def setUp(self):
self.atoms = [
Atom(type='C', name='a1', component_number=3, x=1.0, y=0.0, z=0.0),
Atom(type='C', name='a2', component_number=2, x=2.0, y=0.0, z=0.0),
Atom(type='N', name='b1', component_number=1, x=3.0, y=0.0, z=0.0),
Atom(type='N', name='c2', component_number=0, x=0.0, y=1.0, z=0.0)
]
self.proxy = AtomProxy(self.atoms)
def __init__(self,
atoms,
pdb=None,
model=None,
type=None,
chain=None,
symmetry=None,
sequence=None,
number=None,
index=None,
insertion_code=None,
polymeric=None,
alt_id=None):
"""Create a new Component.
:atoms: The atoms this component is composed of.
:pdb: The pdb this is a part of.
:model: The model number.
"""
self._atoms = atoms
self.pdb = pdb
self.model = model
self.type = type
self.chain = chain
self.symmetry = symmetry
self.sequence = sequence
self.number = number
self.index = index
self.insertion_code = insertion_code
self.polymeric = polymeric
self.alt_id = alt_id
self.centers = AtomProxy(self._atoms)
if self.sequence in defs.RNAbaseheavyatoms:
atoms = defs.RNAbaseheavyatoms[self.sequence]
self.centers.define('base', atoms)
if self.sequence in defs.nt_backbone:
atoms = defs.nt_backbone[self.sequence]
self.centers.define('nt_backbone', atoms)
if self.sequence in defs.aa_fg:
atoms = defs.aa_fg[self.sequence]
self.centers.define('aa_fg', atoms)
if self.sequence in defs.aa_backbone:
atoms = defs.aa_backbone[self.sequence]
self.centers.define('aa_backbone', atoms)
def __init__(self,
atoms,
pdb=None,
model=None,
type=None,
chain=None,
symmetry=None,
sequence=None,
number=None,
index=None,
insertion_code=None,
polymeric=None,
alt_id=None,
inferhydrogens=True):
"""Create a new Component.
:atoms: The atoms this component is composed of.
:pdb: The pdb this is a part of.
:model: The model number.
"""
self._atoms = atoms
self.pdb = pdb
self.model = model
self.type = type
self.chain = chain
self.symmetry = symmetry
self.sequence = sequence
self.number = number
self.index = index
self.insertion_code = insertion_code
self.polymeric = polymeric
self.alt_id = alt_id
self.base_center = None
self.rotation_matrix = None
# for bases, calculate and store rotation_matrix
# calculate and store base_center; especially for modified nt without all heavy atoms
self.calculate_rotation_matrix()
# initialize centers so they can be used to infer hydrogens
self.centers = AtomProxy(self._atoms)
# add hydrogen atoms to standard bases and amino acids
if inferhydrogens:
self.infer_hydrogens()
# initialize centers again to include hydrogens
self.centers = AtomProxy(self._atoms)
# standard and modified bases should have their rotation matrix
# calculated already, and should have a base center set by that
# if they don't, there is no sensible way to assign a base center,
# for example if the structure just has a backbone trace
if self.base_center is not None:
self.centers.setcenter('base', self.base_center)
if self.sequence in defs.nt_sugar:
atoms = defs.nt_sugar[self.sequence]
self.centers.define('nt_sugar', atoms)
if self.sequence in defs.nt_phosphate:
atoms = defs.nt_phosphate[self.sequence]
self.centers.define('nt_phosphate', atoms)
# attempt to add sugar and phosphate centers for all modified nucleotides
if self.sequence in defs.modified_nucleotides:
atoms = defs.nt_sugar['A']
self.centers.define('nt_sugar', atoms)
atoms = defs.nt_phosphate['A']
self.centers.define('nt_phosphate', atoms)
if self.sequence in defs.aa_fg:
atoms = defs.aa_fg[self.sequence]
self.centers.define('aa_fg', atoms)
if self.sequence in defs.aa_backbone:
atoms = defs.aa_backbone[self.sequence]
self.centers.define('aa_backbone', atoms)
