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authorChristoph Helma <helma@in-silico.ch>2016-11-09 10:03:46 +0100
committerChristoph Helma <helma@in-silico.ch>2016-11-09 10:03:46 +0100
commita90047977da5a635072f2833816726eaf721aa88 (patch)
tree6aa5e5424f6847400efa1c8c2598983d8228dc80
parent7bd244b35d2e2059baf1fa535dca854999b5da75 (diff)
CDK 2.0
-rw-r--r--java/CdkDescriptorInfo.classbin1705 -> 1826 bytes
-rw-r--r--java/CdkDescriptorInfo.java5
-rw-r--r--java/CdkDescriptors.classbin6167 -> 6240 bytes
-rw-r--r--java/CdkDescriptors.java56
-rw-r--r--java/Rakefile6
-rw-r--r--java/cdk-2.0-SNAPSHOT.jar (renamed from java/cdk-1.4.19.jar)bin16877592 -> 26800460 bytes
-rw-r--r--test/descriptor.rb5
7 files changed, 37 insertions, 35 deletions
diff --git a/java/CdkDescriptorInfo.class b/java/CdkDescriptorInfo.class
index 9b9408e..ff67505 100644
--- a/java/CdkDescriptorInfo.class
+++ b/java/CdkDescriptorInfo.class
Binary files differ
diff --git a/java/CdkDescriptorInfo.java b/java/CdkDescriptorInfo.java
index 73a65ac..296c93d 100644
--- a/java/CdkDescriptorInfo.java
+++ b/java/CdkDescriptorInfo.java
@@ -1,11 +1,12 @@
import java.util.*;
-import org.openscience.cdk.qsar.descriptors.molecular.*;
+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(DescriptorEngine.MOLECULAR);
+ DescriptorEngine engine = new DescriptorEngine(IMolecularDescriptor.class,null);
for (Iterator<IDescriptor> it = engine.getDescriptorInstances().iterator(); it.hasNext(); ) {
IDescriptor descriptor = it.next();
diff --git a/java/CdkDescriptors.class b/java/CdkDescriptors.class
index 49bfaf2..e37a69a 100644
--- a/java/CdkDescriptors.class
+++ b/java/CdkDescriptors.class
Binary files differ
diff --git a/java/CdkDescriptors.java b/java/CdkDescriptors.java
index 1236240..b5f8672 100644
--- a/java/CdkDescriptors.java
+++ b/java/CdkDescriptors.java
@@ -1,10 +1,10 @@
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.IImplementationSpecification;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.io.iterator.IteratingSDFReader;
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;
@@ -17,8 +17,8 @@ class CdkDescriptors {
System.exit(1);
}
if (! new File(args[0]).exists()){
- System.err.println("file not found "+args[0]);
- System.exit(1);
+ System.err.println("file not found "+args[0]);
+ System.exit(1);
}
// command line descriptor params can be either "descriptorName" or "descriptorValueName"
@@ -34,19 +34,19 @@ class CdkDescriptors {
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("."));
+ descriptorValueNames.add(args[i]);
+ descriptorName = args[i].substring(0,args[i].indexOf("."));
}
else {
- descriptorNames.add(args[i]);
- descriptorName = args[i];
+ descriptorNames.add(args[i]);
+ descriptorName = args[i];
}
classNames.add(getDescriptorClassName(descriptorName));
}
- engine = new DescriptorEngine(new ArrayList<String>(classNames));
+ engine = new DescriptorEngine(new ArrayList<String>(classNames),null);
List<IDescriptor> instances = engine.instantiateDescriptors(new ArrayList<String>(classNames));
- List<DescriptorSpecification> specs = engine.initializeSpecifications(instances);
+ List<IImplementationSpecification> specs = engine.initializeSpecifications(instances);
engine.setDescriptorInstances(instances);
engine.setDescriptorSpecifications(specs);
@@ -54,13 +54,13 @@ class CdkDescriptors {
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());
+ 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));
- IMolecule molecule = (IMolecule)reader.next();
- molecule = (IMolecule) AtomContainerManipulator.removeHydrogens(molecule);
+ IAtomContainer molecule = (IAtomContainer)reader.next();
+ molecule = (IAtomContainer) AtomContainerManipulator.removeHydrogens(molecule);
try {
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
}
@@ -110,21 +110,21 @@ class CdkDescriptors {
* 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) {}
- }
+ 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;
+ }
+ System.err.println("Descriptor not found: "+descriptorName);
+ System.exit(1);
+ return null;
}
/** inserts space in between camel words */
diff --git a/java/Rakefile b/java/Rakefile
index a865528..214c3aa 100644
--- a/java/Rakefile
+++ b/java/Rakefile
@@ -1,7 +1,7 @@
# Java class, classpath
java_classes = [
- ["CdkDescriptors", "cdk-1.4.19.jar"],
- ["CdkDescriptorInfo", "cdk-1.4.19.jar"],
+ ["CdkDescriptors", "cdk-2.0-SNAPSHOT.jar"],
+ ["CdkDescriptorInfo", "cdk-2.0-SNAPSHOT.jar"],
["JoelibDescriptors", "joelib2.jar:."],
["JoelibDescriptorInfo", "joelib2.jar:."],
]
@@ -10,6 +10,6 @@ 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`
+ puts `javac -Xlint:deprecation -classpath #{c.last} #{c.first}.java`
end
end
diff --git a/java/cdk-1.4.19.jar b/java/cdk-2.0-SNAPSHOT.jar
index 3281c87..f55e55e 100644
--- a/java/cdk-1.4.19.jar
+++ b/java/cdk-2.0-SNAPSHOT.jar
Binary files differ
diff --git a/test/descriptor.rb b/test/descriptor.rb
index 42d4661..6eb4316 100644
--- a/test/descriptor.rb
+++ b/test/descriptor.rb
@@ -4,10 +4,11 @@ class DescriptorTest < MiniTest::Test
def test_list
# check available descriptors
- assert_equal 355,PhysChem.descriptors.size,"incorrect number of physchem descriptors"
assert_equal 15,PhysChem.openbabel_descriptors.size,"incorrect number of Openbabel descriptors"
- assert_equal 295,PhysChem.cdk_descriptors.size,"incorrect number of Cdk descriptors"
assert_equal 45,PhysChem.joelib_descriptors.size,"incorrect number of Joelib descriptors"
+ p PhysChem.cdk_descriptors
+ assert_equal 286,PhysChem.cdk_descriptors.size,"incorrect number of Cdk descriptors"
+ assert_equal 346,PhysChem.descriptors.size,"incorrect number of physchem descriptors"
end
def test_smarts