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authorChristoph Helma <helma@in-silico.ch>2015-08-15 11:52:18 +0200
committerChristoph Helma <helma@in-silico.ch>2015-08-15 11:52:18 +0200
commit9a5b7b1bfb352b3a6555babe8bc2344414f66185 (patch)
tree52546698cd6f77ce72bfc0684021f3f439a4496d /java
parent81a2454a9abde6bb79793eb4c72e4a8725f5fe7f (diff)
java libraries added
Diffstat (limited to 'java')
-rw-r--r--java/.gitignore2
-rw-r--r--java/CdkDescriptorInfo.classbin0 -> 1705 bytes
-rw-r--r--java/CdkDescriptorInfo.java22
-rw-r--r--java/CdkDescriptors.classbin0 -> 6167 bytes
-rw-r--r--java/CdkDescriptors.java141
-rw-r--r--java/Jmol.jarbin0 -> 3422261 bytes
-rw-r--r--java/JoelibDescriptorInfo.classbin0 -> 1039 bytes
-rw-r--r--java/JoelibDescriptorInfo.java15
-rw-r--r--java/JoelibDescriptors.classbin0 -> 2578 bytes
-rw-r--r--java/JoelibDescriptors.java60
-rw-r--r--java/Rakefile15
-rw-r--r--java/cdk-1.4.19.jarbin0 -> 16877592 bytes
-rw-r--r--java/joelib2.jarbin0 -> 1866172 bytes
-rw-r--r--java/log4j.jarbin0 -> 391834 bytes
14 files changed, 255 insertions, 0 deletions
diff --git a/java/.gitignore b/java/.gitignore
new file mode 100644
index 0000000..533ae63
--- /dev/null
+++ b/java/.gitignore
@@ -0,0 +1,2 @@
+bak
+docs
diff --git a/java/CdkDescriptorInfo.class b/java/CdkDescriptorInfo.class
new file mode 100644
index 0000000..9b9408e
--- /dev/null
+++ b/java/CdkDescriptorInfo.class
Binary files differ
diff --git a/java/CdkDescriptorInfo.java b/java/CdkDescriptorInfo.java
new file mode 100644
index 0000000..73a65ac
--- /dev/null
+++ b/java/CdkDescriptorInfo.java
@@ -0,0 +1,22 @@
+import java.util.*;
+import org.openscience.cdk.qsar.descriptors.molecular.*;
+import org.openscience.cdk.qsar.*;
+
+class CdkDescriptorInfo {
+ public static void main(String[] args) {
+
+ DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR);
+
+ 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
new file mode 100644
index 0000000..49bfaf2
--- /dev/null
+++ b/java/CdkDescriptors.class
Binary files differ
diff --git a/java/CdkDescriptors.java b/java/CdkDescriptors.java
new file mode 100644
index 0000000..1236240
--- /dev/null
+++ b/java/CdkDescriptors.java
@@ -0,0 +1,141 @@
+import java.util.*;
+import java.io.*;
+import org.openscience.cdk.DefaultChemObjectBuilder;
+import org.openscience.cdk.interfaces.IMolecule;
+import org.openscience.cdk.io.iterator.IteratingMDLReader;
+import org.openscience.cdk.qsar.*;
+import org.openscience.cdk.qsar.DescriptorValue;
+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));
+ List<IDescriptor> instances = engine.instantiateDescriptors(new ArrayList<String>(classNames));
+ List<DescriptorSpecification> 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
+ IteratingMDLReader reader = new IteratingMDLReader( br, DefaultChemObjectBuilder.getInstance());
+ int c = 0;
+ while (reader.hasNext()) {
+ try {
+ System.out.println("computing "+(args.length-1)+" descriptors for compound "+(++c));
+ IMolecule molecule = (IMolecule)reader.next();
+ molecule = (IMolecule) 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
new file mode 100644
index 0000000..2c7e5aa
--- /dev/null
+++ b/java/Jmol.jar
Binary files differ
diff --git a/java/JoelibDescriptorInfo.class b/java/JoelibDescriptorInfo.class
new file mode 100644
index 0000000..0ee67bf
--- /dev/null
+++ b/java/JoelibDescriptorInfo.class
Binary files differ
diff --git a/java/JoelibDescriptorInfo.java b/java/JoelibDescriptorInfo.java
new file mode 100644
index 0000000..851d650
--- /dev/null
+++ b/java/JoelibDescriptorInfo.java
@@ -0,0 +1,15 @@
+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
new file mode 100644
index 0000000..d88ac63
--- /dev/null
+++ b/java/JoelibDescriptors.class
Binary files differ
diff --git a/java/JoelibDescriptors.java b/java/JoelibDescriptors.java
new file mode 100644
index 0000000..e90e35f
--- /dev/null
+++ b/java/JoelibDescriptors.java
@@ -0,0 +1,60 @@
+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
new file mode 100644
index 0000000..a865528
--- /dev/null
+++ b/java/Rakefile
@@ -0,0 +1,15 @@
+# Java class, classpath
+java_classes = [
+ ["CdkDescriptors", "cdk-1.4.19.jar"],
+ ["CdkDescriptorInfo", "cdk-1.4.19.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 -classpath #{c.last} #{c.first}.java`
+ end
+end
diff --git a/java/cdk-1.4.19.jar b/java/cdk-1.4.19.jar
new file mode 100644
index 0000000..3281c87
--- /dev/null
+++ b/java/cdk-1.4.19.jar
Binary files differ
diff --git a/java/joelib2.jar b/java/joelib2.jar
new file mode 100644
index 0000000..fae8d3c
--- /dev/null
+++ b/java/joelib2.jar
Binary files differ
diff --git a/java/log4j.jar b/java/log4j.jar
new file mode 100644
index 0000000..c930a6a
--- /dev/null
+++ b/java/log4j.jar
Binary files differ