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| 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://127.0.0.1:7860" | |
| else: | |
| public_link = "ProteinDesignLab/protpardelle" | |
| 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): | |
| """ | |
| AUTHOR | |
| Simon Duerr | |
| https://twitter.com/simonduerr | |
| DESCRIPTION | |
| Set a public link to use a locally hosted version of this space | |
| USAGE | |
| protpardelle_setlink link_or_username/spacename | |
| """ | |
| 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) | |