From fc4ce9afef0451e0997607819a68a478d83c3d0d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Semih=20Cant=C3=BCrk?= <semih.canturk@umontreal.ca>
Date: Fri, 24 Jan 2025 09:00:15 -0500
Subject: [PATCH] Revert "add dipeptides dataset"

This reverts commit ba1430a96dea47a134cd89231a43406f273f400c.
---
 openqdc/datasets/potential/__init__.py   |  2 -
 openqdc/datasets/potential/dipeptides.py | 81 ------------------------
 2 files changed, 83 deletions(-)
 delete mode 100644 openqdc/datasets/potential/dipeptides.py

diff --git a/openqdc/datasets/potential/__init__.py b/openqdc/datasets/potential/__init__.py
index a4ead5a..7beba8c 100644
--- a/openqdc/datasets/potential/__init__.py
+++ b/openqdc/datasets/potential/__init__.py
@@ -2,7 +2,6 @@
 from .ani import ANI1, ANI1CCX, ANI1CCX_V2, ANI1X, ANI2X
 from .bpa import BPA
 from .comp6 import COMP6
-from .dipeptides import Dipeptides
 from .dummy import Dummy, PredefinedDataset
 from .gdml import GDML
 from .geom import GEOM
@@ -38,7 +37,6 @@
     "ANI2X": ANI2X,
     "BPA": BPA,
     "COMP6": COMP6,
-    "Dipeptides": Dipeptides,
     "GDML": GDML,
     "GEOM": GEOM,
     "ISO17": ISO17,
diff --git a/openqdc/datasets/potential/dipeptides.py b/openqdc/datasets/potential/dipeptides.py
deleted file mode 100644
index 2d8d9eb..0000000
--- a/openqdc/datasets/potential/dipeptides.py
+++ /dev/null
@@ -1,81 +0,0 @@
-import numpy as np 
-from openqdc.datasets.base import BaseDataset
-from openqdc.methods import PotentialMethod
-
-def shape_atom_inputs(coords, atom_species):
-    reshaped_coords = coords.reshape(-1, 3)
-    frame, atoms, _ = coords.shape
-    z = np.tile(atom_species, frame)
-    xs = np.stack((z, np.zeros_like(z)), axis=-1)
-    return np.concatenate((xs, reshaped_coords), axis=-1, dtype=np.float32)
-
-
-def read_npz_entry(folder):
-    data, name = create_path(folder)
-    data = np.load(data)
-
-    nuclear_charges, coords, energies, forces = (
-        data["nuclear_charges"],
-        data["coords"],
-        data["energies"],
-        data["forces"],
-    )
-    frames = coords.shape[0]
-    res = dict(
-        name=np.array([name] * frames),
-        subset=np.array(["dipeptides"] * frames),
-        energies=energies[:, None].astype(np.float32),
-        forces=forces.reshape(-1, 3, 1).astype(np.float32),
-        atomic_inputs=shape_atom_inputs(coords, nuclear_charges),
-        n_atoms=np.array([len(nuclear_charges)] * frames, dtype=np.int32),
-    )
-    return res
-
-
-def create_path(folder):
-    name = folder.split("/")[-1]
-    return folder, name 
-
-folder="/network/scratch/s/semih.canturk/cache/openqdc/dipeptides/npz_files/mol_73.npz"
-
-trajectories={
-    "mol_73": folder
-}
-
-class Dipeptides(BaseDataset):
-    """
-    """
-
-    __name__ = "dipeptides"
-
-    __energy_methods__ = [PotentialMethod.WB97M_D3BJ_DEF2_TZVPPD]
-
-    energy_target_names = [
-        "",
-    ]
-
-    __energy_unit__ = "kj/mol"
-    __distance_unit__ = "ang"
-    __forces_unit__ = "kj/mol/ang"
-    
-    __force_mask__ = [False]
-
-    @property
-    def data_types(self):
-        return {
-            "atomic_inputs": np.float32,
-            "position_idx_range": np.int32,
-            "energies": np.float32,
-            "forces": np.float32,
-        }
-
-    def read_raw_entries(self):
-        entries_list = []
-        
-        for dummy_name, path_to_npz in trajectories.items():
-            entries_list.append(read_npz_entry(path_to_npz))
-        return entries_list
-    
-
-# to store it in the cache and loading back (add the dataset in the __init__)
-# Dipeptides.no_init().preprocess(upload=False, overwrite=True)
\ No newline at end of file