A B C D E F G H I J L M N O P Q R S T U V W X Y Z

A

About - Class in pl.krakow.cmuj.bioinformatics.jellipse

Displays a window with a short conventional information about the program.

About() - Constructor for class pl.krakow.cmuj.bioinformatics.jellipse.About

Creates new form About

AbsDeviation - Class in pl.krakow.cmuj.bioinformatics.jellipse

Enables plotting the absolute value of the difference between the Ln of the radius of curvature of the current structure (observable) and the value of the parameter obtained analyzing model peptides.

AbsDeviation() - Constructor for class pl.krakow.cmuj.bioinformatics.jellipse.AbsDeviation

absdeviation - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Aminoacid

avergage dihedral angle between two consecutive peptide bond planes (taken twice)

accept(File) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.FFilter

Return true if this file should be shown in the directory pane, false if it shouldn't.

actionPerformed(ActionEvent) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.ChainChooser.ButtonListener

Should be syncronized with getSelectedChainId() and notify() but it won't work.

actionPerformed(ActionEvent) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.StructureRenderer.wl

add(Vector3) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.mathtoolkit.Vector3

adds a vectors to the current one (doesn't alter existing vectors)

addExtension(String) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.FFilter

Adds a filetype "dot" extension to filter against.

addToMe(Vector3) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.mathtoolkit.Vector3

adds a vector to the current one (and alters it!)

AdjustHeight - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.StructureRenderer

AdjustWidth - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.StructureRenderer

Alanine - Class in pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids

An alanine molecule.

Alanine(String, Map) - Constructor for class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Alanine

Creates a new instance of the Alanine aminoacid.

Aminoacid - Class in pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids

A skeleton for building every concrete aminoacid.

Aminoacid(String, Map) - Constructor for class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Aminoacid

Creates a new instance of the Cysteine aminoacid.

AminoacidProperties - Interface in pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids

Reading chemical properties of aminoacids.

animatorMolecule - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.jEllipse

animatorPlot - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.jEllipse

AntiAlias - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.Surface

appendAmino(String, String, Map) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.Peptide

Appends an aminoacid of known coordinates to the chain.

Arginine - Class in pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids

An arginine molecule.

Arginine(String, Map) - Constructor for class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Arginine

Creates a new instance of the Histidine aminoacid.

Asparagine - Class in pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids

An asparagine molecule.

Asparagine(String, Map) - Constructor for class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Asparagine

Creates a new instance of the Asparagine aminoacid.

Aspartate - Class in pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids

An aspartate molecule.

Aspartate(String, Map) - Constructor for class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Aspartate

Creates a new instance of the Aspartatne aminoacid.

Atom - Class in pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit

Coordinates for an atom, and read-only methods.

Atom(float[]) - Constructor for class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.Atom

Creates a new instance of Atom

Atom(Object) - Constructor for class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.Atom

Atom(Atom) - Constructor for class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.Atom

Atom(float, float, float) - Constructor for class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.Atom

atom1 - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.Bond

atom2 - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.Bond

ATOMNAMESTART - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.PdbFile

ATOMNAMESTOP - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.PdbFile

AvgDihedralAngle - Class in pl.krakow.cmuj.bioinformatics.jellipse

Enables plotting averaged dihedral angle between consecutive peptide bond planes computed along the whole polypeptide chain.

AvgDihedralAngle() - Constructor for class pl.krakow.cmuj.bioinformatics.jellipse.AvgDihedralAngle

avgdihedralangle - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Aminoacid

avergage dihedral angle between two consecutive peptide bond planes (taken twice)