ImportCIFTest

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// Title:       Force Field X.
// Description: Force Field X - Software for Molecular Biophysics.
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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 ImportCIF command to determine that files are being translated correctly.
 *
 * @author Aaron J. Nessler
 */

public class ImportCIFTest extends PotentialTest {

  /**
   * Test a basic CIF to XYZ conversion.
   */
  @Test
  public void testImportCIF() {
    // Set up the input arguments for the ImportCIF script.
    String cifpath = getResourcePath("CBZ16.cif");
    String xyzpath = getResourcePath("cbz.xyz");
    String[] args = {cifpath, xyzpath};
    binding.setVariable("args", args);
    binding.setVariable("baseDir", registerTemporaryDirectory().toFile());

    // Construct and evaluate the ImportCIF script.

    ImportCIF ImportCIF = new ImportCIF(binding).run();
    potentialScript = ImportCIF;

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

  /**
   * Test writing out a CIF file (XYZ to CIF).
   */
  @Test
  public void testImportCIFWriteAsCIF() {
    // Set up the input arguments for the ImportCIF script.
    String filepath = getResourcePath("paracetamol.xyz");
    String[] args = {"--sc", filepath};
    binding.setVariable("args", args);
    binding.setVariable("baseDir", registerTemporaryDirectory().toFile());

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

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

  /**
   * Test ImportCIF when the CIF file is missing hydrogen atoms.
   */
  @Test
  public void testImportCIFNoHydrogen() {
    // Set up the input arguments for the ImportCIF script.
    String cifpath = getResourcePath("CBZ03.cif");
    String xyzpath = getResourcePath("cbz.xyz");
    String[] args = {"--fl", cifpath, xyzpath};
    binding.setVariable("args", args);
    binding.setVariable("baseDir", registerTemporaryDirectory().toFile());

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

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

  /**
   * Test ImportCIF when several molecules are included in asymmetric unit.
   */
  @Test
  public void testImportCIFMultipleMolecules() {
    // Set up the input arguments for the ImportCIF script.
    String cifpath = getResourcePath("1183240.cif");
    String xyzpath = getResourcePath("asplyswat.xyz");
    String[] args = {cifpath, xyzpath};
    binding.setVariable("args", args);
    binding.setVariable("baseDir", registerTemporaryDirectory().toFile());

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

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

  /**
   * Test ImportCIF when similar (but different) molecules are in asymmetric unit.
   */
  @Test
  public void testImportCIFzPrimeChallenge() {
    // Set up the input arguments for the ImportCIF script.
    String cifpath = getResourcePath("1183241.cif");
    String xyzpath = getResourcePath("glulys.xyz");
    String[] args = {"--fl", cifpath, xyzpath};
    binding.setVariable("args", args);
    binding.setVariable("baseDir", registerTemporaryDirectory().toFile());

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

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

  /**
   * Test ImportCIF on concatenated CIF files (produces multiple ARC files).
   */
  @Test
  public void testImportCIFarc() {
    // Set up the input arguments for the ImportCIF script.
    String cifpath = getResourcePath("cbzs.cif");
    String xyzpath = getResourcePath("cbz.xyz");
    String[] args = {"--fl", cifpath, xyzpath};
    binding.setVariable("args", args);
    binding.setVariable("baseDir", registerTemporaryDirectory().toFile());

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

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

  /**
   * Test ImportCIF across a molecular disulfide bond.
   */
  @Test
  public void testImportCIFdisulfide() {
    // Set up the input arguments for the ImportCIF script.
    String cifpath = getResourcePath("UFAGIS01.cif");
    String xyzpath = getResourcePath("uf.xyz");
    String[] args = {cifpath, xyzpath};
    binding.setVariable("args", args);
    binding.setVariable("baseDir", registerTemporaryDirectory().toFile());

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

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

  /**
   * Test ImportCIF conversion to PDB.
   */
  @Test
  public void testImportCIFpdb() {
    // Set up the input arguments for the ImportCIF script.
    String cifpath = getResourcePath("288726.cif");
    String pdbpath = getResourcePath("ALA-HIE.pdb");
    String[] args = {cifpath, pdbpath};
    binding.setVariable("args", args);
    binding.setVariable("baseDir", registerTemporaryDirectory().toFile());

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

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

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

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