def get_structure(filename):
with open(filename, 'rb') as raw:
structure = Cif(raw).structure()
"""All RNA bases are placed in the standard orientation. All Hydrogen
atoms are inferred. Rotation matrix is calculated for each base."""
structure.infer_hydrogens()
return structure
def get_structure(filename):
with open(filename, 'rb') as raw:
structure = Cif(raw).structure()
"""All RNA bases are placed in the standard orientation. All Hydrogen
atoms are inferred. Rotation matrix is calculated for each base."""
structure.infer_hydrogens()
return structure
def main(filename):
with open(filename, 'rb') as raw:
structure = Cif(raw).structure()
print('Iterating over atoms')
for residue in structure.residues(chain='A', sequence='C'):
for atom in residue.atoms():
print residue.unit_id()
print(atom.name)
def main(filename):
with open(filename, 'rb') as raw:
structure = Cif(raw).structure()
print('Iterating over atoms')
for residue in structure.residues(chain='A', sequence = 'U'):
for atom in residue.atoms():
print residue
print(atom.name)
def main(filename):
with open(filename, 'rb') as raw:
structure = Cif(raw).structure()
print(structure)
print(structure.pdb)
# print(structure._assemblies)
print('Iterating over all units')
# print(structure._residues)
for residue in structure._residues:
if 'base' in residue.centers:
print('residue: %s %s' % (residue, residue.centers['base']))
structure.infer_hydrogens() # iterate through all residues ...
# when you
a = input()
print(structure.experimental_sequence('A'))
# print(structure.residues)
print('Iterating over all parts')
for model in structure.models:
print('model: %s' % model.model)
for chain in model.chains:
print(' chain: %s' % chain.chain)
for residue in chain.residues():
print(' residue: %s' % residue.unit_id())
# You can use residues to iterate over the residues of a structure
# directly.
print('Short cut iteration')
for residue in structure.residues():
print(residue.unit_id())
# The residues method accepts keyword arguments. These arguments are things
# to filter the residues by. Below limits the residues to only those that
# have sequence equal to 'A'.
print('Iterating over specific residues')
for residue in structure.residues(sequence='A'):
print(residue.unit_id())
# You can give more than one condition. Below limits the residues to only
# those in chain B which are a G or C.
print('Iterating over atoms')
for residue in structure.residues(chain='B', sequence=['G', 'C']):
for atom in residue.atoms():
print(atom.unit_id())
# You can also filter the atoms in the same way.
print('Iterating over specific atoms')
for residue in structure.residues(chain='A', sequence=['G', 'C']):
for atom in residue.atoms(name=['N1', 'C2']):
print(atom.unit_id())
def cif(self, pdb):
"""A method to load the cif file for a given pdb id. If given a CIF
file this will return the given CIF file.
Parameters
----------
pdb : str or fr3d.cif.reader.CIF
PDB id to parse or the file to return.
Returns
-------
cif : fr3d.cif.reader.Cif
The parsed mmCIF file.
"""
if isinstance(pdb, Cif):
return pdb
try:
with open(self._cif(pdb), 'rb') as raw:
return Cif(raw)
except ComplexOperatorException as err:
if self.skip_complex:
self.logger.warning("Got a complex operator for %s, skipping",
pdb)
raise Skip("Complex operator must be skipped")
raise err
def setUpClass(cls):
if cls.filename:
with open(cls.filename, 'rb') as raw:
cls.cif = Cif(raw)
cls.structure = cls.cif.structure()
else:
cls.cif = None
cls.structure = None
def deserialize(handle):
"""Load a serialized cif file.
:handle: The filehandle to read from.
:returns: A new Cif object from the persisted data.
"""
data = pickle.load(handle)
return Cif(data=data)
def main(filename):
with open(filename, 'rb') as raw:
structure = Cif(raw).structure()
print('Iterating over all parts')
for model in structure.models:
print('model: %s' % model.model)
for chain in model.chains:
print(' chain: %s' % chain.chain)
for residue in chain.residues():
print(' residue: %s' % residue.unit_id())
# You can use residues to iterate over the residues of a structure
# directly.
print('Short cut iteration')
for residue in structure.residues():
print(residue.unit_id())
# The residues method accepts keyword arguments. These arguments are things
# to filter the residues by. Below limits the residues to only those that
# have sequence equal to 'A'.
print('Iterating over specific residues')
for residue in structure.residues(sequence='A'):
print(residue.unit_id())
# You can give more than one condition. Below limits the residues to only
# those in chain B which are a G or C.
print('Iterating over atoms')
for residue in structure.residues(chain='B', sequence=['G', 'C']):
for atom in residue.atoms():
print(atom.unit_id())
# You can also filter the atoms in the same way.
print('Iterating over specific atoms')
for residue in structure.residues(chain='A', sequence=['G', 'C']):
for atom in residue.atoms(name=['N1', 'C2']):
print(atom.unit_id())
def get_structure(filename):
if not os.path.exists(filename):
mmCIFname = filename[-8:]
print("Downloading " + mmCIFname)
f = urllib.urlopen("https://files.rcsb.org/download/%s" % mmCIFname)
myfile = f.read()
with open(filename, 'w') as outfile:
outfile.write(myfile)
with open(filename, 'rb') as raw:
structure = Cif(raw).structure()
"""All RNA bases are placed in the standard orientation. All Hydrogen
atoms are inferred. Rotation matrix is calculated for each base."""
# structure.infer_hydrogens()
return structure
def main(filename, limits):
with open(filename, 'rb') as raw:
structure = Cif(raw).structure()
aa_mapping, aa_tree = generate_peptide_tree(structure,
limits.get('residue', {}))
rna_mapping, rna_tree = generate_rna_tree(structure, limits.get('nt', {}))
# This produces a list of (rna_atom_index, aa_atom_index)
# The query_ball_tree method goes through all points in rna_tree and finds
# all points in aa_tree that have distance 5. It will return something for
# all rna atoms, even those without any nearby aa atoms.
results = enumerate(rna_tree.query_ball_tree(aa_tree, 5))
# Filter out all rna atoms that have nothing near by
filtered = it.ifilter(lambda (r, a): a, results)
# Map the results so we transform the rna atom to a residue
mapped = it.imap(lambda (r, _): (rna_mapping[r], _), filtered)
# Group the list by the residue
grouped = it.groupby(mapped, lambda (r, _): r)
# Display what we find
for residue, nearby in grouped:
# This creates a dictionary we use to count the number of near by
# atoms.
counts = coll.defaultdict(int)
# Near by is a iterable of the form (residue, [indexes])
for (_, indexes) in nearby:
for index in indexes:
peptide = aa_mapping[index]
counts[peptide] += 1
for peptide, count in counts.items():
print('%s: %s %s' % (residue.unit_id(), peptide.unit_id(), count))
def main(filename):
with open(filename, 'rb') as raw:
structure = Cif(raw).structure()
print('Iterating over all parts')
for model in structure.models:
print('model: %s' % model.model)
for chain in model.chains:
print(' chain: %s' % chain.chain)
for residue in chain.residues():
print(' residue: %s' % residue.unit_id())
# You can use residues to iterate over the residues of a structure
# directly.
print('Short cut iteration')
for residue in structure.residues():
print(residue.unit_id())
# The residues method accepts keyword arguments. These arguments are things
# to filter the residues by. Below limits the residues to only those that
# have sequence equal to 'A'.
print('Iterating over specific residues')
for residue in structure.residues(sequence='A'):
print(residue.unit_id())
# You can give more than one condition. Below limits the residues to only
# those in chain B which are a G or C.
print('Iterating over atoms')
for residue in structure.residues(chain='B', sequence=['G', 'C']):
for atom in residue.atoms():
print(atom.unit_id())
# You can also filter the atoms in the same way.
print('Iterating over specific atoms')
for residue in structure.residues(chain='A', sequence=['G', 'C']):
for atom in residue.atoms(name=['N1', 'C2']):
print(atom.unit_id())
def setUpClass(cls):
print(cls.name)
with open(os.path.join('files', cls.name + '.cif'), 'rb') as raw:
cls.cif = Cif(raw)
cls.structure = cls.cif.structure()
def setUpClass(cls):
with open('files/1FJG.cif', 'rb') as raw:
cls.structure = Cif(raw).structure()
cls.structure.infer_hydrogens()
def setUpClass(cls):
with open('test/files/cif/1GID.cif', 'rb') as raw:
cls.structure = Cif(raw).structure()
