jPdbApi

A Java wrapper for the RCSB PDB APIs. I wrote this module specifically for the Android application Palantir, so I've only implemented what was necessary. Contributions are extremely welcome!

Example

try {
    TextSearch textSearch = new TextSearch(queryString);
    String[] results = textSearch.getPage();  // PDB IDs
    for (String pdbId : results) {
        Pdb pdb = new Pdb(pdbId);
        pdb.load()
        System.out.println(pdbId.getTitle());
    }
} catch (IOException e) {
    e.printStackTrace();
}

Development guide

Testing

mvn test runs the test. To run a single test, use the -Dtest=ClassName#methodName flag, e.g.

mvn test -Dtest=TextSearchTests#nextPageWorksOnline

In the event that several tests seem to fail with a SocketTimeoutException, check if the RCSB search service is online by running this simple query listed on the RCSB "Search API Documentation" page.

Illegal reflective access operation from guice

You might see the warning:

WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.google.inject.internal.cglib.core.$ReflectUtils$1 (file:/usr/share/maven/lib/guice.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of com.google.inject.internal.cglib.core.$ReflectUtils$1
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release

when building or testing the package. This is a documented bug. I expect (hope) that the fix will propagate soon (guice is not a direct dependency).