Examples with ChemFile org.openscience.cdk.silent.ChemFile used on opensource projects

Example 1 with ChemFile

use of org.openscience.cdk.silent.ChemFile in project cdk by cdk.

the class CIFReaderTest method cod1100784.

/**
 * Ensure a CIF file from the crystallography open database can be read.
 * Example input <a href="http://www.crystallography.net/1100784.cif">1100784</a>.
 */
@Test
public void cod1100784() throws IOException, CDKException {
    InputStream in = getClass().getResourceAsStream("1100784.cif");
    CIFReader cifReader = new CIFReader(in);
    // try {
    IChemFile chemFile = cifReader.read(new ChemFile());
    org.hamcrest.MatcherAssert.assertThat(chemFile.getChemSequenceCount(), is(1));
    org.hamcrest.MatcherAssert.assertThat(chemFile.getChemSequence(0).getChemModelCount(), is(1));
    Assert.assertNotNull(chemFile.getChemSequence(0).getChemModel(0).getCrystal());
    // } finally {
    cifReader.close();
// }
}

Example 2 with ChemFile

use of org.openscience.cdk.silent.ChemFile in project cdk by cdk.

the class CIFReaderTest method cod1100784AtomCount.

@Test
public void cod1100784AtomCount() throws IOException, CDKException {
    InputStream in = getClass().getResourceAsStream("1100784.cif");
    CIFReader cifReader = new CIFReader(in);
    IChemFile chemFile = cifReader.read(new ChemFile());
    ICrystal crystal = chemFile.getChemSequence(0).getChemModel(0).getCrystal();
    Assert.assertEquals(72, crystal.getAtomCount());
    cifReader.close();
}

Example 3 with ChemFile

use of org.openscience.cdk.silent.ChemFile in project cdk by cdk.

the class CIFReaderTest method cod1100784CellLengths.

@Test()
public void cod1100784CellLengths() throws IOException, CDKException {
    InputStream in = getClass().getResourceAsStream("1100784.cif");
    CIFReader cifReader = new CIFReader(in);
    IChemFile chemFile = cifReader.read(new ChemFile());
    ICrystal crystal = chemFile.getChemSequence(0).getChemModel(0).getCrystal();
    Assert.assertTrue(java.lang.Math.abs(crystal.getA().length() - 10.9754) < 1E-5);
    Assert.assertTrue(java.lang.Math.abs(crystal.getB().length() - 11.4045) < 1E-5);
    Assert.assertTrue(java.lang.Math.abs(crystal.getC().length() - 12.9314) < 1E-5);
    cifReader.close();
}

Example 4 with ChemFile

use of org.openscience.cdk.silent.ChemFile in project cdk by cdk.

the class CDKAtomTypeMatcherFilesTest method testSmilesFiles.

@Test
public void testSmilesFiles() throws Exception {
    CDKAtomTypeMatcher atomTypeMatcher = CDKAtomTypeMatcher.getInstance(SilentChemObjectBuilder.getInstance());
    // Read the first file
    String filename = "smiles1.cml";
    InputStream ins = this.getClass().getResourceAsStream(filename);
    CMLReader reader = new CMLReader(ins);
    IChemFile chemFile = reader.read(new ChemFile());
    Assert.assertNotNull(chemFile);
    IAtomContainer mol1 = ChemFileManipulator.getAllAtomContainers(chemFile).get(0);
    // Read the second file
    filename = "smiles2.cml";
    ins = this.getClass().getResourceAsStream(filename);
    reader = new CMLReader(ins);
    chemFile = reader.read(new ChemFile());
    Assert.assertNotNull(chemFile);
    IAtomContainer mol2 = ChemFileManipulator.getAllAtomContainers(chemFile).get(0);
    IAtomType[] types1 = atomTypeMatcher.findMatchingAtomTypes(mol1);
    IAtomType[] types2 = atomTypeMatcher.findMatchingAtomTypes(mol2);
    for (int i = 0; i < mol1.getAtomCount(); i++) {
        Assert.assertNotNull("Atom typing in mol1 failed for atom " + (i + 1), types1[i]);
        Assert.assertNotNull("Atom typing in mol2 failed for atom " + (i + 1), types2[i]);
        Assert.assertEquals("Atom type mismatch for the " + (i + 1) + " atom", types1[i].getAtomTypeName(), types2[i].getAtomTypeName());
    }
}

Example 5 with ChemFile

use of org.openscience.cdk.silent.ChemFile in project cdk by cdk.

the class CDKAtomTypeMatcherFilesTest method testFile3.

@Test
public void testFile3() throws Exception {
    String filename = "3.cml";
    InputStream ins = this.getClass().getResourceAsStream(filename);
    CMLReader reader = new CMLReader(ins);
    IChemFile chemFile = reader.read(new ChemFile());
    // test the resulting ChemFile content
    Assert.assertNotNull(chemFile);
    IAtomContainer mol = ChemFileManipulator.getAllAtomContainers(chemFile).get(0);
    String[] expectedTypes = { "C.sp2", "N.sp2", "C.sp2", "N.sp3", "C.sp2", "N.sp2", "O.sp3", "C.sp2", "C.sp2", "C.sp2" };
    assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}