cleanup (ae927734) · Commits · 钟慕尧 / deepchem

deepchem/dock/binding_pocket.py

+1 −0

Original line number	Diff line number	Diff line
		@@ -14,6 +14,7 @@ from deepchem.utils.fragment_util import get_contact_atom_indices

		logger = logging.getLogger(__name__)


		def extract_active_site(protein_file, ligand_file, cutoff=4):
		"""Extracts a box for the active site.

+1 −0

Original line number	Diff line number	Diff line
		@@ -21,6 +21,7 @@ logger = logging.getLogger(__name__)

		class PoseGenerator(object):
		"""A Pose Generator computes low energy conformations for molecular complexes.

		Many questions in structural biophysics reduce to that of computing
		the binding free energy of molecular complexes. A key step towards
		computing the binding free energy of two complexes is to find low

+4 −0

Original line number	Diff line number	Diff line
		@@ -120,6 +120,7 @@ def vina_hbond(d):
		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.

		@@ -139,6 +140,7 @@ def vina_gaussian_first(d):
		out_tensor = np.exp(-(d / 0.5)**2)
		return out_tensor


		def vina_gaussian_second(d):
		"""Computes Autodock Vina's second Gaussian interaction term.

		@@ -158,6 +160,7 @@ def vina_gaussian_second(d):
		out_tensor = np.exp(-((d - 3) / 2)**2)
		return out_tensor


		def weighted_linear_sum(w, x):
		"""Computes weighted linear sum.

		@@ -170,6 +173,7 @@ def weighted_linear_sum(w, x):
		"""
		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