def getTransformation(self):
"""Returns the :class:`~.Transformation` used to superpose this
conformation onto reference coordinates. The transformation can
be used to superpose original PDB file onto the reference PDB file."""
if self._ensemble._trans is not None:
return Transformation(self._ensemble._trans[self._index])
def buildBiomolecules(header, atoms, biomol=None):
"""Returns *atoms* after applying biomolecular transformations from *header*
dictionary. Biomolecular transformations are applied to all coordinate
sets in the molecule.
Some PDB files contain transformations for more than 1 biomolecules. A
specific set of transformations can be choosen using *biomol* argument.
Transformation sets are identified by numbers, e.g. ``"1"``, ``"2"``, ...
If multiple biomolecular transformations are provided in the *header*
dictionary, biomolecules will be returned as
:class:`.AtomGroup` instances in a :func:`list`.
If the resulting biomolecule has more than 26 chains, the molecular
assembly will be split into multiple :class:`.AtomGroup`
instances each containing at most 26 chains. These
:class:`.AtomGroup` instances will be returned in a tuple.
Note that atoms in biomolecules are ordered according to chain identifiers.
"""
if not isinstance(header, dict):
raise TypeError('header must be a dictionary')
if not isinstance(atoms, Atomic):
raise TypeError('atoms must be an Atomic instance')
biomt = header.get('biomoltrans')
if not isinstance(biomt, dict) or len(biomt) == 0:
raise ValueError("header doesn't contain biomolecular transformations")
if not isinstance(atoms, AtomGroup):
atoms = atoms.copy()
biomols = []
if biomol is None:
keys = list(biomt)
else:
biomol = str(biomol)
if biomol in biomt:
keys = [biomol]
else:
LOGGER.warn('Transformations for biomolecule {0} was not '
'found in the header dictionary.'.format(biomol))
return None
keys.sort()
for i in keys:
segnm = list('ABCDEFGHIJKLMNOPQRSTUVWXYZ' * 20)
ags = []
mt = biomt[i]
# mt is a list, first item is list of chain identifiers
# following items are lines corresponding to transformation
# mt must have 3n + 1 lines
if (len(mt)) % 4 != 0:
LOGGER.warn('Biomolecular transformations {0} were not '
'applied'.format(i))
continue
for times in range(int((len(mt)) / 4)):
rotation = np.zeros((3, 3))
translation = np.zeros(3)
line0 = np.fromstring(mt[times * 4 + 1], sep=' ')
rotation[0, :] = line0[:3]
translation[0] = line0[3]
line1 = np.fromstring(mt[times * 4 + 2], sep=' ')
rotation[1, :] = line1[:3]
translation[1] = line1[3]
line2 = np.fromstring(mt[times * 4 + 3], sep=' ')
rotation[2, :] = line2[:3]
translation[2] = line2[3]
t = Transformation(rotation, translation)
newag = atoms.select('chain ' + ' '.join(mt[0])).copy()
if newag is None:
continue
newag.all.setSegnames(segnm.pop(0))
for acsi in range(newag.numCoordsets()):
newag.setACSIndex(acsi)
newag = t.apply(newag)
newag.setACSIndex(0)
ags.append(newag)
if ags:
newag = ags.pop(0)
while ags:
newag += ags.pop(0)
newag.setTitle('{0} biomolecule {1}'.format(atoms.getTitle(), i))
biomols.append(newag)
if biomols:
if len(biomols) == 1:
return biomols[0]
else:
return biomols
else:
return None
