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abradleabradle
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Merge remote-tracking branch 'fork/entity_features' into alt_loc_bonds
2 parents c1ea01e + 20a68c2 commit 9948dc0

23 files changed

Lines changed: 275 additions & 163 deletions

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

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -119,13 +119,13 @@ public void testReadPDBFile() throws Exception {
119119
assertEquals(64, c2.getAtomGroups(GroupType.HETATM).size());
120120
assertEquals(0, c2.getAtomGroups(GroupType.NUCLEOTIDE).size());
121121

122-
List<Compound> compounds= structure.getCompounds();
122+
List<EntityInfo> compounds= structure.getEntityInformation();
123123

124124
// from Biojava 4.2 on we are creating compounds whenever an entity is found to be without an assigned compound in the file
125125
// see issues https://github.com/biojava/biojava/issues/305 and https://github.com/biojava/biojava/pull/394
126126
assertEquals(2, compounds.size());
127-
Compound mol = compounds.get(0);
128-
assertTrue(mol.getMolName().startsWith("TRYPSIN INHIBITOR"));
127+
EntityInfo mol = compounds.get(0);
128+
assertTrue(mol.getDescription().startsWith("TRYPSIN INHIBITOR"));
129129
}
130130

131131
@Test
@@ -203,14 +203,14 @@ public void testPDBHeader(){
203203
assertEquals("the technique in the Header is " + technique, techShould, technique);
204204

205205

206-
List <Compound> compounds = structure.getCompounds();
206+
List <EntityInfo> compounds = structure.getEntityInformation();
207207

208208
// from Biojava 4.2 on we are creating compounds whenever an entity is found to be without an assigned compound in the file
209209
// see issues https://github.com/biojava/biojava/issues/305 and https://github.com/biojava/biojava/pull/394
210210
assertEquals("did not find the right number of compounds! ", 2, compounds.size());
211211

212-
Compound comp = compounds.get(0);
213-
assertEquals("did not get the right compounds info",true,comp.getMolName().startsWith("TRYPSIN INHIBITOR"));
212+
EntityInfo comp = compounds.get(0);
213+
assertEquals("did not get the right compounds info",true,comp.getDescription().startsWith("TRYPSIN INHIBITOR"));
214214

215215
List<String> chainIds = comp.getChainIds();
216216
List<Chain> chains = comp.getChains();

‎biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestLongPdbVsMmCifParsing.java‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -210,15 +210,15 @@ private void testStructureMethods(Structure sPdb, Structure sCif) {
210210
// compounds: there's quite some inconsistencies here between pdb and cif:
211211
// sugar polymers are not in pdb at all: we avoid them
212212
boolean canCompareCompoundsSize = true;
213-
for (Compound compound: sCif.getCompounds()) {
214-
if (compound.getMolName()==null || compound.getMolName().contains("SUGAR")) {
213+
for (EntityInfo compound: sCif.getEntityInformation()) {
214+
if (compound.getDescription()==null || compound.getDescription().contains("SUGAR")) {
215215
canCompareCompoundsSize = false;
216216
break;
217217
}
218218
}
219219

220220
if (canCompareCompoundsSize)
221-
assertEquals("failed number of Compounds pdb vs cif", sPdb.getCompounds().size(), sCif.getCompounds().size());
221+
assertEquals("failed number of Compounds pdb vs cif", sPdb.getEntityInformation().size(), sCif.getEntityInformation().size());
222222

223223

224224
// ss bonds

‎biojava-structure/src/main/java/demo/DemoMMCIFReader.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -102,7 +102,7 @@ public void loadFromDirectAccess(){
102102
System.out.println(h.getAtomSequence());
103103
System.out.println(h.getAtomGroups(GroupType.HETATM));
104104

105-
System.out.println("Compounds: " + s.getCompounds());
105+
System.out.println("Compounds: " + s.getEntityInformation());
106106

107107
} catch (Exception e) {
108108
e.printStackTrace();

‎biojava-structure/src/main/java/org/biojava/nbio/structure/Chain.java‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -195,15 +195,15 @@ public interface Chain {
195195
* @param compound the Compound
196196
* @see #getCompound()
197197
*/
198-
public void setCompound(Compound compound);
198+
public void setCompound(EntityInfo compound);
199199

200200
/**
201201
* Returns the Compound for this chain.
202202
*
203203
* @return the Compound object
204-
* @see #setCompound(Compound)
204+
* @see #setCompound(EntityInfo)
205205
*/
206-
public Compound getCompound();
206+
public EntityInfo getCompound();
207207

208208
/**
209209
* Sets the name of this chain (Chain id in PDB file ).

‎biojava-structure/src/main/java/org/biojava/nbio/structure/ChainImpl.java‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -65,7 +65,7 @@ public class ChainImpl implements Chain, Serializable {
6565
private List<Group> seqResGroups;
6666

6767
private Long id;
68-
private Compound mol;
68+
private EntityInfo mol;
6969
private Structure parent;
7070

7171
private Map<String, Integer> pdbResnumMap;
@@ -217,15 +217,15 @@ private static int findMathingGroupIndex(List<Group> atomGroups, Group g) {
217217
*
218218
*/
219219
@Override
220-
public void setCompound(Compound mol) {
220+
public void setCompound(EntityInfo mol) {
221221
this.mol = mol;
222222
}
223223

224224
/** {@inheritDoc}
225225
*
226226
*/
227227
@Override
228-
public Compound getCompound() {
228+
public EntityInfo getCompound() {
229229
return this.mol;
230230
}
231231

@@ -516,8 +516,8 @@ public String toString(){
516516
StringBuilder str = new StringBuilder();
517517
str.append("Chain >").append(getChainID()).append("<").append(newline);
518518
if ( mol != null ){
519-
if ( mol.getMolName() != null){
520-
str.append(mol.getMolName()).append(newline);
519+
if ( mol.getDescription() != null){
520+
str.append(mol.getDescription()).append(newline);
521521
}
522522
}
523523
str.append("total SEQRES length: ").append(getSeqResGroups().size()).append(" total ATOM length:")

biojava-structure/src/main/java/org/biojava/nbio/structure/Compound.java renamed to biojava-structure/src/main/java/org/biojava/nbio/structure/EntityInfo.java

Lines changed: 32 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -48,11 +48,12 @@
4848
*
4949
* @author Jules Jacobsen
5050
* @author Jose Duarte
51+
* @author Anthony Bradley
5152
* @since 1.5
5253
*/
53-
public class Compound implements Serializable {
54+
public class EntityInfo implements Serializable {
5455

55-
private final static Logger logger = LoggerFactory.getLogger(Compound.class);
56+
private final static Logger logger = LoggerFactory.getLogger(EntityInfo.class);
5657

5758

5859
//TODO we should consider having the data here as it is in mmCIF dictionary - JD 2014-12-11
@@ -80,21 +81,21 @@ public class Compound implements Serializable {
8081
private Map<String, Map<ResidueNumber,Integer>> chains2pdbResNums2ResSerials;
8182

8283
private String refChainId;
83-
84-
private String molName = null;
84+
private String description = null;
8585
private String title = null;
86+
/**
87+
* The type of group (polymer, non-polymer, water)
88+
*/
89+
private String type = null;
8690
private List<String> synonyms = null;
8791
private List<String> ecNums = null;
8892
private String engineered = null;
8993
private String mutation = null;
9094
private String biologicalUnit = null;
9195
private String details = null;
92-
9396
private String numRes = null;
9497
private String resNames = null;
95-
9698
private String headerVars = null;
97-
9899
private String synthetic = null;
99100
private String fragment = null;
100101
private String organismScientific = null;
@@ -130,7 +131,7 @@ public class Compound implements Serializable {
130131

131132
private Long id;
132133

133-
public Compound () {
134+
public EntityInfo () {
134135
chains = new ArrayList<Chain>();
135136
chains2pdbResNums2ResSerials = new HashMap<String, Map<ResidueNumber,Integer>>();
136137
molId = -1;
@@ -141,7 +142,7 @@ public Compound () {
141142
* but not setting the Chains
142143
* @param c
143144
*/
144-
public Compound (Compound c) {
145+
public EntityInfo (EntityInfo c) {
145146

146147
this.chains = new ArrayList<Chain>();
147148

@@ -151,7 +152,7 @@ public Compound (Compound c) {
151152

152153
this.refChainId = c.refChainId;
153154

154-
this.molName = c.molName;
155+
this.description = c.description;
155156
this.title = c.title;
156157

157158
if (c.synonyms!=null) {
@@ -213,7 +214,7 @@ public Compound (Compound c) {
213214
public String toString(){
214215
StringBuilder buf = new StringBuilder();
215216
buf.append("Compound: ").append(molId).append(" ");
216-
buf.append(molName==null?"(no name)":"("+molName+")");
217+
buf.append(description==null?"(no name)":"("+description+")");
217218
buf.append(" chains: ");
218219
if (chains!=null) {
219220
for (int i=0;i<chains.size();i++) {
@@ -292,8 +293,8 @@ public void showCompound() {
292293
}
293294
System.out.println("Chains: " + buf.toString());
294295
}
295-
if (this.molName != null) {
296-
System.out.println("Mol Name: " + this.molName);
296+
if (this.description != null) {
297+
System.out.println("Mol Name: " + this.description);
297298
}
298299
if (this.title != null) {
299300
System.out.println("Title: " + this.title);
@@ -619,12 +620,12 @@ public void setMolId(int molId) {
619620
this.molId = molId;
620621
}
621622

622-
public String getMolName() {
623-
return molName;
623+
public String getDescription() {
624+
return description;
624625
}
625626

626-
public void setMolName(String molName) {
627-
this.molName = molName;
627+
public void setDescription(String molName) {
628+
this.description = molName;
628629
}
629630

630631
public String getTitle() {
@@ -988,4 +989,18 @@ public void addChain(Chain chain){
988989
public void setChains(List<Chain> chains){
989990
this.chains = chains;
990991
}
992+
993+
/**
994+
* @return the type
995+
*/
996+
public String getType() {
997+
return type;
998+
}
999+
1000+
/**
1001+
* @param type the type to set
1002+
*/
1003+
public void setType(String type) {
1004+
this.type = type;
1005+
}
9911006
}

‎biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -40,7 +40,7 @@
4040
* <ul>
4141
* <li>{@link PDBHeader}</li>
4242
* <li>{@link DBRef}</li>
43-
* <li>{@link Compound}</li>
43+
* <li>{@link EntityInfo}</li>
4444
* </ul>
4545
*
4646
* The structure object provides access to the data from the ATOM records through
@@ -518,20 +518,20 @@ public Chain getChainByPDB(String chainId, int modelnr)
518518
*
519519
* @param molList
520520
*/
521-
public void setCompounds(List<Compound> molList);
521+
public void setCompounds(List<EntityInfo> molList);
522522

523523
/**
524524
* Get all the Compounds for this Structure.
525525
* Compounds are called Entities in mmCIF dictionary.
526526
*
527527
* @return a list of Compounds
528528
*/
529-
public List<Compound> getCompounds();
529+
public List<EntityInfo> getEntityInformation();
530530

531531
/**
532532
* Add a Compound to this Structure
533533
*/
534-
public void addCompound(Compound compound);
534+
public void addCompound(EntityInfo compound);
535535

536536
/**
537537
* Set the list of database references for this structure
@@ -553,7 +553,7 @@ public Chain getChainByPDB(String chainId, int modelnr)
553553
* @param molId
554554
* @return a compound
555555
*/
556-
public Compound getCompoundById(int molId);
556+
public EntityInfo getCompoundById(int molId);
557557

558558

559559
/**

‎biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java‎

Lines changed: 14 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -57,7 +57,7 @@ public class StructureImpl implements Structure, Serializable {
5757
private List<List<Chain>> models;
5858

5959
private List<Map <String,Integer>> connections ;
60-
private List<Compound> compounds;
60+
private List<EntityInfo> compounds;
6161
private List<DBRef> dbrefs;
6262
private List<Bond> ssbonds;
6363
private List<Site> sites;
@@ -79,7 +79,7 @@ public StructureImpl() {
7979
models = new ArrayList<List<Chain>>();
8080
name = "";
8181
connections = new ArrayList<Map<String,Integer>>();
82-
compounds = new ArrayList<Compound>();
82+
compounds = new ArrayList<EntityInfo>();
8383
dbrefs = new ArrayList<DBRef>();
8484
pdbHeader = new PDBHeader();
8585
ssbonds = new ArrayList<Bond>();
@@ -169,9 +169,9 @@ public Structure clone() {
169169

170170
// deep-copying of Compounds is tricky: there's cross references also in the Chains
171171
// beware: if we copy the compounds we would also need to reset the references to compounds in the individual chains
172-
List<Compound> newCompoundList = new ArrayList<Compound>();
173-
for (Compound compound:this.compounds) {
174-
Compound newCompound = new Compound(compound); // this sets everything but the chains
172+
List<EntityInfo> newCompoundList = new ArrayList<EntityInfo>();
173+
for (EntityInfo compound:this.compounds) {
174+
EntityInfo newCompound = new EntityInfo(compound); // this sets everything but the chains
175175
for (String chainId:compound.getChainIds()) {
176176

177177
for (int modelNr=0;modelNr<n.nrModels();modelNr++) {
@@ -443,8 +443,8 @@ public String toString(){
443443

444444
str.append("chain ").append(j).append(": >").append(cha.getChainID()).append("< ");
445445
if ( cha.getCompound() != null){
446-
Compound comp = cha.getCompound();
447-
String molName = comp.getMolName();
446+
EntityInfo comp = cha.getCompound();
447+
String molName = comp.getDescription();
448448
if ( molName != null){
449449
str.append(molName);
450450
}
@@ -465,7 +465,7 @@ public String toString(){
465465
str.append(dbref.toPDB()).append(newline);
466466
}
467467
str.append("Molecules: ").append(newline);
468-
for (Compound mol : compounds) {
468+
for (EntityInfo mol : compounds) {
469469
str.append(mol).append(newline);
470470
}
471471

@@ -665,19 +665,19 @@ public boolean hasChain(String chainId) {
665665

666666
/** {@inheritDoc} */
667667
@Override
668-
public void setCompounds(List<Compound> molList){
668+
public void setCompounds(List<EntityInfo> molList){
669669
this.compounds = molList;
670670
}
671671

672672
/** {@inheritDoc} */
673673
@Override
674-
public void addCompound(Compound compound) {
674+
public void addCompound(EntityInfo compound) {
675675
this.compounds.add(compound);
676676
}
677677

678678
/** {@inheritDoc} */
679679
@Override
680-
public List<Compound> getCompounds() {
680+
public List<EntityInfo> getEntityInformation() {
681681
// compounds are parsed from the PDB/mmCIF file normally
682682
// but if the file is incomplete, it won't have the Compounds information and we try
683683
// to guess it from the existing seqres/atom sequences
@@ -686,7 +686,7 @@ public List<Compound> getCompounds() {
686686
this.compounds = cf.findCompounds();
687687

688688
// now we need to set references in chains:
689-
for (Compound compound:compounds) {
689+
for (EntityInfo compound:compounds) {
690690
for (Chain c:compound.getChains()) {
691691
c.setCompound(compound);
692692
}
@@ -697,8 +697,8 @@ public List<Compound> getCompounds() {
697697

698698
/** {@inheritDoc} */
699699
@Override
700-
public Compound getCompoundById(int molId) {
701-
for (Compound mol : this.compounds){
700+
public EntityInfo getCompoundById(int molId) {
701+
for (EntityInfo mol : this.compounds){
702702
if (mol.getMolId()==molId){
703703
return mol;
704704
}

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