Package demo
package demo
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ClassesClassDescriptionDemo displaying a structural alignment from a FASTA file using
FastaAFPChainConverter.Get an instance of the two alignment GUIs.Created by andreas on 8/9/14.Demo of how to use theFastaStructureParserclass to read protein structures from a FASTA file.Example of how to load PDB files using the AtomCache class.A demo for how to use the Berkeley version of SCOP instead of the default UK-SCOPAn example for how to access CATH data.Example of how to run a structure alignment using the CE algorithm.Quick demo of how to call CE-Symm programmatically.This demo shows how to use an alternative ChemCompProvider.This demo contains the CookBook example to create a phylogenetic tree from a multiple sequence alignment (MSA).Demonstration of how to load a Structure with the SS information, either from the PDB file annotation (Author's assignment) or from the DSSP file in the PDB servers (DSSP assignment).Example for how to load protein structures (from PDB files).An example of how to read MMcif filesAn example of how to convert mmCIF file to PDB fileDemo for running the MultipleMC Algorithm on a protein family.Demo on how to use programaticallyQsAlignfor the alignment of quaternary structures.This demo shows how to display theQuatSymmetryResultsof a structure.A demo for how to useRotationAxisto display the rotation for an alignment.A class demonstrating the use of the SCOP parsing toolsDemonstration on how to use the Secondary Structure Prediction (DSSP) implementation in BioJava and obtain different SS representations and outputs.Created by andreas on 8/10/15.Demo of how to use theFastaStructureParserclass to read protein structures from a FASTA file.A demo on how to use the quaternary symmetry detection algorithms.The cookbook recipe for how to request Pfam annotations for a protein sequence using the Hmmer3 serviceA simple demo showingNCBIQBlastServiceusageCreated by andreas on 6/17/15.Demo how to load and display a structure in JmolUncompresses a single tarred or zipped file, writing output to stdandard out