alphafold: Alphafold Client

In gotoolchest/toolchest-client-r: R Client for Toolchest

Alphafold Client

Description

Runs AlphaFold via Toolchest.

Usage

alphafold(
  inputs,
  output_path = NULL,
  model_preset = NULL,
  max_template_date = NULL,
  use_reduced_dbs = FALSE,
  is_prokaryote_list = NULL,
  ...
)

Arguments

inputs	Path or list of paths (client-side) to be passed in as input.
output_path	(optional) Path to directory where the output file(s) will be downloaded
model_preset	(optional) Allows you to choose a specific AlphaFold model from monomer, monomer_casp14, monomer_ptm, multimer. Default mode if not provided is monomer.
max_template_date	(optional) Allows for predicting structure of protiens already in the database by setting a date before it was added in YYYY-MM-DD format. Will use today's date if not provided.
use_reduced_dbs	(optional) Uses a smaller version of the BFD database that will reduce run time at the cost of result quality.
is_prokaryote_list	(optional) takes a list of booleans that determine whether all input sequences in the given fasta file are prokaryotic. Expects the string that would normally input into AlphaFold (e.g. "true,true" if there are two prokaryote inputs)
is_async	(optional) Whether to run a job asynchronously. Defaults to false.

Value

Reference to an object with output location data.

gotoolchest/toolchest-client-r documentation built on July 14, 2022, 7 a.m.