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__init__(self,
name='
' ,
alt_loc='
' ,
res_name='
' ,
fragment_id='
' ,
chain_id='
' ,
model_id=1,
element='
' ,
position=None,
x=None,
y=None,
z=None,
sig_position=None,
sig_x=None,
sig_y=None,
sig_z=None,
temp_factor=None,
column6768=None,
sig_temp_factor=None,
occupancy=None,
sig_occupancy=None,
charge=None,
label_entity_id=None,
label_asym_id=None,
label_seq_id=None,
U=None,
u11=None,
u22=None,
u33=None,
u12=None,
u13=None,
u23=None,
sig_U=None,
sig_u11=None,
sig_u22=None,
sig_u33=None,
sig_u12=None,
sig_u13=None,
sig_u23=None,
**args)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature |
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__len__(self)
Returns the number of alternate conformations of this atom. |
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__getitem__(self,
alt_loc)
This is an alternative to calling get_alt_loc, but a KeyError
exception is raised if the alt_loc Atom is not found. |
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__iter__(self)
Iterates over all Altloc representations of this Atom. |
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__contains__(self,
atom_alt_loc)
Returns True if the argument matches an alternate conformation of the
Atom. |
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remove_alt_loc(self,
atom)
Removes the argument Atom from the Altloc. |
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get_alt_loc(self,
alt_loc)
Returns the Atom object matching the alt_loc argument. |
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iter_alt_loc(self)
Iterate over all alt_loc versions of this atom in the alphabetical
order of the alt_loc labels, within the current model. |
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create_bond(self,
atom=None,
bond_type=None,
atom1_symop=None,
atom2_symop=None,
standard_res_bond=False)
Creates a bond between this atom and the argumentatom. |
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create_bonds(self,
atom=None,
bond_type=None,
atom1_symop=None,
atom2_symop=None,
standard_res_bond=False)
Like create_bonds, but it bonds all alternate locations of this atom. |
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get_bond(self,
atom)
Returns the Bond connecting self with the argument atom. |
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iter_bonds(self)
Iterates over all the Bond edges connected to self. |
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iter_bonded_atoms(self)
Iterates over all the Atoms bonded to self. |
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get_bonded_atom(self,
name_list)
From atom, follow the bonding path specified by a sequence of atom
names given in name_list and return the last atom instance in the
list. |
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get_fragment(self)
Returns the parent Fragment object. |
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get_chain(self)
Returns the parent Chain object. |
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get_model(self)
Returns the parent Model object. |
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get_structure(self)
Returns the parent Structure object. |
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set_U(self,
u11,
u22,
u33,
u12,
u13,
u23)
Sets the symmetric U tensor from the six unique values. |
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set_sig_U(self,
u11,
u22,
u33,
u12,
u13,
u23)
Sets the symmetric sig_U tensor from the six unique values. |
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calc_Uiso(self)
Calculates the Uiso tensor from the Atom's temperature factor. |
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get_U(self)
Returns the Atoms's U tensor if it exists, otherwise returns the
isotropic U tensor calculated by self.calc_Uiso |
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calc_anisotropy3(self)
Calculates the eigenvalues of the U matrix and returns the 3-tuple of
the eigenvalue ratios: (e1/e2, e1/e3, e2/e3) |
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iter_atoms_by_distance(self,
max_distance=None)
Iterates all atoms in the Structure object from the closest to the
farthest up to the cutoff distance max_distance if given. |
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set_model_id(self,
model_id)
Sets the chain_id of the Atom and all alt_loc Atom objects. |
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set_chain_id(self,
chain_id)
Sets the chain_id of the Atom and all alt_loc Atom objects. |
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set_fragment_id(self,
fragment_id)
Sets the fragment_id of the Atom and all alt_loc Atom objects. |
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set_res_name(self,
res_name)
Sets the fragment_id of the Atom and all alt_loc Atom objects. |
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Inherited from object :
__delattr__ ,
__format__ ,
__getattribute__ ,
__hash__ ,
__new__ ,
__reduce__ ,
__reduce_ex__ ,
__repr__ ,
__setattr__ ,
__sizeof__ ,
__subclasshook__
|