Turn 1 document per line text file into CoNLL-X formatted sentences. There's probably a much better way of doing this though...

RunDependencyParser.java

import java.io.File;
import java.io.IOException;
import java.io.StringReader;
import java.util.ArrayList;
import java.util.List;

import org.apache.commons.io.FileUtils;

import edu.stanford.nlp.ling.CoreAnnotations;
import edu.stanford.nlp.ling.CoreLabel;
import edu.stanford.nlp.ling.HasTag;
import edu.stanford.nlp.ling.HasWord;
import edu.stanford.nlp.ling.TaggedWord;
import edu.stanford.nlp.parser.nndep.DependencyParser;
import edu.stanford.nlp.process.DocumentPreprocessor;
import edu.stanford.nlp.tagger.maxent.MaxentTagger;
import edu.stanford.nlp.trees.GrammaticalStructure;
import edu.stanford.nlp.util.CoreMap;

public class RunDependencyParser {

  static final String taggerPath = "/stanford-parser-full-2015-04-20/pos-tagger/english-left3words/english-left3words-distsim.tagger";
  static MaxentTagger tagger = new MaxentTagger(taggerPath);

  static final String modelPath = "/stanford-parser-full-2015-04-20/models/parser/nndep/english_UD.gz";
  static DependencyParser parser = DependencyParser.loadFromModelFile(modelPath);

  /*
   * Input file is 1 document (a few sentences) per line.
   */
  public static void main(String[] args) throws IOException {

    File input = new File("/input.txt");
    File output = new File("/output.txt");

    for (String document : FileUtils.readLines(input)) {
      // Append output file
      FileUtils.writeStringToFile(output, getConllXString(document), true);
    }

  }

  /*
   * Get a chunk of text in CoNLL-X Format:
   */
  public static String getConllXString(String text) {
    StringBuilder sb = new StringBuilder();
    // Split text into sentences:
    DocumentPreprocessor tokenizer = new DocumentPreprocessor(new StringReader(text));

    for (List<HasWord> sentence : tokenizer) {
      // POS Tag & Parse each sentence
      List<TaggedWord> tagged = tagger.tagSentence(sentence);
      GrammaticalStructure gs = parser.predict(tagged);

      // CoNLL-X Output format:
      String s = GrammaticalStructure.dependenciesToCoNLLXString(gs, getCoreMap(tagged));
      sb.append(s);
      sb.append("\n\n");
    }

    return sb.toString();
  }

  /*
   * Turn a sentence (List of annotated tokens) into a CoreMap object:
   */
  public static CoreMap getCoreMap(List<? extends HasWord> sentence) {
    CoreLabel sentenceLabel = new CoreLabel();
    List<CoreLabel> tokens = new ArrayList<>();
    int i = 1;
    for (HasWord wd : sentence) {
      CoreLabel label;
      if (wd instanceof CoreLabel) {
        label = (CoreLabel) wd;
        if (label.tag() == null) {
          throw new IllegalArgumentException("Parser requires words " + "with part-of-speech tag annotations");
        }
      } else {
        label = new CoreLabel();
        label.setValue(wd.word());
        label.setWord(wd.word());
        if (!(wd instanceof HasTag)) {
          throw new IllegalArgumentException("Parser requires words " + "with part-of-speech tag annotations");
        }
        label.setTag(((HasTag) wd).tag());
      }
      label.setIndex(i);
      i++;
      tokens.add(label);
    }
    sentenceLabel.set(CoreAnnotations.TokensAnnotation.class, tokens);
    return sentenceLabel;
  }

}