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<!DOCTYPE HTML>

<head>

<title>demo (biojava 5.2.0 API)</title>

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</head>

<body>

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<h1 title="Package" class="title">Package demo</h1>

</div>

<caption><span>Class Summary</span><span class="tabEnd"> </span></caption>

<tr>

<th class="colFirst" scope="col">Class</th>

<th class="colLast" scope="col">Description</th>

</tr>

<tbody>

<th class="colFirst" scope="row"><a href="AFPFromFasta.html" title="class in demo">AFPFromFasta</a></th>

<div class="block">Demo displaying a structural alignment from a FASTA file using <a href="../org/biojava/nbio/structure/io/FastaAFPChainConverter.html" title="class in org.biojava.nbio.structure.io"><code>FastaAFPChainConverter</code></a>.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="AlignmentGuiDemo.html" title="class in demo">AlignmentGuiDemo</a></th>

<div class="block">Get an instance of the two alignment GUIs.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="BioJavaAADemo.html" title="class in demo">BioJavaAADemo</a></th>

<div class="block">Created by andreas on 8/9/14.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="ChemCompDistribution.html" title="class in demo">ChemCompDistribution</a></th>

</tr>

<th class="colFirst" scope="row"><a href="CookBook.html" title="class in demo">CookBook</a></th>

</tr>

<th class="colFirst" scope="row"><a href="CookbookMSA.html" title="class in demo">CookbookMSA</a></th>

</tr>

<th class="colFirst" scope="row"><a href="DemoAlignmentFromFasta.html" title="class in demo">DemoAlignmentFromFasta</a></th>

<div class="block">Demo of how to use the <a href="../org/biojava/nbio/structure/io/FastaStructureParser.html" title="class in org.biojava.nbio.structure.io"><code>FastaStructureParser</code></a> class to read protein

structures from a FASTA file.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="DemoAlignProteins.html" title="class in demo">DemoAlignProteins</a></th>

</tr>

<th class="colFirst" scope="row"><a href="DemoAsa.html" title="class in demo">DemoAsa</a></th>

</tr>

<th class="colFirst" scope="row"><a href="DemoAtomCache.html" title="class in demo">DemoAtomCache</a></th>

<div class="block">Example of how to load PDB files using the AtomCache class.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="DemoBerkeleyScop.html" title="class in demo">DemoBerkeleyScop</a></th>

<div class="block">A demo for how to use the Berkeley version of SCOP instead of the default UK-SCOP</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="DemoBioAssemblies.html" title="class in demo">DemoBioAssemblies</a></th>

</tr>

<th class="colFirst" scope="row"><a href="DemoCATH.html" title="class in demo">DemoCATH</a></th>

<div class="block">An example for how to access CATH data.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="DemoCE.html" title="class in demo">DemoCE</a></th>

<div class="block">Example of how to run a structure alignment using the CE algorithm.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="DemoCeSymm.html" title="class in demo">DemoCeSymm</a></th>

<div class="block">Quick demo of how to call CE-Symm programmatically.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="DemoChangeChemCompProvider.html" title="class in demo">DemoChangeChemCompProvider</a></th>

<div class="block">This demo shows how to use an alternative ChemCompProvider.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="DemoCommandLineStartup.html" title="class in demo">DemoCommandLineStartup</a></th>

</tr>

<th class="colFirst" scope="row"><a href="DemoContacts.html" title="class in demo">DemoContacts</a></th>

</tr>

<th class="colFirst" scope="row"><a href="DemoCrystalInterfaces.html" title="class in demo">DemoCrystalInterfaces</a></th>

</tr>

<th class="colFirst" scope="row"><a href="DemoDistanceTree.html" title="class in demo">DemoDistanceTree</a></th>

<div class="block">This demo contains the CookBook example to create a phylogenetic tree from a

multiple sequence alignment (MSA).</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="DemoDomainsplit.html" title="class in demo">DemoDomainsplit</a></th>

</tr>

<th class="colFirst" scope="row"><a href="DemoFATCAT.html" title="class in demo">DemoFATCAT</a></th>

</tr>

<th class="colFirst" scope="row"><a href="DemoLoadSecStruc.html" title="class in demo">DemoLoadSecStruc</a></th>

<div class="block">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).</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="DemoLoadStructure.html" title="class in demo">DemoLoadStructure</a></th>

<div class="block">Example for how to load protein structures (from PDB files).</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="DemoLoadSubstMax.html" title="class in demo">DemoLoadSubstMax</a></th>

</tr>

<th class="colFirst" scope="row"><a href="DemoMMCIFReader.html" title="class in demo">DemoMMCIFReader</a></th>

<div class="block">An example of how to read MMcif files</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="DemoMmcifToPdbConverter.html" title="class in demo">DemoMmcifToPdbConverter</a></th>

<div class="block">An example of how to convert mmCIF file to PDB file</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="DemoMmtfReader.html" title="class in demo">DemoMmtfReader</a></th>

<div class="block">Class to show how to read a Biojava structure using MMTF</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="DemoMmtfWriter.html" title="class in demo">DemoMmtfWriter</a></th>

</tr>

<th class="colFirst" scope="row"><a href="DemoMultipleMC.html" title="class in demo">DemoMultipleMC</a></th>

<div class="block">Demo for running the MultipleMC Algorithm on a protein family.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="DemoNWALignment.html" title="class in demo">DemoNWALignment</a></th>

</tr>

<th class="colFirst" scope="row"><a href="DemoQsAlign.html" title="class in demo">DemoQsAlign</a></th>

<div class="block">Demo on how to use programatically <a href="../org/biojava/nbio/structure/align/quaternary/QsAlign.html" title="class in org.biojava.nbio.structure.align.quaternary"><code>QsAlign</code></a> for the alignment of

quaternary structures.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="DemoQuatSymmetryJmol.html" title="class in demo">DemoQuatSymmetryJmol</a></th>

<div class="block">This demo shows how to display the <a href="../org/biojava/nbio/structure/symmetry/core/QuatSymmetryResults.html" title="class in org.biojava.nbio.structure.symmetry.core"><code>QuatSymmetryResults</code></a> of a

structure.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="DemoRotationAxis.html" title="class in demo">DemoRotationAxis</a></th>

<div class="block">A demo for how to use <a href="../org/biojava/nbio/structure/align/util/RotationAxis.html" title="class in org.biojava.nbio.structure.align.util"><code>RotationAxis</code></a> to display the rotation for an

alignment.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="DemoSCOP.html" title="class in demo">DemoSCOP</a></th>

<div class="block">A class demonstrating the use of the SCOP parsing tools</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="DemoSecStrucCalc.html" title="class in demo">DemoSecStrucCalc</a></th>

<div class="block">Demonstration on how to use the Secondary Structure Prediction (DSSP)

implementation in BioJava and obtain different SS representations and

outputs.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="DemoShowBiolAssembly.html" title="class in demo">DemoShowBiolAssembly</a></th>

</tr>

<th class="colFirst" scope="row"><a href="DemoShowCATHDomain.html" title="class in demo">DemoShowCATHDomain</a></th>

</tr>

<th class="colFirst" scope="row"><a href="DemoShowLargeAssembly.html" title="class in demo">DemoShowLargeAssembly</a></th>

</tr>

<th class="colFirst" scope="row"><a href="DemoShowValidationResults.html" title="class in demo">DemoShowValidationResults</a></th>

</tr>

<th class="colFirst" scope="row"><a href="DemoSixFrameTranslation.html" title="class in demo">DemoSixFrameTranslation</a></th>

<div class="block">Created by andreas on 8/10/15.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="DemoStructureFromFasta.html" title="class in demo">DemoStructureFromFasta</a></th>

structures from a FASTA file.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="DemoSW3DAligner.html" title="class in demo">DemoSW3DAligner</a></th>

</tr>

<th class="colFirst" scope="row"><a href="DemoSymmetry.html" title="class in demo">DemoSymmetry</a></th>

<div class="block">A demo on how to use the quaternary symmetry detection algorithms.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="HmmerDemo.html" title="class in demo">HmmerDemo</a></th>

<div class="block">The cookbook recipe for how to request Pfam annotations for a protein sequence using the Hmmer3 service</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="NCBIQBlastServiceDemo.html" title="class in demo">NCBIQBlastServiceDemo</a></th>

<div class="block">A simple demo showing <a href="../org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.html" title="class in org.biojava.nbio.ws.alignment.qblast"><code>NCBIQBlastService</code></a> usage</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="ParseFastaFileDemo.html" title="class in demo">ParseFastaFileDemo</a></th>

<div class="block">Created by andreas on 6/17/15.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="ParseGO.html" title="class in demo">ParseGO</a></th>

</tr>

<th class="colFirst" scope="row"><a href="PredictDisorder.html" title="class in demo">PredictDisorder</a></th>

</tr>

<th class="colFirst" scope="row"><a href="ShowStructureInJmol.html" title="class in demo">ShowStructureInJmol</a></th>

<div class="block">Demo how to load and display a structure in Jmol</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="TestDNANeedlemanWunsch.html" title="class in demo">TestDNANeedlemanWunsch</a></th>

</tr>

<th class="colFirst" scope="row"><a href="WebStartClientDemo.html" title="class in demo">WebStartClientDemo</a></th>

</tr>

</tbody>

</table>

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