Uses of Class
pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.Atom

Packages that use Atom

pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit	Provides basic chemical building blocks.
pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids	Provides general-purpose aminoacids' classes.

Uses of Atom in pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit

Fields in pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit declared as Atom

private Atom	Bond.atom1
private Atom	Bond.atom2

Constructors in pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit with parameters of type Atom

Atom(Atom atom)

Bond(Atom atom1, Atom atom2)
Creates a new instance of Bond

CovalentBond(Atom atom1, Atom atom2)
Creates a new instance of CovalentBond

Uses of Atom in pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids

Fields in pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids declared as Atom

protected Atom	Aminoacid.C Carbon from {carbonyl group at Calpha}
protected Atom	Aminoacid.Ca Carbon alpha
private Atom	Alanine.Cb
private Atom	Arginine.Cb
private Atom	Asparagine.Cb
private Atom	Aspartate.Cb
private Atom	Cysteine.Cb
private Atom	Glutamate.Cb
private Atom	Glutamine.Cb
private Atom	Histidine.Cb
private Atom	Isoleucine.Cb
private Atom	Leucine.Cb
private Atom	Lysine.Cb
private Atom	Methionine.Cb
private Atom	Phenylalanine.Cb
private Atom	Proline.Cb
private Atom	Serine.Cb
private Atom	Threonine.Cb
private Atom	Tryptophan.Cb
private Atom	Tyrosine.Cb
private Atom	Valine.Cb
private Atom	Arginine.Cd
private Atom	Glutamate.Cd
private Atom	Glutamine.Cd
private Atom	Lysine.Cd
private Atom	Proline.Cd
private Atom	Isoleucine.Cd1
private Atom	Leucine.Cd1
private Atom	Phenylalanine.Cd1
private Atom	Tryptophan.Cd1
private Atom	Tyrosine.Cd1
private Atom	Histidine.Cd2
private Atom	Leucine.Cd2
private Atom	Phenylalanine.Cd2
private Atom	Tryptophan.Cd2
private Atom	Tyrosine.Cd2
private Atom	Lysine.Ce
private Atom	Methionine.Ce
private Atom	Histidine.Ce1
private Atom	Phenylalanine.Ce1
private Atom	Tyrosine.Ce1
private Atom	Phenylalanine.Ce2
private Atom	Tryptophan.Ce2
private Atom	Tyrosine.Ce2
private Atom	Tryptophan.Ce3
private Atom	Arginine.Cg
private Atom	Asparagine.Cg
private Atom	Aspartate.Cg
private Atom	Glutamate.Cg
private Atom	Glutamine.Cg
private Atom	Histidine.Cg
private Atom	Leucine.Cg
private Atom	Lysine.Cg
private Atom	Methionine.Cg
private Atom	Phenylalanine.Cg
private Atom	Proline.Cg
private Atom	Tryptophan.Cg
private Atom	Tyrosine.Cg
private Atom	Isoleucine.Cg1
private Atom	Valine.Cg1
private Atom	Isoleucine.Cg2
private Atom	Threonine.Cg2
private Atom	Valine.Cg2
private Atom	Tryptophan.Ch2
private Atom	Arginine.Cz
private Atom	Phenylalanine.Cz
private Atom	Tyrosine.Cz
private Atom	Tryptophan.Cz2
private Atom	Tryptophan.Cz3
protected Atom	Aminoacid.N Nitrogen from amid group at Calpha
private Atom	Histidine.Nd1
private Atom	Asparagine.Nd2
private Atom	Arginine.Ne
private Atom	Tryptophan.Ne1
private Atom	Glutamine.Ne2
private Atom	Histidine.Ne2
private Atom	Arginine.Nh1
private Atom	Arginine.Nh2
private Atom	Lysine.Nz
protected Atom	Aminoacid.O Oxygen from {carbonyl group at Calpha}
private Atom	Asparagine.Od1
private Atom	Aspartate.Od1
private Atom	Aspartate.Od2
private Atom	Glutamate.Oe1
private Atom	Glutamine.Oe1
private Atom	Glutamate.Oe2
private Atom	Serine.Og
private Atom	Threonine.Og1
private Atom	Tyrosine.Oh
private Atom	Methionine.Sd
private Atom	Cysteine.Sg

Methods in pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids that return Atom

Atom	Aminoacid.getCcarbonyl()
Atom	Aminoacid.getNamid()

Methods in pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids that return types with arguments of type Atom

java.util.List<Atom>

Aminoacid.getBackboneAtomsWithoutOcarbonyl()

Methods in pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids with parameters of type Atom

void	Aminoacid.setPhiAngle(Atom prevC) Calls calcTorsionalAngle with appropriate atoms.
void	Aminoacid.setPsiAngle(Atom nextN) Calls calcTorsionalAngle with appropriate atoms.