From 791398c12af4f8290095425dac87e3c852905ab6 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Sat, 7 Sep 2019 18:20:10 +0200 Subject: obsolete data and java directories deleted --- java/CdkDescriptorInfo.class | Bin 1826 -> 0 bytes java/CdkDescriptorInfo.java | 23 ------- java/CdkDescriptors.class | Bin 6240 -> 0 bytes java/CdkDescriptors.java | 141 ---------------------------------------- java/Jmol.jar | Bin 3422261 -> 0 bytes java/JoelibDescriptorInfo.class | Bin 1039 -> 0 bytes java/JoelibDescriptorInfo.java | 15 ----- java/JoelibDescriptors.class | Bin 2578 -> 0 bytes java/JoelibDescriptors.java | 60 ----------------- java/Rakefile | 15 ----- java/cdk-2.0-SNAPSHOT.jar | Bin 26800460 -> 0 bytes java/joelib2.jar | Bin 1866172 -> 0 bytes java/log4j.jar | Bin 391834 -> 0 bytes 13 files changed, 254 deletions(-) delete mode 100644 java/CdkDescriptorInfo.class delete mode 100644 java/CdkDescriptorInfo.java delete mode 100644 java/CdkDescriptors.class delete mode 100644 java/CdkDescriptors.java delete mode 100644 java/Jmol.jar delete mode 100644 java/JoelibDescriptorInfo.class delete mode 100644 java/JoelibDescriptorInfo.java delete mode 100644 java/JoelibDescriptors.class delete mode 100644 java/JoelibDescriptors.java delete mode 100644 java/Rakefile delete mode 100644 java/cdk-2.0-SNAPSHOT.jar delete mode 100644 java/joelib2.jar delete mode 100644 java/log4j.jar (limited to 'java') diff --git a/java/CdkDescriptorInfo.class b/java/CdkDescriptorInfo.class deleted file mode 100644 index ff67505..0000000 Binary files a/java/CdkDescriptorInfo.class and /dev/null differ 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 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 Binary files a/java/CdkDescriptors.class and /dev/null 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: ..."); - 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 classNames = new LinkedHashSet(); // descriptors to be computed - Set descriptorNames = new LinkedHashSet(); // all values of this descriptor will be printed - Set descriptorValueNames = new LinkedHashSet(); // 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(classNames),null); - List instances = engine.instantiateDescriptors(new ArrayList(classNames)); - List 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 properties = molecule.getProperties(); - Boolean first = true; - for (Map.Entry 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 Binary files a/java/Jmol.jar and /dev/null differ diff --git a/java/JoelibDescriptorInfo.class b/java/JoelibDescriptorInfo.class deleted file mode 100644 index 0ee67bf..0000000 Binary files a/java/JoelibDescriptorInfo.class and /dev/null 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 Binary files a/java/JoelibDescriptors.class and /dev/null 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 Binary files a/java/cdk-2.0-SNAPSHOT.jar and /dev/null differ diff --git a/java/joelib2.jar b/java/joelib2.jar deleted file mode 100644 index fae8d3c..0000000 Binary files a/java/joelib2.jar and /dev/null differ diff --git a/java/log4j.jar b/java/log4j.jar deleted file mode 100644 index c930a6a..0000000 Binary files a/java/log4j.jar and /dev/null differ -- cgit v1.2.3