr)
if set_indices:
segindex += 1
segindices[idx] = segindex
_dict[s] = segment
_segments.append(segment)
LOGGER.info('Hierarchical view contains segments.')
if set_indices:
ag._data['segindices'] = segindices
chindex = -1
chindices = zeros(n_atoms, int)
# identify chains
chids = ag._getChids()
if chids is None:
_chains = None
else:
if selstr:
chids = chids[_indices]
if _segments is None:
if len(unique(chids)) == 1:
chain = Chain(ag, _indices, acsi=acsi, unique=True,
selstr=selstr)
_dict[(None, chids[0] or None)] = chain
_chains.append(chain)
else:
pc = None
for i, c in enumerate(chids):
if c == pc or (None, c) in _dict:
continue
pc = c
idx = _indices[i:][chids[i:] == c]
chain = Chain(ag, idx, acsi=acsi, unique=True,
selstr=selstr)
if set_indices:
chindex += 1
chindices[idx] = chindex
_dict[(None, c)] = chain
_chains.append(chain)
else:
pc = chids[0]
ps = sgnms[0]
_i = 0
for i, c in enumerate(chids):
s = sgnms[i]
if c == pc and s == ps:
continue
s_c = (ps, pc or None)
chain = _dict.get(s_c)
if chain is None:
segment = _dict[ps]
idx = _indices[_i:i]
chain = Chain(ag, idx, acsi=acsi, segment=segment,
unique=True, selstr=selstr)
if set_indices:
chindex += 1
chindices[idx] = chindex
_dict[s_c] = chain
_chains.append(chain)
else:
idx = _indices[_i:i]
chindices[idx] = chain._indices[0]
chain._indices = concatenate((chain._indices, idx))
pc = c
ps = s
_i = i
s_c = (ps, pc or None)
chain = _dict.get(s_c)
idx = _indices[_i:]
if chain is None:
segment = _dict[ps]
if set_indices:
chindex += 1
chindices[idx] = chindex
chain = Chain(ag, idx, acsi=acsi, segment=segment,
unique=True, selstr=selstr)
_dict[s_c] = chain
_chains.append(chain)
else:
if set_indices:
chindices[idx] = chain._indices[0]
chain._indices = concatenate((chain._indices, idx))
if set_indices:
ag._data['chindices'] = chindices
if kwargs.get('chain') == True:
return
if set_indices:
resindex = -1
resindices = zeros(n_atoms, int)
rnums = ag._getResnums()
if rnums is None:
raise ValueError('resnums are not set')
if selstr:
rnums = rnums[_indices]
nones = None
if _segments is None:
if nones is None:
nones = [None] * len(rnums)
sgnms = nones
if _chains is None:
if nones is None:
nones = [None] * len(rnums)
chids = nones
icods = ag._getIcodes()
if icods is None:
if nones is None:
nones = [None] * len(rnums)
icods = nones
elif selstr:
icods = icods[_indices]
pr = rnums[0]
pi = icods[0] or None
pc = chids[0]
ps = sgnms[0]
_j = 0
_append = _residues.append
_get = _dict.get
_set = _dict.__setitem__
for j, r in enumerate(rnums):
i = icods[j] or None
c = chids[j]
s = sgnms[j]
if r != pr or i != pi or c != pc or s != ps:
s_c_r_i = (ps, pc, pr, pi)
res = _get(s_c_r_i)
if res is None:
chain = _get((ps, pc))
idx = _indices[_j:j]
res = Residue(ag, idx, acsi=acsi, chain=chain,
unique=True, selstr=selstr)
if set_indices:
resindex += 1
resindices[idx] = resindex
_append(res)
_set(s_c_r_i, res)
else:
res._indices = concatenate((res._indices, _indices[_j:j]))
ps = s
pc = c
pr = r
pi = i
_j = j
s_c_r_i = (ps, pc, pr, pi)
res = _get(s_c_r_i)
idx = _indices[_j:]
if res is None:
chain = _get((ps, pc))
res = Residue(ag, idx, acsi=acsi, chain=chain, unique=True,
selstr=selstr)
if set_indices:
resindex += 1
resindices[idx] = resindex
_append(res)
_set(s_c_r_i, res)
else:
if set_indices:
resindices[idx] = res._indices[0]
res._indices = concatenate((res._indices, idx))
if set_indices:
ag._data['resindices'] = resindices
