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DemoAtomCache.java
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89 lines (70 loc) · 2.08 KB
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/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package demo;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.align.util.AtomCache;
import org.biojava.nbio.structure.io.FileParsingParameters;
import org.biojava.nbio.structure.StructureIO;
/** Example of how to load PDB files using the AtomCache class.
*
* @author Andreas Prlic
*
*/
public class DemoAtomCache {
public static void main(String[] args){
demoAtomCache();
demoStructureIO();
}
@SuppressWarnings("unused")
private static void demoStructureIO() {
try {
Structure s1 = StructureIO.getStructure("4hhb");
Structure bioAssembly = StructureIO.getBiologicalAssembly("1stp",1);
// do something with them...
} catch (Exception e){
e.printStackTrace();
}
}
private static void demoAtomCache() {
AtomCache cache = new AtomCache();
FileParsingParameters params = cache.getFileParsingParams();
params.setAlignSeqRes(true);
params.setHeaderOnly(false);
params.setParseCAOnly(false);
params.setParseSecStruc(false);
String[] pdbIDs = new String[]{"4hhb", "1cdg","5pti","1gav", "WRONGID" };
for (String pdbID : pdbIDs){
try {
Structure s = cache.getStructure(pdbID);
if ( s == null) {
System.out.println("could not find structure " + pdbID);
continue;
}
// do something with the structure
System.out.println(s);
} catch (Exception e){
// something crazy happened...
System.err.println("Can't load structure " + pdbID + " reason: " + e.getMessage());
//e.printStackTrace();
}
}
}
}