Command-line interface

The Python API is primary. After pip install -e ., a Click CLI mirrors common workflows:

phenoms --help
python -m phenoms --help

phenoms prep

Normalize GROMACS / OpenMM / AMBER replicate folders to multi-frame PDBs (imaging / center / fit, protein-only):

phenoms prep --input-dir ./wt_set --prepared-dir ./prepared/wt \
  --frame-dt-ps 1000 --start-ps 1000 --end-ps 500000

Flags: --no-imaging, --no-center, --no-fit.

phenoms run

Analyze PDB replicates or native trajectories (not both in one invocation):

# PDB form
phenoms run --pdb rep1.pdb --pdb rep2.pdb \
  --sub-frames 100 --output-dir ./out

# Native traj + shared topology
phenoms run --traj rep1.xtc --traj rep2.xtc --topology top.pdb

# All-bond mode (default is backbone N–O only)
phenoms run --pdb rep1.pdb --all-bonds

# Optional QC
phenoms run --pdb rep1.pdb --pdb rep2.pdb --qc

phenoms compare

Prep two class directories, run analysis, and export comparison artifacts:

phenoms compare \
  --dir-a ./wt --dir-b ./mut \
  --prepared-dir-a ./prepared/wt --prepared-dir-b ./prepared/mut \
  --label-a wt --label-b mut \
  --output-dir ./phenom_outputs/cli_compare