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* Copyright (C) 2004-2007 The Chemistry Development Kit (CDK) project
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* Contact: cdk-devel@lists.sourceforge.net
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* This program is free software; you can redistribute it and/or
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* modify it under the terms of the GNU Lesser General Public License
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* as published by the Free Software Foundation; either version 2.1
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* of the License, or (at your option) any later version.
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* This program is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU Lesser General Public License for more details.
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* You should have received a copy of the GNU Lesser General Public License
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* along with this program; if not, write to the Free Software
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* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
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package org.openscience.cdk.qsar.model.R;
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import org.omegahat.R.Java.REvaluator;
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import org.omegahat.R.Java.ROmegahatInterpreter;
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import org.openscience.cdk.qsar.model.IModel;
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import org.openscience.cdk.qsar.model.QSARModelException;
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import org.openscience.cdk.tools.LoggingTool;
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/** Base class for modeling classes that use R as the backend.
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* This cannot be directly instantiated as its sole function is
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* to initialize the SJava system and source R matcher/converter
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* functions into the loaded R session. The class variable <code>revaluator</code>
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* can be accessed from subclasses to make calls to the R session.
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* Any class that builds models using R should be a subclass of this.
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* An important feature to note when using the R backend is that the SJava
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* initialization must be done only <b>once</b> in a Java thread. As a result
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* when any model class based on RModel is instantiated the constructor for the
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* super class (i.e., Rmodel) makes sure that SJava is not already initialized.
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* By default the intialization uses a temporary file which is sourced in the
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* R session. In some cases, such as web applications, temporary files might be
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* problematic. In this case the R backend can be initialized via strings. To
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* do this the application should specify <b>-DinitRFromString=true</b> on the command
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* line. Note that this approach will be slightly slower compared to initializsation
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* via a temporary file.
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* <b>NOTE</b>: For the R backend to work, ensure that R is correctly installed
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* and that SJava is also installed, using the -c option. Finally, ensure
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* that the R_HOME environment variable points to the R installation.
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* @author Rajarshi Guha
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* @cdk.require r-project
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public abstract class RModel implements IModel {
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private String modelName = null;
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* The object that performs the calls to the R engine.
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public static REvaluator revaluator = null;
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* This object represents an instance of the R interpreter.
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* Due to the design of R, only one interpreter can be instantiated in a given
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* thread. That is, the underlying R engine is not thread safe. As a result
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* care must be taken to have only one instance of the interpreter.
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public static ROmegahatInterpreter interp = null;
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* A boolean that indicates whether the R/Java subsystem has been initialized or not.
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private static boolean doneInit = false;
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private LoggingTool logger;
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private void loadRFunctions(REvaluator evaluator) {
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String scriptLocator = "org/openscience/cdk/qsar/model/data/cdkSJava.R";
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File scriptFile = File.createTempFile("XXXXX",".R");
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scriptFile.deleteOnExit();
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InputStreamReader reader = new InputStreamReader(
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this.getClass().getClassLoader().getResourceAsStream(scriptLocator));
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BufferedReader inFile = new BufferedReader(reader);
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FileWriter outFile = new FileWriter(scriptFile);
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BufferedWriter outBuffer = new BufferedWriter(outFile);
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while ( (inputLine = inFile.readLine()) != null) {
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outBuffer.write(inputLine,0,inputLine.length());
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evaluator.voidEval("source(\""+scriptFile.getAbsolutePath()+"\")");
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} catch (Exception exception) {
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logger.error("Could not load CDK-SJava R script: ", scriptLocator);
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logger.debug(exception);
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private void loadRFunctionsAsStrings(REvaluator evaluator) {
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"cnn_3.R", "cnn_4.R",
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String scriptPrefix = "org/openscience/cdk/qsar/model/data/";
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for (int i = 0; i < scripts.length; i++) {
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String scriptLocator = scriptPrefix + scripts[i];
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InputStreamReader reader = new InputStreamReader(
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this.getClass().getClassLoader().getResourceAsStream(scriptLocator));
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BufferedReader inFile = new BufferedReader(reader);
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StringWriter sw = new StringWriter();
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while ( (inputLine = inFile.readLine()) != null) {
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evaluator.voidEval("eval(parse(text=\""+sw.toString()+"\"))");
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} catch (Exception exception) {
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logger.error("Could not load CDK-SJava R scripts: ", scriptLocator);
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logger.debug(exception);
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* Initializes SJava and R with the specified command line arguments (see R documentation).
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* This constructor will initialize the R session via a temporary file
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* @param args A String[] containing the command line parameters as elements
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public RModel(String[] args) {
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logger = new LoggingTool(this);
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String initRFromString = System.getProperty("initRFromString");
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boolean useDisk = true;
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if (initRFromString != null && initRFromString.equals("true")) {
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RModel.interp = new ROmegahatInterpreter(ROmegahatInterpreter.fixArgs(args), false);
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RModel.revaluator = new REvaluator();
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loadRFunctions(RModel.revaluator);
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logger.info("Initializing from disk");
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loadRFunctionsAsStrings(RModel.revaluator);
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logger.info("Initializing from strings");
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logger.info("SJava initialized");
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logger.info("SJava already initialized");
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* Initializes SJava with the <i>--vanilla, -q, --slave</i> flags.
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* This constructor will initialize the R session via a temporary file
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String[] args = {"--vanilla","-q", "--slave"};
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logger = new LoggingTool(this);
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String initRFromString = System.getProperty("initRFromString");
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boolean useDisk = true;
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if (initRFromString != null && initRFromString.equals("true")) {
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RModel.interp = new ROmegahatInterpreter(ROmegahatInterpreter.fixArgs(args), false);
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RModel.revaluator = new REvaluator();
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loadRFunctions(RModel.revaluator);
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logger.info("Initializing from disk");
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loadRFunctionsAsStrings(RModel.revaluator);
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logger.info("Initializing from strings");
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logger.info("SJava initialized");
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logger.info("SJava already initialized");
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* Saves a R model to disk.
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* This function can be used to save models built in a session, and then loaded
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* again in a different session.
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* @param modelname The name of the model as returned by \code{getModelName}.
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* @param filename The file to which the model should be saved
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* @throws QSARModelException if the R session cannot save the model
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public static void saveModel(String modelname, String filename) throws QSARModelException {
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if (filename.equals("") || filename == null) {
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filename = modelname+".rda";
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//Boolean result = null;
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revaluator.call("saveModel",
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new Object[] { (Object)modelname, (Object)filename });
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} catch (Exception e) {
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System.out.println("Caught the exception");
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throw new QSARModelException("Error saving model");
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* Get the name of the model.
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* This function returns the name of the variable that the actual
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* model is stored in within the R session. In general this is
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* not used for the end user. In the future this might be changed
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* to a private method.
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* @return A String containing the name of the R variable
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public String getModelName() {
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return(this.modelName);
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* Set the name of the model.
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* Ordinarily the user does not need to call this function as each model
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* is assigned a unique ID at instantiation. However, if a user saves a model
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* to disk and then later loads it, the loaded
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* model may overwrite a model in that session. In this situation, this method
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* can be used to assign a name to the model.
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* @param newName The name of the model
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public void setModelName(String newName) {
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if (this.modelName != null && this.modelName.equals(newName)) return;
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String oldName = this.modelName;
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if (oldName != null) {
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revaluator.voidEval("if ('"+oldName+"' %in% ls()) {"+newName+"<-"+oldName+";rm("+oldName+")}");
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this.modelName = newName;
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abstract public void build() throws QSARModelException;
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abstract public void predict() throws QSARModelException;
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* Specifies the parameters value.
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* @param key A String representing the name of the parameter (corresponding to the
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* name described in the R manpages)
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* @param obj The value of the parameter
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* @throws QSARModelException if the parameters are of the wrong type for the given modeling function
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abstract public void setParameters(String key, Object obj) throws QSARModelException;
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* Abstract method to handle loading R models.
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* This method can be used to load a previously saved R model object. Since
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* the user can save any arbitrary R object, checks must be made that the
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* object being returned is an instance of one of the current modeling classes.
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* This is best achieved by forcing each modeling class to write its own loader.
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* @param fileName The file containing the R object to load
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* @throws QSARModelException if the R session could not load the object or if the loaded model
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* does not correspond to the class that it was loaded from
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abstract public void loadModel(String fileName) throws QSARModelException;
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* Abstract method to handle loading R models that were previously serialized.
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* This method can be used to load a previously serialized R model object (usinging
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* serialize()). Since
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* the user can save any arbitrary R object, checks must be made that the
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* object being returned is an instance of one of the current modeling classes.
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* This is best achieved by forcing each modeling class to write its own loader.
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* objects saved using serialize() do not have a name. As a result a name for the object must
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* be specified when using this method.
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* @param serializedModel A String containing the ASCII sreialized R object
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* @param modelName The name of the model. (Within the R session, the model will be assigned to
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* a variable of this name)
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* @throws QSARModelException if the R session could not load the object or if the loaded model
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* does not correspond to the class that it was loaded from
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abstract public void loadModel(String serializedModel, String modelName) throws QSARModelException;
added
removed
src/org/openscience/cdk/qsar/model/R/RModel.java
