Uses of Class
org.strbio.mol.Atom

Packages that use Atom

org.strbio.mol

These classes represent objects or concepts useful to structural biologists.

Uses of Atom in org.strbio.mol

Subclasses of Atom in org.strbio.mol

class

AtomNode Class to represent a node in a list of atoms.

Methods in org.strbio.mol that return Atom

Atom	Monomer.atomSearch(java.lang.String name) Search the atoms of this monomer for the first atom with a given name.
Atom	Molecule.atomSearch(java.lang.String name) Search the atoms of this molecule for the first atom with a given name.

Methods in org.strbio.mol with parameters of type Atom

static double	Atom.bondAngle(Atom a, Atom b, Atom c) returns the bond angle in radians between three atoms, or Double.NaN if the coordinates of any are unknown.
static double	Atom.dihedralAngle(Atom a, Atom b, Atom c, Atom d) returns the dihedral angle in radians between four atoms, or Double.NaN if the coordinates of any are unknown.
static double	Atom.distance(Atom a, Atom b) returns the distance between two atoms, or Double.NaN if the coordinates of either are unknown.
static void	Atom.find4(Atom a, Atom b, Atom c, Atom d, double r, double theta, double phi) relocate an atom (D) , given three nearby atoms (A, B, and C) with known location, a bond length CD, bond angle BCD, and dihedral angle ABCD.
void	Atom.find4(Atom a, Atom b, Atom c, double r, double theta, double phi) relocate this atom (D) , given three nearby atoms (A, B, and C) with known location, a bond length CD, bond angle BCD, and dihedral angle ABCD.

Constructors in org.strbio.mol with parameters of type Atom

Atom(Atom q)
copies another atom, making its own copy of the data

AtomNode(Atom x)
when constructed from an Atom, it makes a new copy of the data in the Atom, but doesn't set next, prev.