[Biojava-dev] [BioJava - Bug #3334] (New) ReducedChemCompProvider irreversibly set in PDBFileParser in BioJava 3.0.3 release

[redmine at redmine.open-bio.org]

Issue #3334 has been reported by Steven Darnell.

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Bug #3334: ReducedChemCompProvider irreversibly set in PDBFileParser in BioJava 3.0.3 release
https://redmine.open-bio.org/issues/3334

Author: Steven Darnell
Status: New
Priority: Immediate
Assignee: biojava-dev list
Category: structure
Target version: 
URL: 


Revision 9531 (making sure the MAX parameters are set correctly) added a call to setFileParsingParameters in the PDBFileParser constructor using a newly created FileParsingParameter instance. This irreversibly sets the ChemCompGroupFactory class to use a ReducedChemCompProvider while parsing a PDB file from PDBFileReader.getStructure(). The conditional statement in PDBFileParser.setFileParsingParameters is insufficient to correct the situation. As a result, BioJava 3.0.3 users are limited to a default set of 50 chemical components rather than the nearly 14,000 components available. The behavior is correct in BioJava 3.0.2.

In my opinion, allowing the PDBFileParser constructor to always and undesirably change the ChemCompGroupFactory provider should be avoided (synchronization problems are just waiting to happen).

The fact that a base workflow (opening a PDB file) has been broken in the last release suggests (to me at least) that a patch release is required. Perhaps a patch could be deferred if a workaround within the 3.0.3 API is possible. I could not think of one short of subclassing, which does not seem like an acceptable solution.


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