abpark/transferable-cg

---

Dataset Overview

The data repository contains four trajectory datasets plus metadata files for train/test splits:

transferable-cg/
├── MFM/
├── MFM_100K/
├── MFM_test/
├── instantaneous_md/
├── training_cath_1000.npy
└── test_cath_50.npy

Dataset Descriptions

Dataset	Structures per Domain	Number of Domains	Purpose
MFM	Up to 20	1,000	Mean force estimates (training)
MFM_100K	Up to 100	1,000	Mean force estimates (training, extended)
MFM_test	Up to 100	50	Mean force estimates (held-out test set)
instantaneous_md	Up to 20 simulations	1,000	Concatenated MD trajectories

Important Notes on Mean Force Datasets

⚠️ For MFM, MFM_100K, and MFM_test datasets:

• Forces are recorded only for backbone atoms (Cα, C, N) of each residue and represent the estimated mean force on the Cα, C, and N for each structure
• Forces for all other atoms are set to zero and should be ignored
• Only positions/forces for Cα, C, and N atoms contain valid data

File Descriptions

File	Description
training_cath_1000.npy	List of 1000 CATH domains IDs used for training
test_cath_50.npy	List of 50 CATH domains held out for testing

---

File Structure

Each dataset folder contains subfolders organized by CATH domain ID:

{Dataset}/
└── {CATH_ID}/
    ├── {CATH_ID}_traj_all.hdf5
    └── {CATH_ID}.pdb
    └── subset_1000_cg.npy        # Only in instantaneous_md/

Per-Domain Files

File	Description	Datasets
{CATH_ID}.pdb	Reference structure defining atom ordering and topology	All
{CATH_ID}_traj_all.hdf5	Trajectory data and simulation metadata in HDF5 format	All
subset_1000_cg.npy	Indices of frames used for training	instantaneous_md only

---

HDF5 File Contents

Datasets

Each HDF5 file contains the following trajectory data:

Dataset	Shape	Description
positions	(n_frames, n_atoms, 3)	Atomic coordinates
forces	(n_frames, n_atoms, 3)	Forces on atoms
velocities	(n_frames, n_atoms, 3)	Atomic velocities
pe	(n_frames,)	Potential energy
ke	(n_frames,)	Kinetic energy

Attributes (Metadata)

Each HDF5 file includes the following attributes:

Attribute	Type	Description
energy_units	str	Units for energy values
length_units	str	Units for positions/distances
time_units	str	Units for time
save_energy	bool	If False, energy arrays contain zeros
save_forces	bool	If False, force arrays contain zeros
save_positions	bool	If False, position arrays contain zeros
save_velocities	bool	If False, velocity arrays contain zeros

---

For details on usage see docs/tutorials/training_dataset.md at https://github.com/rotskoff-group/transferable-cg.