Commit a731768c authored by leswing's avatar leswing
Browse files

wget -nv

parent a375ba4e

deepchem/dock/binding_pocket.py

+1 −1
Original line number Diff line number Diff line
@@ -224,7 +224,7 @@ class RFConvexHullPocketFinder(BindingPocketFinder): 
    print("About to download trained model.")

    # TODO(rbharath): Shift refined to full once trained.

    call((

        "wget -c http://deepchem.io.s3-website-us-west-1.amazonaws.com/trained_models/pocket_random_refined_RF.tar.gz"

        "wget -nv -c http://deepchem.io.s3-website-us-west-1.amazonaws.com/trained_models/pocket_random_refined_RF.tar.gz"

    ).split())

    call(("tar -zxvf pocket_random_refined_RF.tar.gz").split())

    call(("mv pocket_random_refined_RF %s" % (self.base_dir)).split())

deepchem/dock/docking.py

+2 −2
Original line number Diff line number Diff line
@@ -41,7 +41,7 @@ class VinaGridRFDocker(Docker): 
    self.base_dir = tempfile.mkdtemp()

    print("About to download trained model.")

    call((

        "wget -c http://deepchem.io.s3-website-us-west-1.amazonaws.com/trained_models/random_full_RF.tar.gz"

        "wget -nv -c http://deepchem.io.s3-website-us-west-1.amazonaws.com/trained_models/random_full_RF.tar.gz"

    ).split())

    call(("tar -zxvf random_full_RF.tar.gz").split())

    call(("mv random_full_RF %s" % (self.base_dir)).split())
@@ -79,7 +79,7 @@ class VinaGridDNNDocker(object): 
    self.base_dir = tempfile.mkdtemp()

    print("About to download trained model.")

    call((

        "wget -c http://deepchem.io.s3-website-us-west-1.amazonaws.com/trained_models/random_full_DNN.tar.gz"

        "wget -nv -c http://deepchem.io.s3-website-us-west-1.amazonaws.com/trained_models/random_full_DNN.tar.gz"

    ).split())

    call(("tar -zxvf random_full_DNN.tar.gz").split())

    call(("mv random_full_DNN %s" % (self.base_dir)).split())

deepchem/dock/pose_generation.py

+1 −1
Original line number Diff line number Diff line
@@ -66,7 +66,7 @@ class VinaPoseGenerator(PoseGenerator): 
      print("Vina not available. Downloading")

      # TODO(rbharath): May want to move this file to S3 so we can ensure it's

      # always available.

      wget_cmd = "wget -c http://vina.scripps.edu/download/autodock_vina_1_1_2_linux_x86.tgz"

      wget_cmd = "wget -nv -c http://vina.scripps.edu/download/autodock_vina_1_1_2_linux_x86.tgz"

      call(wget_cmd.split())

      print("Downloaded Vina. Extracting")

      download_cmd = "tar xzvf autodock_vina_1_1_2_linux_x86.tgz"

deepchem/dock/tests/test_pose_scoring.py

+1 −1
Original line number Diff line number Diff line
@@ -28,7 +28,7 @@ class TestPoseScoring(unittest.TestCase): 
  def setUp(self):

    """Downloads dataset."""

    call(

        "wget -c http://deepchem.io.s3-website-us-west-1.amazonaws.com/featurized_datasets/core_grid.tar.gz".

        "wget -nv -c http://deepchem.io.s3-website-us-west-1.amazonaws.com/featurized_datasets/core_grid.tar.gz".

        split())

    call("tar -zxvf core_grid.tar.gz".split())

    self.core_dataset = dc.data.DiskDataset("core_grid/")

deepchem/models/autoencoder_models/autoencoder.py

+2 −2
Original line number Diff line number Diff line
@@ -62,7 +62,7 @@ class TensorflowMoleculeEncoder(Model): 
    weights_file = os.path.join(current_dir, weights_filename)



    if not os.path.exists(weights_file):

      wget_command = "wget -c http://karlleswing.com/misc/keras-molecule/model.h5"

      wget_command = "wget -nv -c http://karlleswing.com/misc/keras-molecule/model.h5"

      call(wget_command.split())

      mv_cmd = "mv model.h5 %s" % weights_file

      call(mv_cmd.split())
@@ -132,7 +132,7 @@ class TensorflowMoleculeDecoder(Model): 
    weights_file = os.path.join(current_dir, weights_filename)



    if not os.path.exists(weights_file):

      wget_command = "wget -c http://karlleswing.com/misc/keras-molecule/model.h5"

      wget_command = "wget -nv -c http://karlleswing.com/misc/keras-molecule/model.h5"

      call(wget_command.split())

      mv_cmd = "mv model.h5 %s" % weights_file

      call(mv_cmd.split())

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