def main():
plugin = nanome.Plugin(
"MD Simulation",
"Run molecular dynamics on the selected complexes, using OpenMM", "MD",
True)
plugin.set_plugin_class(MDSimulation)
plugin.run('127.0.0.1', 8888)
def main():
plugin = nanome.Plugin(
"GlycamCB",
"Input an oligasaccharide sequence and obtain a minimized pdb.",
"pdb_from_sequence", False)
plugin.set_plugin_class(GlycamCB)
plugin.run('127.0.0.1', 8888)
def main():
parser = argparse.ArgumentParser(
description=
'Parse Arguments to determine flavor of Docking to instantiate')
parser.add_argument('--algorithm',
choices=['smina', 'autodock4'],
default='smina')
args, _ = parser.parse_known_args()
plugin_class = None
name = ''
algo = args.algorithm
if algo == "smina":
name = "Smina"
plugin_class = SminaDocking
elif algo == "autodock4":
name = "Autodock4"
plugin_class = Autodock4Docking
elif algo == "rhodium":
name = "Rhodium"
plugin_class = RhodiumDocking
# Create the plugin, register Docking as the class to instantiate, and start listening
plugin_name = f'{name} Docking'
description = f'Run docking using {plugin_name}. Lets user choose the receptor, ligands, and diverse options'
category = "Docking"
advanced_settings = True
plugin = nanome.Plugin(plugin_name, description, category,
advanced_settings)
plugin.set_plugin_class(plugin_class)
plugin.run()
def main():
parser = Plugin.create_parser()
args, _ = parser.parse_known_args()
default_name = 'Cookbook'
arg_name = args.name or []
plugin_name = ' '.join(arg_name) or default_name
description = 'Interact with your Nanome session via Jupyter Notebook.'
tags = ['Interactions']
plugin = nanome.Plugin(plugin_name, description, tags)
plugin.set_plugin_class(PluginService)
# CLI Args take priority over environment variables for NTS settnigs
host = args.host or os.environ.get('NTS_HOST')
port = args.port or os.environ.get('NTS_PORT') or 0
key = args.key or os.environ.get('NTS_KEY')
configs = {}
if host:
configs['host'] = host
if port:
configs['port'] = int(port)
if key:
configs['key'] = key
plugin.run(**configs)
def main():
plugin = nanome.Plugin(
"Chemical Properties",
"Calculates and displays different properties of chemicals using the RDKit Python library",
"Analysis", True)
plugin.set_plugin_class(ChemicalProperties)
plugin.run('127.0.0.1', 8888)
def main():
if not NANOBABEL:
Logs.error('Error: nanobabel not found, please set NANOBABEL env var')
sys.exit(1)
plugin = nanome.Plugin("Minimization", "Run minimization on selected structures. See Advanced Parameters for forcefield, number of steps, and steepest descent", "Minimization", True)
plugin.set_plugin_class(Minimization)
plugin.run()
def main():
plugin = nanome.Plugin('Electrostatic Potential',
'Calculates Electrostatic Potential Map',
'ESP',
False,
integrations=[Integrations.calculate_esp])
plugin.set_plugin_class(ElectrostaticPotential)
plugin.run()
def main():
plugin = nanome.Plugin(
"Structure Prep",
"Select your structures from the Entry List, then press Run to regenerate bonds and secondary structure.",
"Structure",
True,
integrations=[Integrations.structure_prep])
plugin.set_plugin_class(StructurePrep)
plugin.run()
def main():
plugin = nanome.Plugin(
"Chemical Properties",
"Calculates and displays different properties of chemicals using the RDKit Python library",
"Analysis",
True,
integrations=[Integrations.analysis])
plugin.set_plugin_class(ChemicalProperties)
plugin.run()
def launch_plugin(class_name, args):
module_name = "test_plugins." + class_name
import nanome
sys.argv = args
module = importlib.import_module(module_name)
plugin = nanome.Plugin(module.NAME, module.DESCRIPTION, module.CATEGORY, module.HAS_ADVANCED_OPTIONS)
clsmembers = inspect.getmembers(module, inspect.isclass)
class_target = None
for clsmember in clsmembers:
if class_name == clsmember[0]:
class_target = clsmember[1]
break
if class_target == None:
nanome.util.Logs.error ("Plugin must have the same name as the containing file")
plugin.set_plugin_class(class_target)
plugin.run("config", "config", "config")
def main():
enable_accounts = True
try:
for i in range(len(sys.argv)):
if sys.argv[i] in ["-d", "--disable-accounts"]:
enable_accounts = False
except:
pass
plugin_class = WorkspaceManagerAccounts if enable_accounts else WorkspaceManagerNoAccounts
# Plugin
plugin = nanome.Plugin(
"Workspace Manager",
"Allows standalone VR headset to save and load workspaces", "Loading",
False)
plugin.set_plugin_class(plugin_class)
plugin.run()
def main():
# Plugin server (for Web)
api_key = None
https = False
url = None
port = None
try:
for i, arg in enumerate(sys.argv):
if arg == '--api-key':
api_key = sys.argv[i + 1]
elif arg in ['--https', '-s', '--ssl-cert']:
https = True
elif arg in ['-u', '--url']:
url = sys.argv[i + 1]
elif arg in ['-w', '--web-port']:
port = int(sys.argv[i + 1])
except:
pass
if port is None:
port = 443 if https else DEFAULT_WEB_PORT
# Plugin
integrations = [
Integrations.import_file,
Integrations.export_locations,
Integrations.export_file,
]
plugin = nanome.Plugin(
'Vault',
'Use your browser to upload files and folders to make them available in Nanome.',
'Files',
False,
integrations=integrations)
plugin.set_plugin_class(Vault)
plugin.set_custom_data(url, port, api_key)
plugin.run()
def main():
# Plugin server (for Web)
web_port = DEFAULT_SERVER_PORT
keep_files_days = DEFAULT_KEEP_FILES_DAYS
try:
for i in range(len(sys.argv)):
if sys.argv[i] == "-w":
web_port = int(sys.argv[i + 1])
elif sys.argv[i] == "-k":
keep_files_days = int(sys.argv[i + 1])
except:
pass
server = WebLoaderServer(web_port, keep_files_days)
server.start()
# Plugin
plugin = nanome.Plugin(
"Load from Web",
"Use your browser to upload files and folders to make them available in Nanome.",
"Loading", False)
plugin.set_plugin_class(WebLoader)
plugin.run('127.0.0.1', 8888)
def main():
description = "Display realtime scoring info about a selected ligand."
plugin = nanome.Plugin("Realtime Scoring", description, "Scoring", True)
plugin.set_plugin_class(RealtimeScoring)
plugin.run()
def main():
plugin = nanome.Plugin("URL Loader", "Load molecule from database",
"Loading", False)
plugin.set_plugin_class(URLLoader)
plugin.run('127.0.0.1', 8888)
def main():
plugin = nanome.Plugin("URL Loader", "Load molecule from database",
"Loading", True)
plugin.set_plugin_class(URLLoader)
plugin.run()
self.request_files(["./api_bad_test.txt", "api_test.txt"],
self.on_files_received) # Read two files
def on_files_received(self, file_list):
# For each file we read, display if error, and file content
for file in file_list:
nanome.util.Logs.debug(
"Error?", str(nanome.util.FileErrorCode(file.error_code)),
"Content:", file.data)
# Prepare to write file "api_test.txt", with content "AAAA"
file = nanome.util.FileSaveData()
file.path = "./api_test.txt"
file.write_text("AAAA")
self.save_files([file], self.on_save_files_result) # Write file
def on_save_files_result(self, result_list):
# Check for writing errors
for result in result_list:
nanome.util.Logs.debug(
"Saving", result.path, "Error?",
str(nanome.util.FileErrorCode(result.error_code)))
if __name__ == "__main__":
plugin = nanome.Plugin(
"Example File API",
"Test File API by reading current directory, reading api_test.txt and api_bad_test.txt and modifying api_test.txt",
"Examples", False)
plugin.set_plugin_class(FilesAPITest)
plugin.run()
def main():
plugin = nanome.Plugin('{{name}}', '{{description}}', '{{category}}', False)
plugin.set_plugin_class({{class}})
plugin.run('127.0.0.1', 8888)
def main():
plugin = nanome.Plugin("RMSD", "Aligns complexes using RMSD calculations.",
"Alignment", False)
plugin.set_plugin_class(RMSD)
plugin.run()
def main():
plugin = nanome.Plugin('Matryx', 'Interact with the Matryx platform',
'Utilities', False)
plugin.set_plugin_class(Matryx)
plugin.run('127.0.0.1', 8888)
sys.stdout.flush()
time.sleep(3)
class Test(nanome.PluginInstance):
pass
process = None
def pre_run():
print("Pre run")
sys.stdout.flush()
global process
process = Process(target=start_process)
process.start()
def post_run():
print("Post run")
sys.stdout.flush()
process.kill()
if __name__ == "__main__":
plugin = nanome.Plugin("Test Autoreload", "", "Test", False)
plugin.pre_run = pre_run
plugin.post_run = post_run
plugin.set_plugin_class(Test)
plugin.run('127.0.0.1', 8888)
self.all_atoms = []
for complex in workspace.complexes:
for atom in complex.atoms:
self.all_atoms.append(atom)
all_atom_indices.append(atom.index)
self.create_stream(all_atom_indices, self.stream_created)
def stream_created(self, stream, error):
a_pos = []
for atom in self.all_atoms:
atom.position.y += 1
a_pos.append(atom.position.x)
a_pos.append((atom.position.y) % 100)
a_pos.append(atom.position.z)
def repeat():
self.stream_created(stream, None)
stream.update(a_pos, repeat)
def on_run(self):
self.request_workspace(self.on_workspace_received)
def __init__(self):
pass
if __name__ == "__main__":
plugin = nanome.Plugin("Profile Streams", "", "Test", False)
plugin.set_plugin_class(UpdateWorkspace)
plugin.run('127.0.0.1', 8888)
