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

Example 31 with Protein

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

the class ProteinParserTest method shouldHandleProteinWithNonStandardAminoAcids.

@Test
public void shouldHandleProteinWithNonStandardAminoAcids() {
    Protein protein = ProteinParser.source(NON_STANDARD_PDB_ID).parse();
    // ensure that the initial selenomethionine stored as HETATM is correctly parsed
    System.out.println(protein.getAminoAcidSequence());
    Assert.assertThat(protein.getAminoAcidSequence(), startsWith("M"));
}

Example 32 with Protein

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

the class ProteinParserTest method shouldParseInsertedAminoAcids.

@Test
public void shouldParseInsertedAminoAcids() {
    Protein protein = ProteinParser.source("2w0l").parse();
    List<Group> groups = protein.select().chainName("A").residueNumber(95).asFilteredGroups().collect(Collectors.toList());
    Assert.assertEquals(2, groups.size());
    groups.forEach(System.out::println);
}