.. _`ris-rosettafold-all-atom`:

====================
RoseTTAFold All-Atom
====================

.. contents::
   :depth: 1
   :local:

.. admonition:: Compute Resources

    - Have questions or need help with compute, including activation or issues?
      Follow `this link. <https://washu.atlassian.net/servicedesk/customer/portal/2/group/6/create/43>`__
    - :ref:`User Agreement <compute-user-agreement>`

.. admonition:: Docker Usage

    - The information on this page assumes that you have a knowledge base of
      using Docker to create images and push them to a repository for use. If
      you need to review that information, please see the links below.
    - :ref:`Docker and the RIS Compute Service <docker-on-compute>`
    - :ref:`Docker Basics: Building, Tagging, & Pushing A Custom Docker Image <ris-docker-basics>`

.. admonition:: storageN

    - The use of ``storageN`` within these documents indicates that any storage platform can be used.
    - Current available storage platforms:
        - storage1
        - storage2

.. _`ris-rosettafold-software`:

Image Details
-------------

- Includes RoseTTAFold All-Atom

Docker Image
~~~~~~~~~~~~

.. code::

    ghcr.io/washu-it-ris/rosettafold-all-atom-docker:<tag>

.. _`rosettafold-docker-tag`:

.. admonition:: Docker Tag

    The ``<tag>`` will refer to the version of the Docker container.
    Please click :ref:`here <rosettafold-versions>` to see a current list of
    available versions and their corresponding Docker images.

.. _`rosettafold-non-interactive`:

Running RoseTTAFold All-Atom Non-interactively
----------------------------------------------

- Copy the script runscript.sh

.. code::

    #! /bin/bash

    cd /app/RoseTTAFold/RoseTTAFold-All-Atom/
    source /app/RoseTTAFold/mambaforge/condabin/activate RFAA
    python -m rf2aa.run_inference --config-name $1

- Copy the script bsub-non-interactive.sh

.. code::

    #! /bin/bash

    # SPECIFY ACCORDINGLY
    COMPUTE_GROUP=MY-COMPUTE-GROUP

    # where are the fasta or sfd files among others?
    INPUT_PATH=MY-INPUT-PATH

    # where do you want the resulting files?
    OUTPUT_PATH=MY-OUTPUT-PATH

    # where are the config inference files?
    INFERENCES_PATH=MY-CONFIG-INFERENCE-PATH

    # Required by LSF
    QUEUE=general
    MEMORY=64GB
    SLOTS=4

    # The image tag should be a tag of the rosettafold-all-atom-docker
    # or an image based on the rosettafold-all-atom-docker image.
    IMAGE_TAG="ghcr.io/washu-it-ris/rosettafold-all-atom-docker:1.0.0"

    # DO NOT CHANGE BELOW THIS LINE
    ROSETTAFOLD_ASSETS_PATH="/scratch1/fs1/ris/references/RoseTTAFold/bfd:/app/RoseTTAFold/RoseTTAFold-All-Atom/bfd \
        /scratch1/fs1/ris/references/RoseTTAFold/checkpoint:/app/RoseTTAFold/RoseTTAFold-All-Atom/checkpoint \
        /scratch1/fs1/ris/references/RoseTTAFold/pdb100_2021Mar03:/app/RoseTTAFold/RoseTTAFold-All-Atom/pdb100_2021Mar03 \
        /scratch1/fs1/ris/references/RoseTTAFold/UniRef30_2020_06:/app/RoseTTAFold/RoseTTAFold-All-Atom/UniRef30_2020_06 \
        /scratch1/fs1/ris/references/RoseTTAFold/blast-2.2.26:/app/RoseTTAFold/RoseTTAFold-All-Atom/blast-2.2.26 \
        /scratch1/fs1/ris/references/RoseTTAFold/csblast-2.2.3:/app/RoseTTAFold/RoseTTAFold-All-Atom/csblast-2.2.3"

    USER_CONFIGURED_PATH="$OUTPUT_PATH:/app/RoseTTAFold/RoseTTAFold-All-Atom/outputs \
        $INPUT_PATH:/app/RoseTTAFold/RoseTTAFold-All-Atom/inputs \
        $INFERENCES_PATH:/app/RoseTTAFold/RoseTTAFold-All-Atom/rf2aa/config/inference"

    DOCKER_VOLUMES="$USER_CONFIGURED_PATH \
        $ROSETTAFOLD_ASSETS_PATH \
        $LSF_DOCKER_VOLUMES"

    # BSUB
    PATH="$PATH:/app/RoseTTAFold/mambaforge/condabin:/app/RoseTTAFold/mambaforge/bin" \
    LSF_DOCKER_VOLUMES="$DOCKER_VOLUMES" \
    bsub \
    -n $SLOTS \
    -M $MEMORY \
    -R "rusage[mem=$MEMORY]" \
    -R "gpuhost" \
    -G $COMPUTE_GROUP \
    -q $QUEUE \
    -gpu 'num=1' \
    -Is -a "docker($IMAGE_TAG)" /bin/bash

- Keep both scripts in the same directory.
- Change the variables such as the COMPUTE_GROUP, OUTPUT_PATH, INFERENCES_PATH among others.
- E.g.

.. code::

    # SPECIFY ACCORDINGLY
    COMPUTE_GROUP=compute-a.santiago

    # where are the fasta or sfd files among others?
    INPUT_PATH=$STORAGEN/rfaa/fastas/

    # where do you want the resulting files?
    OUTPUT_PATH=$STORAGEN/rfaa/outputs

    # where are the config inference files?
    INFERENCES_PATH=$HOME/rfaa/configs

    # Required by LSF
    QUEUE=qa
    MEMORY=32GB
    SLOTS=4

- Copy the base.yaml config file and put it in the config/inference directory.

.. code::

    job_name: "structure_prediction"
    output_path: outputs/
    checkpoint_path: checkpoint/RFAA_paper_weights.pt
    database_params:
      sequencedb: ""
      hhdb: "pdb100_2021Mar03/pdb100_2021Mar03"
      command: make_msa.sh
      num_cpus: 4
      mem: 64
    protein_inputs: null
    na_inputs: null
    sm_inputs: null
    covale_inputs:  null
    residue_replacement: null

    chem_params:
      use_phospate_frames_for_NA: True
      use_cif_ordering_for_trp: True

    loader_params:
      n_templ: 4
      MAXLAT: 128
      MAXSEQ: 1024
      MAXCYCLE: 4
      BLACK_HOLE_INIT: False
      seqid: 150.0


    legacy_model_param:
      n_extra_block: 4
      n_main_block: 32
      n_ref_block: 4
      n_finetune_block: 0
      d_msa: 256
      d_msa_full: 64
      d_pair: 192
      d_templ: 64
      n_head_msa: 8
      n_head_pair: 6
      n_head_templ: 4
      d_hidden_templ: 64
      p_drop: 0.0
      use_chiral_l1: True
      use_lj_l1: True
      use_atom_frames: True
      recycling_type: "all"
      use_same_chain: True
      lj_lin: 0.75
      SE3_param:
        num_layers: 1
        num_channels: 32
        num_degrees: 2
        l0_in_features: 64
        l0_out_features: 64
        l1_in_features: 3
        l1_out_features: 2
        num_edge_features: 64
        n_heads: 4
        div: 4
      SE3_ref_param:
        num_layers: 2
        num_channels: 32
        num_degrees: 2
        l0_in_features: 64
        l0_out_features: 64
        l1_in_features: 3
        l1_out_features: 2
        num_edge_features: 64
        n_heads: 4
        div: 4

- Create a config inference yaml file.
    - The inference config file should inherit the base settings from the base.yaml file.
    - The defaults should be ``base`` and ``_self_``.
    - Set the job name; otherwise, the default job name will be “structure_prediction.”
    - All the input files should have be prefixed with inputs/.
    - For example, the K7N608.fasta file should be set as inputs/K7N608.fasta
    - Example config file named Vmn1r78_E1050.rtaa.yaml

.. code::

    defaults:
      - base
      - _self_

    job_name: "K7N608"

    protein_inputs:
      A:
        fasta_file: inputs/K7N608.fasta

    sm_inputs:
      B:
        input: inputs/66430.sdf
        input_type: "sdf"

- Launch the non-interactive app

.. code::

    # Usage ./bsub-non-interactive.sh <<inference config name>>
    # Do not include the yaml file extention.

    ./bsub-non-interactive.sh Vmn1r78_E1050.rtaa

- Go to the OUTPUT_PATH to find the results. A successful run should generate a pdb file.

.. code::

    drwx------+  Aug 26 11:16 2024-08-26
    drwx------+  Aug 26 10:32 K7N608
    -rw-------+  Aug 26 10:38 K7N608_aux.pt
    -rw-------+  Aug 26 10:38 K7N608.pdb

- The output log should look like the following

.. code::

    Predicting:   0%|          | 0/1 [00:00<?, ?sequences/s]
    Predicting: 100%|██████████| 1/1 [00:00<00:00,  1.49sequences/s]
    Predicting: 100%|██████████| 1/1 [00:00<00:00,  1.48sequences/s]
    Running HHblits against UniRef30 with E-value cutoff 1e-10
    - 20:47:40.116 INFO: Input file = outputs/K7N608/A/hhblits/t000_.1e-10.a3m

    - 20:47:40.116 INFO: Output file = outputs/K7N608/A/hhblits/t000_.1e-10.id90cov75.a3m

    - 20:47:40.240 WARNING: Maximum number 100000 of sequences exceeded in file outputs/K7N608/A/hhblits/t000_.1e-10.a3m

    - 20:48:50.358 INFO: Input file = outputs/K7N608/A/hhblits/t000_.1e-10.a3m

    - 20:48:50.359 INFO: Output file = outputs/K7N608/A/hhblits/t000_.1e-10.id90cov50.a3m

    - 20:48:50.646 WARNING: Maximum number 100000 of sequences exceeded in file outputs/K7N608/A/hhblits/t000_.1e-10.a3m

    Running PSIPRED
    Running hhsearch
    Using the cif atom ordering for TRP.
    ./make_msa.sh inputs/K7N608.fasta outputs/K7N608/A 4 64  pdb100_2021Mar03/pdb100_2021Mar03
    Aug 26 15:51:16 docker1_starter[2469871]: DEBUG:       run_docker returns 0
    Aug 26 15:51:16 docker1_starter[2469871]: DEBUG:       Cleaning up temp files
    Aug 26 15:51:16 docker1_starter[2469871]: DEBUG:       About to exit 0

.. _`rosettafold-versions`:

Available RoseTTAFold Versions
--------------------------

Current Version:
~~~~~~~~~~~~~~~~

- 1.0.0