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

C

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

Carbon from {carbonyl group at C_alpha}

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

Carbon _alpha

calcTorsionalAngle(Vector3, Vector3, Vector3, Vector3) - Static method in class pl.krakow.cmuj.bioinformatics.jellipse.mathtoolkit.Math3d

Calculates torsional angle set up by four atoms

calculateAbsDeviations() - Method in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.Peptide

calculateDeviations() - Method in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.Peptide

calculatePeptideBondPlanesDihedral() - Method in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.Peptide

Cb - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Alanine

Cb - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Arginine

Cb - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Asparagine

Cb - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Aspartate

Cb - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Cysteine

Cb - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Glutamate

Cb - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Glutamine

Cb - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Histidine

Cb - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Isoleucine

Cb - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Leucine

Cb - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Lysine

Cb - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Methionine

Cb - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Phenylalanine

Cb - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Proline

Cb - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Serine

Cb - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Threonine

Cb - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Tryptophan

Cb - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Tyrosine

Cb - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Valine

Cd - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Arginine

Cd - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Glutamate

Cd - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Glutamine

Cd - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Lysine

Cd - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Proline

Cd1 - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Isoleucine

Cd1 - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Leucine

Cd1 - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Phenylalanine

Cd1 - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Tryptophan

Cd1 - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Tyrosine

Cd2 - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Histidine

Cd2 - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Leucine

Cd2 - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Phenylalanine

Cd2 - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Tryptophan

Cd2 - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Tyrosine

Ce - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Lysine

Ce - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Methionine

Ce1 - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Histidine

Ce1 - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Phenylalanine

Ce1 - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Tyrosine

Ce2 - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Phenylalanine

Ce2 - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Tryptophan

Ce2 - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Tyrosine

Ce3 - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Tryptophan

centerOfThreePointCircle(Vector3, Vector3, Vector3) - Static method in class pl.krakow.cmuj.bioinformatics.jellipse.mathtoolkit.Math3d

calculates the location of a circle that intersects three points (in 3d) and is (of course) co-planar with them ============= Here comes Maple code, that produced solutions ============== restart: with(linalg): 2 equations on radii equivalence, the 3rd on coplanar location eqns :={ (r0-a0)^2 + (r1-a1)^2 + (r2-a2)^2 = (r0-b0)^2 + (r1-b1)^2 + (r2-b2)^2, (r0-a0)^2 + (r1-a1)^2 + (r2-a2)^2 = (r0-c0)^2 + (r1-c1)^2 + (r2-c2)^2, det(matrix( [ [r0-a0, r1-a1, r2-a2], [b0-a0, b1-a1, b2-a2], [c0-a0, c1-a1, c2-a2] ] ))=0 }: rcoords := solve( eqns, {r0,r1,r2} ): x := simplify(subs(rcoords,r0)); y := simplify(subs(rcoords,r1)); z := simplify(subs(rcoords,r2)); distance test randomize(123): los := rand(-100..100): a0 := los(): a1 := los(): a2 := los(): b0 := los(): b1 := los(): b2 := los(): c0 := los(): c1 := los(): c2 := los(): dista:=evalf(sqrt((a0-x)^2 + (a1-y)^2 + (a2-z)^2)); distb:=evalf(sqrt((b0-x)^2 + (b1-y)^2 + (b2-z)^2)); distc:=evalf(sqrt((c0-x)^2 + (c1-y)^2 + (c2-z)^2)); visual test PLOT3D(POINTS( [a0,a1,a2], [b0,b1,b2], [c0,c1,c2], [x, y, z], SYMBOL(DIAMOND) ) ); ---------------------------------------------------------------------------

centerWindow(Component) - Static method in class pl.krakow.cmuj.bioinformatics.jellipse.ChainChooser

Displays any component in the center of the screen.

centerWindow(Component) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.jEllipse

Displays any java.awt.component in the center of the screen

centerWindow(Component) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.PdbFetcher

Displays any component in the center of the screen.

Cg - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Arginine

Cg - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Asparagine

Cg - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Aspartate

Cg - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Glutamate

Cg - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Glutamine

Cg - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Histidine

Cg - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Leucine

Cg - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Lysine

Cg - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Methionine

Cg - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Phenylalanine

Cg - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Proline

Cg - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Tryptophan

Cg - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Tyrosine

Cg1 - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Isoleucine

Cg1 - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Valine

Cg2 - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Isoleucine

Cg2 - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Threonine

Cg2 - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Valine

Ch2 - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Tryptophan

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

chain - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.LnRvsVPlot

chain - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.PlotRenderer

chain - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.RamachandranMap

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

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

If there is more than one chain in the PDB file, enables user to choose.

ChainChooser(int, String) - Constructor for class pl.krakow.cmuj.bioinformatics.jellipse.ChainChooser

Creates new form selectChain

ChainChooser.ButtonListener - Class in pl.krakow.cmuj.bioinformatics.jellipse

Dynamic listener (handles unknown number of buttons, that depends on the number of chains among which the user has to choose.

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

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

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

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

clear() - Method in class pl.krakow.cmuj.bioinformatics.jellipse.SwingWorker.ThreadVar

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

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

color - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.PinkBlue

values of red, green, blue calculated by getColor

color - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.RedGreen

values of red, green, blue calculated by getColor

ColorScheme - Interface in pl.krakow.cmuj.bioinformatics.jellipse

Interface allowing switching between predefined color schemes.

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

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

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

construct() - Method in class pl.krakow.cmuj.bioinformatics.jellipse.SwingWorker

Compute the value to be returned by the get method.

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

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

Creates a new instance of CovalentBond

createBinaryImage(int, int, int) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.Surface

createBufferedImage(Graphics2D, int, int, int) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.Surface

createGraphics2D(int, int, BufferedImage, Graphics) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.Surface

createSGISurface(int, int, int) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.Surface

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

performs cross multiplication on current and given vectors (doesn't alter existing vectors)

cross(Vector3, Vector3) - Static method in class pl.krakow.cmuj.bioinformatics.jellipse.mathtoolkit.Vector3

perform cross multiplication on vectors (and doesn't alter any existing)

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

performs cross multiplication on current and given vectors (alters current one!)

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

A cysteine molecule.

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

Creates a new instance of the Cysteine aminoacid.

Cz - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Arginine

Cz - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Phenylalanine

Cz - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Tyrosine

Cz2 - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Tryptophan

Cz3 - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Tryptophan