Examples with AtomContainer de.bioforscher.jstructure.model.structure.container.AtomContainer used on opensource projects

Example 6 with AtomContainer

use of de.bioforscher.jstructure.model.structure.container.AtomContainer in project jstructure by JonStargaryen.

the class StructureCollectorsTest method shouldCreateDistinctContainer.

@Test
public void shouldCreateDistinctContainer() {
    // create copy
    AminoAcid original = protein.select().aminoAcids().asAminoAcid();
    String initialPdbRecord = original.getPdbRepresentation();
    AtomContainer copy = original.createDeepCopy();
    // manipulate coordinates of copy
    copy.getAtoms().get(0).setCoordinates(new double[] { 0, 0, 0 });
    // should not affect original
    Assert.assertNotEquals(initialPdbRecord, copy.getPdbRepresentation());
    Assert.assertEquals(initialPdbRecord, original.getPdbRepresentation());
}

Example 7 with AtomContainer

use of de.bioforscher.jstructure.model.structure.container.AtomContainer in project jstructure by JonStargaryen.

the class SelectionTest method shouldSelectAtomsFromGroupsFromChains.

@Test
public void shouldSelectAtomsFromGroupsFromChains() {
    System.out.println("alpha carbons and beta carbons of PHEs in chain 'A' and 'C'");
    AtomContainer atoms = protein.select().chainName("A", "C").groupName(Phenylalanine.THREE_LETTER_CODE).atomName(AminoAcid.ALPHA_CARBON_NAME, AminoAcid.BETA_CARBON_NAME).asIsolatedStructure();
    System.out.println(atoms.getPdbRepresentation());
}