Hacking on boxes

import tempfile

import numpy as np

from subprocess import call

from scipy.spatial import ConvexHull

from deepchem.feat.fingerprints import CircularFingerprint

from deepchem.models.sklearn_models import SklearnModel

from deepchem.utils import rdkit_util

  Parameters

  ----------

  d: jax.np.ndarray

  d: np.ndarray

    Of shape `(N, M)`.

  Returns

      np.where(d < 0, (1.0 / 0.7) * (0 - d), np.zeros_like(d)))

  return out_tensor

def vina_gaussian_first(d):

  """Computes Autodock Vina's first Gaussian interaction term.

  out_tensor = np.exp(-(d / 0.5)**2)

  return out_tensor

def vina_gaussian_second(d):

  """Computes Autodock Vina's second Gaussian interaction term.

  out_tensor = np.exp(-((d - 3) / 2)**2)

  return out_tensor

def weighted_linear_sum(w, x):

  """Computes weighted linear sum.

  """

  return np.sum(np.dot(w, x))

def vina_energy_term(coords1, coords2, weights, wrot, Nrot):

  """Computes the Vina Energy function for two molecular conformations