rush-py 1.3.2

Python SDK for interacting with the QDX Rush API and modules

rush-py

Quickstart

This document will walk through executing jobs on the Rush platform. For a comprehensive guide on the concepts and constructing a full workflow, see the full rush-py explainer document

First, install the following modules via pip - we require Python > 3.10

pip install rush-py pdb-tools

0) Setup

This is where we prepare the rush client, directories, and input data we’ll be working with

0.0) Imports

import os
import tarfile
from datetime import datetime
from pathlib import Path

from pdbtools import pdb_fetch, pdb_delhetatm, pdb_selchain, pdb_rplresname, pdb_keepcoord, pdb_selresname
import requests
import py3Dmol

import rush

NOTE: This walkthrough assumes that you are running code in a Jupyter notebook, which allows for top level await calls. If you are writing a normal Python script, you will need to wrap your code in something like the following:

import asyncio
def main():
    #your code here
asyncio.run(main)

0.1) Credentials

Retrieve your api token from the Rush UI.

You can either set the RUSH_TOKEN and RUSH_URL environment variables, or provide them as variables to the client directly.

To see how to set environment variables, Wikipedia has an extensive article

RUSH_TOKEN = os.getenv("RUSH_TOKEN") or "YOUR_TOKEN_HERE"
RUSH_URL = os.getenv("RUSH_URL") or "https://tengu.qdx.ai"

0.2) Configuration

Lets set some global variables that define our project, these are not required, but are good practice to help organize the jobs that will be persisted under your account.

Make sure you create a unique set of tags for each run. Good practice is to have at least each of the experiment name and system name as a tag.

EXPERIMENT = "tengu-py-v2-quickstart"
SYSTEM = "1B39"
TAGS = ["qdx", EXPERIMENT, SYSTEM]

0.2) Build your client

Get our client, for calling modules and using the Rush API.

As mentioned earlier access_token and url are optional, if you have set the env variables RUSH_TOKEN and RUSH_URL.

batch_tags will be applied to each run that is spawned by this client.

A folder called .rush will be created in your workspace directory (defaults to the current working directory, can be overridden by passing workspace= to the provider builder

# By using the `build_provider_with_functions` method, we will also build helper functions calling each module
client = await rush.build_provider_with_functions(
    access_token=RUSH_TOKEN, url=RUSH_URL, batch_tags=TAGS
)

0.3) Input selection

Fetch data files from RCSB to pass as input to the modules

PROTEIN_PDB_PATH = client.workspace / f"{SYSTEM}_P.pdb"

complex = list(pdb_fetch.fetch_structure(SYSTEM))
protein = pdb_delhetatm.remove_hetatm(pdb_selchain.select_chain(complex, "A"))
with open(PROTEIN_PDB_PATH, "w") as f:
    for l in protein:
        f.write(str(l))

help(client.convert)

Help on function convert in module rush.provider:

async convert(*args: [list[typing.Union[str, ~T]], <class 'pathlib.Path'>], target: rush.graphql_client.enums.ModuleInstanceTarget | None = <ModuleInstanceTarget.NIX: 'NIX'>, resources: rush.graphql_client.input_types.ModuleInstanceResourcesInput | None = ModuleInstanceResourcesInput(gpus=0, gpu_mem=None, gpu_mem_units=None, cpus=None, nodes=None, mem=None, mem_units=None, storage=10, storage_units=<MemUnits.MB: 'MB'>, walltime=None, storage_mounts=None), tags: list[str] | None = None, restore: bool | None = None) -> [<class 'pathlib.Path'>]
    Convert biomolecular and chemical file formats to the QDX file format. Supports PDB and SDF
    
    Module version: github:talo/tengu-prelude/efc6d8b3a8cc342cd9866d037abb77dac40a4d56#convert
    
    QDX Type Description:
    
        format: PDB|SDF;
    
        input: @bytes 
    
    ->
    
        output: @[Conformer]
    
    
    
    :param format: the format of the input file
    :param input: the input file
    :return output: the output conformers

1) Running Rush Modules

You can view which modules are available, alongside their documentation, in the API Dodumentation

1.1) Prep the protein

First we will run the protein preparation routine (using pdbfixer and pdb2pqr internally) to prepare the protein for molecular dynamics

# we can check the arguments and outputs for prepare_protein with help()
help(client.prepare_protein)

Help on function prepare_protein in module rush.provider:

async prepare_protein(*args: [<class 'pathlib.Path'>], target: rush.graphql_client.enums.ModuleInstanceTarget | None = <ModuleInstanceTarget.NIX_SSH_2_GPU: 'NIX_SSH_2_GPU'>, resources: rush.graphql_client.input_types.ModuleInstanceResourcesInput | None = ModuleInstanceResourcesInput(gpus=1, gpu_mem=None, gpu_mem_units=None, cpus=None, nodes=None, mem=None, mem_units=None, storage=138, storage_units=<MemUnits.MB: 'MB'>, walltime=None, storage_mounts=None), tags: list[str] | None = None, restore: bool | None = None) -> [<class 'pathlib.Path'>, <class 'pathlib.Path'>]
    Prepare a PDB for downstream tasks: protonate, fill missing atoms, etc.
    
    Module version: github:talo/pdb2pqr/ff5abe87af13f31478ede490d37468a536621e9c#prepare_protein_tengu
    
    QDX Type Description:
    
        input_pdb: @bytes 
    
    ->
    
        output_qdxf: @[Conformer];
    
        output_pdb: @bytes
    
    
    
    :param input_pdb: An input protein as a file: one PDB file
    :return output_qdxf: An output protein a vec: one qdxf per model in pdb
    :return output_pdb: An output protein as a file: one PDB file

# Here we run the function, it will return a Provider.Arg which you can use to fetch the results
# We set restore = True so that we can restore a previous run to the same path with the same tags
(prepared_protein_qdxf, prepared_protein_pdb) = await client.prepare_protein(
    PROTEIN_PDB_PATH
)
print(f"{datetime.now().time()} | Running protein prep!")
prepared_protein_qdxf  # this initially only have the id of your result, we will show how to fetch the actual value later

23:32:40.657673 | Running protein prep!

Arg(id=1c19095e-4bd0-4fa1-bd60-e52338e2d9c2, value=None)

1.3) Run statuses

This will show the status of all of your runs. You can also view run statuses on the Rush UI

await client.status()

{'6e643129-f6e9-47f4-9b6f-414bacc29944': (<ModuleInstanceStatus.RESOLVING: 'RESOLVING'>,
  'prepare_protein',
  1),
 '0cae0860-f8c7-4afb-8fe2-144ab175a415': (<ModuleInstanceStatus.COMPLETED: 'COMPLETED'>,
  'prepare_protein',
  1),
 '0c2b5aa5-36c2-4180-b242-c2ff622a14f4': (<ModuleInstanceStatus.COMPLETED: 'COMPLETED'>,
  'prepare_protein',
  1)}

1.4) Run Values

This will return the “value” of the output from the function - for files you will recieve a url that you can download, otherwise you will recieve them as python types

protein_qdxf_value = await prepared_protein_qdxf.get()
len(protein_qdxf_value[0]["topology"]["symbols"])

2024-01-27 23:32:40,880 - rush - INFO - Argument 1c19095e-4bd0-4fa1-bd60-e52338e2d9c2 is now ModuleInstanceStatus.RESOLVING
2024-01-27 23:32:46,504 - rush - INFO - Argument 1c19095e-4bd0-4fa1-bd60-e52338e2d9c2 is now ModuleInstanceStatus.ADMITTED
2024-01-27 23:33:00,993 - rush - INFO - Argument 1c19095e-4bd0-4fa1-bd60-e52338e2d9c2 is now ModuleInstanceStatus.DISPATCHED
2024-01-27 23:33:06,618 - rush - INFO - Argument 1c19095e-4bd0-4fa1-bd60-e52338e2d9c2 is now ModuleInstanceStatus.RUNNING
2024-01-27 23:33:30,495 - rush - INFO - Argument 1c19095e-4bd0-4fa1-bd60-e52338e2d9c2 is now ModuleInstanceStatus.AWAITING_UPLOAD

4852

1.5) Downloads

We provide a utility to download files into your workspace, you can either provide a filename, which will be saved in workspace/objects/[filename], or you can provide your own filepath which the client will use as-is

await prepared_protein_pdb.download(filename="01_prepared_protein.pdb", overwrite=True)

# we can read our prepared protein pdb like this
with open(client.workspace / "objects" / "01_prepared_protein.pdb", "r") as f:
    print(f.readline(), "...")

REMARK   1 PDBFIXER FROM: /home/ubuntu/.cache/tengu_store/run/6e643129-f6e9-47f4-9b6f-414bacc29944/.tmp/m2_protein.pdb
 ...