fd3f643d7ccc44e3ec7e6e6b074ee2efe7f077db,deepchem/dock/pose_generation.py,VinaPoseGenerator,__init__,#VinaPoseGenerator#Any#Any#,91

Before Change


      mv_cmd = "mv %s %s" % (dirname, data_dir)
      check_output(mv_cmd.split())
      logger.info("Cleanup: removing downloaded vina tar.gz")
      rm_cmd = "rm %s" % filename
      call(rm_cmd.split())
    self.vina_cmd = os.path.join(self.vina_dir, "bin/vina")

  def generate_poses(self,
                     molecular_complex,

After Change


    self.pocket_finder = pocket_finder
    if not os.path.exists(self.vina_dir):
      logger.info("Vina not available. Downloading")
      download_url(url, data_dir)
      downloaded_file = os.path.join(data_dir, filename)
      logger.info("Downloaded Vina. Extracting")
      with tarfile.open(downloaded_file) as tar:
        tar.extractall(data_dir)
Italian Trulli
In pattern: SUPERPATTERN

Frequency: 3

Non-data size: 4

Instances


Project Name: deepchem/deepchem
Commit Name: fd3f643d7ccc44e3ec7e6e6b074ee2efe7f077db
Time: 2020-06-16
Author: peastman@stanford.edu
File Name: deepchem/dock/pose_generation.py
Class Name: VinaPoseGenerator
Method Name: __init__


Project Name: deepchem/deepchem
Commit Name: d1dc4e10fb6edeafe36429b672448b87bb8a795a
Time: 2017-08-28
Author: peastman@stanford.edu
File Name: deepchem/models/autoencoder_models/autoencoder.py
Class Name: TensorflowMoleculeEncoder
Method Name: zinc_encoder


Project Name: deepchem/deepchem
Commit Name: d1dc4e10fb6edeafe36429b672448b87bb8a795a
Time: 2017-08-28
Author: peastman@stanford.edu
File Name: deepchem/models/autoencoder_models/autoencoder.py
Class Name: TensorflowMoleculeDecoder
Method Name: zinc_decoder