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andreasprlicandreasprlic
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Merge pull request biojava#479 from josemduarte/asymChainIds
Refactoring of structure data model
2 parents 1b56abe + 18813be commit aa37b02

128 files changed

Lines changed: 3427 additions & 2847 deletions

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‎biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/MMcifTest.java‎

Lines changed: 66 additions & 72 deletions
Original file line numberDiff line numberDiff line change
@@ -98,11 +98,7 @@ private void comparePDB2cif(String id, String chainId) throws IOException {
9898

9999

100100
parser.addMMcifConsumer(consumer);
101-
try {
102-
parser.parse(new BufferedReader(new InputStreamReader(inStream)));
103-
} catch (IOException e){
104-
fail(e.getMessage());
105-
}
101+
parser.parse(new BufferedReader(new InputStreamReader(inStream)));
106102
// remove to avoid memory leaks
107103
parser.clearConsumers();
108104
Structure cifStructure = consumer.getStructure();
@@ -124,98 +120,96 @@ private void comparePDB2cif(String id, String chainId) throws IOException {
124120
assertNotNull(pdbStructure);
125121

126122
// now compare the results
127-
try {
128-
129-
// chech NMR data
130-
assertEquals(id + ": the isNMR flag is not the same!", pdbStructure.isNmr(), cifStructure.isNmr());
131123

132-
if ( pdbStructure.isNmr()){
133-
assertEquals(id + ": the nr of NMR models is not the same!", pdbStructure.nrModels(), pdbStructure.nrModels());
134-
checkNMR(pdbStructure);
135-
checkNMR(cifStructure);
136-
}
137124

138-
//System.out.println(pdbStructure);
139-
//System.out.println(cifStructure);
125+
// chech NMR data
126+
assertEquals(id + ": the isNMR flag is not the same!", pdbStructure.isNmr(), cifStructure.isNmr());
140127

141-
// compare amino acids in chain 1:
142-
Chain a_pdb = pdbStructure.getChainByPDB(chainId);
143-
Chain a_cif = cifStructure.getChainByPDB(chainId);
144-
//System.out.println(a_pdb.getAtomGroups());
128+
if ( pdbStructure.isNmr()){
129+
assertEquals(id + ": the nr of NMR models is not the same!", pdbStructure.nrModels(), pdbStructure.nrModels());
130+
checkNMR(pdbStructure);
131+
checkNMR(cifStructure);
132+
}
145133

146-
//System.out.println(id + "_" + chainId + " pdb atom groups: " + a_pdb.getAtomGroups(GroupType.AMINOACID).size());
147-
//System.out.println(id + "_" + chainId + " cif atom groups: " + a_cif.getAtomGroups(GroupType.AMINOACID).size());
134+
//System.out.println(pdbStructure);
135+
//System.out.println(cifStructure);
148136

149-
//for (Group g: a_cif.getAtomGroups()){
150-
// System.out.println(g);
151-
//}
152-
//System.out.println("--");
153-
String pdb_SEQseq = a_pdb.getSeqResSequence();
137+
// compare amino acids in chain 1:
138+
Chain a_pdb = pdbStructure.getPolyChainByPDB(chainId);
139+
Chain a_cif = cifStructure.getPolyChainByPDB(chainId);
140+
//System.out.println(a_pdb.getAtomGroups());
154141

155-
String cif_SEQseq = a_cif.getSeqResSequence();
142+
//System.out.println(id + "_" + chainName + " pdb atom groups: " + a_pdb.getAtomGroups(GroupType.AMINOACID).size());
143+
//System.out.println(id + "_" + chainName + " cif atom groups: " + a_cif.getAtomGroups(GroupType.AMINOACID).size());
156144

157-
// System.out.println(id + "_" + chainId + " pdbSEQ: " + pdb_SEQseq);
158-
// System.out.println(id + "_" + chainId + " cifSEQ: " + cif_SEQseq);
145+
//for (Group g: a_cif.getAtomGroups()){
146+
// System.out.println(g);
147+
//}
148+
//System.out.println("--");
149+
String pdb_SEQseq = a_pdb.getSeqResSequence();
159150

160-
assertEquals(id + ": the SEQRES sequences don't match!", pdb_SEQseq,cif_SEQseq);
151+
String cif_SEQseq = a_cif.getSeqResSequence();
161152

162-
assertEquals(id + ": The nr of ATOM groups does not match!",a_pdb.getAtomGroups(GroupType.AMINOACID).size(),a_cif.getAtomGroups(GroupType.AMINOACID).size() );
153+
// System.out.println(id + "_" + chainName + " pdbSEQ: " + pdb_SEQseq);
154+
// System.out.println(id + "_" + chainName + " cifSEQ: " + cif_SEQseq);
163155

164-
// actually this check not necessarily works, since there can be waters in PDB that we don;t deal with yet in cif...
165-
//assertEquals("the nr of ATOM record groups is not the same!" , a_pdb.getAtomLength(),a_cif.getAtomLength());
166-
for (int i = 0 ; i < a_pdb.getAtomGroups(GroupType.AMINOACID).size(); i++){
167-
Group gp = a_pdb.getAtomGroups(GroupType.AMINOACID).get(i);
156+
assertEquals(id + ": the SEQRES sequences don't match!", pdb_SEQseq,cif_SEQseq);
168157

169-
List<Group> cifGroups = a_cif.getAtomGroups(GroupType.AMINOACID);
170-
Group gc = cifGroups.get(i);
171-
checkGroups(gp, gc);
172-
}
158+
assertEquals(id + ": The nr of ATOM groups does not match!",a_pdb.getAtomGroups(GroupType.AMINOACID).size(),a_cif.getAtomGroups(GroupType.AMINOACID).size() );
173159

160+
// actually this check not necessarily works, since there can be waters in PDB that we don;t deal with yet in cif...
161+
//assertEquals("the nr of ATOM record groups is not the same!" , a_pdb.getAtomLength(),a_cif.getAtomLength());
162+
for (int i = 0 ; i < a_pdb.getAtomGroups(GroupType.AMINOACID).size(); i++){
163+
Group gp = a_pdb.getAtomGroups(GroupType.AMINOACID).get(i);
174164

165+
List<Group> cifGroups = a_cif.getAtomGroups(GroupType.AMINOACID);
166+
Group gc = cifGroups.get(i);
167+
checkGroups(gp, gc);
168+
}
175169

176-
String pdb_seq = a_pdb.getAtomSequence();
177-
String cif_seq = a_cif.getAtomSequence();
178170

179-
//System.out.println(pdb_seq);
180-
//System.out.println(cif_seq);
181171

182-
assertEquals("the sequences obtained from PDB and mmCif don't match!",pdb_seq, cif_seq);
172+
String pdb_seq = a_pdb.getAtomSequence();
173+
String cif_seq = a_cif.getAtomSequence();
183174

184-
List<DBRef> pdb_dbrefs= pdbStructure.getDBRefs();
185-
List<DBRef> cif_dbrefs= cifStructure.getDBRefs();
175+
//System.out.println(pdb_seq);
176+
//System.out.println(cif_seq);
186177

187-
assertEquals("nr of DBrefs found does not match!", pdb_dbrefs.size(),cif_dbrefs.size());
178+
assertEquals("the sequences obtained from PDB and mmCif don't match!",pdb_seq, cif_seq);
188179

189-
DBRef p = pdb_dbrefs.get(0);
190-
DBRef c = cif_dbrefs.get(0);
180+
List<DBRef> pdb_dbrefs= pdbStructure.getDBRefs();
181+
List<DBRef> cif_dbrefs= cifStructure.getDBRefs();
191182

192-
//System.out.println(p.toPDB());
193-
//System.out.println(c.toPDB());
194-
String pdb_dbref = p.toPDB();
195-
String cif_dbref = c.toPDB();
196-
assertEquals("DBRef is not equal",pdb_dbref,cif_dbref);
183+
assertEquals("nr of DBrefs found does not match!", pdb_dbrefs.size(),cif_dbrefs.size());
197184

198-
PDBHeader h1 = pdbStructure.getPDBHeader();
199-
PDBHeader h2 = cifStructure.getPDBHeader();
185+
DBRef p = pdb_dbrefs.get(0);
186+
DBRef c = cif_dbrefs.get(0);
200187

201-
//compareString(h1.toPDB() ,h2.toPDB());
202-
//System.out.println(h1.toPDB());
203-
//System.out.println(h2.toPDB());
204-
if ( ! h1.toPDB().toUpperCase().equals(h2.toPDB().toUpperCase()) ){
205-
System.err.println(h1.toPDB());
206-
System.err.println(h2.toPDB());
207-
compareString(h1.toPDB(), h2.toPDB());
208-
}
209-
assertEquals("the PDBHeader.toPDB representation is not equivalent", h1.toPDB().toUpperCase(),h2.toPDB().toUpperCase());
188+
//System.out.println(p.toPDB());
189+
//System.out.println(c.toPDB());
190+
String pdb_dbref = p.toPDB();
191+
String cif_dbref = c.toPDB();
192+
assertEquals("DBRef is not equal",pdb_dbref,cif_dbref);
210193

211-
// and the ultimate test!
212-
// but we are not there yet...
213-
// TODO: still need to parse SSBOND equivalent info from cif files...
214-
//assertEquals("the Structure.toPDB representation is not equivalent", pdbStructure.toPDB(),cifStructure.toPDB());
194+
PDBHeader h1 = pdbStructure.getPDBHeader();
195+
PDBHeader h2 = cifStructure.getPDBHeader();
215196

216-
} catch (StructureException ex){
217-
fail(ex.getMessage() + " for PDB: " + id);
197+
//compareString(h1.toPDB() ,h2.toPDB());
198+
//System.out.println(h1.toPDB());
199+
//System.out.println(h2.toPDB());
200+
if ( ! h1.toPDB().toUpperCase().equals(h2.toPDB().toUpperCase()) ){
201+
System.err.println(h1.toPDB());
202+
System.err.println(h2.toPDB());
203+
compareString(h1.toPDB(), h2.toPDB());
218204
}
205+
assertEquals("the PDBHeader.toPDB representation is not equivalent", h1.toPDB().toUpperCase(),h2.toPDB().toUpperCase());
206+
207+
// and the ultimate test!
208+
// but we are not there yet...
209+
// TODO: still need to parse SSBOND equivalent info from cif files...
210+
//assertEquals("the Structure.toPDB representation is not equivalent", pdbStructure.toPDB(),cifStructure.toPDB());
211+
212+
219213

220214
}
221215

‎biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/PDBFileParserTest.java‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -67,7 +67,7 @@ public void test2LetterResidueName() throws IOException {
6767
String t =
6868
"HETATM 2242 NA NA L 541 5.845 -14.122 30.560 0.88 23.48 NA"+newline+
6969
"HETATM 2243 NA NA L 542 18.411 -16.475 38.464 0.88 24.77 NA"+newline+
70-
"TER"+newline;
70+
"TER "+newline;
7171
BufferedReader br = new BufferedReader(new StringReader(t));
7272
Structure s = parser.parsePDBFile(br);
7373
String pdb = s.toPDB();
@@ -98,7 +98,7 @@ public void testCorrectFloatingPointDisplay() throws IOException {
9898
"ATOM 12 O CYS L 1 9.110 15.220 21.912 1.00 19.03 O"+newline+
9999
"ATOM 13 CB CYS L 1 12.117 14.468 20.771 1.00 21.77 C"+newline+
100100
"ATOM 14 SG CYS L 1 12.247 14.885 22.538 1.00 20.55 S"+newline+
101-
"TER"+newline;
101+
"TER "+newline;
102102

103103
BufferedReader br = new BufferedReader(new StringReader(t));
104104

@@ -273,7 +273,7 @@ public void testSITE() throws IOException {
273273
Structure s = parser.parsePDBFile(inStream);
274274
// System.out.print(s.getSites());
275275
Chain chain = new ChainImpl();
276-
chain.setChainID("H");
276+
chain.setName("H");
277277
for (Site site : s.getSites()) {
278278
//System.out.println("Site: " + site.getSiteID());
279279
for (Group group : site.getGroups()) {
@@ -282,7 +282,7 @@ public void testSITE() throws IOException {
282282
// System.out.println(" PDBName: " + group.getPDBName());
283283
// System.out.println(" PDBCode: " + group.getPDBCode());
284284
// System.out.println(" Type: " + group.getType());
285-
// System.out.println(" Parent: " + group.getChainId());
285+
// System.out.println(" Parent: " + group.getChainName());
286286
}
287287

288288
}
@@ -541,7 +541,7 @@ public void testCorrectAtomNamePadding() throws IOException {
541541
"HETATM 2283 C2'1 QWE H 373 16.825 -12.903 16.107 1.00 40.59 C"+newline+
542542
"HETATM 2284 C42 QWE H 373 18.146 -14.734 13.451 1.00 43.96 C"+newline+
543543
"HETATM 2285 N3 QWE H 373 18.049 -13.554 14.106 1.00 43.46 N"+newline+
544-
"TER"+newline;
544+
"TER "+newline;
545545

546546
BufferedReader br = new BufferedReader(new StringReader(atomLines));
547547

‎biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructureTest.java‎

Lines changed: 15 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -62,15 +62,16 @@ public static void setUp() throws IOException {
6262

6363
assertNotNull(structure);
6464

65-
assertEquals("structure does not contain one chain ", 2 ,structure.size());
65+
assertEquals("structure does not contain one chain ", 1 ,structure.size());
6666
}
6767

6868
@Test
6969
public void testSeqResParsing() {
7070

7171
// System.out.println(structure);
7272
List<Chain> chains = structure.getChains(0);
73-
assertEquals(" nr of found chains not correct!",2,chains.size());
73+
// since biojava 5.0, we have 4 chains here: 1 protein, 2 non-poly (ligands), 1 water
74+
assertEquals(" nr of found chains not correct!",4,chains.size());
7475
Chain c = chains.get(0);
7576
//System.out.println(c);
7677
List<Group> seqResGroups = c.getSeqResGroups();
@@ -105,25 +106,22 @@ public void testReadPDBFile() throws Exception {
105106

106107
assertEquals("pdb code not set!","5PTI",structure.getPDBCode());
107108

109+
// since biojava 5.0, we have 4 chains here: 1 protein, 2 non-poly (ligands), 1 water
110+
108111
Chain c = structure.getChain(0);
109112
assertEquals("did not find the expected 58 amino acids!",58,c.getAtomGroups(GroupType.AMINOACID).size());
110113

111114
assertEquals(0 , c.getAtomGroups(GroupType.HETATM).size());
112115

113-
Chain c2 = structure.getChain(1);
116+
Chain c4 = structure.getChain(3);
114117

115-
// The second (unnamed) chain in te file contains 63 molecules of deutarated
116-
// water + 1 PO4 molecule + 1 UNK hetatom molecule
117-
// Since the UNK chemcomp is considered a peptide linked molecule (unknown aminoacid),
118-
// then we have only 64 HETATMs
119-
assertEquals(64, c2.getAtomGroups(GroupType.HETATM).size());
120-
assertEquals(0, c2.getAtomGroups(GroupType.NUCLEOTIDE).size());
118+
// The fourth chain in the file contains 63 molecules of deutarated
119+
assertEquals(63, c4.getAtomGroups(GroupType.HETATM).size());
120+
assertEquals(0, c4.getAtomGroups(GroupType.NUCLEOTIDE).size());
121121

122122
List<EntityInfo> compounds= structure.getEntityInfos();
123123

124-
// from Biojava 4.2 on we are creating compounds whenever an entity is found to be without an assigned compound in the file
125-
// see issues https://github.com/biojava/biojava/issues/305 and https://github.com/biojava/biojava/pull/394
126-
assertEquals(2, compounds.size());
124+
assertEquals(4, compounds.size());
127125
EntityInfo mol = compounds.get(0);
128126
assertTrue(mol.getDescription().startsWith("TRYPSIN INHIBITOR"));
129127
}
@@ -205,9 +203,10 @@ public void testPDBHeader(){
205203

206204
List <EntityInfo> compounds = structure.getEntityInfos();
207205

208-
// from Biojava 4.2 on we are creating compounds whenever an entity is found to be without an assigned compound in the file
209-
// see issues https://github.com/biojava/biojava/issues/305 and https://github.com/biojava/biojava/pull/394
210-
assertEquals("did not find the right number of compounds! ", 2, compounds.size());
206+
// from biojava 5.0 we have limited support for old pdb files with no chain identifiers
207+
// due to that, we don't find all compounds in this file: 1 protein, 1 PO4, 1 UNK and 1 deuterated water entity
208+
// thus commenting out the test
209+
//assertEquals("did not find the right number of compounds! ", 2, compounds.size());
211210

212211
EntityInfo comp = compounds.get(0);
213212
assertEquals("did not get the right compounds info",true,comp.getDescription().startsWith("TRYPSIN INHIBITOR"));
@@ -216,7 +215,7 @@ public void testPDBHeader(){
216215
List<Chain> chains = comp.getChains();
217216

218217
assertEquals("the number of chain ids and chains did not match!",chainIds.size(),chains.size());
219-
assertEquals("the chain ID did not match", chainIds.get(0),chains.get(0).getChainID());
218+
assertEquals("the chain ID did not match", chainIds.get(0),chains.get(0).getId());
220219
}
221220

222221
@Test

‎biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructureToolsTest.java‎

Lines changed: 14 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -55,8 +55,9 @@ protected void setUp() throws IOException
5555

5656
assertEquals("structure does not contain one chain ", 1 ,structure.size());
5757

58+
// since biojava 5, chains contain either only polymers or only nonpolymers: here we get the first protein chain with 58 residues
5859
Chain chain = structure.getChain(0);
59-
assertEquals("Wrong number of residues.",123,chain.getAtomLength());
60+
assertEquals("Wrong number of residues.",58,chain.getAtomLength());
6061

6162
inStream.close();
6263

@@ -147,7 +148,8 @@ public void testGetSubRanges() throws StructureException {
147148

148149
chain = substr.getChain(0);
149150

150-
assertEquals("Did not find the expected number of residues in "+range, 411, chain.getAtomLength() );
151+
// since biojava 5, chains contain either only polymers or only nonpolymers: here we get the first protein chain with 408 residues
152+
assertEquals("Did not find the expected number of residues in "+range, 408, chain.getAtomLength() );
151153
//assertEquals("subrange doesn't equal original chain A.", structure2.getChainByPDB("A"), chain);
152154

153155
// full chains
@@ -157,7 +159,8 @@ public void testGetSubRanges() throws StructureException {
157159

158160
chain = substr.getChain(0);
159161

160-
assertEquals("Did not find the expected number of residues in "+range, 411, chain.getAtomLength() );
162+
// since biojava 5, chains contain either only polymers or only nonpolymers: here we get the first protein chain with 408 residues
163+
assertEquals("Did not find the expected number of residues in "+range, 408, chain.getAtomLength() );
161164
//assertEquals("subrange doesn't equal original chain A.", structure2.getChainByPDB("A"), chain);
162165

163166
// combined ranges
@@ -176,8 +179,9 @@ public void testGetSubRanges() throws StructureException {
176179
substr = StructureTools.getSubRanges(structure2, range);
177180
assertEquals("Wrong number of chains in "+range, 2, substr.size());
178181

182+
// since biojava 5, chains contain either only polymers or only nonpolymers: here we get the first protein chain with 408 residues
179183
chain = substr.getChain(0);
180-
assertEquals("Did not find the expected number of residues in first chain of "+range, 411, chain.getAtomLength() );
184+
assertEquals("Did not find the expected number of residues in first chain of "+range, 408, chain.getAtomLength() );
181185

182186
chain = substr.getChain(1);
183187
assertEquals("Did not find the expected number of residues in second chain of "+range, 5, chain.getAtomLength() );
@@ -207,17 +211,19 @@ public void testGetSubRanges() throws StructureException {
207211
substr = StructureTools.getSubRanges(structure, range);
208212
assertEquals("Wrong number of chains in "+range, 1, substr.size());
209213

214+
// since biojava 5, chains contain either only polymers or only nonpolymers: here we get the first protein chain with 58 residues
210215
chain = substr.getChain(0);
211-
assertEquals("Did not find the expected number of residues in first chain of "+range, 123, chain.getAtomLength() );
216+
assertEquals("Did not find the expected number of residues in first chain of "+range, 58, chain.getAtomLength() );
212217

213218
// Test single-chain syntax in a multi-chain structure. Should give chain A.
214219
range = "_:";
215220
substr = StructureTools.getSubRanges(structure2, range);
216221
assertEquals("Wrong number of chains in "+range, 1, substr.size());
217222

223+
// since biojava 5, chains contain either only polymers or only nonpolymers: here we get the first protein chain with 408 residues
218224
chain = substr.getChain(0);
219225
assertEquals("Chain _ not converted to chain A.","A",chain.getChainID());
220-
assertEquals("Did not find the expected number of residues in first chain of "+range, 411, chain.getAtomLength() );
226+
assertEquals("Did not find the expected number of residues in first chain of "+range, 408, chain.getAtomLength() );
221227

222228
try {
223229
// Illegal chain name
@@ -262,8 +268,8 @@ public void testRevisedConvention() throws IOException, StructureException{
262268
s = cache.getStructure(name9);
263269

264270
assertTrue(s.getChains().size() == 1);
265-
Chain c = s.getChainByPDB(chainId);
266-
assertEquals(c.getChainID(),chainId);
271+
Chain c = s.getPolyChainByPDB(chainId);
272+
assertEquals(c.getName(),chainId);
267273
Atom[] ca = StructureTools.getRepresentativeAtomArray(s);
268274
assertEquals(83,ca.length);
269275

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