Lim Heo
:exclamation: Make to check out our [User Guide](https://github.com/soedinglab/hh-suite/wiki). ## Expected Behavior When a PDB has multiple chains of the same protein, I expect the script to leave only one of...
I realized that paths for the database are hard-coded in the bash scripts. For example, in the "run_pyrosetta_ver.sh", the PDB100 database is referred as ` DB="$PIPEDIR/pdb100_2021Mar03/pdb100_2021Mar03" ` I am suggesting...
When I was doing trajectory.atom_slice, if a residue's resSeq == 0, the line 93 reassigns resSeq as residue.index because ```python resSeq = 0 or residue.index # =residue.index ``` As we...
I'm using a CUDA 9.2, and the nvcc did not support -arch=sm_20 option. I simply fixed the issue by replacing sm_20 to sm_70 in CMakeLists.txt file.
I developed the method during my postdoctoral research and transitioned to industry. I am trying to maintain the method as quick as I can during my free time; however, please...
## Summary - remove inner frame loop in `patch_TER` - compute all Cartesian coordinates in vectorized fashion ## Testing - `pytest -q` ------ https://chatgpt.com/codex/tasks/task_e_684239b2a96883228d0bbcb30b262b1f
## Summary - fix typo `torch.minumum` -> `torch.minimum` - add simple unit test for `rmsd_torsion_angle` ## Testing - `pytest -q` ------ https://chatgpt.com/codex/tasks/task_e_6842362abeec832294eda407f4cb5aa1
## Summary - drop `Martini2`/`martini2` from supported options in `convert_cg2all.py` - drop `Martini2`/`martini2` from supported options in `convert_all2cg.py` ## Testing - `pytest -q` ------ https://chatgpt.com/codex/tasks/task_e_68423636b1788322a8243f8aadd140c6
## Summary - fix update_by_permute_method to append the minimum-distance transform ## Testing - `pytest -q` ------ https://chatgpt.com/codex/tasks/task_e_6842345d4b508322949a8a592cc3f137
## Summary - fix `_get_gpu_mem` to return reserved GPU memory instead of allocated twice ## Testing - `pytest -q` ------ https://chatgpt.com/codex/tasks/task_e_6842362dc6fc8322a0a827f0e4d633b9