Repository navigation
Expand file tree
/
Copy pathTestBond.java
More file actions
240 lines (189 loc) · 5.92 KB
/
Copy pathTestBond.java
File metadata and controls
240 lines (189 loc) · 5.92 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
/*
* 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 java.util.ArrayList;
import java.util.List;
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() {
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.getPolyChainsByPDB("A").get(0).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.getPolyChainsByPDB("A").get(0).getSeqResGroup(273);
AminoAcidImpl residue2 = (AminoAcidImpl) s.getPolyChainsByPDB("A").get(0).getSeqResGroup(274);
Atom carboxylC = residue1.getC();
Atom aminoN = residue2.getN();
assertTrue(areBonded(carboxylC, aminoN));
}
@Test
public void testDisulfideBonds() throws StructureException, IOException {
Structure s = StructureIO.getStructure("1kh9");
Atom atom1 = s.getPolyChainsByPDB("A").get(0).getSeqResGroup(177).getAtom("SG");
Atom atom2 = s.getPolyChainsByPDB("A").get(0).getSeqResGroup(167).getAtom("SG");
assertTrue(areBonded(atom1, atom2));
}
@Test
public void testLigandBonds() throws StructureException, IOException {
Structure s = StructureIO.getStructure("1kh9");
Atom phosphateP = s.getChain("I").getAtomGroup(0).getAtom("P");
Atom phosphateO = s.getChain("I").getAtomGroup(0).getAtom("O1");
assertTrue(areBonded(phosphateP, phosphateO));
}
/**
* Test whether nucleotide bonds are being generated
* @throws IOException
* @throws StructureException
*/
@Test
public void testNucleotideBonds() throws IOException, StructureException {
Structure bio = StructureIO.getStructure("4y60");
for( Chain c : bio.getChains()) {
int groupCounter = 0;
List<Group> currentGroups = c.getAtomGroups();
for ( Group g : currentGroups) {
if(groupCounter!=0 && groupCounter<currentGroups.size()) {
List<Atom> atoms = g.getAtoms();
for ( Atom a : atoms) {
if ( a.getName().equals("P")){
// Check to see if one of the phosphate atoms has bonding to something
// outside of the group.
List<Integer> indexList = new ArrayList<>();
for (Bond b : a.getBonds()){
indexList.add(atoms.indexOf(b.getOther(a)));
}
assertTrue(indexList.contains(-1));
}
}
}
groupCounter++;
}
}
}
/**
* Test whether these partial occupancy hydrogens are bonded to the residue.
* @throws StructureException
* @throws IOException
*/
@Test
public void testHeavyAtomBondMissing() throws IOException, StructureException {
testPartialOccBonds("3jtm");
testPartialOccBonds("3jq8");
testPartialOccBonds("3jq9");
testPartialOccBonds("3i06");
testPartialOccBonds("3nu3");
testPartialOccBonds("3nu4");
testPartialOccBonds("3nvd");
}
/**
* Test whether these partial occupancy hydrogens are bonded to the residue.
* @throws StructureException
* @throws IOException
*/
@Test
public void testHydrogenToProteinBondMissing() throws IOException, StructureException {
testPartialOccBonds("4txr");
testPartialOccBonds("3nvd");
}
/**
*
* @throws IOException
* @throws StructureException
*/
private void testPartialOccBonds(String pdbId) throws IOException, StructureException {
Structure inputStructure = StructureIO.getStructure(pdbId);
// Loop through the structure
for(int i=0;i<inputStructure.nrModels();i++){
for(Chain c: inputStructure.getChains(i)){
for(Group g: c.getAtomGroups()){
// Skip single atom groups
if(g.size()<=1){
continue;
}
// Get all the atoms
List<Atom> atomsList = new ArrayList<>(g.getAtoms());
for(Group altLocOne: g.getAltLocs()){
atomsList.addAll(altLocOne.getAtoms());
}
// Check they all have bonds
for(Atom a: atomsList){
assertNotEquals(a.getBonds(), null);
}
}
}
}
}
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");
}
}