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'STRAP:multiple sequence alignments ' | ||||||||
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Interface Summary | |
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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 | |
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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
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'STRAP:multiple sequence alignments ' | ||||||||
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