Package mmLib :: Module Structure :: Class Atom
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Type Atom

object --+
         |
        Atom


Class representing a single atom.  Atoms have the following default
attributes.  If a attribue has the value None, then the attribue was
never set.  If the attribue has a default, then it is required.

Atom[alt_loc]    - Atom objects in alternate locations can be accessed
                   by using Python's dictionary syntax with the alt_loc
                   charactor
iter(Atom)       - iterates over all alt_loc versions of the Atom
Atom.name        - label of the atom
Atom.alt_loc     - alternate location indicater for the atom
Atom.res_name    - the name of the resiude/fragment this atom is part of
Atom.res_seq     - the residue/fragment sequence number
Atom.icode       - the insertion code for the residue/fragment
Atom.chain_id    - the chain ID of the chain containing this atom
Atom.element     - symbol for the element
Atom.position    - a numpy.array[3] (Numeric Python)
Atom.occupancy   - [1.0 - 0.0] float 
Atom.temp_factor - float represting B-style temp factor
Atom.U           - a 6-tuple of the anisotropic values
Atom.charge      - charge on the atom
Atom.label_entity_id -
                   entity id corresponding to entity_poly_seq.entity_id
Atom.label_seq_id -
                   sequence id corresponding to entity_poly_seq_num
                   and struct_conn.ptnr?_label_seq_id

Method Summary
  __init__(self, name, alt_loc, res_name, fragment_id, chain_id, model_id, element, position, x, y, z, sig_position, sig_x, sig_y, sig_z, temp_factor, sig_temp_factor, occupancy, sig_occupancy, charge, label_entity_id, label_seq_id, U, u11, u22, u33, u12, u13, u23, sig_U, sig_u11, sig_u22, sig_u33, sig_u12, sig_u13, sig_u23, **args)
  __contains__(self, atom_alt_loc)
Returns True if the argument matches a alternate conformation of the Atom.
  __deepcopy__(self, memo)
  __ge__(self, other)
  __getitem__(self, alt_loc)
This is a alternative to calling get_alt_loc, but a KeyError exception is raised if the alt_loc Atom is not found.
  __gt__(self, other)
  __iter__(self)
Iterates over all Altloc representations of this Atom.
  __le__(self, other)
  __len__(self)
Returns the number of alternate conformations of this atom.
  __lt__(self, other)
  __str__(self)
  calc_anisotropy(self)
Calculates the anisotropy of that atom.
  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)
  calc_Uiso(self)
Calculates the Uiso tensor from the Atom's temperature factor.
  create_bond(self, atom, bond_type, atom1_symop, atom2_symop, standard_res_bond)
Creates a bond between this atom and the argumentatom.
  create_bonds(self, atom, bond_type, atom1_symop, atom2_symop, standard_res_bond)
Like create_bonds, but it bonds all alternate locations of this atom.
  get_alt_loc(self, alt_loc)
Returns the Atom object matching the alt_loc argument.
  get_bond(self, atom)
Returns the Bond connecting self with the argument atom.
  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.
  get_chain(self)
Returns the parent Chain object.
  get_fragment(self)
Returns the parent Fragment object.
  get_model(self)
Returns the parent Model object.
  get_structure(self)
Returns the parent Structure object.
  get_U(self)
Returns the Atoms's U tensor if it exists, otherwise returns the isotropic U tensor calculated by self.calc_Uiso
  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.
  iter_atoms_by_distance(self, max_distance)
Iterates all atoms in the Structure object from the closest to the farthest up to the cutoff distance max_distance if given.
  iter_bonded_atoms(self)
Iterates over all the Atoms bonded to self.
  iter_bonds(self)
Iterates over all the Bond edges connected to self.
  remove_alt_loc(self, atom)
Removes the argument Atom from the Altloc.
  set_chain_id(self, chain_id)
Sets the chain_id of the Atom and all alt_loc Atom objects.
  set_fragment_id(self, fragment_id)
Sets the fragment_id of the Atom and all alt_loc Atom objects.
  set_model_id(self, model_id)
Sets the chain_id of the Atom and all alt_loc Atom objects.
  set_res_name(self, res_name)
Sets the fragment_id of the Atom and all alt_loc Atom objects.
  set_sig_U(self, u11, u22, u33, u12, u13, u23)
Sets the symmetric sig_U tensor from the six unique values.
  set_U(self, u11, u22, u33, u12, u13, u23)
Sets the symmetric U tensor from the six unique values.
    Inherited from object
  __delattr__(...)
x.__delattr__('name') <==> del x.name
  __getattribute__(...)
x.__getattribute__('name') <==> x.name
  __hash__(x)
x.__hash__() <==> hash(x)
  __new__(T, S, ...)
T.__new__(S, ...) -> a new object with type S, a subtype of T
  __reduce__(...)
helper for pickle
  __reduce_ex__(...)
helper for pickle
  __repr__(x)
x.__repr__() <==> repr(x)
  __setattr__(...)
x.__setattr__('name', value) <==> x.name = value

Method Details

__contains__(self, atom_alt_loc)
(In operator)

Returns True if the argument matches a alternate conformation of the Atom. The argument can be a alt_loc label, or a Atom object.

__getitem__(self, alt_loc)
(Indexing operator)

This is a alternative to calling get_alt_loc, but a KeyError exception is raised if the alt_loc Atom is not found.

__iter__(self)

Iterates over all Altloc representations of this Atom.

__len__(self)
(Length operator)

Returns the number of alternate conformations of this atom.

calc_anisotropy(self)

Calculates the anisotropy of that atom. Anisotropy is defined as the ratio of the minimum/maximum eigenvalues of the 3x3 symmetric tensor defined by U.

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)

calc_Uiso(self)

Calculates the Uiso tensor from the Atom's temperature factor.

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. The arugment bond_type is a string, atom1_symop and atom2_symop are symmetry operations to be applied to self and the argument atom before distance calculations, and standard_res_bond is a flag used to indicate this bond is a standard bond.

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.

get_alt_loc(self, alt_loc)

Returns the Atom object matching the alt_loc argument.

get_bond(self, atom)

Returns the Bond connecting self with the argument atom.

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. Returns None if any atom in the bonding path cannot be found.

get_chain(self)

Returns the parent Chain object.

get_fragment(self)

Returns the parent Fragment object.

get_model(self)

Returns the parent Model object.

get_structure(self)

Returns the parent Structure object.

get_U(self)

Returns the Atoms's U tensor if it exists, otherwise returns the isotropic U tensor calculated by self.calc_Uiso

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.

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. Yields the 2-tuple (dist, atm).

iter_bonded_atoms(self)

Iterates over all the Atoms bonded to self.

iter_bonds(self)

Iterates over all the Bond edges connected to self.

remove_alt_loc(self, atom)

Removes the argument Atom from the Altloc.

set_chain_id(self, chain_id)

Sets the chain_id of the Atom and all alt_loc Atom objects.

set_fragment_id(self, fragment_id)

Sets the fragment_id of the Atom and all alt_loc Atom objects.

set_model_id(self, model_id)

Sets the chain_id of the Atom and all alt_loc Atom objects.

set_res_name(self, res_name)

Sets the fragment_id of the Atom and all alt_loc Atom objects.

set_sig_U(self, u11, u22, u33, u12, u13, u23)

Sets the symmetric sig_U tensor from the six unique values.

set_U(self, u11, u22, u33, u12, u13, u23)

Sets the symmetric U tensor from the six unique values.

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