search

rdk / p2rank

P2Rank: Protein-ligand binding site prediction tool based on machine learning. Stand-alone command line program / Java library for predicting ligand binding pockets from protein structure.
https://rdk.github.io/p2rank/
MIT License
242 stars 34 forks source link

Update biojava dependencies #5

Closed jendelel closed 7 years ago

jendelel commented 7 years ago

Hi,

please update your biojava dependencies to 4.2.8. The url paths to RCSB have changed and parsing PDB files does not work in the older versions any longer (See this bug). I would send you a pull request, however, I don't have the source code for your forked biojava-strcture-rdk library, which need to be updated as well.

Thanks,

Lukas

rdk commented 7 years ago

Solved on develop branch, p2rank now depends on standard non-forked biojava 4.2.8.

Forked version was there because older versions of biojava were crashing when parsing some pdb files from standard datasets, but now it seems to be ok. Note: now biojava is probably ignoring the lines form those files that it is not able to parse.

Thanks for the hint.