<commit_before>package org.cheminfo.actelion.client;

import org.timepedia.exporter.client.Export;
import org.timepedia.exporter.client.ExportPackage;
import org.timepedia.exporter.client.Exportable;

import com.actelion.research.chem.SSSearcherWithIndex;
import com.actelion.research.chem.StereoMolecule;

@ExportPackage(value="actelion")
@Export
public class SSSearchWithIndex implements Exportable {
	
	private SSSearcherWithIndex searcher = new SSSearcherWithIndex();
	
	public SSSearchWithIndex() {}
	
	public static String[] getKeyIDCode() {
		return SSSearcherWithIndex.cKeyIDCode;
	}
	
	public void setFragment(Molecule fragment) {
		StereoMolecule mol = fragment.getStereoMolecule();
		this.searcher.setFragment(mol, searcher.createIndex(mol));
	}
	
	public void setFragment(Molecule fragment, int[] index) {
		this.searcher.setFragment(fragment.getStereoMolecule(), index);
	}
	
	public void setMolecule(Molecule molecule) {
		StereoMolecule mol = molecule.getStereoMolecule();
		this.searcher.setMolecule(mol, searcher.createIndex(mol));
	}
	
	public void setMolecule(Molecule molecule, int[] index) {
		this.searcher.setFragment(molecule.getStereoMolecule(), index);
	}
	
	public boolean isFragmentInMolecule() {
		return this.searcher.isFragmentInMolecule();
	}
	
	public int[] getIndex(Molecule molecule) {
		return searcher.createIndex(molecule.getStereoMolecule());
	}
	
	public float getTanimotoSimilarity(int[] index1, int[] index2) {
		return SSSearcherWithIndex.getSimilarityTanimoto(index1, index2);
	}
	
	public float getTanimotoSimilarity(Molecule mol1, Molecule mol2) {
		return SSSearcherWithIndex.getSimilarityTanimoto(getIndex(mol1), getIndex(mol2));
	}
}<commit_msg>fix SSSearchWithIndex<commit_after>package org.cheminfo.actelion.client;

import org.timepedia.exporter.client.Export;
import org.timepedia.exporter.client.ExportPackage;
import org.timepedia.exporter.client.Exportable;

import com.actelion.research.chem.SSSearcherWithIndex;
import com.actelion.research.chem.StereoMolecule;

@ExportPackage(value="actelion")
@Export
public class SSSearchWithIndex implements Exportable {
	
	private SSSearcherWithIndex searcher = new SSSearcherWithIndex();
	
	public SSSearchWithIndex() {}
	
	public static String[] getKeyIDCode() {
		return SSSearcherWithIndex.cKeyIDCode;
	}
	
	public void setFragment(Molecule fragment) {
		StereoMolecule mol = fragment.getStereoMolecule();
		this.searcher.setFragment(mol, searcher.createIndex(mol));
	}
	
	public void setFragment(Molecule fragment, int[] index) {
		this.searcher.setFragment(fragment.getStereoMolecule(), index);
	}
	
	public void setMolecule(Molecule molecule) {
		StereoMolecule mol = molecule.getStereoMolecule();
		this.searcher.setMolecule(mol, searcher.createIndex(mol));
	}
	
	public void setMolecule(Molecule molecule, int[] index) {
		this.searcher.setMolecule(molecule.getStereoMolecule(), index);
	}
	
	public boolean isFragmentInMolecule() {
		return this.searcher.isFragmentInMolecule();
	}
	
	public int[] getIndex(Molecule molecule) {
		return searcher.createIndex(molecule.getStereoMolecule());
	}
	
	public float getTanimotoSimilarity(int[] index1, int[] index2) {
		return SSSearcherWithIndex.getSimilarityTanimoto(index1, index2);
	}
	
	public float getTanimotoSimilarity(Molecule mol1, Molecule mol2) {
		return SSSearcherWithIndex.getSimilarityTanimoto(getIndex(mol1), getIndex(mol2));
	}
}
{'fraction_non_alphanumeric': 0.10306242638398115, 'fraction_numerical': 0.004711425206124852, 'mean_word_length': 6.3847826086956525, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, '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': '1885841', 'n_tokens_mistral': 1252, 'n_tokens_neox': 1109, 'n_words': 191}