[Biojava-dev] [BioJava - Bug #3307] (New) Wrong first atom in alternate location when parsing PDB file

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Issue #3307 has been reported by Martin Riese.

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Bug #3307: Wrong first atom in alternate location when parsing PDB file
https://redmine.open-bio.org/issues/3307

Author: Martin Riese
Status: New
Priority: Normal
Assignee: biojava-dev list
Category: structure
Target version: 
URL: 


For a pdb file with alternate locations

@ATOM   1573  N  AILE B 314      -4.258  84.780  67.290  0.50 61.63           N  
ATOM   1574  N  BILE B 314     -11.611  76.616  54.938  0.50 59.27           N  
@
the first atom is the same and the following two statements give the same Atom

@group.getAtoms().get(0)
group.getAltLocs().getAtoms().get(0)@

I think this is because in PDBFileParser.getCorrectAltLocGroup(), to create a new alternate group the first one gets cloned together with its atoms.

@Group altLocG = (Group) current_group.clone();
current_group.addAltLoc(altLocG);@


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