Recent Releases of gtalign_alpha
gtalign_alpha - GTalign v0.19.0
- Structure IDs generated from clustering a tar archive corrected
- Cuda
Published by minmarg 7 months ago
gtalign_alpha - GTalign v0.18.0
- File reading issue for clustering fixed when caching is disabled
- Cuda
Published by minmarg 8 months ago
gtalign_alpha - GTalign v0.17.0
- Improved interpretation of the mmCIF format
- Additional synchronization added to a kernel to handle an extremely rare but plausible scenario
- build script added for the Hopper architecture (e.g., H100)
- Cuda
Published by minmarg 9 months ago
gtalign_alpha - GTalign v0.16.0-alpha
- JSON output format introduced
- Reading database files skipped when the database has been cached with the -c option
- Total number of query positions defined by the --dev-queries-total-length-per-chunk option aligned to 32 bits to avoid a memory alignment issue
- Bug fix: a rare case of the master resetting a response flag set by a reader when caching is on
- Cuda
Published by minmarg about 1 year ago
gtalign_alpha - GTalign v0.15.0-alpha
- Introduction of the secondary TM-score, 2TM-score (--2tm-score)
- Option to sort alignments by the harmonic mean (--sort)
See the section Alignment sorting in the README file for a more detailed description.
- Cuda
Published by minmarg almost 2 years ago
gtalign_alpha - GTalign v0.14.0-alpha-doi
- Adding a persistent identifier to the repository with Zenodo
- Cuda
Published by minmarg about 2 years ago
gtalign_alpha - GTalign v0.14.0-alpha-full
- Publication of the full software package, including source code
- Cuda
Published by minmarg about 2 years ago
gtalign_alpha - GTalign v0.14.0-alpha
- Bug fix: Score reinitialization was missing; occasionally actual for deep searches (--speed<7)
- Cuda
Published by minmarg over 2 years ago
gtalign_alpha - GTalign v0.13.0-alpha
- Data caching when reading large datasets implemented (option -c), which can provide considerable speedup
- Cuda
Published by minmarg over 2 years ago
gtalign_alpha - GTalign v0.12.0-alpha
- Bug fix for reading PDB files: Case of ENDMDL immediately following TER
- Cuda
Published by minmarg over 2 years ago
gtalign_alpha - GTalign v0.11.0-alpha
- Complete-linkage clustering algorithm implemented and made default
- Cuda
Published by minmarg over 2 years ago
gtalign_alpha - GTalign v0.10.0-alpha
- Cross-platform code
- Non-essential issue fixes (Clustering sync; Model number parsing; Adjustment for Clang)
- Option --no-file-sort
- Cuda
Published by minmarg over 2 years ago
gtalign_alpha - GTalign v0.9.0-alpha
- Flexible clustering of structures implemented
- Cuda
Published by minmarg over 2 years ago
gtalign_alpha - GTalign v0.8.0-alpha
- Bug fix: coherency issue when using multiple GPUs and filters
- Cuda
Published by minmarg over 2 years ago
gtalign_alpha - GTalign v0.7.0-alpha
- Option (--add-search-by-ss) added for superposition search by a combination of secondary structure and sequence similarity
- Prescreening for similarities in sequence space made available (option --pre-similarity)
- Cuda
Published by minmarg over 2 years ago
gtalign_alpha - GTalign v0.6.0-alpha
- CPU/multiprocessing version made available
- Cuda
Published by minmarg over 2 years ago
gtalign_alpha - GTalign v0.5.0-alpha
- Option for minimum reference length introduced: --dev-min-length
- Race condition fixed when using --pre-score
- Cuda
Published by minmarg almost 3 years ago
gtalign_alpha - GTalign v0.4.0-alpha
- Non-critical bug fix: missed synchronization
- Cuda
Published by minmarg almost 3 years ago
gtalign_alpha - GTalign v0.3.0-alpha
- Output options added: wrap alignments (--wrap), remove deletion positions from alignments (--no-deletions), transformation matrices for reference structures (--referenced)
- Superposition optimality improved for --depth={deep,high}
- Number of independent superposition branches for exploration made configurable (--nbranches)
- Similarity pre-screening in structure space optimized
- Utilization of multiple GPUs
- Cuda
Published by minmarg almost 3 years ago
gtalign_alpha - GTalign v0.2.0-alpha
Changes:
- new options and functionalities introduced: --pre-score, --depth, --trigger, --no-detailed-search, --convergence
- Memory footprint reduced
- Multi-threaded reading and reading from tar archives implemented
- small bug fixes
- Cuda
Published by minmarg about 3 years ago