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Fixing issue in bonds between atoms with different alt locs by josemduarte · Pull Request #854 · biojava/biojava · GitHub

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Fixing issue in bonds between atoms with different alt locs #854

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Merged
josemduarte merged 8 commits into from
Dec 19, 2019
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Fixing issue in bonds between atoms with different alt locs #854

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761799b
Fixing issue: no bonds between different altloc atoms
josemduarte Nov 10, 2019
408c8ac
Extending test
josemduarte Nov 10, 2019
7c7caa2
Now all tests pass
josemduarte Nov 12, 2019
0ff1823
Clarifying docs and some more cleanup
josemduarte Nov 12, 2019
a29f881
Covering another alt loc bond edge case
josemduarte Nov 13, 2019
b889140
Extracted common method, now covering nucleotide bonds
josemduarte Nov 13, 2019
7180aeb
Consolidating on a single method call for all alt loc bond business
josemduarte Nov 13, 2019
c363396
Docs
josemduarte Nov 13, 2019
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    • Atom.java
    • AtomImpl.java
    • HetatomImpl.java
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Clarifying docs and some more cleanup
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josemduarte committed Nov 12, 2019
commit 0ff1823543a133e42e7f09e32003fca4a0fd894f
3 changes: 2 additions & 1 deletion biojava-structure/src/main/java/org/biojava/nbio/structure/Atom.java
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Original file line number Diff line number Diff line change
Expand Up @@ -163,7 +163,8 @@ public interface Atom extends Cloneable, PDBRecord {

/**
* Get alternate Location.
* @return a Character object representing the alt loc value
* @return a Character object representing the alt loc value. Default altLoc ('.' in mmCIF files)
* is represented by ' ' (space character, ascii 32).
* @see #setAltLoc
*/
public Character getAltLoc();
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9 changes: 0 additions & 9 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/AtomImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -157,10 +157,6 @@ public void setZ(double z) {
@Override
public double getZ() { return coords.z; }

/**
* Set alternate Location.
* @see #getAltLoc
*/
@Override
public void setAltLoc(Character c) {
// after changing altLoc from Character to char, we do this to keep the interface the same as it used to be - JD 2016-01-27
Expand All @@ -170,11 +166,6 @@ public void setAltLoc(Character c) {
altLoc = c ;
}

/**
* Get alternate Location.
* @return a Character object representing the alt loc value
* @see #setAltLoc
*/
@Override
public Character getAltLoc() {
// after changing altLoc from Character to char, we do this to keep the interface the same as it used to be - JD 2016-01-27
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30 changes: 1 addition & 29 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/HetatomImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -254,16 +254,13 @@ public boolean hasAtom(String fullName) {
Atom a = atomNameLookup.get(fullName.trim());
return a != null;
} else {
/** This is the performance penalty we pay for NOT using the atomnameLookup in PerformanceBehaviour.LESS_MEMORY_SLOWER_PERFORMANCE
*/
// This is the performance penalty we pay for NOT using the atomnameLookup in PerformanceBehaviour.LESS_MEMORY_SLOWER_PERFORMANCE
for (Atom a : atoms) {
if (a.getName().equals(fullName)) {
return true;
}
}
return false;


}

}
Expand Down Expand Up @@ -375,42 +372,21 @@ public void setProperties(Map<String,Object> props) {
properties = props ;
}

/** return properties.
*
* @return a HashMap object representing the properties value
* @see #setProperties
*/
@Override
public Map<String, Object> getProperties() {
return properties ;
}

/** set a single property .
*
* @see #getProperties
* @see #getProperty
*/
@Override
public void setProperty(String key, Object value){
properties.put(key,value);
}

/** get a single property .
* @param key a String
* @return an Object
* @see #setProperty
* @see #setProperties
*/
@Override
public Object getProperty(String key){
return properties.get(key);
}


/** return an AtomIterator.
*
* @return an Iterator object
*/
@Override
public Iterator<Atom> iterator() {
return new AtomIterator(this);
Expand Down Expand Up @@ -615,10 +591,6 @@ public boolean isWater() {
return GroupType.WATERNAMES.contains(pdb_name);
}

/** attempts to reduce the memory imprint of this group by trimming
* all internal Collection objects to the required size.
*
*/
@Override
public void trimToSize(){

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