Examples with ColumnarStructure edu.sdsc.mmtf.spark.utils.ColumnarStructure used on opensource projects

Example 1 with ColumnarStructure

use of edu.sdsc.mmtf.spark.utils.ColumnarStructure in project mmtf-spark by sbl-sdsc.

the class ColumnarStructureTest method testGetAtomNames.

@Test
public void testGetAtomNames() {
    StructureDataInterface s = pdb.values().first();
    ColumnarStructure cs = new ColumnarStructure(s, true);
    assertEquals("CG2", cs.getAtomNames()[900]);
}

Example 2 with ColumnarStructure

use of edu.sdsc.mmtf.spark.utils.ColumnarStructure in project mmtf-spark by sbl-sdsc.

the class ColumnarStructureTest method testIsPolymer.

@Test
public void testIsPolymer() {
    StructureDataInterface s = pdb.values().first();
    ColumnarStructure cs = new ColumnarStructure(s, true);
    // chain A
    assertEquals(true, cs.isPolymer()[100]);
    // BTN
    assertEquals(false, cs.isPolymer()[901]);
    // HOH
    assertEquals(false, cs.isPolymer()[917]);
}

Example 3 with ColumnarStructure

use of edu.sdsc.mmtf.spark.utils.ColumnarStructure in project mmtf-spark by sbl-sdsc.

the class ColumnarStructureTest method testGetChemCompTypes.

@Test
public void testGetChemCompTypes() {
    StructureDataInterface s = pdb.values().first();
    ColumnarStructure cs = new ColumnarStructure(s, true);
    assertEquals("PEPTIDE LINKING", cs.getChemCompTypes()[100]);
    // BTN
    assertEquals("NON-POLYMER", cs.getChemCompTypes()[901]);
    // HOH
    assertEquals("NON-POLYMER", cs.getChemCompTypes()[917]);
}

Example 4 with ColumnarStructure

use of edu.sdsc.mmtf.spark.utils.ColumnarStructure in project mmtf-spark by sbl-sdsc.

the class ColumnarStructureTest method testGetEntityTypes.

@Test
public void testGetEntityTypes() {
    StructureDataInterface s = pdb.values().first();
    ColumnarStructure cs = new ColumnarStructure(s, true);
    assertEquals("PRO", cs.getEntityTypes()[100]);
    // BTN
    assertEquals("LGO", cs.getEntityTypes()[901]);
    // HOH
    assertEquals("WAT", cs.getEntityTypes()[917]);
}

Example 5 with ColumnarStructure

use of edu.sdsc.mmtf.spark.utils.ColumnarStructure in project mmtf-spark by sbl-sdsc.

the class ColumnarStructureTest method testGetElements.

@Test
public void testGetElements() {
    StructureDataInterface s = pdb.values().first();
    ColumnarStructure cs = new ColumnarStructure(s, true);
    assertEquals("C", cs.getElements()[20]);
}