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Search doesn't work #1

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sbliven opened this issue Sep 30, 2021 · 0 comments
Open

Search doesn't work #1

sbliven opened this issue Sep 30, 2021 · 0 comments

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@sbliven
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sbliven commented Sep 30, 2021

The version used in the paper relied on RCSB services which are no longer available. It needs to be updated to use biojava 6 and current APIs before the results can be reproduced.
sbliven added a commit to sbliven/motif-search that referenced this issue Sep 30, 2021
@sbliven
Fix lafita#1: Search doesn't work
29866ee 
- update to biojava-6.0.0-alpha4
- Add mvn packaging and assembly code to produce stand-alone jar files
- Add wrapper script for running the code
- Replace obsolete biojava `PdbIdLists.getCurrentPDBIds` with calls
  to the RCSB REST API.
- Remove obsolete DSSP server calls. Either use author-assigned secondary
  structure or calculate DSSP locally
- Add citation for preprint
sbliven added a commit to sbliven/motif-search that referenced this issue Sep 30, 2021
@sbliven
Fix lafita#1: Search doesn't work
3d3f48f 
- update to biojava-6.0.0-alpha4
- Add mvn packaging and assembly code to produce stand-alone jar files
- Add wrapper script for running the code
- Replace obsolete biojava `PdbIdLists.getCurrentPDBIds` with calls
  to the RCSB REST API.
- Remove obsolete DSSP server calls. Either use author-assigned secondary
  structure or calculate DSSP locally
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