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Analyzed 1 day ago. based on code collected 2 days ago.

Commit Message	Contributor	Files Modified	Lines Added	Lines Removed	Code Location	Date
Nov 05, 2025 — Nov 05, 2026 Showing page 158 of 243 Search / Filter on:
Also don't add 'final' everywhere. I think that's probably a little overzealous and intrusive.	dmyersturnbull	More...				about 13 years ago
Trim to size all bond arraylists after creating the bonds	ulyssecarion	More...				about 13 years ago
By default, keep the bond arraylist as small as possible	ulyssecarion	More...				about 13 years ago
Loop through all non-water groups for intra-residue bonds, not just sequence residues	ulyssecarion	More...				about 13 years ago
Add a test making sure ligands get bonds too	ulyssecarion	More...				about 13 years ago
Use the new bond constructor in PDBFileReader	ulyssecarion	More...				about 13 years ago
For LINK records, work strictly with atoms that aren't alt locs	ulyssecarion	More...				about 13 years ago
By default, Bonds will now add themselves to their Atoms' bond lists.	ulyssecarion	More...				about 13 years ago
Remove BondType from Bond	ulyssecarion	More...				about 13 years ago
Merge remote-tracking branch 'updates/master'	Karl Nicholas	More...				about 13 years ago
Ran cleanup on AtomCache; this time didn't sort members.	dmyersturnbull	More...				about 13 years ago
Added a GenbankProxySequenceReader class that takes an accessionid and reads genbank data from either a file if it exists or the ncbi/eutils web interface.	Karl Nicholas	More...				about 13 years ago
Changed Eclipse formatter preferences: 1) Use tabs for indentation (I think this is what we've been using), and 2) Don't format header comments because it makes them less readable.	dmyersturnbull	More...				about 13 years ago
Merge pull request #37 from ulyssecarion/peptide-bond-007	Andreas Prlic	More...				about 13 years ago
Set createAtomBonds to be true in TestBond	ulyssecarion	More...				about 13 years ago
Only form bonds if params has createAtomBonds set to true	ulyssecarion	More...				about 13 years ago
Add a createAtomBonds flag to FileParsingParameters	ulyssecarion	More...				about 13 years ago
Add bond-parsing to PDBFileParser	ulyssecarion	More...				about 13 years ago
Add a getAltLocGroup method to Groups, implement it in HetatomImpl	ulyssecarion	More...				about 13 years ago
Add a utility class to store information stored from LINK records	ulyssecarion	More...				about 13 years ago
Add a utility method to convert a ChemCompBond's order into an int	ulyssecarion	More...				about 13 years ago
ChempComp and ChemCompConsumer now use ChemCompBonds.	ulyssecarion	More...				about 13 years ago
Comment out StructureTools.findBonds	ulyssecarion	More...				about 13 years ago
Add a getBonds() method to Atoms and implement it.	ulyssecarion	More...				about 13 years ago
Introduce a new Bond class	ulyssecarion	More...				about 13 years ago
Add tests for atom bonds	ulyssecarion	More...				about 13 years ago
Fixing formatting with biojava lGPL header	Andreas Prlic	More...				about 13 years ago
Merge remote-tracking branch 'andreas/mmcif' into 'andreas/master'	sbliven as Spencer Bliven	More...				over 13 years ago
adding support for different types of file access	Andreas Prlic	More...				over 13 years ago
Merge pull request #36 from dmyersturnbull/master	Douglas Myers-Turnbull	More...				over 13 years ago

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