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adding a java example
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‎wiki/BioJava:CookBook:PDB:hibernate.md‎

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@@ -7,10 +7,228 @@ How to serialize a protein structure to a database
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There is a little project that provides
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[Hibernate](http://www.hibernate.org) mappings for the protein structure
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classes at
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[<http://www.spice-3d.org/hibernatePDB/>](http://www.spice-3d.org/hibernatePDB/).
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It mainly consists of the Hibernate mappings files,with a few Java
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helper classes.
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classes at [BioJava Structure
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Hibernate](http://www.spice-3d.org/hibernatePDB/). It mainly consists of
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the Hibernate mappings files,with a few Java helper classes.
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I am not sure if this should be joint with the core BioJava
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CVS. --[Andreas](User:Andreas "wikilink") 17:42, 8 October 2007 (EDT)
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I am not sure if this code should be joint with the core BioJava CVS,
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but then BioJava should not directly depend on
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Hibernate... --[Andreas](User:Andreas "wikilink") 17:42, 8 October 2007
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(EDT)
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If you have BioJava Structure Hibernate installed, you can do something
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like:
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See also the [example
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page](http://www.spice-3d.org/hibernatePDB/examples.jsp)
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<java>
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import org.biojava.bio.structure.Chain; import
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org.biojava.bio.structure.Compound; import
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org.biojava.bio.structure.Group; import
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org.biojava.bio.structure.Structure; import
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org.biojava.bio.structure.hibernate.HibernateUtil; import
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org.biojava.bio.structure.hibernate.StructureFile; import
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org.biojava.bio.structure.io.PDBFileReader; import
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org.hibernate.HibernateException; import org.hibernate.Session; import
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java.io.File; import java.io.FileFilter; import java.util.ArrayList;
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import java.util.List;
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/\*\* A class that finds all PDB files from the filesystem and stores
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them in the database.
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`* A current release of PDB (2007 - September) takes about one night for an upload`
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`* (without the atoms).`
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`* `
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`*`
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`*/`
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public class DemoWritePDBFiles {
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`   public static void main(String[] args) {`
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`   `
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`       // init log4j`
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`       //org.apache.log4j.BasicConfigurator.configure();`
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`       if (args.length < 1 ) {`
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`           System.err.println("please provide PDB directory as argument");`
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`           System.exit(0);`
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`       }`
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// init the installation
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`       File pdbLocation = new File(args[0]);`
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`       System.out.println("searching in " + pdbLocation);`
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`       // init the demo class`
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`       DemoWritePDBFiles demo = new DemoWritePDBFiles();`
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`       `
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`       // now we find all PDB files under the provided directory`
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`       List`<File>` pdbfiles = demo.getAllPDB(pdbLocation);`
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`       System.out.println("serializing "+ pdbfiles.size() + " PDB files...");`
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`       try {`
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`           demo.storeFiles(pdbfiles);`
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`       } catch (Exception e) {`
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`           e.printStackTrace();`
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`       }`
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`       `
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`   }`
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`   /** get all PDBfiles from a directory`
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`    * `
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`    * @param dir the directory where the PDB files are located`
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`    * @return all PDB files`
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`    */`
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`   public  List`<File>` getAllPDB(File dir)  {`
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`       List`<File>` allpdbs = new ArrayList`<File>`();`
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`       if ( ! dir.isDirectory()){`
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`           throw new IllegalArgumentException("path is not a directory " + dir);`
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`       }`
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`       //  This filter only returns directories`
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`       FileFilter fileFilter = new FileFilter() {`
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`           public boolean accept(File file) {`
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`               return file.isDirectory();`
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`           }`
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`       };`
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`       File[] subfiles = dir.listFiles(fileFilter);`
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`       for (File f: subfiles){`
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`           List`<File>` pdbs = getAllPDB(f);`
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`           allpdbs.addAll(pdbs);`
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`       }`
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`       String[] all = dir.list();`
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`       for (int i = 0 ; i < all.length;i++ ){`
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`           // filenames are like 'pdb1234.ent.gz'`
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`           String file = all[i];`
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`           if ( (file.endsWith(".pdb.gz")) || `
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`                   ( file.endsWith(".ent.gz")) ||`
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`                   (file.endsWith(".pdb")) ||`
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`                   (file.endsWith(".ent"))                                 `
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`           ){`
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`               allpdbs.add(new File(dir+File.separator + file));`
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`           }`
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`       }`
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`       return allpdbs;`
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`   }`
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`   /** upload the set of PDB files into the database`
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`    * `
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`    * @param pdbfiles - list of PDBFiles`
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`    * @throws HibernateException`
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`    */`
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`   public void storeFiles(List`<File>` pdbfiles) throws HibernateException{`
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`       //Object ownership = HibernateSession.createSession();`
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`       //Session session = HibernateSession.getSession();`
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`       int l = pdbfiles.size();`
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`       //long loopStart = System.currentTimeMillis();`
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`       PDBFileReader pdbreader = new PDBFileReader();`
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`       int i=0;`
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`       for (File f: pdbfiles){`
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`           i++;`
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`           `
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`           System.out.println(f);`
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`           StructureFile struFile = new StructureFile();`
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`           struFile.setPath(f.toString());`
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`           System.out.println("# "+i + " / " + l + " " + f);`
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`           try {`
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`               `
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`               // associate the biojava Structure container class with`
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`               // the location of the PDB file in the filesystem               `
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`               Structure s = pdbreader.getStructure(f);`
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`               struFile.setPDBCode(s.getPDBCode());`
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`               struFile.setStructure(s);`
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`               // now we write it`
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`               createAndStoreStructure(struFile);`
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`           } catch (Exception e){`
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`               e.printStackTrace();`
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`           }`
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`       }`
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`   }`
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`   /** does the actual Hibernate serialisation`
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`    * `
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`    * @param struFile `
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`    */`
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`   private void createAndStoreStructure(StructureFile struFile ) {`
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`       //System.out.println(s);`
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`       Structure s = struFile.getStructure();`
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`       // open a new Hibernate session`
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`       Session session = HibernateUtil.getSessionFactory().openSession();`
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`       session.beginTransaction();`
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`       //System.err.println("saving struc");`
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`       for (Compound compound : s.getCompounds()){`
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`           session.save(compound);`
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`       }`
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`       `
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`       // save the toplevel container`
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`       session.saveOrUpdate(s);`
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`       `
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`       `
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`       // save the file path`
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`       session.saveOrUpdate(struFile);`
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`       `
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`       for (Chain chain:s.getChains(0)){   `
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`           `
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`           session.saveOrUpdate(chain);`
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`           `
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`           for (Group g: chain.getAtomGroups()){   `
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`               g.setParent(chain);`
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`               session.saveOrUpdate(g);    `
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`               `
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`               /* at the moment writing Atoms is very slow,`
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`                * it needs some more optimization ... :-(`
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`                * patches are welcome!`
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`                * `
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`                * Therefore by default writing the Atoms is disabled.`
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`                * if you want to do that, uncomment these lines, as well as the `
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`                * lines in HetatomImpl.hbm.xml`
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`                */`
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`                //for ( Atom a: g.getAtoms())`
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`                //     session.saveOrUpdate(a);`
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`               `
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`               `
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`           }`
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`           //System.err.println("saving groups seqres");`
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`           for (Group g: chain.getSeqResGroups()){`
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`               g.setParent(chain);`
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`               session.saveOrUpdate(g);                `
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`               `
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`               /* see above`
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`                */`
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`                //for ( Atom a: g.getAtoms())                  `
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`               //  session.saveOrUpdate(a);`
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`               `
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`           }`
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`       }`
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`       `
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`       `
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`       `
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`       session.flush();`
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`       `
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`       session.getTransaction().commit();`
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`       session.clear();        `
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`       `
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`       HibernateUtil.getSessionFactory().close();`
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`       `
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`   }`
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} </java>

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