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

P

paint(Graphics) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.Surface

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

It's possible to turn off double-buffering for just the repaint calls invoked directly on the non double buffered component.

parse(String) - Method in class pl.krakow.cmuj.bioinformatics.jellipse.ChainChooser

This method exists only because ButtonListener.actionPerformed cannot handle its synchronization and cannot produce working notify().

pbCaps - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.ScreenShot

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

pbufferHeight - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.ScreenShot

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

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

pbufferWidth - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.ScreenShot

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

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

pdb - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.PdbFetcher

pdbContent - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.PdbFetcher

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

Loads PDB file content via http protocol from RCSB or from a local file.

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

Creates new PdbFetcher and displays as a JFrame

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

String operations' implementations are dirty and require more study on regexps, although they work and are quite fast.

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

Creates a new instance of PdbFile

pdbid - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.PdbFetcher

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

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

Sequential residue number, must be String because of so called iColde.

pdbsize - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.PdbFetcher

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

Fully described polipeptide chain with aminoacids.

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

Creates a new instance of Peptide

peptide - Variable in class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.Peptide

if one day we would like to read complexes with e.g aacids

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

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

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

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

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

A phenylalanine molecule.

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

Creates a new instance of the Methionine aminoacid.

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

backbone phi torsional angle

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

Pastel, a bit synthetic color scheme.

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

create new instance of ColorScheme due to the PinkBlue scheme

pl.krakow.cmuj.bioinformatics.jellipse - package pl.krakow.cmuj.bioinformatics.jellipse

Provides main application networking, file-handling and GUI support.

pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit - package pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit

Provides basic chemical building blocks.

pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids - package pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids

Provides general-purpose aminoacids' classes.

pl.krakow.cmuj.bioinformatics.jellipse.mathtoolkit - package pl.krakow.cmuj.bioinformatics.jellipse.mathtoolkit

Provides linear algebra front-end for polypeptide and scene geometry.

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

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

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

PlotRenderer(jEllipse, Peptide) - Constructor for class pl.krakow.cmuj.bioinformatics.jellipse.PlotRenderer

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

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

Common functions for all properties that can be represented in a 2D plot.

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

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

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

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

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

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

A proline molecule.

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

Creates a new instance of the Proline aminoacid.

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

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

backbone psi torsional angle