Atom¶
This class stores all properties (attributes) related to an atom.
When pmx reads a PDB file, each line starting with “ATOM” or “HETATM”
is converted to an Atom instance. In addition, the atom class also has a number
of methods that can be used to calculate distances, angles and dihedrals.
API Reference¶
-
class
pmx.atom.Atom(line=None, mol2line=None, **kwargs)¶ Atom Class.
- Parameters
line (str, optional) – input line in PDB format. Default is None.
mol2line (str, optional) – input line in MOL2 format. Default is None.
-
id¶ atom id
- Type
int
-
name¶ atom name
- Type
str
-
resname¶ name of residue atom is part of
- Type
str
-
chain_id¶ ID of the chain atom belongs to
- Type
str
-
x¶ atom coordinates
- Type
array
-
occ¶ occupancy
- Type
float
-
bfac¶ B-factor
- Type
float
-
symbol¶ chemical element of the atom
- Type
str
-
unity¶ unit of the coordinates, either ‘A’ or ‘nm’. Default is ‘A’.
- Type
str
Methods
dist(other)Calculates the distance between two atoms.
dist2(other)Calculates the squared distance between two atoms.
translate(v)Translates the position of the atom.
angle(other1, other2[, degree])Calcluates the angle between 3 atoms.
dihedral(other1, other2, other3[, degree])Calculates the dihedral angle between four atoms.
nm2a()Converts the Atom coordinates from nanometers (nm) to Angstrom (A).
a2nm()Converts the Atom coordinates from Angstrom (A) to nanometers (nm).