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several fixes for biological assemblies calculations #709

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Merged
josemduarte merged 1 commit into from
Oct 9, 2017
Merged

several fixes for biological assemblies calculations #709

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3 changes: 3 additions & 0 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/ChainImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -187,6 +187,9 @@ public Object clone() {

for (Group seqResGroup : seqResGroups) {

if (seqResGroup==null)
continue;

int i = groups.indexOf(seqResGroup);

Group g ;
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6 changes: 1 addition & 5 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitExtractor.java
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Expand Up @@ -68,19 +68,15 @@ public static List<Subunit> extractSubunits(Structure structure,
// The extracted subunit container
List<Subunit> subunits = new ArrayList<Subunit>();


for (Chain c : structure.getChains()) {

for (Chain c : structure.getPolyChains()) {
// Only take protein chains
if (c.isProtein()) {
Atom[] ca = StructureTools.getRepresentativeAtomArray(c);
logger.debug("Chain " + c.getId() + "; CA Atoms: "
+ ca.length + "; SEQRES: " + c.getSeqResSequence());
subunits.add(new Subunit(ca, c.getName(), null, structure));

}
}


// Calculate the minimum length of a Subunit
int adjustedMinLen = calcAdjustedMinimumSequenceLength(subunits,
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15 changes: 9 additions & 6 deletions ...structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryResults.java
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Expand Up @@ -22,15 +22,15 @@
*/
package org.biojava.nbio.structure.symmetry.core;

import java.util.ArrayList;
import java.util.Collections;
import java.util.List;

import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.cluster.Subunit;
import org.biojava.nbio.structure.cluster.SubunitCluster;
import org.biojava.nbio.structure.cluster.SubunitClusterUtils;

import java.util.ArrayList;
import java.util.Collections;
import java.util.List;

/**
* Holds the results of quaternary symmetry perception obtained with
* {@link QuatSymmetryDetector}.
Expand Down Expand Up @@ -111,14 +111,17 @@ public QuatSymmetryResults(List<SubunitCluster> clusters,
public List<SubunitCluster> getSubunitClusters() {
return Collections.unmodifiableList(clusters);
}

/**
* Returns the List of Subunits used to calculate symmetry.
*
* @return an unmodifiable view of the List
*/
public List<Subunit> getSubunits() {
return Collections.unmodifiableList(subunits);
if (subunits != null)
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@lafita lafita Oct 10, 2017

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Subunits should never be null. The bug is that some code is missing from the helical symmetry constructor. The right fix is to add the following code into line 101:

 subunits = new ArrayList();
 for (SubunitCluster c : clusters) {
 	subunits.addAll(c.getSubunits());
 }


    

  
  




    


        

      
  
  

    
  
    
    

  

  

  



          

      
    





    

        

  

    

      

          
    
    

  


        
            
  
      
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          @josemduarte
      

      
            josemduarte
  

      

      

      


        Oct 10, 2017


      
    


  




        

      

  

  
 

  
    

    
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Thanks for the tip, now done in 96c6816

    

  
  




    


        

      
  
  

    
  
    
    

  

  

  



          

      
    








    


  









  


    


  		



    

    

    

  
    			return Collections.unmodifiableList(subunits);






    

    

    

  
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    			return Collections.unmodifiableList(new ArrayList<>());






    

    

    

  
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