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周锐 — Wed, 29 Jun 2011 02:20:00 GMT

分子�l�构式相似度搜烦使用的是fingerprint�q�行比较�Q��?div style="display: inline-block; ">fingerprint是一个二�q�制数据�Q�CDK中��用BitSet来存储该信息�Q�如果要每次比对都去生成BitSet�Q�那也太耗时间了�Q�所以我们需要存�?div style="display: inline-block; ">fingerprint信息到数据库中，比较的时候，直接��d��Q�而MySQL不支持存储BitSet数据�Q�网站找了一下，有�h惛_��?div style="display: inline-block; ">BitSet转换成Blob信息�q�行存储�Q�然后取的时候再转换回来�Q�不愧是个好的方法。下面来看看代码实现�Q?br />

* This software is the confidential and proprietary information of

* Founder. You shall not disclose such Confidential Information

* and shall use it only in accordance with the terms of the agreements

* you entered into with Founder.

package com.founder.mysql;

import java.sql.Blob;

import java.sql.Connection;

import java.sql.SQLException;

import java.util.BitSet;

public class MySQLUtil {

public static Blob bitsetToBlob(BitSet myBitSet, Connection con) throws SQLException {

byte[] byteArray = toByteArray(myBitSet);

Blob blob = con.createBlob();

blob.setBytes(1, byteArray);

return blob;

}

private static byte[] toByteArray(BitSet bits) {

byte[] bytes = new byte[bits.length()/8+1];

for (int i=0; i

if (bits.get(i)) {

bytes[bytes.length-i/8-1] |= 1<<(i%8);

}

return bytes;

}

public static BitSet blobToBitSet(Blob blob) throws SQLException {

byte[] bytes = blob.getBytes(1, (int)blob.length());

BitSet bitSet = fromByteArray(bytes);

return bitSet;

}

private static BitSet fromByteArray(byte[] bytes) {

BitSet bits = new BitSet(1024);

for (int i=0; i

if ((bytes[bytes.length-i/8-1]&(1<<(i%8))) > 0) {

bits.set(i);

}

return bits;

}

通过以上代码�Q�我们就可以把fingerprint的��D��出来，然后存储到MySQL数据库中了�?br />�q�行�怼�度搜索的时候，值需要取出已�l�存储的��D��行比对就可以了�?br />

float coefficient = Tanimoto.calculate(query, MySQLUtil.blobToBitSet(results.getBlob("bits")));
�W�者测试了187586条结构数据，大概需�?2�U�左叻I��基本满��一般需求�?/div>

周锐 2011-06-29 10:20 发表评论

Improved SMILES Substructure Searching-提高子结构搜索速度

周锐 — Mon, 27 Jun 2011 13:50:00 GMT

daylight上面有一��文章，讲解如何提高子结构搜索速度�Q?a >http://www.daylight.com/meetings/emug00/Sayle/substruct.html
其大概意思就是先通过Fingerprint�q�行�{�选，�q�样可以快速的�{�选掉一部分数据�Q�对于复杂结构更有效�Q�另外就是根据原子个数或者特�D�原子个数进行比较，如果查询�l�构包含三个“N”原子�Q�那么所要查询出的结构所含有“N”的个数必��d��于等�?�Q�这样对于包含一些特�D�元素的效果是特别的好；�q�有��是�Ҏ(gu��)��分子的一些性质�q�行�{�选过滤，比如芳香性等�Q�最后再�q�行匚w��Q�这样一来对于复杂结构以�?qi��ng)含��?gu��)��元素的查询速度�?x��)提高很多�?br /> 最后文章中�q�给出测试数据，从中可以看出�Q�速度一般提高了三倍左叻I��(x��)

Name	SMILES	Correct	FP	Triage	Before	After	Latest
Propane	CCC	65337	66352	42411	42.59	17.99	14.34
Selenium	[Se]	246	995	225	0.80	0.83	0.52
Benzene	c1ccccc1	79426	79486	50893	72.69	27.56	20.29
Methane	C	118519	118524	118511	61.29	5.47	4.25
Amido	NC=O	25695	26975	14702	18.89	9.84	8.16
Methylbenzene	Cc1ccccc1	54529	56869	20490	54.76	35.58	25.90
Carboxy	OC=O	33009	34369	17809	23.86	12.48	10.24
Chlorine	Cl	19424	23318	19424	11.23	1.38	1.12
Cyclopropane	C1CC1	863	4358	484	8.24	7.78	5.02
Biphenyl	c1ccccc1c2ccccc2	2967	5142	146	21.94	21.65	11.44
Dopamine	NCCc1ccc(O)c(O)c1	829	913	23	1.85	2.09	1.47
Sulfisoxazole		7	8	3	0.50	0.88	0.51
BetaCarotene		2	16	1	0.48	0.68	0.58
Nitrofurantoin		0	0	0	0.42	0.58	0.52

周锐 2011-06-27 21:50 发表评论

周锐 — Tue, 12 Apr 2011 14:54:00 GMT

摘要: 参照Rajarshi Guha的CDKDescUI代码�Q�已�l�把CDK的分子描�q�符计算�Q�molecular descriptor calculator�Q�集成到chemtoolkits中了�Q�其中包�?4个描�q�符�?nbsp; 阅读全文

周锐 2011-04-12 22:54 发表评论

周锐 — Mon, 11 Apr 2011 13:41:00 GMT

摘要: rcdk, 是在R下面集成了CDK工具包，以此来通过CDK生成的化学性质数据�q�行更深层次的统计分析，下面来看看在rcdk中如何进行多个化合物�l�构的聚�c�R�?nbsp; 阅读全文

周锐 2011-04-11 21:41 发表评论

周锐 — Sat, 09 Apr 2011 09:16:00 GMT

摘要: Chemtoolkits(CTK)部分功能和界面已�l�完成，目前�|�站的主要辅助性的功能已经加入�Q�比如新闅R��文章、留�a�以及(qi��ng)其他信息内容。化学信息学斚w��的目前只整合了里宾斯��Z��规则计算�Q�以�?qi��ng)比较流行的OSIRIS Property Explorer (LogP, 溶解度、成药可能性预��?��工兗��?nbsp; 阅读全文

周锐 2011-04-09 17:16 发表评论

周锐 — Mon, 26 Oct 2009 14:24:00 GMT

package com.founder.cdk;

import Java.util.BitSet;

import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.exception.InvalidSmilesException;
import org.openscience.cdk.fingerprint.ExtendedFingerprinter;
import org.openscience.cdk.smiles.SmilesParser;

public class FingerprinterTest {

/**
* @param args
* @throws CDKException
* @throws InvalidSmilesException
*/
public static void main(String[] args) throws InvalidSmilesException, CDKException {
  ExtendedFingerprinter fingerprinter = new ExtendedFingerprinter();
  SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
  BitSet bt = fingerprinter.getFingerprint(sp.parseSmiles("c2ccc1ccccc1c2"));
}

}

周锐 2009-10-26 22:24 发表评论

周锐 — Thu, 22 Oct 2009 00:51:00 GMT

import Java.awt.Dimension;
import Java.awt.Graphics2D;
import Java.awt.geom.Rectangle2D;
import Java.awt.image.BufferedImage;
import Java.io.OutputStream;
import Java.io.StringReader;
import Java.util.Iterator;

import javax.servlet.http.HttpServletResponse;
import javax.vecmath.Point2d;

import org.apache.log4j.Logger;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.io.MDLReader;
import org.openscience.cdk.layout.StructureDiagramGenerator;
import org.openscience.cdk.renderer.Renderer2DModel;
import org.openscience.cdk.renderer.SimpleRenderer2D;

public class ImageTypeExporterUtil {
private static final Logger logger = Logger.getLogger(ImageTypeExporterUtil.class);

/**
* show molecule structure to image type (png, jpeg)
*
* @param mol String molecule stucture
* @param length width and height
* @param response HttpServletResponse object
* @throws Exception
*             if occurred exception ,then throw Exception
*/
public static void showAsImage(String stucture, Integer length, HttpServletResponse response) throws Exception {
  logger.debug("ImageTypeExporterUtil.showAsImage..");

  StringReader mdl = new StringReader(stucture);
  MDLReader cdkMDL = new MDLReader(mdl);
  Molecule mol = new Molecule();
  cdkMDL.read(mol);
  // null coordinates
  Iterator itatoms = mol.atoms();
  while (itatoms.hasNext()) {
   IAtom atom = itatoms.next();
   atom.setPoint2d(null);
   atom.setPoint3d(null);
  }
  // generate 2D coordinates
  StructureDiagramGenerator sdg = new StructureDiagramGenerator();
  sdg.setMolecule(mol);
  try {
   sdg.generateCoordinates();
  } catch (Exception ex) {
   ex.printStackTrace();
  }
  IMolecule layedOutMol = sdg.getMolecule();
  // scale molecule
  final double UNDEF_POS = 100000;
  double minX = UNDEF_POS, minY = UNDEF_POS, maxX = UNDEF_POS, maxY = UNDEF_POS;
  itatoms = layedOutMol.atoms();
  while (itatoms.hasNext()) {
   IAtom atom = itatoms.next();
   Point2d point2d = atom.getPoint2d();
   if (minX == UNDEF_POS || minX > point2d.x)
    minX = point2d.x;
   if (minY == UNDEF_POS || minY > point2d.y)
    minY = point2d.y;
   if (maxX == UNDEF_POS || maxX < point2d.x)
    maxX = point2d.x;
   if (maxY == UNDEF_POS || maxY < point2d.y)
    maxY = point2d.y;
  }
  double scaleX = length / (maxX - minX + 1);
  double scaleY = length / (maxY - minY + 1);
  double scale = scaleX > scaleY ? scaleY : scaleX;
  double centreX = scale * (maxX + minX) / 2.;
  double centreY = scale * (maxY + minY) / 2.;
  double offsetX = length / 2. - centreX;
  double offsetY = length / 2. - centreY;
  itatoms = layedOutMol.atoms();
  while (itatoms.hasNext()) {
   IAtom atom = itatoms.next();
   Point2d a = atom.getPoint2d();
   Point2d b = new Point2d();
   b.x = a.x * scale + offsetX;
   b.y = a.y * scale + offsetY;
   atom.setPoint2d(b);
  }
  // set rendering properties
  Renderer2DModel r2dm = new Renderer2DModel();
  r2dm.setDrawNumbers(false);
  r2dm.setUseAntiAliasing(true);
  r2dm.setColorAtomsByType(true);
  r2dm.setShowAtomTypeNames(false);
  r2dm.setShowAromaticity(true);
  r2dm.setShowImplicitHydrogens(false);
  r2dm.setShowReactionBoxes(false);
  r2dm.setKekuleStructure(false);
  Dimension dim = new Dimension();
  dim.setSize(length, length);
  r2dm.setBackgroundDimension(dim);
  r2dm.setBackColor(java.awt.Color.WHITE);
  // render the image
  SimpleRenderer2D renderer = new SimpleRenderer2D();
  renderer.setRenderer2DModel(r2dm);
  BufferedImage bufferedImage = new BufferedImage(length, length,
    BufferedImage.TYPE_INT_RGB);
  Graphics2D graphics = bufferedImage.createGraphics();
  graphics.setPaint(java.awt.Color.WHITE);
  Rectangle2D.Float rectangle = new Rectangle2D.Float(0, 0, length, length);
  graphics.fill(rectangle);
  renderer.paintMolecule(layedOutMol, graphics);
  // write the image to response
  response.setContentType("image/png");
  OutputStream out = response.getOutputStream();
  try {
   javax.imageio.ImageIO.write(bufferedImage, "png", out);
  } finally {
   out.close();
  }
}
}

周锐 2009-10-22 08:51 发表评论

周锐 — Tue, 20 Oct 2009 00:33:00 GMT

CDK提供了通过smiles��D��行子�l�构搜烦, org.openscience.cdk.smiles.smarts.SMARTSQueryTool

package com.founder.cdk;

import Java.io.File;
import Java.io.FileNotFoundException;
import Java.io.FileReader;
import Java.util.ArrayList;
import Java.util.List;

import org.openscience.cdk.ChemFile;
import org.openscience.cdk.ChemObject;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.io.MDLV2000Reader;
import org.openscience.cdk.smiles.smarts.SMARTSQueryTool;
import org.openscience.cdk.tools.manipulator.ChemFileManipulator;

public class SMARTSQueryToolTest {

static SMARTSQueryTool sqt;static {
        try {
            sqt = new SMARTSQueryTool("c2ccc1ccccc1c2");
        } catch (CDKException e) {
        }
    }

/**
* @param args
*/
public static void main(String[] args) {
  String filename = "H:\\molecules.sdf";
  try {
            MDLV2000Reader reader = new MDLV2000Reader(new FileReader(new File(filename)));
            ChemFile chemFile = (ChemFile) reader.read((ChemObject) new ChemFile());
            List containersList = ChemFileManipulator.getAllAtomContainers(chemFile);

            List substructureList = new ArrayList();

            sqt.setSmarts("c1ccc3c(c1)ccc4c2ccccc2ccc34"); //重新讄��匚w��的smiles�?br />             boolean matched = false;
            for (IAtomContainer molecule : containersList) {
                matched = sqt.matches(molecule);
                if (matched){
                substructureList.add(molecule);
                }
            }
            System.out.println(substructureList.size());

            for (IAtomContainer molecule : substructureList) {
                 System.out.println(molecule.getProperty("ID"));
            }

        } catch (CDKException e) {
            e.printStackTrace();
        } catch (FileNotFoundException e) {
           e.printStackTrace();
        }

}

}

通过��试, matches�Ҏ(gu��)��速度很慢, 一般一个结构需�?00ms-1000ms左右.

周锐 2009-10-20 08:33 发表评论

使用CDK解析SDF文�g

周锐 — Mon, 19 Oct 2009 01:45:00 GMT

package com.founder.cdk;

import Java.io.File;
import Java.io.FileNotFoundException;
import Java.io.FileReader;
import Java.util.List;

import org.openscience.cdk.ChemFile;
import org.openscience.cdk.ChemObject;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.io.MDLReader;
import org.openscience.cdk.io.MDLV2000Reader;
import org.openscience.cdk.tools.manipulator.ChemFileManipulator;

public class ReadSDFTest {

/**
* @param args
* @throws CDKException
* @throws FileNotFoundException
*/
public static void main(String[] args) throws CDKException, FileNotFoundException {
  String filename = "H:\\molecules.sdf";

//  InputStream ins = ReadSDFTest.class.getClassLoader().getResourceAsStream(filename);
//  MDLReader reader = new MDLReader(ins);

//alternatively, you can specify a file directly
MDLV2000Reader reader = new MDLV2000Reader(new FileReader(new File(filename)));

  ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile());

  List containersList = ChemFileManipulator.getAllAtomContainers(chemFile);

  Molecule molecule = null;
  for (IAtomContainer mol : containersList) {
   molecule = (Molecule) mol;
   System.out.println(molecule.getProperties());
   System.out.println(molecule.getProperty("CD_MOLWEIGHT"));
//   Fingerprinter fp = new Fingerprinter();
//   BitSet bt = fp.getFingerprint(molecule);
//   System.out.println(bt);
  }
}

}

周锐 2009-10-19 09:45 发表评论

周锐 — Mon, 19 Oct 2009 01:37:00 GMT

package com.founder.cdk;

import Java.io.StringReader;
import Java.sql.Connection;
import Java.sql.ResultSet;
import Java.sql.SQLException;
import Java.util.ArrayList;
import Java.util.BitSet;
import Java.util.List;

import org.openscience.cdk.Molecule;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.fingerprint.Fingerprinter;
import org.openscience.cdk.io.MDLReader;
import org.openscience.cdk.similarity.Tanimoto;

public class CDKTest {

/**
* @param args
*/
public static void main(String[] args) {

  // MySQL
  long t1 = System.currentTimeMillis();
  try {
   Class.forName("com.mysql.jdbc.Driver").newInstance();
   Connection con = Java.sql.DriverManager
     .getConnection(
       "jdbc:mysql://localhost/coocoo?useUnicode=true&characterEncoding=utf-8&zeroDateTimeBehavior=convertToNull",
       "root", "root");

   ResultSet results = null;
   String querySQL = "select id, structure from structure ";

   results = con.createStatement().executeQuery(querySQL);

   // dump out the results

   List list = new ArrayList();
   Fingerprinter fp = new Fingerprinter();
   BitSet bt = null;
   while (results.next()) {
    Long id = results.getLong("id");

    //�Ҏ(gu��)��l�构数据生成分子对象
    StringReader mdl = new StringReader(results.getString("structure"));
    MDLReader cdkMDL = new MDLReader(mdl);
    Molecule molecule = new Molecule();
    cdkMDL.read(molecule);
    if (id == 1220) {
     bt = fp.getFingerprint(molecule);
    }
    list.add(molecule);

   }
   System.out.println("size:=" + list.size());

   List resultList = new ArrayList();

         long t2 = System.currentTimeMillis();
         System.out.println("Thread: collection data in " + (t2 - t1) + " ms.");
         for (Molecule molecule : list) {
             try {
                 float coefficient = Tanimoto.calculate(fp.getFingerprint(molecule), bt); //计算�怼��?br />                  if (coefficient > 0.9) {
                 resultList.add(molecule);
                 }
             } catch (CDKException e) {

             }
         }
         long t3 = System.currentTimeMillis();

         System.out.println(resultList.size());
         System.out.println("Thread: Search in " + (t3 - t2) + " ms.");

   con.close();
  } catch (InstantiationException e) {
   e.printStackTrace();
  } catch (IllegalAccessException e) {
   e.printStackTrace();
  } catch (ClassNotFoundException e) {
   e.printStackTrace();
  } catch (SQLException e) {
   e.printStackTrace();
  } catch (CDKException e) {
   e.printStackTrace();
  }
  long t4 = System.currentTimeMillis();
        System.out.println("Thread: all in " + (t4 - t1) + " ms.");
}

}

周锐 2009-10-19 09:37 发表评论

Faster Fingerprint Search with Java & CDK

周锐 — Sun, 18 Oct 2009 06:09:00 GMT

原文来自:http://chemhack.com/cn/2008/11/faster-fingerprint-search-with-java-cdk/

Rich Apodaca wrote a great serious posts named Fast Substructure Search Using Open Source Tools providing details on substructure search with MySQL. But, however, poor binary data operation functions of MySQL limited the implementation of similar structure search which typically depends on the calculation of Tanimato coefficient. We are going to use Java & CDK to add this feature.

As default output of CDK fingerprint, java.util.BitSet with Serializable interface is perfect data format of fingerprint data storage. Java itself provides several collections such as ArrayList, LinkedList, Vector class in package Java.util. To provide web access to the search engine, thread unsafe ArrayList and LinkedList have to be kicked out. How about Vector? Once all the fingerprint data is well prepared, the collection function we need to do similarity search is just iteration. No add, no delete. So, a light weight array is enough.

Most of the molecule information is stored in MySQL database, so we are going to map fingerprint to corresponding row in data table. Here is the MolDFData class, we use a long variable to store corresponding primary key in data table.

public class MolDFData implements Serializable {

    private long id;

   private BitSet fingerprint;

    public MolDFData(long id, BitSet fingerprint) {

        this.id = id;

        this.fingerprint = fingerprint;

    }

    public long getId() {

        return id;

    }

    public void setId(long id) {

        this.id = id;

    }

    public BitSet getFingerprint() {

        return fingerprint;

    }

    public void setFingerprint(BitSet fingerprint) {

        this.fingerprint = fingerprint;

    }

}

This is how we storage our fingerprints.

private MolFPData[] arrayData;

No big deal with similarity search. Just calculate the Tanimoto coefficient, if it’s bigger than minimal similarity you set, add this one into result.

    public List searchTanimoto(BitSet bt, float minSimlarity) {

        List resultList = new LinkedList();
        int i;
        for (i = 0; i < arrayData.length; i++) {
            MolDFData aListData = arrayData[i];
            try {
                float coefficient = Tanimoto.calculate(aListData.getFingerprint(), bt);
                if (coefficient > minSimlarity) {
                    resultList.add(new SearchResultData(aListData.getId(), coefficient));
                }
            } catch (CDKException e) {
            }
            Collections.sort(resultList);
        }
        return resultList;
    }
Pretty ugly code? Maybe. But it really works, at a acceptable speed.

Tests were done using the code blow on a macbook(Intel Core Due 1.83 GHz, 2G RAM).

long t3 = System.currentTimeMillis();
List listResult = se.searchTanimoto(bs, 0.8f);
long t4 = System.currentTimeMillis();
System.out.println("Thread: Search done in " + (t4 - t3) + " ms.");

In my database of 87364 commercial compounds, it takes 335 ms.

周锐 2009-10-18 14:09 发表评论

周锐 — Sun, 18 Oct 2009 05:36:00 GMT

/* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* Copyright (C) 1997-2007 The Chemistry Development Kit (CDK) project
*
* 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 org.openscience.cdk.similarity;

import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.exception.CDKException;

import Java.util.BitSet;

/**
* Calculates the Tanimoto coefficient for a given pair of two
* fingerprint bitsets or real valued feature vectors.
*
* The Tanimoto coefficient is one way to
* quantitatively measure the "distance" or similarity of
* two chemical structures.
*
*

You can use the FingerPrinter class to retrieve two fingerprint bitsets.
* We assume that you have two structures stored in cdk.Molecule objects.
* A tanimoto coefficient can then be calculated like:
*



 *   BitSet fingerprint1 = Fingerprinter.getFingerprint(molecule1);

 *   BitSet fingerprint2 = Fingerprinter.getFingerprint(molecule2);

 *   float tanimoto_coefficient = Tanimoto.calculate(fingerprint1, fingerprint2);

 *

*
*

The FingerPrinter assumes that hydrogens are explicitely given, if this
* is desired!
*

Note that the continuous Tanimoto coefficient does not lead to a metric space
*
*@author         steinbeck
* @cdk.githash
*@cdk.created    2005-10-19
*@cdk.keyword    jaccard
*@cdk.keyword    similarity, tanimoto
* @cdk.module fingerprint
*/
@TestClass("org.openscience.cdk.similarity.TanimotoTest")
public class Tanimoto
{

    /**
     * Evaluates Tanimoto coefficient for two bit sets.
     *
     * @param bitset1 A bitset (such as a fingerprint) for the first molecule
     * @param bitset2 A bitset (such as a fingerprint) for the second molecule
     * @return The Tanimoto coefficient
     * @throws org.openscience.cdk.exception.CDKException if bitsets are not of the same length
     */
    @TestMethod("testTanimoto1,testTanimoto2")
    public static float calculate(BitSet bitset1, BitSet bitset2) throws CDKException
    {
        float _bitset1_cardinality = bitset1.cardinality();
        float _bitset2_cardinality = bitset2.cardinality();
        if (bitset1.size() != bitset2.size()) {
            throw new CDKException("Bisets must have the same bit length");
        }
        BitSet one_and_two = (BitSet)bitset1.clone();
        one_and_two.and(bitset2);
        float _common_bit_count = one_and_two.cardinality();
        return _common_bit_count/(_bitset1_cardinality + _bitset2_cardinality - _common_bit_count);
    }

    /**
     * Evaluates the continuous Tanimoto coefficient for two real valued vectors.
     *
     * @param features1 The first feature vector
     * @param features2 The second feature vector
     * @return The continuous Tanimoto coefficient
     * @throws org.openscience.cdk.exception.CDKException if the features are not of the same length
     */
    @TestMethod("testTanimoto3")
    public static float calculate(double[] features1, double[] features2) throws CDKException {

        if (features1.length != features2.length) {
            throw new CDKException("Features vectors must be of the same length");
        }

        int n = features1.length;
        double ab = 0.0;
        double a2 = 0.0;
        double b2 = 0.0;

        for (int i = 0; i < n; i++) {
            ab += features1[i] * features2[i];
            a2 += features1[i]*features1[i];
            b2 += features2[i]*features2[i];
        }
        return (float)ab/(float)(a2+b2-ab);
    }
}

通过源码可以看出calculate(BitSet bitset1, BitSet bitset2)�Ҏ(gu��)��,是通过比较两个分子的fingerprint的位,来计��相似度.通过BitSet的and操作得到共同的个�?然后在除以��d��为true的个�?�q�样��得到相似�?

周锐 2009-10-18 13:36 发表评论

JChemPaint (�?D化学�l�构的Java�E�序)

周锐 — Sat, 17 Oct 2009 13:53:00 GMT

JChemPaint (or JCP for short here) is the editor and viewer included in CDK for 2D chemical structures. It is implemented in several forms: a Java application and two varieties of Java applet.

JChemPaint was started by Christoph Steinbeck in the late 1990's to be the complementary structure editor to Jmol. It was then co-developed by Egon Willighagen and others. Jmol again is a visualisation and analysis tool for 3D molecular structures, started by Dan Gezelter at Notre Dame University, initiator of the Open Science Project and, like JChemPaint, developed by an international team of opensource programmers.

In at least three aspects JChemPaint is different from other 2D editors:

JChemPaint is open source and free software. We believe that scientific software, especially when its development was publicly funded, should be free. As the GNU people put it: «`Free software´ is a matter of liberty, not price. To understand the concept, you should think of `free speech´, not `free beer´». Everyone can participate in the development of the program. Everyone can download and change the source code, provided that they make the changes publicly available again, according to the GNU Lesser General Public License, LGPL. This ensures that the community can take advantage of any bugfix or enhancement made to the system. It also ensures that a scientist, who needs a standard piece of software like a structure editor as a helper application in his/her new program, does not have to reinvent the wheel over and over again because all the structure editors that have been written before are now proprietary software. If there is a free structure editor, he/she can focus on the real science.
JChemPaint is in constant development and you can help (see below).
Since JChemPaint is written in Java, it runs on any computing platform and operating system for which a Java Virtual Machine (of version >= 1.3 up to JCP 2.4 and version >= 1.5 for JCP > 2.4) has been implemented (like Linux, Windows, Solaris, AIX and others).
JChemPaint is available free of charge.
JChemPaint is translated into several languages: Dutch, French, German, Polish, Portuguese and Spanish.

集成EditorApplett到jsp��面�?

archive="jchempaint-applet-core.jar" name="Editor"
width="550" height="400">

集成ViewerApplet到jsp��面�?
archive="jchempaint-applet-core.jar"
width="550" height="400">

Applet methods:

Reading from the applet

getMolFile()
getSmiles()
getSmilesChiral()
getParameter()
getParameterInfo()
getAppletInfo()
getLocale()
getImage()
getTheJcpp()

Writing to the applet

setMolFile()
setMolFileWithReplace()
addMolFileWithReplace()
loadModelFromUrl()
loadModelFromSmiles()
clear()
selectAtom()
init()
start()
stop()
initPanelAndModel()
setTheJcpp()
setTheModel()

周锐 2009-10-17 21:53 发表评论