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josemduartejosemduarte
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Some fixes in altloc test and 2 additions
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‎biojava-structure/src/test/java/org/biojava/nbio/structure/TestAltLocs.java‎

Lines changed: 168 additions & 31 deletions
Original file line numberDiff line numberDiff line change
@@ -23,13 +23,19 @@
2323
import org.biojava.nbio.structure.align.util.AtomCache;
2424
import org.biojava.nbio.structure.io.FileParsingParameters;
2525
import org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory;
26+
import org.biojava.nbio.structure.io.mmcif.MMCIFFileTools;
27+
import org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer;
28+
import org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser;
2629
import org.biojava.nbio.structure.io.mmcif.chem.PolymerType;
2730
import org.biojava.nbio.structure.io.mmcif.chem.ResidueType;
31+
import org.biojava.nbio.structure.io.mmcif.model.AtomSite;
2832
import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
2933
import org.biojava.nbio.structure.io.mmcif.model.ChemCompBond;
3034
import org.junit.Test;
3135

36+
import java.io.BufferedReader;
3237
import java.io.IOException;
38+
import java.io.StringReader;
3339
import java.util.ArrayList;
3440
import java.util.List;
3541

@@ -85,28 +91,26 @@ public void testAltLocParsing() throws StructureException, IOException{
8591

8692
assertTrue("The group does not have an altLoc ", g.hasAltLoc());
8793

88-
assertTrue("The nr of altLocs is not 1, but " + g.getAltLocs().size(), g.getAltLocs().size() == 1);
94+
assertEquals(1, g.getAltLocs().size());
8995

9096
assertEquals( g.getPDBName(), "KOR");
9197

9298
Group altLocG = g.getAltLocs().get(0);
9399

94100
assertEquals(altLocG.getPDBName(),"K1R");
95101

96-
assertEquals(275,groupCount);
102+
assertEquals(275, groupCount);
97103

98104
// citric acid is now in its own chain
99105

100106
Chain b = s.getChain("B");
101-
assertTrue(b.getAtomGroups().size() == 1);
102-
107+
assertEquals(1, b.getAtomGroups().size());
103108

104109
ResidueNumber resNum2 = ResidueNumber.fromString("265");
105110

106111
Group g2 = a.getGroupByPDB(resNum2);
107112
assertTrue(g2.hasAltLoc());
108113

109-
110114
}
111115

112116
@Test
@@ -127,8 +131,7 @@ public void test2W72() throws IOException, StructureException{
127131

128132
Atom[] caA = StructureTools.getRepresentativeAtomArray(a);
129133

130-
assertEquals(caA.length,141);
131-
134+
assertEquals(141, caA.length);
132135

133136
}
134137

@@ -148,7 +151,6 @@ public void test1U7F() throws IOException, StructureException{
148151
ensureAllAtomsSameAltCode(altGroup, g);
149152
}
150153

151-
152154
}
153155

154156
@Test
@@ -166,7 +168,6 @@ public void test1JXX() throws IOException, StructureException{
166168
ensureAllAtomsSameAltCode(altGroup, g);
167169
}
168170

169-
170171
}
171172

172173

@@ -208,15 +209,20 @@ private void ensureAllAtomsSameAltCode(Group groupInputAltLocGroup, Group inputM
208209
@Test
209210
public void test1AAC() throws IOException, StructureException{
210211

212+
AtomCache cache = new AtomCache();
213+
cache.setUseMmCif(false);
214+
StructureIO.setAtomCache(cache);
215+
211216
Structure s = StructureIO.getStructure("1AAC");
212217

213218
Chain a = s.getPolyChainByPDB("A");
214219

215220
Group g = a.getGroupByPDB( ResidueNumber.fromString("27"));
216221
testCBAtomInMainGroup(g);
217222

218-
AtomCache cache = new AtomCache();
223+
cache = new AtomCache();
219224
cache.setUseMmCif(true);
225+
StructureIO.setAtomCache(cache);
220226

221227
Structure s1 = cache.getStructure("1AAC");
222228
Chain a1 = s1.getPolyChainByPDB("A");
@@ -225,20 +231,6 @@ public void test1AAC() throws IOException, StructureException{
225231

226232
testCBAtomInMainGroup(g1);
227233

228-
229-
230-
// int pos = 0;
231-
// for (Group alt: g.getAltLocs()) {
232-
// pos++;
233-
// System.out.println("altLoc: " + pos + " " + alt);
234-
// for (Atom atom : alt.getAtoms()) {
235-
// System.out.print(atom.toPDB());
236-
// }
237-
// }
238-
239-
240-
241-
242234
}
243235

244236
private void testCBAtomInMainGroup(Group g) {
@@ -248,7 +240,7 @@ private void testCBAtomInMainGroup(Group g) {
248240

249241
for (Atom atom : g.getAtoms()) {
250242
//System.out.print(atom.toPDB());
251-
if ( atom.getName().equals(StructureTools.CA_ATOM_NAME)){
243+
if ( atom.getName().equals(StructureTools.CB_ATOM_NAME)){
252244

253245
cbInMain = true;
254246
break;
@@ -316,7 +308,7 @@ public void test3PIUpdb() throws IOException, StructureException{
316308
}
317309
}
318310

319-
assertTrue(ca.length == caList.size());
311+
assertEquals(ca.length, caList.size());
320312

321313
}
322314

@@ -354,7 +346,7 @@ private void doTestAllAltLocsSamAtomsMainGroup(String pdbId) throws IOException,
354346
for (Group g: c.getAtomGroups()){
355347

356348
for (Group altLocGroup:g.getAltLocs()) {
357-
assertEquals(altLocGroup.size(), g.size());
349+
assertEquals(g.size(), altLocGroup.size());
358350
}
359351
}
360352
}
@@ -482,7 +474,7 @@ public void test4CUPBonds() throws IOException, StructureException{
482474
}
483475
}
484476

485-
assertTrue(ca.length == caList.size());
477+
assertEquals(ca.length, caList.size());
486478

487479

488480
}
@@ -534,7 +526,6 @@ public void test3PIUmmcif() throws IOException, StructureException{
534526

535527
}
536528

537-
538529
}
539530
if (! caInMain && g.hasAtom(StructureTools.CA_ATOM_NAME)){
540531
// g.hasAtom checks altLocs
@@ -546,7 +537,6 @@ public void test3PIUmmcif() throws IOException, StructureException{
546537

547538
assertEquals(ca.length, caList.size());
548539

549-
550540
}
551541

552542
@Test
@@ -592,7 +582,6 @@ public void test3U7Tmmcif() throws IOException, StructureException{
592582

593583
}
594584

595-
596585
}
597586
if (! caInMain && g.hasAtom(StructureTools.CA_ATOM_NAME)){
598587
// g.hasAtom checks altLocs
@@ -604,6 +593,154 @@ public void test3U7Tmmcif() throws IOException, StructureException{
604593

605594
assertEquals(ca.length, caList.size());
606595

596+
}
597+
598+
@Test
599+
public void testMmcifWritingPartialAltlocs() throws IOException {
600+
String mmcifData =
601+
"data_test\n" +
602+
"loop_\n" +
603+
"_atom_site.group_PDB \n" +
604+
"_atom_site.id \n" +
605+
"_atom_site.type_symbol \n" +
606+
"_atom_site.label_atom_id \n" +
607+
"_atom_site.label_alt_id \n" +
608+
"_atom_site.label_comp_id \n" +
609+
"_atom_site.label_asym_id \n" +
610+
"_atom_site.label_entity_id \n" +
611+
"_atom_site.label_seq_id \n" +
612+
"_atom_site.pdbx_PDB_ins_code \n" +
613+
"_atom_site.Cartn_x \n" +
614+
"_atom_site.Cartn_y \n" +
615+
"_atom_site.Cartn_z \n" +
616+
"_atom_site.occupancy \n" +
617+
"_atom_site.B_iso_or_equiv \n" +
618+
"_atom_site.pdbx_formal_charge \n" +
619+
"_atom_site.auth_seq_id \n" +
620+
"_atom_site.auth_comp_id \n" +
621+
"_atom_site.auth_asym_id \n" +
622+
"_atom_site.auth_atom_id \n" +
623+
"_atom_site.pdbx_PDB_model_num \n" +
624+
"ATOM 102 N N . ARG A 1 13 ? 9.889 23.379 13.115 1.00 6.57 ? 102 ARG A N 1\n" +
625+
"ATOM 103 C CA . ARG A 1 13 ? 9.540 23.003 14.482 1.00 7.05 ? 102 ARG A CA 1\n" +
626+
"ATOM 104 C C . ARG A 1 13 ? 10.407 23.758 15.489 1.00 6.88 ? 102 ARG A C 1\n" +
627+
"ATOM 105 O O . ARG A 1 13 ? 9.915 24.196 16.532 1.00 7.69 ? 102 ARG A O 1\n" +
628+
"ATOM 106 C CB . ARG A 1 13 ? 9.706 21.494 14.688 1.00 9.07 ? 102 ARG A CB 1\n" +
629+
"ATOM 107 C CG A ARG A 1 13 ? 8.757 20.644 13.854 0.50 14.39 ? 102 ARG A CG 1\n" +
630+
"ATOM 108 C CG B ARG A 1 13 ? 8.693 20.645 13.938 0.50 13.58 ? 102 ARG A CG 1\n" +
631+
"ATOM 109 C CD A ARG A 1 13 ? 9.109 19.164 13.950 0.50 18.14 ? 102 ARG A CD 1\n" +
632+
"ATOM 110 C CD B ARG A 1 13 ? 8.710 19.216 14.456 0.50 16.34 ? 102 ARG A CD 1\n" +
633+
"ATOM 111 N NE A ARG A 1 13 ? 8.983 18.644 15.310 0.50 20.72 ? 102 ARG A NE 1\n" +
634+
"ATOM 112 N NE B ARG A 1 13 ? 8.315 19.158 15.861 0.50 23.99 ? 102 ARG A NE 1\n" +
635+
"ATOM 113 C CZ A ARG A 1 13 ? 7.826 18.445 15.933 0.50 23.45 ? 102 ARG A CZ 1\n" +
636+
"ATOM 114 C CZ B ARG A 1 13 ? 8.404 18.072 16.622 0.50 24.56 ? 102 ARG A CZ 1\n" +
637+
"ATOM 115 N NH1 A ARG A 1 13 ? 6.683 18.718 15.321 0.50 23.60 ? 102 ARG A NH1 1\n" +
638+
"ATOM 116 N NH1 B ARG A 1 13 ? 8.881 16.942 16.118 0.50 28.42 ? 102 ARG A NH1 1\n" +
639+
"ATOM 117 N NH2 A ARG A 1 13 ? 7.812 17.972 17.172 0.50 24.80 ? 102 ARG A NH2 1\n" +
640+
"ATOM 118 N NH2 B ARG A 1 13 ? 8.013 18.115 17.888 0.50 26.52 ? 102 ARG A NH2 1\n";
641+
642+
SimpleMMcifParser parser = new SimpleMMcifParser();
643+
SimpleMMcifConsumer consumer = new SimpleMMcifConsumer();
644+
parser.addMMcifConsumer(consumer);
645+
646+
BufferedReader buf = new BufferedReader(new StringReader(mmcifData));
647+
parser.parse(buf);
648+
buf.close();
649+
650+
Structure s = consumer.getStructure();
651+
Chain c = s.getPolyChains().get(0);
652+
assertEquals(1, c.getAtomGroups().size());
653+
Group g = c.getAtomGroup(0);
654+
assertEquals(11, g.size());
655+
assertEquals(1, g.getAltLocs().size());
656+
657+
for (Atom a : g.getAtoms()) {
658+
if (a.getName().equals("C") || a.getName().equals("N") || a.getName().equals("O") || a.getName().equals("CA") || a.getName().equals("CB"))
659+
assertEquals(' ', a.getAltLoc().charValue());
660+
else
661+
assertEquals('A', a.getAltLoc().charValue());
662+
}
663+
664+
assertEquals(11, g.getAltLocs().get(0).size());
665+
for (Atom a : g.getAltLocs().get(0).getAtoms()) {
666+
if (a.getName().equals("C") || a.getName().equals("N") || a.getName().equals("O") || a.getName().equals("CA") || a.getName().equals("CB"))
667+
assertEquals(' ', a.getAltLoc().charValue());
668+
else
669+
assertEquals('B', a.getAltLoc().charValue());
670+
}
671+
672+
List<AtomSite> atomSites = MMCIFFileTools.convertChainToAtomSites(c, 1, "A", "A");
673+
assertEquals(17, atomSites.size());
674+
675+
}
676+
677+
@Test
678+
public void testMmcifWritingAllAltlocs() throws IOException {
679+
String mmcifData =
680+
"data_test\n" +
681+
"loop_\n" +
682+
"_atom_site.group_PDB \n" +
683+
"_atom_site.id \n" +
684+
"_atom_site.type_symbol \n" +
685+
"_atom_site.label_atom_id \n" +
686+
"_atom_site.label_alt_id \n" +
687+
"_atom_site.label_comp_id \n" +
688+
"_atom_site.label_asym_id \n" +
689+
"_atom_site.label_entity_id \n" +
690+
"_atom_site.label_seq_id \n" +
691+
"_atom_site.pdbx_PDB_ins_code \n" +
692+
"_atom_site.Cartn_x \n" +
693+
"_atom_site.Cartn_y \n" +
694+
"_atom_site.Cartn_z \n" +
695+
"_atom_site.occupancy \n" +
696+
"_atom_site.B_iso_or_equiv \n" +
697+
"_atom_site.pdbx_formal_charge \n" +
698+
"_atom_site.auth_seq_id \n" +
699+
"_atom_site.auth_comp_id \n" +
700+
"_atom_site.auth_asym_id \n" +
701+
"_atom_site.auth_atom_id \n" +
702+
"_atom_site.pdbx_PDB_model_num \n" +
703+
"ATOM 204 N N A PRO A 1 23 ? 15.057 31.425 23.772 0.50 3.09 ? 112 PRO A N 1 \n" +
704+
"ATOM 205 N N B PRO A 1 23 ? 14.762 31.778 23.217 0.50 15.25 ? 112 PRO A N 1 \n" +
705+
"ATOM 206 C CA A PRO A 1 23 ? 16.391 30.930 23.416 0.50 5.82 ? 112 PRO A CA 1 \n" +
706+
"ATOM 207 C CA B PRO A 1 23 ? 16.049 31.406 22.622 0.50 15.44 ? 112 PRO A CA 1 \n" +
707+
"ATOM 208 C C A PRO A 1 23 ? 17.360 30.580 24.546 0.50 6.73 ? 112 PRO A C 1 \n" +
708+
"ATOM 209 C C B PRO A 1 23 ? 16.971 30.922 23.734 0.50 15.04 ? 112 PRO A C 1 \n" +
709+
"ATOM 210 O O A PRO A 1 23 ? 18.566 30.784 24.409 0.50 10.00 ? 112 PRO A O 1 \n" +
710+
"ATOM 211 O O B PRO A 1 23 ? 18.076 31.430 23.925 0.50 14.61 ? 112 PRO A O 1 \n" +
711+
"ATOM 212 C CB A PRO A 1 23 ? 16.931 32.050 22.542 0.50 8.38 ? 112 PRO A CB 1 \n" +
712+
"ATOM 213 C CB B PRO A 1 23 ? 16.519 32.710 21.986 0.50 14.09 ? 112 PRO A CB 1 \n" +
713+
"ATOM 214 C CG A PRO A 1 23 ? 16.424 33.256 23.263 0.50 7.59 ? 112 PRO A CG 1 \n" +
714+
"ATOM 215 C CG B PRO A 1 23 ? 15.960 33.743 22.908 0.50 15.66 ? 112 PRO A CG 1 \n" +
715+
"ATOM 216 C CD A PRO A 1 23 ? 14.980 32.886 23.580 0.50 6.98 ? 112 PRO A CD 1 \n" +
716+
"ATOM 217 C CD B PRO A 1 23 ? 14.558 33.235 23.153 0.50 14.91 ? 112 PRO A CD 1 \n";
717+
718+
SimpleMMcifParser parser = new SimpleMMcifParser();
719+
SimpleMMcifConsumer consumer = new SimpleMMcifConsumer();
720+
parser.addMMcifConsumer(consumer);
721+
722+
BufferedReader buf = new BufferedReader(new StringReader(mmcifData));
723+
parser.parse(buf);
724+
buf.close();
725+
726+
Structure s = consumer.getStructure();
727+
Chain c = s.getPolyChains().get(0);
728+
assertEquals(1, c.getAtomGroups().size());
729+
730+
Group g = c.getAtomGroup(0);
731+
assertEquals(7, g.size());
732+
733+
assertEquals(1, g.getAltLocs().size());
734+
735+
for (Atom a : g.getAtoms()) {
736+
assertEquals('A', a.getAltLoc().charValue());
737+
}
738+
for (Atom a : g.getAltLocs().get(0).getAtoms()) {
739+
assertEquals('B', a.getAltLoc().charValue());
740+
}
741+
742+
List<AtomSite> atomSites = MMCIFFileTools.convertChainToAtomSites(c, 1, "A", "A");
743+
assertEquals(14, atomSites.size());
607744

608745
}
609746

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