<commit_before>package demo;

import org.biojava.bio.structure.Structure;
import org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol;
import org.biojava.bio.structure.align.util.AtomCache;


/** Demo how to load and display a structure in Jmol
 * 
 * @author <NAME>
 *
 */
public class ShowStructureInJmol {
	public static void main(String[] args){
		try {
			
			AtomCache cache = new AtomCache();

			Structure struc = cache.getStructure("1aoi");

			StructureAlignmentJmol jmolPanel = new StructureAlignmentJmol();

			jmolPanel.setStructure(struc);

			// send some RASMOL style commands to Jmol
			jmolPanel.evalString("select * ; color chain;");
			jmolPanel.evalString("select nucleic; cartoon on;");
			jmolPanel.evalString("select *; spacefill off; wireframe off; cartoon on;  ");
		} catch (Exception e){
			e.printStackTrace();
		}<commit_msg>updating example to latest API<commit_after>package demo;

import org.biojava.bio.structure.Structure;
import org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol;
import org.biojava3.structure.StructureIO;


/** Demo how to load and display a structure in Jmol
 * 
 * @author <NAME>
 *
 */
public class ShowStructureInJmol {
	public static void main(String[] args){
		try {
			
			Structure struc = StructureIO.getStructure("1aoi");

			StructureAlignmentJmol jmolPanel = new StructureAlignmentJmol();

			jmolPanel.setStructure(struc);

			// send some RASMOL style commands to Jmol
			jmolPanel.evalString("select * ; color chain;");
			jmolPanel.evalString("select nucleic; cartoon on;");
			jmolPanel.evalString("select *; spacefill off; wireframe off; cartoon on;  ");
		} catch (Exception e){
			e.printStackTrace();
		}
{'fraction_non_alphanumeric': 0.11326291079812206, 'fraction_numerical': 0.0017605633802816902, 'mean_word_length': 4.447284345047923, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 5, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2404396', 'n_tokens_mistral': 605, 'n_tokens_neox': 511, 'n_words': 132}