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170 lines (120 loc) · 4.06 KB
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/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.nbio.structure;
import java.io.IOException;
import org.biojava.nbio.structure.align.util.AtomCache;
import org.biojava.nbio.structure.io.FileParsingParameters;
import org.junit.BeforeClass;
import org.junit.Test;
import static org.junit.Assert.*;
public class TestBond {
private static AtomCache cache;
@BeforeClass
public static void setUp() throws IOException, StructureException {
cache = new AtomCache();
cache.setUseMmCif(true);
FileParsingParameters params = cache.getFileParsingParams();
params.setAlignSeqRes(true);
params.setCreateAtomBonds(true);
StructureIO.setAtomCache(cache);
}
@Test
public void testIntraResidueBonds() throws StructureException, IOException {
Structure s = StructureIO.getStructure("1kh9");
Group g = s.getChainByPDB("A").getSeqResGroup(274);
Atom cg = g.getAtom("CG");
Atom cb = g.getAtom("CB");
Atom cd1 = g.getAtom("CD1");
Atom cd2 = g.getAtom("CD2");
assertEquals(3, cg.getBonds().size());
for (Bond bond : cg.getBonds()) {
if (bond.getOther(cg) == cb) {
assertEquals(1, bond.getBondOrder());
} else if (bond.getOther(cg) == cd1) {
assertEquals(2, bond.getBondOrder());
} else if (bond.getOther(cg) == cd2) {
assertEquals(1, bond.getBondOrder());
}
}
}
@Test
public void testPeptideBonds() throws StructureException, IOException {
Structure s = StructureIO.getStructure("1kh9");
AminoAcidImpl residue1 = (AminoAcidImpl) s.getChainByPDB("A").getSeqResGroup(273);
AminoAcidImpl residue2 = (AminoAcidImpl) s.getChainByPDB("A").getSeqResGroup(274);
Atom carboxylC = residue1.getC();
Atom aminoN = residue2.getN();
assertTrue(areBonded(carboxylC, aminoN));
}
@Test
public void testLINKBonds() throws StructureException, IOException {
cache.setUseMmCif(false);
Structure s = StructureIO.getStructure("1kh9");
Group g1 = s.getChainByPDB("A").getSeqResGroup(50);
assertNotNull(g1);
assertTrue(g1 instanceof AminoAcid);
AminoAcid aa = (AminoAcid)g1;
assertTrue(aa.getRecordType().equals(AminoAcid.ATOMRECORD));
Atom atom1 = g1.getAtom("OD1");
Atom atom2 = s.getChainByPDB("A").getAtomGroup(446).getAtom("MG");
assertNotNull(atom1);
assertNotNull(atom2);
assertTrue(areBonded(atom1, atom2));
cache.setUseMmCif(true);
}
@Test
public void testDisulfideBonds() throws StructureException, IOException {
Structure s = StructureIO.getStructure("1kh9");
Atom atom1 = s.getChainByPDB("A").getSeqResGroup(177).getAtom("SG");
Atom atom2 = s.getChainByPDB("A").getSeqResGroup(167).getAtom("SG");
assertTrue(areBonded(atom1, atom2));
}
@Test
public void testLigandBonds() throws StructureException, IOException {
Structure s = StructureIO.getStructure("1kh9");
Atom phosphateP = s.getChainByPDB("A").getAtomGroup(447).getAtom("P");
Atom phosphateO = s.getChainByPDB("A").getAtomGroup(447).getAtom("O1");
assertTrue(areBonded(phosphateP, phosphateO));
}
private boolean areBonded(Atom a, Atom b) {
for (Bond bond : a.getBonds()) {
if (bond.getOther(a) == b) {
return true;
}
}
return false;
}
/*
* Each of the following PDB IDs used to make formBonds() crash.
*/
@Test
public void test145D() throws IOException, StructureException {
StructureIO.getStructure("145D");
}
@Test
public void test1APJ() throws IOException, StructureException {
StructureIO.getStructure("1APJ");
}
@Test
public void test1BDX() throws IOException, StructureException {
StructureIO.getStructure("1BDX");
}
}