Examples with InteractionContainer de.bioforscher.jstructure.feature.plip.model.InteractionContainer used on opensource projects

Example 1 with InteractionContainer

use of de.bioforscher.jstructure.feature.plip.model.InteractionContainer in project jstructure by JonStargaryen.

the class ProteinLigandInteractionProfilerTest method test_ligand_5in3.

@Test
public void test_ligand_5in3() {
    Structure structure = StructureParser.fromPdbId("5in3").parse();
    InteractionContainer interactions = instance.annotateLigandInteractions(structure);
    System.out.println(interactions);
}

Example 2 with InteractionContainer

use of de.bioforscher.jstructure.feature.plip.model.InteractionContainer in project jstructure by JonStargaryen.

the class ProteinLigandInteractionProfilerTest method test_ligand_1eve.

@Test
public void test_ligand_1eve() {
    Structure structure = StructureParser.fromPdbId("1eve").parse();
    Group ligand = structure.select().chainId("A").residueNumber(2001).asGroup();
    Group res84 = structure.select().residueNumber(84).asGroup();
    Group res279 = structure.select().residueNumber(279).asGroup();
    Group res330 = structure.select().residueNumber(330).asGroup();
    InteractionContainer interactions = instance.annotateLigandInteractions(structure).getSubsetOfInteractions(ligand);
    Assert.assertFalse(interactions.getSubsetOfInteractions(res84).getPiStackingInteractions().isEmpty());
    Assert.assertFalse(interactions.getSubsetOfInteractions(res279).getPiStackingInteractions().isEmpty());
    Assert.assertFalse(interactions.getSubsetOfInteractions(res330).getPiCationInteractions().isEmpty());
}

Example 3 with InteractionContainer

use of de.bioforscher.jstructure.feature.plip.model.InteractionContainer in project jstructure by JonStargaryen.

the class ProteinLigandInteractionProfilerTest method test_ligand_1h2t.

@Test
public void test_ligand_1h2t() {
    Structure structure = StructureParser.fromPdbId("1h2t").parse();
    Group ligand = structure.select().chainId("Z").residueNumber(1151).asGroup();
    InteractionContainer interactions = instance.annotateLigandInteractions(structure).getSubsetOfInteractions(ligand);
    Assert.assertFalse(interactions.getInteractions().isEmpty());
// TODO offset in renumbering of residues
// Group res20 = structure.getGroups().get(21);
// Group res43 = structure.select().residueNumber(43).asGroup();
// Group res112 = structure.select().residueNumber(112).asGroup();
// Group res116 = structure.select().residueNumber(116).asGroup();
// Assert.assertFalse(interactions.getSubsetOfInteractions(res20).getPiStackingInteractions().isEmpty());
// Assert.assertFalse(interactions.getSubsetOfInteractions(res43).getPiStackingInteractions().isEmpty());
// Assert.assertFalse(interactions.getSubsetOfInteractions(res112).getHydrogenBonds().isEmpty());
// Assert.assertFalse(interactions.getSubsetOfInteractions(res116).getSaltBridges().isEmpty());
}

Example 4 with InteractionContainer

use of de.bioforscher.jstructure.feature.plip.model.InteractionContainer in project jstructure by JonStargaryen.

the class ProteinLigandInteractionProfilerTest method test_ligand_3g1h.

@Test
public void test_ligand_3g1h() {
    Structure structure = StructureParser.fromPdbId("3g1h").parse();
    InteractionContainer interactionContainer = instance.annotateLigandInteractions(structure);
    // there are strange effects regarding how interactions are associated to individual ligands
    Group ligand_H2U_A_229 = structure.select().chainId("A").residueNumber(229).asGroup();
    InteractionContainer ic_H2U_A_229 = interactionContainer.getSubsetOfInteractions(ligand_H2U_A_229);
    Assert.assertEquals("hydrophobic count does not match", 1, ic_H2U_A_229.getHydrophobicInteractions().size());
    Assert.assertEquals("hydrogen bond count does not match", 9, ic_H2U_A_229.getHydrogenBonds().size());
    Assert.assertEquals("water bridge count does not match", // offset between PLIP CLI and web server
    4 + 1, ic_H2U_A_229.getWaterBridges().size());
    Assert.assertEquals("salt bridge count does not match", 1, ic_H2U_A_229.getSaltBridges().size());
}