| AFPFromFasta |
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| AlignmentGuiDemo |
Get an instance of the two alignment GUIs.
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| BioJavaAADemo |
Created by andreas on 8/9/14.
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| ChemCompDistribution |
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| CookBook |
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| CookbookMSA |
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| DemoAlignmentFromFasta |
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| DemoAlignProteins |
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| DemoAsa |
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| DemoAtomCache |
Example of how to load PDB files using the AtomCache class.
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| DemoBerkeleyScop |
A demo for how to use the Berkeley version of SCOP instead of the default UK-SCOP
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| DemoBioAssemblies |
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| DemoCATH |
An example for how to access CATH data.
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| DemoCE |
Example of how to run a structure alignment using the CE algorithm.
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| DemoCeSymm |
Quick demo of how to call CE-Symm programmatically.
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| DemoChangeChemCompProvider |
This demo shows how to use an alternative ChemCompProvider.
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| DemoCommandLineStartup |
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| DemoContacts |
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| DemoCrystalInterfaces |
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| DemoDistanceTree |
This demo contains the CookBook example to create a phylogenetic tree from a
multiple sequence alignment (MSA).
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| DemoDomainsplit |
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| DemoFATCAT |
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| DemoLoadSecStruc |
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).
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| DemoLoadStructure |
Example for how to load protein structures (from PDB files).
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| DemoLoadSubstMax |
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| DemoMMCIFReader |
An example of how to read MMcif files
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| DemoMmcifToPdbConverter |
An example of how to convert mmCIF file to PDB file
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| DemoMmtfReader |
Class to show how to read a Biojava structure using MMTF
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| DemoMmtfWriter |
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| DemoMultipleMC |
Demo for running the MultipleMC Algorithm on a protein family.
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| DemoNWALignment |
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| DemoQsAlign |
Demo on how to use programatically QsAlign for the alignment of
quaternary structures. |
| DemoQuatSymmetryJmol |
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| DemoRotationAxis |
A demo for how to use RotationAxis to display the rotation for an
alignment. |
| DemoSCOP |
A class demonstrating the use of the SCOP parsing tools
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| DemoSecStrucCalc |
Demonstration on how to use the Secondary Structure Prediction (DSSP)
implementation in BioJava and obtain different SS representations and
outputs.
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| DemoShowBiolAssembly |
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| DemoShowCATHDomain |
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| DemoShowLargeAssembly |
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| DemoSixFrameTranslation |
Created by andreas on 8/10/15.
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| DemoStructureFromFasta |
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| DemoSW3DAligner |
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| DemoSymmetry |
A demo on how to use the quaternary symmetry detection algorithms.
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| HmmerDemo |
The cookbook recipe for how to request Pfam annotations for a protein sequence using the Hmmer3 service
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| NCBIQBlastServiceDemo |
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| ParseFastaFileDemo |
Created by andreas on 6/17/15.
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| ParseGO |
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| PredictDisorder |
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| ShowStructureInJmol |
Demo how to load and display a structure in Jmol
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| TestDNANeedlemanWunsch |
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| UncompressFile |
Uncompresses a single tarred or zipped file, writing output to stdandard out
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| WebStartClientDemo |
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