def __init__(self,
radius: float = 8.0,
max_neighbors: float = 12,
step: float = 0.2):
"""
Parameters
----------
radius: float (default 8.0)
Radius of sphere for finding neighbors of atoms in unit cell.
max_neighbors: int (default 12)
Maximum number of neighbors to consider when constructing graph.
step: float (default 0.2)
Step size for Gaussian filter. This value is used when building edge features.
"""
self.radius = radius
self.max_neighbors = int(max_neighbors)
self.step = step
# load atom_init.json
data_dir = get_data_dir()
download_url(ATOM_INIT_JSON_URL, data_dir)
atom_init_json_path = os.path.join(data_dir, 'atom_init.json')
with open(atom_init_json_path, 'r') as f:
atom_init_json = json.load(f)
self.atom_features = {
int(key): np.array(value, dtype=np.float32)
for key, value in atom_init_json.items()
}
self.valid_atom_number = set(self.atom_features.keys())
def __init__(self,
sixty_four_bits: bool = True,
pocket_finder: Optional[BindingPocketFinder] = None):
"""Initializes Vina Pose Generator
Parameters
----------
sixty_four_bits: bool, optional (default True)
Specifies whether this is a 64-bit machine. Needed to download
the correct executable.
pocket_finder: BindingPocketFinder, optional (default None)
If specified should be an instance of
`dc.dock.BindingPocketFinder`.
"""
data_dir = get_data_dir()
if platform.system() == 'Linux':
url = "http://vina.scripps.edu/download/autodock_vina_1_1_2_linux_x86.tgz"
filename = "autodock_vina_1_1_2_linux_x86.tgz"
dirname = "autodock_vina_1_1_2_linux_x86"
self.vina_dir = os.path.join(data_dir, dirname)
self.vina_cmd = os.path.join(self.vina_dir, "bin/vina")
elif platform.system() == 'Darwin':
if sixty_four_bits:
url = "http://vina.scripps.edu/download/autodock_vina_1_1_2_mac_64bit.tar.gz"
filename = "autodock_vina_1_1_2_mac_64bit.tar.gz"
dirname = "autodock_vina_1_1_2_mac_catalina_64bit"
else:
url = "http://vina.scripps.edu/download/autodock_vina_1_1_2_mac.tgz"
filename = "autodock_vina_1_1_2_mac.tgz"
dirname = "autodock_vina_1_1_2_mac"
self.vina_dir = os.path.join(data_dir, dirname)
self.vina_cmd = os.path.join(self.vina_dir, "bin/vina")
elif platform.system() == 'Windows':
url = "http://vina.scripps.edu/download/autodock_vina_1_1_2_win32.msi"
filename = "autodock_vina_1_1_2_win32.msi"
self.vina_dir = "\\Program Files (x86)\\The Scripps Research Institute\\Vina"
self.vina_cmd = os.path.join(self.vina_dir, "vina.exe")
else:
raise ValueError(
"Unknown operating system. Try using a cloud platform to run this code instead."
)
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")
if platform.system() == 'Windows':
msi_cmd = "msiexec /i %s" % downloaded_file
check_output(msi_cmd.split())
else:
with tarfile.open(downloaded_file) as tar:
tar.extractall(data_dir)
logger.info("Cleanup: removing downloaded vina tar.gz")
os.remove(downloaded_file)
def __init__(self):
"""Initialize GNINA pose generator."""
data_dir = get_data_dir()
if platform.system() == 'Linux':
url = "https://github.com/gnina/gnina/releases/download/v1.0/gnina"
filename = 'gnina'
self.gnina_dir = data_dir
self.gnina_cmd = os.path.join(self.gnina_dir, filename)
else:
raise ValueError(
"GNINA currently only runs on Linux. Try using a cloud platform to run this code instead."
)
if not os.path.exists(self.gnina_cmd):
logger.info("GNINA not available. Downloading...")
download_url(url, data_dir)
downloaded_file = os.path.join(data_dir, filename)
os.chmod(downloaded_file, 755)
logger.info("Downloaded GNINA.")