mmLib.Structure.Atom

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)