Class Atom

x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:

• serial_number (int) - atom's UID
• name (str) - atom's name
• element (csb.core.EnumItem) - corresponding ChemElements
• vector (numpy array) - atom's coordinates
• alternate (bool) - if True, means that this is a wobbling atom with multiple alternative locations

Overrides: object.__init__

(inherited documentation)

repr(x)

Overrides: object.__repr__

(inherited documentation)

Extract the coordinates of the specified kind(s) of atoms and return them as a list.

Parameters:

• what - a list of atom kinds, e.g. ['N', 'CA', 'C']

Returns: list

a list of lists, each internal list corresponding to the coordinates of a 3D vector

Raises:

• Broken3DStructureError - if a specific atom kind cannot be retrieved from a residue

Overrides: AbstractEntity.get_coordinates

(inherited documentation)

Apply in place RotationMatrix and translation Vector to all atoms.

Overrides: AbstractEntity.transform

(inherited documentation)

alternate

Alternative location flag

Get Method:

unreachable.alternate(self) - Alternative location flag

Set Method:

unreachable.alternate(self, value)

Type:

str

bfactor

Temperature factor

Get Method:

unreachable.bfactor(self) - Temperature factor

Set Method:

unreachable.bfactor(self, value)

Type:

float

charge

Charge

Get Method:

unreachable.charge(self) - Charge

Set Method:

unreachable.charge(self, value)

Type:

int

element

Chemical element - a member of ChemElements

Get Method:

unreachable.element(self) - Chemical element - a member of ChemElements

Type:

enum item

items

Iterator over all immediate children of the entity

Get Method:

unreachable.items(self)

Type:

iterator of AbstractEntity

name

PDB atom name (trimmed)

Get Method:

unreachable.name(self) - PDB atom name (trimmed)

Type:

str

occupancy

Occupancy number

Get Method:

unreachable.occupancy(self) - Occupancy number

Set Method:

unreachable.occupancy(self, value)

Type:

float

residue

Residue instance that owns this atom (if available)

Get Method:

unreachable.residue(self) - Residue instance that owns this atom (if available)

Set Method:

unreachable.residue(self, residue)

Type:

Residue

serial_number

PDB serial number

Get Method:

unreachable.serial_number(self) - PDB serial number

Set Method:

unreachable.serial_number(self, number)

Type:

int

vector

Atom's 3D coordinates (x, y, z)

Get Method:

unreachable.vector(self) - Atom's 3D coordinates (x, y, z)

Set Method:

unreachable.vector(self, vector)

Type:

numpy.array