Skip to content

Commit 2785fdf

Browse files
josemduartejosemduarte
committed
Fixing #533 
1 parent 14c4e53 commit 2785fdf

File tree

2 files changed

+97
-157
lines changed

2 files changed

+97
-157
lines changed

‎biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -511,7 +511,7 @@ public static List<AtomSite> convertStructureToAtomSites(Structure s) {
511511
List<AtomSite> list = new ArrayList<AtomSite>();
512512

513513
for (int m=0;m<s.nrModels();m++) {
514-
for (Chain c:s.getChains()) {
514+
for (Chain c:s.getChains(m)) {
515515
list.addAll(convertChainToAtomSites(c, m+1, c.getChainID(), c.getInternalChainID()));
516516
}
517517
}

‎biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMCIFWriting.java‎

Lines changed: 96 additions & 156 deletions
Original file line numberDiff line numberDiff line change
@@ -28,10 +28,12 @@
2828
import java.io.FileWriter;
2929
import java.io.IOException;
3030

31+
import org.biojava.nbio.structure.Atom;
3132
import org.biojava.nbio.structure.Chain;
3233
import org.biojava.nbio.structure.Structure;
3334
import org.biojava.nbio.structure.StructureException;
3435
import org.biojava.nbio.structure.StructureIO;
36+
import org.biojava.nbio.structure.StructureTools;
3537
import org.biojava.nbio.structure.align.util.AtomCache;
3638
import org.biojava.nbio.structure.io.mmcif.MMCIFFileTools;
3739
import org.biojava.nbio.structure.io.mmcif.MMcifParser;
@@ -45,59 +47,8 @@ public class TestMMCIFWriting {
4547

4648
@Test
4749
public void test1SMT() throws IOException, StructureException {
48-
AtomCache cache = new AtomCache();
49-
50-
StructureIO.setAtomCache(cache);
51-
52-
cache.setUseMmCif(true);
53-
54-
FileParsingParameters params = new FileParsingParameters();
55-
params.setAlignSeqRes(true);
56-
cache.setFileParsingParams(params);
57-
58-
Structure originalStruct = StructureIO.getStructure("1SMT");
59-
60-
File outputFile = File.createTempFile("biojava_testing_", ".cif");
61-
outputFile.deleteOnExit();
62-
63-
FileWriter fw = new FileWriter(outputFile);
64-
fw.write(originalStruct.toMMCIF());
65-
fw.close();
66-
67-
68-
MMcifParser parser = new SimpleMMcifParser();
69-
70-
SimpleMMcifConsumer consumer = new SimpleMMcifConsumer();
71-
72-
FileParsingParameters fileParsingParams = new FileParsingParameters();
73-
fileParsingParams.setAlignSeqRes(true);
74-
75-
consumer.setFileParsingParameters(fileParsingParams);
76-
77-
parser.addMMcifConsumer(consumer);
78-
79-
//parser.parse(new BufferedReader(new FileReader(new File("/home/duarte_j/test.cif"))));
80-
parser.parse(new BufferedReader(new FileReader(outputFile)));
81-
82-
Structure readStruct = consumer.getStructure();
83-
84-
assertNotNull(readStruct);
85-
86-
assertEquals(originalStruct.getChains().size(), readStruct.getChains().size());
87-
88-
for (int i=0;i<originalStruct.getChains().size();i++) {
89-
assertEquals(originalStruct.getChains().get(i).getAtomGroups().size(),
90-
readStruct.getChains().get(i).getAtomGroups().size());
91-
92-
Chain origChain = originalStruct.getChains().get(i);
93-
Chain readChain = readStruct.getChains().get(i);
94-
95-
assertEquals(origChain.getAtomGroups().size(), readChain.getAtomGroups().size());
96-
//assertEquals(origChain.getSeqResGroups().size(), readChain.getSeqResGroups().size());
97-
}
98-
99-
// Test cell and symmetry
100-
assertEquals(originalStruct.getCrystallographicInfo().getSpaceGroup(),readStruct.getCrystallographicInfo().getSpaceGroup());
50+
// an x-ray structure
51+
testRoundTrip("1SMT");
10152
}
10253

10354
/**
@@ -107,71 +58,57 @@ public void test1SMT() throws IOException, StructureException {
10758
*/
10859
@Test
10960
public void test2N3J() throws IOException, StructureException {
110-
AtomCache cache = new AtomCache();
111-
112-
StructureIO.setAtomCache(cache);
113-
114-
cache.setUseMmCif(true);
115-
116-
FileParsingParameters params = new FileParsingParameters();
117-
params.setAlignSeqRes(true);
118-
cache.setFileParsingParams(params);
119-
120-
Structure originalStruct = StructureIO.getStructure("2N3J");
121-
122-
File outputFile = File.createTempFile("biojava_testing_", ".cif");
123-
outputFile.deleteOnExit();
124-
125-
126-
FileWriter fw = new FileWriter(outputFile);
127-
fw.write(originalStruct.toMMCIF());
128-
fw.close();
129-
130-
131-
MMcifParser parser = new SimpleMMcifParser();
132-
133-
SimpleMMcifConsumer consumer = new SimpleMMcifConsumer();
134-
135-
FileParsingParameters fileParsingParams = new FileParsingParameters();
136-
fileParsingParams.setAlignSeqRes(true);
137-
138-
consumer.setFileParsingParameters(fileParsingParams);
139-
140-
parser.addMMcifConsumer(consumer);
141-
142-
//parser.parse(new BufferedReader(new FileReader(new File("/home/duarte_j/test.cif"))));
143-
parser.parse(new BufferedReader(new FileReader(outputFile)));
144-
145-
Structure readStruct = consumer.getStructure();
146-
147-
assertNotNull(readStruct);
148-
149-
assertEquals(originalStruct.getChains().size(), readStruct.getChains().size());
150-
151-
assertEquals(originalStruct.nrModels(), readStruct.nrModels());
61+
// an NMR structure (multimodel) with 2 chains
62+
testRoundTrip("2N3J");
63+
}
64+
65+
@Test
66+
public void test1A2C() throws IOException, StructureException {
67+
// a structure with insertion codes
68+
testRoundTrip("1A2C");
69+
}
70+
71+
private static class DemoBean {
72+
@IgnoreField
73+
String not_a_field;
74+
75+
@SuppressWarnings("unused")//used by reflection
76+
String default_field;
77+
78+
@CIFLabel(label="custom_label")
79+
String custom_field;
15280

153-
for (int i=0; i<originalStruct.nrModels();i++) {
154-
assertEquals(originalStruct.getModel(i).size(), readStruct.getModel(i).size());
81+
public void setNot_a_field(String not_a_field) {
82+
this.not_a_field = not_a_field;
15583
}
156-
157-
for (int i=0;i<originalStruct.getChains().size();i++) {
158-
assertEquals(originalStruct.getChains().get(i).getAtomGroups().size(),
159-
readStruct.getChains().get(i).getAtomGroups().size());
160-
161-
Chain origChain = originalStruct.getChains().get(i);
162-
Chain readChain = readStruct.getChains().get(i);
163-
164-
assertEquals(origChain.getAtomGroups().size(), readChain.getAtomGroups().size());
165-
//assertEquals(origChain.getSeqResGroups().size(), readChain.getSeqResGroups().size());
84+
public void setDefault_field(String default_field) {
85+
this.default_field = default_field;
86+
}
87+
public void setCustom_field(String custom_field) {
88+
this.custom_field = custom_field;
16689
}
167-
16890
}
169-
91+
17092
@Test
171-
public void test1A2C() throws IOException, StructureException {
93+
public void testBeanAnnotations() {
94+
DemoBean bean = new DemoBean();
95+
bean.setCustom_field("custom_field");
96+
bean.setDefault_field(null);
97+
bean.setNot_a_field("not_a_field");
17298

173-
// a structure with insertion codes
17499

100+
// Test (1) should have custom_label (@CIFLabel)
101+
// (2) shouldn't have not_a_field (@IgnoreField)
102+
String newline = System.getProperty("line.separator");
103+
String mmcif = MMCIFFileTools.toMMCIF("_demo", bean);
104+
String expected =
105+
"_demo.default_field ?" + newline
106+
+ "_demo.custom_label custom_field" + newline
107+
+ "#" + newline;
108+
assertEquals(expected, mmcif);
109+
}
110+
111+
private static void testRoundTrip(String pdbId) throws IOException, StructureException {
175112
AtomCache cache = new AtomCache();
176113

177114
StructureIO.setAtomCache(cache);
@@ -182,7 +119,7 @@ public void test1A2C() throws IOException, StructureException {
182119
params.setAlignSeqRes(true);
183120
cache.setFileParsingParams(params);
184121

185-
Structure originalStruct = StructureIO.getStructure("1A2C");
122+
Structure originalStruct = StructureIO.getStructure(pdbId);
186123

187124
File outputFile = File.createTempFile("biojava_testing_", ".cif");
188125
outputFile.deleteOnExit();
@@ -204,7 +141,6 @@ public void test1A2C() throws IOException, StructureException {
204141

205142
parser.addMMcifConsumer(consumer);
206143

207-
//parser.parse(new BufferedReader(new FileReader(new File("/home/duarte_j/test.cif"))));
208144
parser.parse(new BufferedReader(new FileReader(outputFile)));
209145

210146
Structure readStruct = consumer.getStructure();
@@ -213,56 +149,60 @@ public void test1A2C() throws IOException, StructureException {
213149

214150
assertEquals(originalStruct.getChains().size(), readStruct.getChains().size());
215151

216-
for (int i=0;i<originalStruct.getChains().size();i++) {
217-
assertEquals(originalStruct.getChains().get(i).getAtomGroups().size(),
218-
readStruct.getChains().get(i).getAtomGroups().size());
219-
220-
Chain origChain = originalStruct.getChains().get(i);
221-
Chain readChain = readStruct.getChains().get(i);
152+
assertEquals(originalStruct.nrModels(), readStruct.nrModels());
222153

223-
assertEquals(origChain.getAtomGroups().size(), readChain.getAtomGroups().size());
224-
//assertEquals(origChain.getSeqResGroups().size(), readChain.getSeqResGroups().size());
154+
for (int i=0; i<originalStruct.nrModels();i++) {
155+
assertEquals(originalStruct.getModel(i).size(), readStruct.getModel(i).size());
225156
}
226157

227-
}
228-
229-
private static class DemoBean {
230-
@IgnoreField
231-
String not_a_field;
232158

233-
@SuppressWarnings("unused")//used by reflection
234-
String default_field;
235159

236-
@CIFLabel(label="custom_label")
237-
String custom_field;
160+
for (int modelIdx=0;modelIdx<originalStruct.nrModels();modelIdx++) {
161+
162+
for (int i=0;i<originalStruct.getModel(modelIdx).size();i++) {
163+
assertEquals(originalStruct.getChains().get(i).getAtomGroups().size(),
164+
readStruct.getChains().get(i).getAtomGroups().size());
165+
166+
Chain origChain = originalStruct.getModel(modelIdx).get(i);
167+
Chain readChain = readStruct.getModel(modelIdx).get(i);
168+
169+
assertEquals(origChain.getAtomGroups().size(), readChain.getAtomGroups().size());
170+
//assertEquals(origChain.getSeqResGroups().size(), readChain.getSeqResGroups().size());
171+
assertEquals(origChain.getChainID(), readChain.getChainID());
172+
173+
Atom[] origAtoms = StructureTools.getAllAtomArray(origChain);
174+
Atom[] readAtoms = StructureTools.getAllAtomArray(readChain);
175+
176+
assertEquals(origAtoms.length, readAtoms.length);
177+
178+
for (int atomIdx=0;atomIdx<origAtoms.length;atomIdx++) {
179+
180+
assertEquals("atom serials don't match for atom "+origAtoms[atomIdx].toString(),
181+
origAtoms[atomIdx].getPDBserial(), readAtoms[atomIdx].getPDBserial());
182+
183+
assertEquals("atom names don't match for atom "+origAtoms[atomIdx].toString(),
184+
origAtoms[atomIdx].getName(), readAtoms[atomIdx].getName());
185+
186+
assertEquals("atom elements don't match for atom "+origAtoms[atomIdx].toString(),
187+
origAtoms[atomIdx].getElement(), readAtoms[atomIdx].getElement());
188+
189+
assertEquals("x values don't match for atom "+origAtoms[atomIdx].toString(),
190+
origAtoms[atomIdx].getX(), readAtoms[atomIdx].getX(),0.0001);
191+
192+
assertEquals("y values don't match for atom "+origAtoms[atomIdx].toString(),
193+
origAtoms[atomIdx].getY(), readAtoms[atomIdx].getY(),0.0001);
194+
195+
assertEquals("z values don't match for atom "+origAtoms[atomIdx].toString(),
196+
origAtoms[atomIdx].getZ(), readAtoms[atomIdx].getZ(),0.0001);
197+
}
198+
}
238199

239-
public void setNot_a_field(String not_a_field) {
240-
this.not_a_field = not_a_field;
241-
}
242-
public void setDefault_field(String default_field) {
243-
this.default_field = default_field;
244-
}
245-
public void setCustom_field(String custom_field) {
246-
this.custom_field = custom_field;
247200
}
248-
}
249201

250-
@Test
251-
public void testBeanAnnotations() {
252-
DemoBean bean = new DemoBean();
253-
bean.setCustom_field("custom_field");
254-
bean.setDefault_field(null);
255-
bean.setNot_a_field("not_a_field");
256-
257-
258-
// Test (1) should have custom_label (@CIFLabel)
259-
// (2) shouldn't have not_a_field (@IgnoreField)
260-
String newline = System.getProperty("line.separator");
261-
String mmcif = MMCIFFileTools.toMMCIF("_demo", bean);
262-
String expected =
263-
"_demo.default_field ?" + newline
264-
+ "_demo.custom_label custom_field" + newline
265-
+ "#" + newline;
266-
assertEquals(expected, mmcif);
202+
// Test cell and symmetry
203+
assertEquals(originalStruct.getCrystallographicInfo().getSpaceGroup(),
204+
readStruct.getCrystallographicInfo().getSpaceGroup());
205+
206+
267207
}
268208
}

0 commit comments

Comments
 (0)