com.github.egonw.ops4j.Structures.java Source code

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Here is the source code for com.github.egonw.ops4j.Structures.java

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/* Copyright (C) 2013  Egon Willighagen <egonw@users.sf.net>
 * 
 * Contact: cdk-devel@lists.sourceforge.net
 * 
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 * All we ask is that proper credit is given for our work, which includes
 * - but is not limited to - adding the above copyright notice to the beginning
 * of your source code files, and to any copyright notice that you may distribute
 * with programs based on this work.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Lesser General Public License for more details.
 * 
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
 */
package com.github.egonw.ops4j;

import java.io.IOException;
import java.net.MalformedURLException;
import java.util.HashMap;
import java.util.Map;

import org.apache.http.HttpException;
import org.apache.http.client.ClientProtocolException;

public class Structures extends AbstractOPS4JClient {

    private Structures(String server, String appID, String appKey) throws MalformedURLException {
        super(server, appID, appKey, null);
    }

    public static Structures getInstance(String server, String apiID, String appKey) throws MalformedURLException {
        return new Structures(server, apiID, appKey);
    }

    public static Structures getInstance(Server server) throws MalformedURLException {
        return new Structures(server.getServer(), server.getAppID(), server.getAppKey());
    }

    public String smiles2uri(String smiles, Object... objects)
            throws ClientProtocolException, IOException, HttpException {
        Map<String, String> params = new HashMap<String, String>();
        params.put("smiles", smiles);
        return runRequest(server + "structure", params, objects);
    }

    public String inchi2uri(String inchi, Object... objects)
            throws ClientProtocolException, IOException, HttpException {
        Map<String, String> params = new HashMap<String, String>();
        params.put("inchi", inchi);
        return runRequest(server + "structure", params, objects);
    }

    public String inchikey2uri(String inchikey, Object... objects)
            throws ClientProtocolException, IOException, HttpException {
        Map<String, String> params = new HashMap<String, String>();
        params.put("inchi_key", inchikey);
        return runRequest(server + "structure", params, objects);
    }

    public String tanimotoSimilarityFrom(String smiles, float treshold, int start, int count, Object... objects)
            throws ClientProtocolException, IOException, HttpException {
        Map<String, String> params = new HashMap<String, String>();
        params.put("searchOptions.Molecule", smiles);
        params.put("searchOptions.SimilarityType", "0"); // Tanimoto
        params.put("searchOptions.Threshold", Float.toString(treshold));
        params.put("resultOptions.Start", "" + Integer.toString(start));
        params.put("resultOptions.Count", "" + Integer.toString(count));
        return runRequest(server + "structure/similarity", params, objects);
    }

    public String tanimotoSimilarity(String smiles, float treshold, Object... objects)
            throws ClientProtocolException, IOException, HttpException {
        Map<String, String> params = new HashMap<String, String>();
        params.put("searchOptions.Molecule", smiles);
        params.put("searchOptions.SimilarityType", "0"); // Tanimoto
        params.put("searchOptions.Threshold", Float.toString(treshold));
        return runRequest(server + "structure/similarity", params, objects);
    }

    public String similarity(String smiles, Object... objects)
            throws ClientProtocolException, IOException, HttpException {
        Map<String, String> params = new HashMap<String, String>();
        params.put("searchOptions.Molecule", smiles);
        params.put("resultOptions.Count", "" + Integer.toString(25));
        params.put("searchOptions.SimilarityType", "0"); // Tanimoto
        params.put("searchOptions.Threshold", Float.toString(0.5f));
        return runRequest(server + "structure/similarity", params, objects);
    }

    public String substructure(String smiles, int start, int count, Object... objects)
            throws ClientProtocolException, IOException, HttpException {
        Map<String, String> params = new HashMap<String, String>();
        params.put("searchOptions.Molecule", smiles);
        params.put("searchOptions.MolType", "SMILES");
        params.put("resultOptions.Start", "" + Integer.toString(start));
        params.put("resultOptions.Count", "" + Integer.toString(count));
        return runRequest(server + "structure/substructure", params, objects);
    }

    public String smarts(String smarts, int start, int count, Object... objects)
            throws ClientProtocolException, IOException, HttpException {
        Map<String, String> params = new HashMap<String, String>();
        params.put("searchOptions.Molecule", smarts);
        params.put("searchOptions.MolType", "SMARTS");
        params.put("resultOptions.Start", "" + Integer.toString(start));
        params.put("resultOptions.Count", "" + Integer.toString(count));
        return runRequest(server + "structure/substructure", params, objects);
    }

    public String exact(String smarts, Object... objects)
            throws ClientProtocolException, IOException, HttpException {
        Map<String, String> params = new HashMap<String, String>();
        params.put("searchOptions.Molecule", smarts);
        params.put("searchOptions.MatchType", "0");
        return runRequest(server + "structure/exact", params, objects);
    }

    public String allTautomers(String smarts, Object... objects)
            throws ClientProtocolException, IOException, HttpException {
        Map<String, String> params = new HashMap<String, String>();
        params.put("searchOptions.Molecule", smarts);
        params.put("searchOptions.MatchType", "1");
        return runRequest(server + "structure/exact", params, objects);
    }

    public String sameSkeleton(String smarts, Object... objects)
            throws ClientProtocolException, IOException, HttpException {
        Map<String, String> params = new HashMap<String, String>();
        params.put("searchOptions.Molecule", smarts);
        params.put("searchOptions.MatchType", "3");
        return runRequest(server + "structure/exact", params, objects);
    }
}