├── .classpath ├── .gitignore ├── .project ├── .settings ├── org.eclipse.core.resources.prefs ├── org.eclipse.jdt.core.prefs └── org.eclipse.m2e.core.prefs ├── data └── input │ ├── deep │ ├── deepwalk_external_100.txt │ └── deepwalkidx_external_100.txt │ └── query │ ├── drugs.txt │ └── target.txt ├── lib ├── deeplearning │ ├── DeepWalk_BSI-0.0.1-SNAPSHOT.jar │ ├── deeplearning4j-core-0.4-rc3.9.jar │ ├── deeplearning4j-graph-0.4-rc3.9.jar │ ├── deeplearning4j-nlp-0.4-rc3.9.jar │ ├── deeplearning4j-ui-0.4-rc3.9.jar │ ├── nd4j-api-0.4-rc3.9.jar │ ├── nd4j-buffer-0.4-rc3.9.jar │ ├── nd4j-common-0.4-rc3.9.jar │ ├── nd4j-context-0.4-rc3.9.jar │ ├── nd4j-jackson-0.4-rc3.9.jar │ ├── nd4j-native-0.4-rc3.9-windows-x86_64.jar │ ├── nd4j-native-0.4-rc3.9.jar │ ├── nd4j-native-api-0.4-rc3.9.jar │ └── org.apache.commons.codec-1.8.jar └── rdf │ └── nxparser-parsers-2.2.jar ├── pom.xml ├── readMe.md ├── src └── edu │ └── ucsd │ └── dbmi │ └── drugtarget │ ├── chemicstrc │ ├── ChemicalBasedMethod.java │ ├── DDSimilarityConvertor.java │ ├── DrugCollector.java │ ├── Simcomp.java │ └── SimilarityRunable.java │ ├── deepwalk │ ├── DGraph.java │ ├── DeepGraph.java │ └── DeepWalkMethod.java │ ├── genomicsqs │ ├── Aligner.java │ ├── Alignment.java │ ├── Blosum.java │ ├── Example.java │ ├── FastaSequence.java │ ├── GenomicSeqBasedMethod.java │ ├── InvalidAlphabetException.java │ ├── NToMMappingDetc.java │ ├── PPSimilarityConvertor.java │ ├── ProteinCollector.java │ ├── ProteinSimcomp.java │ ├── ProteinSimilarityRunable.java │ ├── SimpleChaining.java │ └── SmithWaterman.java │ └── main │ ├── Job.java │ └── Prediction.java └── target └── classes ├── .gitignore └── META-INF ├── MANIFEST.MF └── maven └── drug-target-prediction └── drug-target-prediction ├── pom.properties └── pom.xml /.classpath: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zongnansu1982/drug-target-prediction/HEAD/.classpath 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