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-rw-r--r--java/CdkDescriptorInfo.classbin1826 -> 0 bytes
-rw-r--r--java/CdkDescriptorInfo.java23
-rw-r--r--java/CdkDescriptors.classbin6240 -> 0 bytes
-rw-r--r--java/CdkDescriptors.java141
-rw-r--r--java/Jmol.jarbin3422261 -> 0 bytes
-rw-r--r--java/JoelibDescriptorInfo.classbin1039 -> 0 bytes
-rw-r--r--java/JoelibDescriptorInfo.java15
-rw-r--r--java/JoelibDescriptors.classbin2578 -> 0 bytes
-rw-r--r--java/JoelibDescriptors.java60
-rw-r--r--java/Rakefile15
-rw-r--r--java/cdk-2.0-SNAPSHOT.jarbin26800460 -> 0 bytes
-rw-r--r--java/joelib2.jarbin1866172 -> 0 bytes
-rw-r--r--java/log4j.jarbin391834 -> 0 bytes
13 files changed, 0 insertions, 254 deletions
diff --git a/java/CdkDescriptorInfo.class b/java/CdkDescriptorInfo.class
deleted file mode 100644
index ff67505..0000000
--- a/java/CdkDescriptorInfo.class
+++ /dev/null
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diff --git a/java/CdkDescriptorInfo.java b/java/CdkDescriptorInfo.java
deleted file mode 100644
index 296c93d..0000000
--- a/java/CdkDescriptorInfo.java
+++ /dev/null
@@ -1,23 +0,0 @@
-import java.util.*;
-import org.openscience.cdk.DefaultChemObjectBuilder;
-import org.openscience.cdk.qsar.*;
-//import org.openscience.cdk.qsar.descriptors.molecular.*;
-
-class CdkDescriptorInfo {
- public static void main(String[] args) {
-
- DescriptorEngine engine = new DescriptorEngine(IMolecularDescriptor.class,null);
-
- for (Iterator<IDescriptor> it = engine.getDescriptorInstances().iterator(); it.hasNext(); ) {
- IDescriptor descriptor = it.next();
- String cdk_class = descriptor.getClass().toString().replaceAll("class ","");
- System.out.println("- :java_class: \""+cdk_class+"\"");
- String description = engine.getDictionaryDefinition(cdk_class).replaceAll("^\\s+", "" ).replaceAll("\\s+$", "").replaceAll("\\s+", " ");
- System.out.println(" :description: \""+description+"\"");
- System.out.println(" :names:");
- for (String name : descriptor.getDescriptorNames()) {
- System.out.println(" - \""+name+"\"");
- }
- }
- }
-}
diff --git a/java/CdkDescriptors.class b/java/CdkDescriptors.class
deleted file mode 100644
index e37a69a..0000000
--- a/java/CdkDescriptors.class
+++ /dev/null
Binary files differ
diff --git a/java/CdkDescriptors.java b/java/CdkDescriptors.java
deleted file mode 100644
index b5f8672..0000000
--- a/java/CdkDescriptors.java
+++ /dev/null
@@ -1,141 +0,0 @@
-import java.util.*;
-import java.io.*;
-import org.openscience.cdk.DefaultChemObjectBuilder;
-import org.openscience.cdk.IImplementationSpecification;
-import org.openscience.cdk.interfaces.IAtomContainer;
-import org.openscience.cdk.io.iterator.IteratingSDFReader;
-import org.openscience.cdk.qsar.*;
-import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
-import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
-import org.openscience.cdk.exception.NoSuchAtomTypeException;
-
-class CdkDescriptors {
- public static void main(String[] args) {
-
- if (args==null || args.length<2) {
- System.err.println("required params: <sd-file> <descriptor1> <descriptor2(optional)> <descriptor3(optional)> ...");
- System.exit(1);
- }
- if (! new File(args[0]).exists()){
- System.err.println("file not found "+args[0]);
- System.exit(1);
- }
-
- // command line descriptor params can be either "descriptorName" or "descriptorValueName"
- // terminology:
- // A descriptor can calculate serveral values, e.g., ALOGP produces ALOGP.ALogP, ALOGP.ALogp2, ALOGP.AMR
- // "descriptorName" ALOGP
- // "valueName" AMR
- // "descriptorValueName" ALOGP.AMR
- DescriptorEngine engine;
- Set<String> classNames = new LinkedHashSet<String>(); // descriptors to be computed
- Set<String> descriptorNames = new LinkedHashSet<String>(); // all values of this descriptor will be printed
- Set<String> descriptorValueNames = new LinkedHashSet<String>(); // only these values of a descriptor will be printed
- for (int i =1; i < args.length; i++) {
- String descriptorName;
- if (args[i].indexOf(".")!=-1) {
- descriptorValueNames.add(args[i]);
- descriptorName = args[i].substring(0,args[i].indexOf("."));
- }
- else {
- descriptorNames.add(args[i]);
- descriptorName = args[i];
- }
- classNames.add(getDescriptorClassName(descriptorName));
- }
-
- engine = new DescriptorEngine(new ArrayList<String>(classNames),null);
- List<IDescriptor> instances = engine.instantiateDescriptors(new ArrayList<String>(classNames));
- List<IImplementationSpecification> specs = engine.initializeSpecifications(instances);
- engine.setDescriptorInstances(instances);
- engine.setDescriptorSpecifications(specs);
-
- try {
- BufferedReader br = new BufferedReader(new FileReader(args[0]));
- PrintWriter yaml = new PrintWriter(new FileWriter(args[0]+"cdk.yaml"));
- // parse 3d sdf from file and calculate descriptors
- IteratingSDFReader reader = new IteratingSDFReader( br, DefaultChemObjectBuilder.getInstance());
- int c = 0;
- while (reader.hasNext()) {
- try {
- System.out.println("computing "+(args.length-1)+" descriptors for compound "+(++c));
- IAtomContainer molecule = (IAtomContainer)reader.next();
- molecule = (IAtomContainer) AtomContainerManipulator.removeHydrogens(molecule);
- try {
- AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
- }
- catch (NoSuchAtomTypeException e) {
- e.printStackTrace();
- }
- CDKHueckelAromaticityDetector.detectAromaticity(molecule);
-
- engine.process(molecule);
- Map<Object,Object> properties = molecule.getProperties();
- Boolean first = true;
- for (Map.Entry<Object, Object> entry : properties.entrySet()) {
- try {
- if ((entry.getKey() instanceof DescriptorSpecification) && (entry.getValue() instanceof DescriptorValue)) {
- DescriptorSpecification property = (DescriptorSpecification)entry.getKey();
- DescriptorValue value = (DescriptorValue)entry.getValue();
- String[] values = value.getValue().toString().split(",");
- for (int i = 0; i < values.length; i++) {
- String cdk_class = property.getImplementationTitle();
- String descriptorName = cdk_class.substring(cdk_class.lastIndexOf(".")+1).replace("Descriptor","");
- String descriptorValueName = descriptorName + "." + value.getNames()[i];
- if (descriptorNames.contains(descriptorName) || descriptorValueNames.contains(descriptorValueName)) {
- if (first) { yaml.print("- "); first = false; }
- else { yaml.print(" "); }
- yaml.println("Cdk." + descriptorValueName + ": " + values[i]);
- }
- }
- }
- }
- catch (ClassCastException e) { } // sdf properties are stored as molecules properties (strings), ignore them
- catch (Exception e) { e.printStackTrace(); } // output nothing to yaml
- }
- }
- catch (Exception e) {
- yaml.println("- {}");
- e.printStackTrace();
- continue;
- }
- }
- yaml.close();
- }
- catch (Exception e) { e.printStackTrace(); }
- }
-
-
- /** HACK to find the class for a descriptor
- * problem: Descriptor is not always at the end of the class (APolDescriptor), but may be in the middle (AutocorrelationDescriptorPolarizability)
- * this method makes a class-lookup using trial and error */
- static String getDescriptorClassName(String descriptorName) {
- String split = splitCamelCase(descriptorName)+" "; // space mark possible positions for 'Descriptor'
- for(int i = split.length()-1; i>0; i--) {
- if (split.charAt(i)==' ') { // iterate over all spaces, starting with the trailing one
- String test = split.substring(0,i)+"Descriptor"+split.substring(i+1,split.length()); // replace current space with 'Descriptor' ..
- test = test.replaceAll("\\s",""); // .. and remove other spaces
- String className = "org.openscience.cdk.qsar.descriptors.molecular." + test;
- try {
- Class.forName(className);
- return className;
- } catch (ClassNotFoundException e) {}
- }
- }
- System.err.println("Descriptor not found: "+descriptorName);
- System.exit(1);
- return null;
- }
-
- /** inserts space in between camel words */
- static String splitCamelCase(String s) {
- return s.replaceAll(
- String.format("%s|%s|%s",
- "(?<=[A-Z])(?=[A-Z][a-z])",
- "(?<=[^A-Z])(?=[A-Z])",
- "(?<=[A-Za-z])(?=[^A-Za-z])"
- ),
- " "
- );
- }
-}
diff --git a/java/Jmol.jar b/java/Jmol.jar
deleted file mode 100644
index 2c7e5aa..0000000
--- a/java/Jmol.jar
+++ /dev/null
Binary files differ
diff --git a/java/JoelibDescriptorInfo.class b/java/JoelibDescriptorInfo.class
deleted file mode 100644
index 0ee67bf..0000000
--- a/java/JoelibDescriptorInfo.class
+++ /dev/null
Binary files differ
diff --git a/java/JoelibDescriptorInfo.java b/java/JoelibDescriptorInfo.java
deleted file mode 100644
index 851d650..0000000
--- a/java/JoelibDescriptorInfo.java
+++ /dev/null
@@ -1,15 +0,0 @@
-import joelib2.feature.FeatureHelper;
-
-class JoelibDescriptorInfo {
- public static void main(String[] args) {
- FeatureHelper helper = FeatureHelper.instance();
- System.out.println("---"); // document separator for Joelib debug messages
- for (Object feature : helper.getNativeFeatures() ) {
- System.out.println("- :java_class: \""+feature.toString()+"\"");
- // methods for accessing feature descriptions e.g. with
- // FeatureFactory.instance().getFeature(feature.toString()).getDescription().getText() or
- // FeatureFactory.instance().getFeature(feature.toString()).getDescription().getHtml()
- // are defunct
- }
- }
-}
diff --git a/java/JoelibDescriptors.class b/java/JoelibDescriptors.class
deleted file mode 100644
index d88ac63..0000000
--- a/java/JoelibDescriptors.class
+++ /dev/null
Binary files differ
diff --git a/java/JoelibDescriptors.java b/java/JoelibDescriptors.java
deleted file mode 100644
index e90e35f..0000000
--- a/java/JoelibDescriptors.java
+++ /dev/null
@@ -1,60 +0,0 @@
-import java.util.*;
-import java.io.*;
-import joelib2.feature.Feature;
-import joelib2.feature.FeatureHelper;
-import joelib2.feature.FeatureFactory;
-import joelib2.feature.FeatureResult;
-import joelib2.io.BasicIOType;
-import joelib2.io.BasicIOTypeHolder;
-import joelib2.io.BasicReader;
-import joelib2.io.MoleculeFileHelper;
-import joelib2.io.MoleculeFileIO;
-import joelib2.io.MoleculeIOException;
-import joelib2.molecule.BasicConformerMolecule;
-
-class JoelibDescriptors {
- public static void main(String[] args) {
-
- String[] features = null;
- features = new String[args.length-1];
- System.arraycopy(args,1,features,0,args.length-1);
-
- FeatureFactory factory = FeatureFactory.instance();
- MoleculeFileIO loader = null;
- String line = new String();
- String sdf = new String();
- try {
- // parse 3d sdf from file and calculate descriptors
- InputStream is = new FileInputStream(args[0]);
- PrintWriter yaml = new PrintWriter(new FileWriter(args[0]+"joelib.yaml"));
- BasicIOType inType = BasicIOTypeHolder.instance().getIOType("SDF");
- loader = MoleculeFileHelper.getMolReader(is, inType);
- BasicConformerMolecule mol = new BasicConformerMolecule(inType, inType);
- while (true) {
- try {
- Boolean success = loader.read(mol);
- if (!success) { break; } // last molecule
- for (int i =0; i < features.length; i++) {
- String name = "joelib2.feature.types." + features[i];
- Feature feature = factory.getFeature(name);
- FeatureResult result = feature.calculate(mol);
- if (i == 0) { yaml.print("- "); }
- else { yaml.print(" "); }
- yaml.print( "Joelib."+features[i]+": " );
- yaml.println( result.toString() );
- }
-
- }
- catch (Exception e) {
- System.err.println(e.toString());
- e.printStackTrace();
- }
- }
- yaml.close();
- }
- catch (Exception e) {
- System.err.println(e.toString());
- e.printStackTrace();
- }
- }
-}
diff --git a/java/Rakefile b/java/Rakefile
deleted file mode 100644
index 214c3aa..0000000
--- a/java/Rakefile
+++ /dev/null
@@ -1,15 +0,0 @@
-# Java class, classpath
-java_classes = [
- ["CdkDescriptors", "cdk-2.0-SNAPSHOT.jar"],
- ["CdkDescriptorInfo", "cdk-2.0-SNAPSHOT.jar"],
- ["JoelibDescriptors", "joelib2.jar:."],
- ["JoelibDescriptorInfo", "joelib2.jar:."],
-]
-
-task :default => java_classes.collect{|c| "#{c.first}.class"}
-
-java_classes.each do |c|
- file "#{c.first}.class" => "#{c.first}.java" do
- puts `javac -Xlint:deprecation -classpath #{c.last} #{c.first}.java`
- end
-end
diff --git a/java/cdk-2.0-SNAPSHOT.jar b/java/cdk-2.0-SNAPSHOT.jar
deleted file mode 100644
index f55e55e..0000000
--- a/java/cdk-2.0-SNAPSHOT.jar
+++ /dev/null
Binary files differ
diff --git a/java/joelib2.jar b/java/joelib2.jar
deleted file mode 100644
index fae8d3c..0000000
--- a/java/joelib2.jar
+++ /dev/null
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diff --git a/java/log4j.jar b/java/log4j.jar
deleted file mode 100644
index c930a6a..0000000
--- a/java/log4j.jar
+++ /dev/null
Binary files differ
generated by cgit v1.2.3 (git 2.25.1) at 2024-04-28 10:44:54 +0000