Package charite.christo.protein

Interface Summary

CoiledCoil_Predictor	Classes that provide a prediction of coiled coils.
HasProtein	Implemented by objects that contain references to Proteins.
NeedsProteins	Implemented by dialogs that act on a Protein.
PhylogeneticTree
PredictionFromAminoacidSequence	Classes that provide a prediction depending on amino acid setSequences.
PredictSubcellularLocation
ProteinAlignment	HELP PACKAGE:charite.christo.strap. PACKAGE:charite.christo.
ProteinParser	HELP Proteins are stored in plain text files.
ProteinViewer	A protein viewer can display proteins three-dimensionally.
ProteinWriter	A ProteinWriter is used to export a protein to a text file using a certain format such as pdb or fasta.
ResidueSelection	HELP PACKAGE:charite.christo.strap. Residue selections are objects attached to proteins which select one or more amino acid positions from the amino acid sequence.
SecondaryStructure_Predictor
SelectorOfNucleotides	Selects nucleotides.
SequenceAligner	Classes that provide a calculation of sequence alignments.
SequenceAligner3D
SequenceAlignerSorting	It can reorder proteins so that similar sequences are in adjacent lines.
SequenceAlignerTakesProfile
SequenceDisSimilarity	Compares two amino acid sequences and returns a float value
SimilarPdbFinder
StrapListener	All plugins that need to react on changes of the alignment should implement this interface.
Superimpose3D	Implemented by plugins that perform a 3D-superposition of the C-alpha atoms of two protein chains.
TransmembraneHelix_Predictor	Classes that provide a prediction of membrane spanning helices.
ValueOfProtein	Plugin that returns a numeric value for the protein or NaN.
ValueOfResidue
VisibleIn123	Determins the style how a selection is visualized and where it is visualized.

Class Summary

AbstractPredictionFromAminoacidSequence
AbstractProteinViewerProxy
AbstractValueOfResidue
AbstractVisibleIn123	An abstract implementation of VisibleIn123.
Backtranslate
Backtranslate.Codonusage
BasicResidueSelection	A skelleton of an Selection of Residues ResidueSelection.
Bl2seq	HELP Given is an amino acid sequence and one (or several) nucleotide sequences of unknown frame shift.
Bl2seq.Hit
Blosum
ChAlignUtils
ChAstex
ChAstexPROXY	HELP Home: http://openastexviewer.net http://www.astex-therapeutics.com/ License of OpenAstexViewer: WIKI:LGPL Authors: Mike Hartshorn, Tom Oldfield
ChJmol	Jmol Home: http://jmol.sourceforge.net/ License: WIKI:LGPL
ChJmolPROXY	HELP Home: http://jmol.sourceforge.net/ License: WIKI:LGPL The protein structure viewer WIKI:Jmol is written in Java and understands Rasmol-instructions.
ChSoapEBI
CrudeSequenceDisSimilarity	Counting dissimilar residues in two aligned sequences.
CrudeSequenceSimilarity	Counting identical residues in two aligned sequences.
DAS
DAS.Capability
DAS.Coordinates
DAS.Entry
DSSP_Parser	HELP DSSP-files are calculated from PDB-files with the program DSSP by Kabsh and Sander which is freely available in the Web (see WIKI:DSSP_(protein)).
FetchSeqs
FindUniprotID
Gaps2Columns	HELP When there are gaps occurring in all loaded sequences at the same position they are usually not displayed.
HeteroCompound	HELP The HeteroCompound class can hold two types of 3D-structures: Ligands like NADH, FAD, FMN and metal ions encoded in PDB files in the form
Matrix3D	A matrix defines an affine transformation in 3D space.
MergeAlignments
MultiFromPairAligner	This class converts SequenceAligner for two proteins into one for many proteins.
MultipleSequenceParser	Reads multiple sequences formats: clustalW, MSF, WIKI:Fasta see http://www.molecularevolution.org/mbl/resources/fileformats/ http://bioinformatics.abc.hu/tothg/biocomp/other/Stockholm.html WIKI:Stockholm_format http://www.ebi.ac.uk/help/formats_frame.html http://www.bioinformatics.nl/tools/crab_pir.html
NumberedSequence_Parser	HELP Sequence files where the sequence block is at the end of the file.
PDB_Parser	HELP Those lines containing CA in the third column describe C-alpha atoms.
PDB_Parser_SeqRes	The SEQRES lines in PDB files look like this:
Picr_EBI
PredictSubcellularLocation.Prediction
Protein	PACKAGE:charite.christo.strap. The class Protein provides a protein model with amino acid sequences and coordinates for c-alpha atoms.
Protein3d	HELP PACKAGE:charite.christo.strap. The simple 3D-viewer visualizes the C-alpha trace of one or several proteins as a polygon.
Protein3d.PView
Protein3dUtils
ProteinLabel	A label for protein objects e.g.
ProteinMC
ProteinUtils
ProteinWriter1	Write a protein file
Pymol	HELP WIKI:PyMOL HOME_PAGE:Pymol is a widely applied protein structure viewer by Warren Delano.
ReferenceSequence
SBD_Parser	HELP .sbd Files created with SeqBuilder
Selection3D
SequenceForPdbID	HELP
ShadingAA	Residues are shaded according to their physical and chemical properties.
SimilarPdb_blastEBI
SimilarPdbFinder.Result
SingleFastaParser	HELP The fasta format is characterized by a greater than character followed by the header ( WIKI:FASTA_format).
StrapEvent	StrapEvent's are broadcasted using JAVADOC:StrapEvent#run().
StupidParser	HELP This parser is indeed stupid.
Superimpose3D.Result
SwissHeaderParser	The header of swissprot files contains the definition, organism ...
XML_SequenceParser	HELP