def setBonds(self, bonds):
"""Set covalent bonds between atoms. *bonds* must be a list or an
array of pairs of indices. All bonds must be set at once. Bonding
information can be used to make atom selections, e.g. ``"bonded to
index 1"``. See :mod:`~.select` module documentation for details.
Also, a data array with number of bonds will be generated and stored
with label *numbonds*. This can be used in atom selections, e.g.
``'numbonds 0'`` can be used to select ions in a system."""
if isinstance(bonds, list):
bonds = np.array(bonds, int)
if bonds.ndim != 2:
raise ValueError('bonds.ndim must be 2')
if bonds.shape[1] != 2:
raise ValueError('bonds.shape must be (n_bonds, 2)')
if bonds.min() < 0:
raise ValueError('negative atom indices are not valid')
n_atoms = self._n_atoms
if bonds.max() >= n_atoms:
raise ValueError('atom indices are out of range')
bonds.sort(1)
bonds = bonds[bonds[:,1].argsort(),]
bonds = bonds[bonds[:,0].argsort(),]
self._bmap, self._data['numbonds'] = evalBonds(bonds, n_atoms)
self._bonds = bonds
self._data['fragindices'] = None
self._fragments = None
def saveAtoms(atoms, filename=None, **kwargs):
"""Save *atoms* in ProDy internal format. All atomic classes are accepted
as *atoms* argument. This function saves user set atomic data as well.
Note that title of the AtomGroup instance is used as the filename when
*atoms* is not an AtomGroup. To avoid overwriting an existing file with
the same name, specify a *filename*."""
if not isinstance(atoms, Atomic):
raise TypeError('atoms must be Atomic instance, not {0:s}'
.format(type(atoms)))
if isinstance(atoms, AtomGroup):
ag = atoms
title = ag.getTitle()
SKIP = SAVE_SKIP_ATOMGROUP
else:
ag = atoms.getAtomGroup()
title = str(atoms)
SKIP = SAVE_SKIP_POINTER
if filename is None:
filename = ag.getTitle().replace(' ', '_')
filename += '.ag.npz'
attr_dict = {'title': title}
attr_dict['n_atoms'] = atoms.numAtoms()
attr_dict['n_csets'] = atoms.numCoordsets()
attr_dict['cslabels'] = atoms.getCSLabels()
coords = atoms._getCoordsets()
if coords is not None:
attr_dict['coordinates'] = coords
bonds = ag._bonds
bmap = ag._bmap
if bonds is not None and bmap is not None:
if isinstance(atoms, AtomGroup):
attr_dict['bonds'] = bonds
attr_dict['bmap'] = bmap
attr_dict['numbonds'] = ag._data['numbonds']
frags = ag._data['fragindices']
if frags is not None:
attr_dict['fragindices'] = frags
else:
bonds = trimBonds(bonds, atoms._getIndices())
attr_dict['bonds'] = bonds
attr_dict['bmap'], attr_dict['numbonds'] = \
evalBonds(bonds, len(atoms))
for key, data in ag._data.iteritems():
if key in SKIP:
continue
if data is not None:
attr_dict[key] = data
ostream = openFile(filename, 'wb', **kwargs)
savez(ostream, **attr_dict)
ostream.close()
return filename
def setBonds(self, bonds):
"""Set covalent bonds between atoms. *bonds* must be a list or an
array of pairs of indices. All bonds must be set at once. An array
with number of bonds will be generated and stored as *numbonds*.
This can be used in atom selections, e.g. ``ag.select('numbonds 0')``
can be used to select ions in a system."""
if isinstance(bonds, list):
bonds = np.array(bonds, int)
if bonds.ndim != 2:
raise ValueError('bonds.ndim must be 2')
if bonds.shape[1] != 2:
raise ValueError('bonds.shape must be (n_bonds, 2)')
if bonds.min() < 0:
raise ValueError('negative atom indices are not valid')
n_atoms = self._n_atoms
if bonds.max() >= n_atoms:
raise ValueError('atom indices are out of range')
bonds.sort(1)
bonds = bonds[bonds[:,1].argsort(),]
bonds = bonds[bonds[:,0].argsort(),]
self._bmap, self._data['numbonds'] = evalBonds(bonds, n_atoms)
self._bonds = bonds
