Original Script-Based PathGennie

This release represents the original script-based PathGennie distribution. It
provides standalone command-line workflows for rare-event pathway generation,
with emphasis on ligand unbinding and protein folding/unfolding through
direction-guided adaptive sampling.

Highlights

• Provides a script-oriented PathGennie workflow under Scripts/.
• Supports ligand unbinding simulations driven by PCA-based collective
  variables.
• Supports protein folding and unfolding workflows using reference and starting
  structures.
• Includes OpenMM helper modules for simulation setup, restraints, barostats,
  wrapping, and related simulation utilities.
• Includes helper scripts for ligand conformation generation, ligand CV
  generation, PCA model generation, and steering workflows.
• Bundles example molecular systems for direct experimentation, including:
  • examples/2JOF
  • examples/3PTB
  • examples/4W52
  • examples/NTL9
• Provides a Conda environment file for reproducing the original runtime setup.
• Documents the publication context and DOI:
  https://doi.org/10.1021/acs.jctc.5c01244

Main Workflows

Ligand Unbinding

The original release focuses on ligand unbinding through PCA-guided steering.
Users prepare a solvated molecular system, generate PCA collective variables
from ligand-protein distance features, and run the unbinding driver:

python pcagen.py pbcmol.gro \
    --ligand_sel "resname LIG" \
    --output pca.pkl

../../Scripts/unbind \
    --structure_file pbcmol.gro \
    --verbose \
    --relax1 10 \
    --relax2 15 \
    --max_probes 50 \
    --temperature 300 \
    --model_file pca.pkl

The primary output is a reactive trajectory, typically written as
trajectory.xtc.

Protein Unfolding

../../Scripts/unfold \
    --ref_config folded.gro \
    --start_config folded.gro \
    --verbose \
    --relax1 10 \
    --relax2 15 \
    --max_probes 50 \
    --temperature 290

Protein Folding

../../Scripts/fold \
    --ref_config folded.gro \
    --start_config equili.gro \
    --verbose \
    --relax1 10 \
    --relax2 15 \
    --max_probes 50 \
    --temperature 290

Repository Layout

Scripts/
  unbind
  unfold
  fold
  steer
  pcagen.py
  ligconfgen.py
  ligcvgen.py
  omm/

examples/
  2JOF/
  3PTB/
  4W52/
  NTL9/

environment.yml
README.md
LICENSE

Installation

The original release is intended to be used directly from the cloned repository:

git clone https://github.com/TeamSuman/PathGennie.git
cd PathGennie
conda env create -f environment.yml
conda activate pathgennie

The command-line tools are invoked from the Scripts/ directory rather than
through an installed Python package.

Notes

• This release predates the package-oriented backend architecture.
• It does not include pyproject.toml or pip-installable package metadata.
• Workflows are centered on standalone scripts and example-local system.py
  simulation definitions.
• Later code reorganizes these workflows into a pathgennie Python package
  with backend-specific AMBER, GROMACS, and OpenMM runners.