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
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:
LOGGER.warn("no biomolecular transformations found so original structure was used")
return atoms
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
def buildBiomolecules(header, atoms, biomol=None):
"""Return *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 = biomt.keys()
else:
biomol = str(biomol)
if biomol in biomt:
keys = [biomol]
else:
LOGGER.warning('Transformations for biomolecule {0:s} was not '
'found in the header dictionary.'.format(biomol))
return None
c_max = 26
keys.sort()
for i in keys:
chids = 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) - 1) % 3 != 0:
LOGGER.warning('Biomolecular transformations {0:s} were not '
'applied'.format(i))
continue
chids_used = []
for times in range((len(mt) - 1)/ 3):
rotation = np.zeros((3,3))
translation = np.zeros(3)
line = np.fromstring(mt[times*3+1], sep=' ')
rotation[0,:] = line[:3]
translation[0] = line[3]
line = np.fromstring(mt[times*3+2], sep=' ')
rotation[1,:] = line[:3]
translation[1] = line[3]
line = np.fromstring(mt[times*3+3], sep=' ')
rotation[2,:] = line[:3]
translation[2] = line[3]
t = Transformation(rotation, translation)
for chid in mt[0]:
chids_used.append(chid)
newag = atoms.select('chain ' + chid).copy()
if newag is None:
continue
for acsi in range(newag.numCoordsets()):
newag.setACSIndex(acsi)
newag = t.apply(newag)
newag.setACSIndex(0)
ags.append(newag)
if ags:
# Handles the case when there is more atom groups than the number
# of chain identifiers
if len(chids_used) != len(set(chids_used)):
for newag in ags:
newag.select('all').setChids(chids.pop(0))
if len(ags) <= c_max:
ags_ = [ags]
else:
ags_ = []
for j in range(len(ags)/c_max + 1):
ags_.append(ags[j*c_max: (j+1)*c_max])
parts = []
for k, ags in enumerate(ags_):
if not ags:
continue
newag = ags.pop(0)
while ags:
newag += ags.pop(0)
if len(ags_) > 1:
newag.setTitle('{0:s} biomolecule {1:s} part {2:d}'
.format(atoms.getTitle(), i, k+1))
else:
newag.setTitle('{0:s} biomolecule {1:s}'
.format(atoms.getTitle(), i))
parts.append(newag)
if len(parts) == 1:
biomols.append(newag)
else:
biomols.append(tuple(parts))
if biomols:
if len(biomols) == 1:
return biomols[0]
else:
return biomols
else:
return None