CIFtoXYZTest

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//
// Title:       Force Field X.
// Description: Force Field X - Software for Molecular Biophysics.
// Copyright:   Copyright (c) Michael J. Schnieders 2001-2023.
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package ffx.potential.groovy;

import ffx.potential.utils.PotentialTest;
import org.junit.Test;

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;

/**
 * Tests CIFtoXYZ command to determine that files are being translated correctly.
 *
 * @author Aaron J. Nessler
 */

public class CIFtoXYZTest extends PotentialTest {

  /**
   * Test a basic CIF to XYZ conversion.
   */
  @Test
  public void testCIFtoXYZ() {
    // Set up the input arguments for the CIFtoXYZ script.
    String[] args = {"src/main/java/ffx/potential/structures/CBZ16.cif",
        "src/main/java/ffx/potential/structures/cbz.xyz"};
    binding.setVariable("args", args);
    binding.setVariable("baseDir", registerTemporaryDirectory().toFile());

    // Construct and evaluate the CIFtoXYZ script.

    CIFtoXYZ cifToXYZ = new CIFtoXYZ(binding).run();
    potentialScript = cifToXYZ;

    assertEquals(1, cifToXYZ.createdFiles.length);
    assertTrue(cifToXYZ.createdFiles[0].toUpperCase().contains(".XYZ"));
  }

  /**
   * Test writing out a CIF file (XYZ to CIF).
   */
  @Test
  public void testCIFtoXYZWriteAsCIF() {
    // Set up the input arguments for the CIFtoXYZ script.
    String[] args = {"--sc", "src/main/java/ffx/potential/structures/paracetamol.xyz"};
    binding.setVariable("args", args);
    binding.setVariable("baseDir", registerTemporaryDirectory().toFile());

    // Construct and evaluate the CIFtoXYZ script.
    CIFtoXYZ cifToXYZ = new CIFtoXYZ(binding).run();
    potentialScript = cifToXYZ;

    assertEquals(1, cifToXYZ.createdFiles.length);
    assertTrue(cifToXYZ.createdFiles[0].toUpperCase().contains(".CIF"));
  }

  /**
   * Test CIFtoXYZ when the CIF file is missing hydrogen atoms.
   */
  @Test
  public void testCIFtoXYZNoHydrogen() {
    // Set up the input arguments for the CIFtoXYZ script.
    String[] args = {"--fl","src/main/java/ffx/potential/structures/CBZ03.cif",
        "src/main/java/ffx/potential/structures/cbz.xyz"};
    binding.setVariable("args", args);
    binding.setVariable("baseDir", registerTemporaryDirectory().toFile());

    // Construct and evaluate the CIFtoXYZ script.
    CIFtoXYZ cifToXYZ = new CIFtoXYZ(binding).run();
    potentialScript = cifToXYZ;

    assertEquals(1, cifToXYZ.createdFiles.length);
    assertTrue(cifToXYZ.createdFiles[0].toUpperCase().contains(".XYZ"));
  }

  /**
   * Test CIFtoXYZ when several molecules are included in asymmetric unit.
   */
  @Test
  public void testCIFtoXYZMultipleMolecules() {
    // Set up the input arguments for the CIFtoXYZ script.
    String[] args = {"src/main/java/ffx/potential/structures/1183240.cif",
            "src/main/java/ffx/potential/structures/asplyswat.xyz"};
    binding.setVariable("args", args);
    binding.setVariable("baseDir", registerTemporaryDirectory().toFile());

    // Construct and evaluate the CIFtoXYZ script.
    CIFtoXYZ cifToXYZ = new CIFtoXYZ(binding).run();
    potentialScript = cifToXYZ;

    assertEquals(1, cifToXYZ.createdFiles.length);
    assertTrue(cifToXYZ.createdFiles[0].toUpperCase().contains(".XYZ"));
  }

  /**
   * Test CIFtoXYZ when similar (but different) molecules are in asymmetric unit.
   */
  @Test
  public void testCIFtoXYZzPrimeChallenge() {
    // Set up the input arguments for the CIFtoXYZ script.
    String[] args = {"--fl","src/main/java/ffx/potential/structures/1183241.cif",
            "src/main/java/ffx/potential/structures/glulys.xyz"};
    binding.setVariable("args", args);
    binding.setVariable("baseDir", registerTemporaryDirectory().toFile());

    // Construct and evaluate the CIFtoXYZ script.
    CIFtoXYZ cifToXYZ = new CIFtoXYZ(binding).run();
    potentialScript = cifToXYZ;

    assertEquals(1, cifToXYZ.createdFiles.length);
    assertTrue(cifToXYZ.createdFiles[0].toUpperCase().contains(".XYZ"));
  }

  /**
   * Test CIFtoXYZ on concatenated CIF files (produces multiple ARC files).
   */
  @Test
  public void testCIFtoXYZarc() {
    // Set up the input arguments for the CIFtoXYZ script.
    String[] args = {"--fl","src/main/java/ffx/potential/structures/cbzs.cif",
            "src/main/java/ffx/potential/structures/cbz.xyz"};
    binding.setVariable("args", args);
    binding.setVariable("baseDir", registerTemporaryDirectory().toFile());

    // Construct and evaluate the CIFtoXYZ script.
    CIFtoXYZ cifToXYZ = new CIFtoXYZ(binding).run();
    potentialScript = cifToXYZ;

    assertEquals(3, cifToXYZ.createdFiles.length);
    assertTrue(cifToXYZ.createdFiles[0].toUpperCase().contains(".ARC"));
  }

  /**
   * Test CIFtoXYZ across a molecular disulfide bond.
   */
  @Test
  public void testCIFtoXYZdisulfide() {
    // Set up the input arguments for the CIFtoXYZ script.
    String[] args = {"src/main/java/ffx/potential/structures/UFAGIS01.cif",
            "src/main/java/ffx/potential/structures/uf.xyz"};
    binding.setVariable("args", args);
    binding.setVariable("baseDir", registerTemporaryDirectory().toFile());

    // Construct and evaluate the CIFtoXYZ script.
    CIFtoXYZ cifToXYZ = new CIFtoXYZ(binding).run();
    potentialScript = cifToXYZ;

    assertEquals(1, cifToXYZ.createdFiles.length);
    assertTrue(cifToXYZ.createdFiles[0].toUpperCase().contains(".XYZ"));
  }

  /**
   * Print out help message.
   */
  @Test
  public void testCIFtoXYZHelp() {
    // Set up the input arguments for the CIFtoXYZ script.
    String[] args = {"-h"};
    binding.setVariable("args", args);

    // Construct and evaluate the CIFtoXYZ script.
    potentialScript = new CIFtoXYZ(binding).run();
  }
}