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josemduartejosemduarte
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Merge pull request biojava#504 from andreasprlic/bugfixes-4.2
Bugfixes 4.2
2 parents 349d4e1 + a27b4c7 commit fbca778

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16 files changed

+1205
-838
lines changed

16 files changed

+1205
-838
lines changed

‎biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java‎

Lines changed: 30 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -95,7 +95,7 @@ public void setbondLengthTolerance(final double bondLengthTolerance) {
9595

9696
/**
9797
*
98-
* @param recordUnidentifiableAtomLinkages true if choosing to record unidentifiable
98+
* @param recordUnidentifiableModifiedCompounds true if choosing to record unidentifiable
9999
* atoms; false, otherwise.
100100
* @see #getRecordUnidentifiableCompounds
101101
* @see #getUnidentifiableModifiedResidues
@@ -276,7 +276,6 @@ public void identify(final List<Chain> chains,
276276

277277
List<Group> ress = StructureUtil.getAminoAcids(chain);
278278

279-
280279
//List<Group> ligs = chain.getAtomLigands();
281280
List<Group> ligs = StructureTools.filterLigands(chain.getAtomGroups());
282281
residues.addAll(ress);
@@ -378,9 +377,10 @@ private void processCrosslink1(Map<Component, Set<Group>> mapCompGroups,
378377

379378
/**
380379
* identify additional groups that are not directly attached to amino acids.
381-
* @param mc {@link ModifiedCompound}.
382-
* @param chain a {@link Chain}.
383-
* @return a list of added groups.
380+
* @param mc {@link ModifiedCompound}
381+
* @param ligands {@link Group}
382+
* @param chains List of {@link Chain}s
383+
* @return a list of added groups
384384
*/
385385
private void identifyAdditionalAttachments(ModifiedCompound mc,
386386
List<Group> ligands, Map<String, Chain> mapChainIdChain) {
@@ -406,7 +406,9 @@ private void identifyAdditionalAttachments(ModifiedCompound mc,
406406
resNum.setSeqNum(num.getResidueNumber());
407407
resNum.setInsCode(num.getInsCode());
408408
//group = chain.getGroupByPDB(numIns);
409+
409410
group = mapChainIdChain.get(num.getChainId()).getGroupByPDB(resNum);
411+
//group = mapChainIdChain.get(num.getChainId()).getGroupByPDB(resNum);
410412
} catch (StructureException e) {
411413
logger.error("Exception: ", e);
412414
// should not happen
@@ -442,6 +444,23 @@ private void identifyAdditionalAttachments(ModifiedCompound mc,
442444
}
443445
}
444446

447+
private Group getGroup(StructureGroup num, List<Chain> chains) throws StructureException {
448+
for (Chain c : chains){
449+
if ( c.getId().equals(num.getChainId())){
450+
451+
ResidueNumber resNum = new ResidueNumber();
452+
453+
resNum.setSeqNum(num.getResidueNumber());
454+
resNum.setInsCode(num.getInsCode());
455+
456+
457+
return c.getGroupByPDB(resNum);
458+
}
459+
}
460+
461+
throw new StructureException("Could not find residue " + num);
462+
}
463+
445464
/**
446465
* Merge identified modified compounds if linked.
447466
*/
@@ -547,6 +566,8 @@ private void recordUnidentifiableModifiedResidues(List<ModifiedCompound> modComp
547566
if (group.getType().equals(GroupType.HETATM)) {
548567
StructureGroup strucGroup = StructureUtil.getStructureGroup(
549568
group, true);
569+
//strucGroup.setChainId(group.getChainId());
570+
550571
if (!identifiedComps.contains(strucGroup)) {
551572
unidentifiableModifiedResidues.add(strucGroup);
552573
}
@@ -777,13 +798,12 @@ private List<List<Atom[]>> getMatchedAtomsOfLinkages(
777798
return matchedAtomsOfLinkages;
778799
}
779800

780-
/**
781-
* Assembly the matched linkages.
801+
/** Assembly the matched linkages
802+
*
782803
* @param matchedAtomsOfLinkages
783804
* @param mod
784-
* @param condition
785-
* @param ret ModifiedCompound will be stored here.
786-
*/
805+
* @param ret ModifiedCompound will be stored here
806+
*/
787807
private void assembleLinkages(List<List<Atom[]>> matchedAtomsOfLinkages,
788808
ProteinModification mod, List<ModifiedCompound> ret) {
789809
ModificationCondition condition = mod.getCondition();

‎biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/StructureUtil.java‎

Lines changed: 83 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -25,10 +25,13 @@
2525
package org.biojava.nbio.protmod.structure;
2626

2727
import org.biojava.nbio.structure.*;
28+
import org.biojava.nbio.structure.io.mmcif.MetalBondParser;
29+
import org.biojava.nbio.structure.io.mmcif.chem.MetalBondDistance;
2830

2931
import java.util.ArrayList;
3032
import java.util.Collections;
3133
import java.util.List;
34+
import java.util.Map;
3235

3336
public final class StructureUtil {
3437
private StructureUtil() {
@@ -53,7 +56,11 @@ public static StructureGroup getStructureGroup(Group group, boolean isAminoAcid)
5356
* @return the {@link StructureAtom} of the atom.
5457
*/
5558
public static StructureAtom getStructureAtom(Atom atom, boolean isParentAminoAcid) {
56-
StructureGroup strucGroup = getStructureGroup(atom.getGroup(), isParentAminoAcid);
59+
60+
Group g = atom.getGroup();
61+
String chainId = g.getChainId();
62+
StructureGroup strucGroup = getStructureGroup(g, isParentAminoAcid);
63+
strucGroup.setChainId(chainId);
5764
return new StructureAtom(strucGroup, atom.getName());
5865
}
5966

@@ -104,6 +111,8 @@ public static double getAtomDistance(Atom atom1, Atom atom2) {
104111
public static Atom[] findNearestAtomLinkage(final Group group1, final Group group2,
105112
List<String> potentialNamesOfAtomOnGroup1, List<String> potentialNamesOfAtomOnGroup2,
106113
final boolean ignoreNCLinkage, double bondLengthTolerance) {
114+
115+
107116
List<Atom[]> linkages = findAtomLinkages(group1, group2,
108117
potentialNamesOfAtomOnGroup1, potentialNamesOfAtomOnGroup2,
109118
ignoreNCLinkage, bondLengthTolerance);
@@ -216,31 +225,96 @@ public static List<Atom[]> findAtomLinkages(final Group group1,
216225
public static Atom[] findLinkage(final Group group1, final Group group2,
217226
String nameOfAtomOnGroup1, String nameOfAtomOnGroup2,
218227
double bondLengthTolerance) {
219-
Atom[] ret = new Atom[2];
220-
double distance;
221228

229+
Atom[] ret = new Atom[2];
222230

223231
ret[0] = group1.getAtom(nameOfAtomOnGroup1);
224232
ret[1] = group2.getAtom(nameOfAtomOnGroup2);
233+
225234
if (ret[0]==null || ret[1]==null) {
226235
return null;
227236
}
228237

229-
distance = Calc.getDistance(ret[0], ret[1]);
230238

239+
Atom a1 = ret[0];
240+
Atom a2 = ret[1];
231241

242+
boolean hasBond = a1.hasBond(a2);
232243

233-
float radiusOfAtom1 = ret[0].getElement().getCovalentRadius();
234-
float radiusOfAtom2 = ret[1].getElement().getCovalentRadius();
244+
if ( hasBond ) {
245+
246+
return ret;
247+
}
248+
249+
// is it a metal ?
250+
251+
if ( a1.getElement().isMetal() || a2.getElement().isMetal()){
252+
253+
MetalBondDistance defined = getMetalDistanceCutoff(a1.getElement().name(),a2.getElement().name());
254+
255+
if ( defined != null) {
256+
257+
if (hasMetalBond(a1, a2, defined))
258+
return ret;
259+
else
260+
return null;
261+
}
235262

236-
if (Math.abs(distance-radiusOfAtom1 -radiusOfAtom2)
237-
> bondLengthTolerance) {
238-
return null;
239263
}
240264

265+
// not a metal
266+
267+
double distance = Calc.getDistance(a1, a2);
268+
269+
float radiusOfAtom1 = ret[0].getElement().getCovalentRadius();
270+
float radiusOfAtom2 = ret[1].getElement().getCovalentRadius();
271+
272+
if (Math.abs(distance - radiusOfAtom1 - radiusOfAtom2)
273+
> bondLengthTolerance) {
274+
return null;
275+
}
276+
277+
241278
return ret;
242279
}
243280

281+
private static boolean hasMetalBond(Atom a1, Atom a2, MetalBondDistance definition) {
282+
283+
double distance = Calc.getDistance(a1,a2);
284+
285+
Float min = definition.getLowerLimit();
286+
Float max = definition.getUpperLimit();
287+
288+
return ( min < distance && max > distance);
289+
290+
}
291+
292+
private static MetalBondDistance getMetalDistanceCutoff(String name1, String name2) {
293+
Map<String,List<MetalBondDistance>> defs= MetalBondParser.getMetalBondDefinitions();
294+
295+
List<MetalBondDistance> distances = defs.get(name1);
296+
297+
if ( distances == null){
298+
299+
distances = defs.get(name2);
300+
String tmp = name1;
301+
name2 = name1;
302+
name1 = tmp;
303+
}
304+
if ( distances == null){
305+
return null;
306+
}
307+
308+
for ( MetalBondDistance d : distances){
309+
if ( name1.equalsIgnoreCase(d.getAtomType1()) && name2.equalsIgnoreCase(d.getAtomType2()) )
310+
return d;
311+
}
312+
313+
// no matching atom definitions found
314+
return null;
315+
316+
}
317+
244318
/**
245319
*
246320
* @param group a {@link Group}.

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