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

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -281,7 +281,7 @@ public interface Chain extends Serializable {
281281
/**
282282
* Returns the sequence of amino acids as it has been provided in the ATOM records.
283283
* Non-standard residues will be present in the string only if the property
284-
* {@value org.biojava.nbio.structure.io.PDBFileReader.LOAD_CHEM_COMP_PROPERTY} has been set.
284+
* {@value org.biojava.nbio.structure.io.PDBFileReader#LOAD_CHEM_COMP_PROPERTY} has been set.
285285
* @return amino acid sequence as string
286286
* @see #getSeqResSequence()
287287
*/

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

Lines changed: 30 additions & 27 deletions
Original file line numberDiff line numberDiff line change
@@ -334,25 +334,25 @@ public static Cell convertCrystalCellToCell(CrystalCell c) {
334334
/**
335335
* Converts an Atom object to an {@link AtomSite} object.
336336
* @param a
337-
* @param model
338-
* @param chainId
339-
* @param internalChainId
337+
* @param model the model number for the output AtomSites
338+
* @param chainName the chain identifier (author id) for the output AtomSites
339+
* @param chainId the internal chain identifier (asym id) for the output AtomSites
340340
* @return
341341
*/
342-
public static AtomSite convertAtomToAtomSite(Atom a, int model, String chainId, String internalChainId) {
343-
return convertAtomToAtomSite(a, model, chainId, internalChainId, a.getPDBserial());
342+
public static AtomSite convertAtomToAtomSite(Atom a, int model, String chainName, String chainId) {
343+
return convertAtomToAtomSite(a, model, chainName, chainId, a.getPDBserial());
344344
}
345345

346346
/**
347347
* Converts an Atom object to an {@link AtomSite} object.
348-
* @param a
349-
* @param model
350-
* @param chainId
351-
* @param internalChainId
348+
* @param a the atom
349+
* @param model the model number for the output AtomSites
350+
* @param chainName the chain identifier (author id) for the output AtomSites
351+
* @param chainId the internal chain identifier (asym id) for the output AtomSites
352352
* @param atomId the atom id to be written to AtomSite
353353
* @return
354354
*/
355-
public static AtomSite convertAtomToAtomSite(Atom a, int model, String chainId, String internalChainId, int atomId) {
355+
public static AtomSite convertAtomToAtomSite(Atom a, int model, String chainName, String chainId, int atomId) {
356356

357357
/*
358358
ATOM 7 C CD . GLU A 1 24 ? -10.109 15.374 38.853 1.00 50.05 ? ? ? ? ? ? 24 GLU A CD 1
@@ -404,7 +404,7 @@ record = "ATOM";
404404
atomSite.setLabel_atom_id(a.getName());
405405
atomSite.setLabel_alt_id(altLocStr);
406406
atomSite.setLabel_comp_id(g.getPDBName());
407-
atomSite.setLabel_asym_id(internalChainId);
407+
atomSite.setLabel_asym_id(chainId);
408408
atomSite.setLabel_entity_id(entityId);
409409
atomSite.setLabel_seq_id(labelSeqId);
410410
atomSite.setPdbx_PDB_ins_code(insCode);
@@ -415,26 +415,29 @@ record = "ATOM";
415415
atomSite.setB_iso_or_equiv(FileConvert.d2.format(a.getTempFactor()));
416416
atomSite.setAuth_seq_id(Integer.toString(g.getResidueNumber().getSeqNum()));
417417
atomSite.setAuth_comp_id(g.getPDBName());
418-
atomSite.setAuth_asym_id(chainId);
418+
atomSite.setAuth_asym_id(chainName);
419419
atomSite.setAuth_atom_id(a.getName());
420420
atomSite.setPdbx_PDB_model_num(Integer.toString(model));
421421

422422
return atomSite;
423423
}
424424

425425
/**
426-
* Converts a Group into a List of {@link AtomSite} objects
427-
* @param g
428-
* @param model
429-
* @param chainId
430-
* @param internalChainId
426+
* Converts a Group into a List of {@link AtomSite} objects.
427+
* Atoms in other altloc groups (different from the main group) are also included, removing possible duplicates
428+
* via using the atom identifier to assess uniqueness.
429+
* @param g the group
430+
* @param model the model number for the output AtomSites
431+
* @param chainName the chain identifier (author id) for the output AtomSites
432+
* @param chainId the internal chain identifier (asym id) for the output AtomSites
431433
* @return
432434
*/
433-
private static List<AtomSite> convertGroupToAtomSites(Group g, int model, String chainId, String internalChainId) {
435+
public static List<AtomSite> convertGroupToAtomSites(Group g, int model, String chainName, String chainId) {
434436

435437
// The alt locs can have duplicates, since at parsing time we make sure that all alt loc groups have
436438
// all atoms (see StructureTools#cleanUpAltLocs)
437439
// Thus we have to remove duplicates here by using the atom id
440+
// See issue https://github.com/biojava/biojava/issues/778 and TestAltLocs.testMmcifWritingAllAltlocs/testMmcifWritingPartialAltlocs
438441
Map<Integer, AtomSite> uniqueAtomSites = new LinkedHashMap<>();
439442

440443
int groupsize = g.size();
@@ -444,12 +447,12 @@ private static List<AtomSite> convertGroupToAtomSites(Group g, int model, String
444447
if ( a == null)
445448
continue ;
446449

447-
uniqueAtomSites.put(a.getPDBserial(), convertAtomToAtomSite(a, model, chainId, internalChainId));
450+
uniqueAtomSites.put(a.getPDBserial(), convertAtomToAtomSite(a, model, chainName, chainId));
448451
}
449452

450453
if ( g.hasAltLoc()){
451454
for (Group alt : g.getAltLocs() ) {
452-
for (AtomSite atomSite : convertGroupToAtomSites(alt, model, chainId, internalChainId)) {
455+
for (AtomSite atomSite : convertGroupToAtomSites(alt, model, chainName, chainId)) {
453456
uniqueAtomSites.put(Integer.parseInt(atomSite.getId()), atomSite);
454457
}
455458
}
@@ -459,15 +462,15 @@ private static List<AtomSite> convertGroupToAtomSites(Group g, int model, String
459462

460463
/**
461464
* Converts a Chain into a List of {@link AtomSite} objects
462-
* @param c
463-
* @param model
464-
* @param authorId
465-
* @param asymId
465+
* @param c the chain
466+
* @param model the model number for the output AtomSites
467+
* @param chainName the chain identifier (author id) for the output AtomSites
468+
* @param chainId the internal chain identifier (asym id) for the output AtomSites
466469
* @return
467470
*/
468-
public static List<AtomSite> convertChainToAtomSites(Chain c, int model, String authorId, String asymId) {
471+
public static List<AtomSite> convertChainToAtomSites(Chain c, int model, String chainName, String chainId) {
469472

470-
List<AtomSite> list = new ArrayList<AtomSite>();
473+
List<AtomSite> list = new ArrayList<>();
471474

472475
if (c.getEntityInfo()==null) {
473476
logger.warn("No Compound (entity) found for chain {}: entity_id will be set to 0, label_seq_id will be the same as auth_seq_id", c.getName());
@@ -477,7 +480,7 @@ public static List<AtomSite> convertChainToAtomSites(Chain c, int model, String
477480

478481
Group g= c.getAtomGroup(h);
479482

480-
list.addAll(convertGroupToAtomSites(g, model, authorId, asymId));
483+
list.addAll(convertGroupToAtomSites(g, model, chainName, chainId));
481484

482485
}
483486

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