--- a
+++ b/unimol/utils/geom.py
@@ -0,0 +1,53 @@
+import random
+import numpy as np
+import rdkit
+import rdkit.Chem as Chem
+import rdkit.Chem.AllChem as AllChem
+import rdkit.Chem.Descriptors as Descriptors
+import tqdm
+
+def change_torsion(pointset, index, angle=None):
+    # pointset: (N, 3)
+    #return the new pointset
+    # angle: rad
+    # index: (2)
+    if angle is None:
+        angle = random.uniform(-np.pi, np.pi)
+    pointset = np.array(pointset)
+    #get rotate axis
+    axis = pointset[index[0][-1]] - pointset[index[1][0]]
+    axis = axis / np.linalg.norm(axis)
+    #get rotate matrix
+    cos = np.cos(angle)
+    sin = np.sin(angle)
+    R = np.array([[cos + axis[0] ** 2 * (1 - cos), axis[0] * axis[1] * (1 - cos) - axis[2] * sin, axis[0] * axis[2] * (1 - cos) + axis[1] * sin],
+                    [axis[1] * axis[0] * (1 - cos) + axis[2] * sin, cos + axis[1] ** 2 * (1 - cos), axis[1] * axis[2] * (1 - cos) - axis[0] * sin],
+                    [axis[2] * axis[0] * (1 - cos) - axis[1] * sin, axis[2] * axis[1] * (1 - cos) + axis[0] * sin, cos + axis[2] ** 2 * (1 - cos)]])
+    #rotate
+    pointset[index[1]] = np.dot(pointset[index[1]] - pointset[index[1][0]], R) + pointset[index[1][0]]
+    return pointset, angle
+
+def gen_conformation(mol, num_conf=20, num_worker=8):
+    try:
+        mol = Chem.AddHs(mol)
+        AllChem.EmbedMultipleConfs(mol, numConfs=num_conf, numThreads=num_worker, pruneRmsThresh=0.1, maxAttempts=5, useRandomCoords=False)
+        AllChem.MMFFOptimizeMoleculeConfs(mol, numThreads=num_worker)
+        mol = Chem.RemoveHs(mol)
+        return mol
+    except:
+        return None
+
+def RotatableBond(mol):
+    """Get the rotatable bond index of a molecule.
+    Args:
+        mol: rdkit.Chem.rdchem.Mol
+    Returns:
+        rotatable_bond: list of tuple
+    """
+    rotatable_bond = []
+    for bond in mol.GetBonds():
+        if bond.IsInRing():
+            continue
+        if bond.GetBondType() == Chem.rdchem.BondType.SINGLE:
+            rotatable_bond.append((bond.GetBeginAtomIdx(), bond.GetEndAtomIdx()))
+    return rotatable_bond
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