from pymol import cmd import os import json import time import threading try: from gradio_client import Client except ImportError: print("gradio_client not installed, trying install:") import pip pip.main(['install', 'gradio_client']) from gradio_client import Client if os.environ.get("GRADIO_LOCAL") != None: public_link = "http://127.0.0.1:7862" else: public_link = "spacesplaceholder" def thread_protpardelle(input_pdb, resample_idxs, modeltype, mode, minlen=50, maxlen= 60, steplen = 2, per_len = 2): client = Client(public_link) job = client.submit( input_pdb, # str in 'PDB Content' Textbox component modeltype, # str in 'Choose a Mode' Radio component f'"{resample_idxs}"', # str in 'Resampled Idxs' Textbox component mode, # str (Option from: ['backbone', 'allatom']) minlen, # int | float (numeric value between 2 and 200) minlen maxlen, # int | float (numeric value between 3 and 200) in 'maxlen' Slider component steplen, # int | float (numeric value between 1 and 50) in 'steplen' Slider component per_len, # int | float (numeric value between 1 and 200) in 'perlen' Slider component api_name="/protpardelle" ) #start time start = time.time() while (job.done() == False): status = job.status() elapsed = time.time()-start # format as hh:mm:ss elapsed = time.strftime("%H:%M:%S", time.gmtime(elapsed)) print(f"\r protpardelle running since {elapsed}", end="") time.sleep(1) results = job.result() # load each result into pymol results = json.loads(results) for (name,pdb_content) in results: print(name) cmd.read_pdbstr(pdb_content, os.path.basename(name)) def query_protpardelle( name_of_input: str, selection_resample_idxs: str="", per_len: int = 2, mode: str="allatom", ): """ AUTHOR Simon Duerr https://twitter.com/simonduerr DESCRIPTION Run Protpardelle USAGE protpardelle name_of_input, selection_resampled_idx, modeltype, mode, per_len PARAMETERS name_of_input = string: name of input object selection_resampled_idx = string: selection of resampled protein residues per_len = int: per_len (default: 2) mode = string: mode (default: 'allatom') """ if name_of_input != "": input_pdb = cmd.get_pdbstr(name_of_input) all_aa = cmd.index(name_of_input+" and name CA") idx = cmd.index(selection_resample_idxs+" and name CA") #map to zero indexed values aa_mapping = {aa[1]:i for i,aa in enumerate(all_aa)} idx = ",".join([str(aa_mapping[aa[1]]) for aa in idx]) print("resampling", idx , "(zero indexed) from", name_of_input) t = threading.Thread(target=thread_protpardelle, args=(input_pdb, idx, "conditional",mode ), kwargs={'per_len':per_len}, daemon=True) t.start() def query_protpardelle_uncond( minlen: int = 50, maxlen: int = 60, steplen: int = 2, per_len: int = 2, mode: str="allatom", ): """ AUTHOR Simon Duerr https://twitter.com/simonduerr DESCRIPTION Run Protpardelle USAGE protpardelle_uncond minlen, maxlen, steplen, per_len,mode PARAMETERS minlen = int: minlen maxlen = int: maxlen steplen = int: steplen per_len = int: per_len mode = string: mode (default: 'allatom') """ modeltype = "unconditional" idx = None input_pdb = None t = threading.Thread(target=thread_protpardelle, args=(input_pdb, idx, modeltype, mode), kwargs={'minlen':minlen, 'maxlen':maxlen, 'steplen':steplen,'per_len':per_len}, daemon=True) t.start() def setprotpardellelink(link:str): global public_link try: client = Client(link) except: print("could not connect to:", public_link) public_link = link cmd.extend("protpardelle_setlink", setprotpardellelink) cmd.extend("protpardelle", query_protpardelle) cmd.extend("protpardelle_uncond", query_protpardelle_uncond)