From 7958e5efcf106eb2df5802c5c800115737baa552 Mon Sep 17 00:00:00 2001
From: xraymemory <me.anzuoni@gmail.com>
Date: Mon, 11 May 2026 23:00:16 -0400
Subject: [PATCH] feat(diffuse): add ACTL-native Sampleworks wrappers

---
 Dockerfile                               |   3 +-
 docker-entrypoint.sh                     |  23 ++-
 rf3_partial_occ_sweep_chiral_off_actl.sh |  46 ++++++
 rf3_partial_occ_sweep_fixed_actl.sh      |  10 ++
 run_all_models_actl.sh                   | 156 ++++++++++++++++++++
 run_all_models_mdc_actl.sh               | 142 ++++++++++++++++++
 run_grid_search_actl.sh                  | 180 +++++++++++++++++++++++
 run_protenix_mini_tiny_actl.sh           |  86 +++++++++++
 run_rf3_partial_actl.sh                  |  49 ++++++
 run_rf3_partial_fixed_actl.sh            |  44 ++++++
 run_rf3_protenix_mdc_actl.sh             |  73 +++++++++
 11 files changed, 810 insertions(+), 2 deletions(-)
 create mode 100755 rf3_partial_occ_sweep_chiral_off_actl.sh
 create mode 100755 rf3_partial_occ_sweep_fixed_actl.sh
 create mode 100755 run_all_models_actl.sh
 create mode 100755 run_all_models_mdc_actl.sh
 create mode 100755 run_grid_search_actl.sh
 create mode 100755 run_protenix_mini_tiny_actl.sh
 create mode 100755 run_rf3_partial_actl.sh
 create mode 100755 run_rf3_partial_fixed_actl.sh
 create mode 100755 run_rf3_protenix_mdc_actl.sh

diff --git a/Dockerfile b/Dockerfile
index 45ca0ae0..51ae4cba 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -106,8 +106,9 @@ COPY pyproject.toml pixi.lock ./
 COPY src/ ./src/
 COPY scripts/ ./scripts/
 COPY run_grid_search.py ./
+COPY *_actl.sh /usr/local/bin/
 COPY docker-entrypoint.sh /usr/local/bin/entrypoint.sh
-RUN chmod +x /usr/local/bin/entrypoint.sh
+RUN chmod +x /usr/local/bin/entrypoint.sh /usr/local/bin/*_actl.sh
 
 # ============================================================================
 # Install all three environments: boltz, protenix, rf3
diff --git a/docker-entrypoint.sh b/docker-entrypoint.sh
index 45ca3bb2..badd841a 100755
--- a/docker-entrypoint.sh
+++ b/docker-entrypoint.sh
@@ -5,6 +5,8 @@
 #   docker run sampleworks -e <pixi_env> <script> [args...]
 #   docker run sampleworks -e boltz run_grid_search.py --proteins /data/proteins.csv ...
 #   docker run sampleworks --params /data/input/params.json --output-dir /data/results
+#   docker run sampleworks run_grid_search_actl.sh --model rf3 --proteins /data/proteins.csv
+#   docker run sampleworks run_all_models_actl.sh  # native ACTL/Kubernetes run
 #   docker run sampleworks bash  # interactive shell
 #
 # Available pixi environments: boltz, protenix, rf3
@@ -30,6 +32,7 @@ Sampleworks - Protein structure prediction with diffusion model guidance
 USAGE:
     docker run --gpus all --shm-size=16g sampleworks -e <environment> <script> [arguments...]
     docker run --gpus all --shm-size=16g sampleworks --params <params.json> --output-dir <dir>
+    docker run sampleworks run_all_models_actl.sh
     docker run sampleworks bash
     docker run sampleworks --help
 
@@ -41,6 +44,9 @@ OPTIONS:
     --params FILE       Run grid search from a flexible params.json file
     -h, --help          Show this help message
     bash                Start an interactive shell
+    run_grid_search_actl.sh
+                        Run run_grid_search.py natively inside this container
+    *_actl.sh           Run one of the bundled ACTL/Kubernetes-native wrappers
 
 ENVIRONMENTS:
     boltz       For boltz1 and boltz2 models
@@ -104,6 +110,13 @@ EXAMPLES:
     # Interactive shell
     docker run --gpus all --shm-size=16g -it sampleworks bash
 
+    # ACTL/Kubernetes-native all-model run. No Docker is started inside the container.
+    docker run --gpus all --shm-size=16g -v /data:/data sampleworks run_all_models_actl.sh
+
+    # ACTL/Kubernetes-native generic grid search launcher.
+    docker run --gpus all --shm-size=16g -v /data:/data sampleworks \
+      run_grid_search_actl.sh --model rf3 --proteins /data/proteins.csv --output-dir /data/results
+
     # Run a custom script
     docker run --gpus all --shm-size=16g -v /data:/data sampleworks \
       -e boltz scripts/boltz2_pure_guidance.py \
@@ -246,6 +259,12 @@ if [ "$1" = "bash" ] || [ "$1" = "sh" ]; then
     exec "$@"
 fi
 
+# ACTL/Kubernetes-native runners are intended to run inside the already-started
+# sampleworks container and must not launch Docker-in-Docker.
+if [[ "$1" == *_actl.sh ]]; then
+    exec "$@"
+fi
+
 # Generic params mode. Diffuse uses this path: it materializes params.json in
 # the pod, then passes --params plus --output-dir to this entrypoint.
 if [ "$1" = "--params" ]; then
@@ -271,10 +290,11 @@ while [[ $# -gt 0 ]]; do
             break
             ;;
         *)
-            echo "Error: First argument must be -e <environment>, --params, bash, or --help"
+            echo "Error: First argument must be -e <environment>, --params, run_all_models_actl.sh, bash, or --help"
             echo ""
             echo "Usage: docker run sampleworks -e <env> <script> [args...]"
             echo "       docker run sampleworks --params <params.json> --output-dir <dir>"
+            echo "       docker run sampleworks run_all_models_actl.sh"
             echo "       docker run sampleworks bash"
             echo "       docker run sampleworks --help"
             exit 1
@@ -291,6 +311,7 @@ if [[ -z "$ENV" ]]; then
     echo "Examples:"
     echo "  docker run sampleworks -e boltz run_grid_search.py --proteins /data/proteins.csv"
     echo "  docker run sampleworks -e rf3 run_grid_search.py --help"
+    echo "  docker run sampleworks run_all_models_actl.sh"
     echo "  docker run sampleworks bash"
     exit 1
 fi
diff --git a/rf3_partial_occ_sweep_chiral_off_actl.sh b/rf3_partial_occ_sweep_chiral_off_actl.sh
new file mode 100755
index 00000000..9853512f
--- /dev/null
+++ b/rf3_partial_occ_sweep_chiral_off_actl.sh
@@ -0,0 +1,46 @@
+#!/bin/bash
+# Run RF3 occ-sweep partial grid search with chiral features disabled.
+
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+RUN_GRID_SEARCH_ACTL="${RUN_GRID_SEARCH_ACTL:-$SCRIPT_DIR/run_grid_search_actl.sh}"
+
+if [[ "${1:-}" == "-h" || "${1:-}" == "--help" ]]; then
+    cat << 'EOF'
+Usage: rf3_partial_occ_sweep_chiral_off_actl.sh
+
+Environment overrides: DATA_DIR, RESULTS_DIR, MSA_CACHE_DIR, PROTEINS_CSV, GPU_DEVICES, RF3_CHECKPOINT
+EOF
+    exit 0
+fi
+
+DATA_DIR="${DATA_DIR:-/mnt/diffuse-private/raw/sampleworks/initial_dataset_40_occ_sweeps}"
+RESULTS_DIR="${RESULTS_DIR:-/data/sampleworks-exp/occ_sweep/grid_search_results_rf3_chiral_off}"
+MSA_CACHE_DIR="${MSA_CACHE_DIR:-${HOME}/sampleworks-exp/msa_cache}"
+PROTEINS_CSV="${PROTEINS_CSV:-$DATA_DIR/proteins.csv}"
+GPU_DEVICES="${GPU_DEVICES:-5}"
+
+if [[ ! -f "$PROTEINS_CSV" ]]; then
+    echo "Error: proteins CSV not found: $PROTEINS_CSV" >&2
+    exit 1
+fi
+
+mkdir -p "$RESULTS_DIR" "$MSA_CACHE_DIR"
+
+echo "[$(date)] Starting RF3 chiral-off occ-sweep run on GPUs $GPU_DEVICES"
+CUDA_VISIBLE_DEVICES="$GPU_DEVICES" "$RUN_GRID_SEARCH_ACTL" \
+    --model rf3 \
+    --proteins "$PROTEINS_CSV" \
+    --scalers pure_guidance \
+    --partial-diffusion-step 120 \
+    --ensemble-sizes "8" \
+    --gradient-weights "0.0 0.005 0.01 0.02 0.035 0.05 0.1 0.2 0.35 0.5" \
+    --gradient-normalization --augmentation --align-to-input \
+    --output-dir "$RESULTS_DIR" \
+    --force-all \
+    --disable-chiral-features \
+    --model-checkpoint "${RF3_CHECKPOINT:-/checkpoints/rf3_foundry_01_24_latest.ckpt}" \
+    2>&1 | tee "$RESULTS_DIR/rf3_partial_run_occ_sweep_chiral_off.log"
+
+echo "[$(date)] RF3 job completed."
diff --git a/rf3_partial_occ_sweep_fixed_actl.sh b/rf3_partial_occ_sweep_fixed_actl.sh
new file mode 100755
index 00000000..f15c36f9
--- /dev/null
+++ b/rf3_partial_occ_sweep_fixed_actl.sh
@@ -0,0 +1,10 @@
+#!/bin/bash
+# Alias for the fixed occ-sweep RF3 ACTL run, matching the remote wrapper name.
+
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+
+RESULTS_DIR="${RESULTS_DIR:-/data/sampleworks-exp/occ_sweep/grid_search_results}" \
+MSA_CACHE_DIR="${MSA_CACHE_DIR:-/data/sampleworks-exp/msa_cache}" \
+exec "$SCRIPT_DIR/run_rf3_partial_fixed_actl.sh" "$@"
diff --git a/run_all_models_actl.sh b/run_all_models_actl.sh
new file mode 100755
index 00000000..7921d98a
--- /dev/null
+++ b/run_all_models_actl.sh
@@ -0,0 +1,156 @@
+#!/bin/bash
+# Run all 4 Sampleworks model grid searches in parallel inside the current container.
+#
+# This is the ACTL/Kubernetes-native version of run_all_models.sh. It intentionally
+# does not run Docker; launch/connect to the sampleworks image first, then run this
+# script in that container.
+#
+# Usage:
+#   run_all_models_actl.sh
+#
+# Environment overrides:
+#   DATA_DIR       Input directory containing proteins.csv (default: /data/input)
+#   RESULTS_DIR    Output directory (default: /data/results)
+#   MSA_CACHE_DIR  MSA cache directory (default: /root/.sampleworks/msa)
+
+set -euo pipefail
+
+if [[ "${1:-}" == "-h" || "${1:-}" == "--help" ]]; then
+    cat << 'EOF'
+Run all 4 Sampleworks model grid searches in parallel inside the current container.
+
+Usage:
+  run_all_models_actl.sh
+
+Environment overrides:
+  DATA_DIR       Input directory containing proteins.csv (default: /data/input)
+  RESULTS_DIR    Output directory (default: /data/results)
+  MSA_CACHE_DIR  MSA cache directory (default: /root/.sampleworks/msa)
+  PROTEINS_CSV   Explicit proteins CSV path (default: $DATA_DIR/proteins.csv)
+EOF
+    exit 0
+fi
+
+DATA_DIR="${DATA_DIR:-/data/input}"
+RESULTS_DIR="${RESULTS_DIR:-/data/results}"
+MSA_CACHE_DIR="${MSA_CACHE_DIR:-/root/.sampleworks/msa}"
+PROTEINS_CSV="${PROTEINS_CSV:-$DATA_DIR/proteins.csv}"
+
+if [[ ! -f "$PROTEINS_CSV" ]]; then
+    echo "Error: proteins CSV not found: $PROTEINS_CSV" >&2
+    echo "Set DATA_DIR or PROTEINS_CSV to the mounted Sampleworks input path." >&2
+    exit 1
+fi
+
+mkdir -p "$RESULTS_DIR" "$MSA_CACHE_DIR"
+
+echo "=========================================="
+echo "Starting all model grid searches natively (4 jobs x 2 GPUs)"
+echo "Data: $DATA_DIR"
+echo "Proteins CSV: $PROTEINS_CSV"
+echo "Results: $RESULTS_DIR"
+echo "MSA Cache: $MSA_CACHE_DIR"
+echo "Checkpoints: BAKED INTO IMAGE (with mount fallback)"
+echo ""
+echo "Models:"
+echo "  - Boltz2 X-ray (GPUs 0,1)"
+echo "  - Boltz2 MD    (GPUs 2,3)"
+echo "  - RF3          (GPUs 4,5)"
+echo "  - Protenix     (GPUs 6,7)"
+echo "=========================================="
+
+PIDS=()
+NAMES=()
+
+start_grid_search() {
+    local name="$1"
+    local gpu_devices="$2"
+    local pixi_env="$3"
+    local log_file="$4"
+    shift 4
+
+    echo "[$(date)] Starting $name on GPUs $gpu_devices"
+    CUDA_VISIBLE_DEVICES="$gpu_devices" \
+        pixi run -e "$pixi_env" python /app/run_grid_search.py "$@" \
+        2>&1 | tee "$log_file" &
+    PIDS+=("$!")
+    NAMES+=("$name")
+    echo "[$(date)] $name job started (PID: ${PIDS[-1]})"
+}
+
+start_grid_search "Boltz2 X-ray" "0,1" "boltz" "$RESULTS_DIR/boltz2_xrd_run.log" \
+    --proteins "$PROTEINS_CSV" \
+    --models boltz2 \
+    --methods "X-RAY DIFFRACTION" \
+    --scalers pure_guidance \
+    --partial-diffusion-step 120 \
+    --ensemble-sizes "8" \
+    --gradient-weights "0.0 0.05 0.1 0.2 0.35 0.5" \
+    --gradient-normalization --augmentation --align-to-input \
+    --output-dir "$RESULTS_DIR"
+
+start_grid_search "Boltz2 MD" "2,3" "boltz" "$RESULTS_DIR/boltz2_md_run.log" \
+    --proteins "$PROTEINS_CSV" \
+    --models boltz2 \
+    --methods "MD" \
+    --scalers pure_guidance \
+    --partial-diffusion-step 120 \
+    --ensemble-sizes "8" \
+    --gradient-weights "0.0 0.05 0.1 0.2 0.35 0.5" \
+    --gradient-normalization --augmentation --align-to-input \
+    --output-dir "$RESULTS_DIR"
+
+start_grid_search "RosettaFold3" "4,5" "rf3" "$RESULTS_DIR/rf3_run.log" \
+    --proteins "$PROTEINS_CSV" \
+    --models rf3 \
+    --partial-diffusion-step 120 \
+    --scalers pure_guidance \
+    --ensemble-sizes "8" \
+    --gradient-weights "0.0 0.005 0.01 0.02 0.035 0.05 0.1" \
+    --gradient-normalization --augmentation --align-to-input \
+    --output-dir "$RESULTS_DIR"
+
+start_grid_search "Protenix" "6,7" "protenix" "$RESULTS_DIR/protenix_run.log" \
+    --proteins "$PROTEINS_CSV" \
+    --models protenix \
+    --scalers pure_guidance \
+    --partial-diffusion-step 120 \
+    --ensemble-sizes "8" \
+    --gradient-weights "0.0 0.05 0.1 0.2 0.35 0.5" \
+    --gradient-normalization --augmentation --align-to-input \
+    --output-dir "$RESULTS_DIR"
+
+echo ""
+echo "=========================================="
+echo "All 4 jobs launched! PIDs: ${PIDS[*]}"
+echo "Logs:"
+echo "  - $RESULTS_DIR/boltz2_xrd_run.log"
+echo "  - $RESULTS_DIR/boltz2_md_run.log"
+echo "  - $RESULTS_DIR/rf3_run.log"
+echo "  - $RESULTS_DIR/protenix_run.log"
+echo ""
+echo "Monitor GPU usage: nvidia-smi -l 1"
+echo "Waiting for all jobs to complete..."
+echo "=========================================="
+
+failed=0
+for index in "${!PIDS[@]}"; do
+    if wait "${PIDS[$index]}"; then
+        echo "[$(date)] ${NAMES[$index]} completed successfully"
+    else
+        status=$?
+        echo "[$(date)] ${NAMES[$index]} failed with exit code $status" >&2
+        failed=1
+    fi
+done
+
+echo ""
+echo "=========================================="
+if [[ "$failed" -eq 0 ]]; then
+    echo "[$(date)] All jobs completed successfully!"
+else
+    echo "[$(date)] One or more jobs failed. Check logs above."
+fi
+echo "=========================================="
+
+exit "$failed"
diff --git a/run_all_models_mdc_actl.sh b/run_all_models_mdc_actl.sh
new file mode 100755
index 00000000..b10df1cc
--- /dev/null
+++ b/run_all_models_mdc_actl.sh
@@ -0,0 +1,142 @@
+#!/bin/bash
+# Run selected Sampleworks model grid searches inside the current container.
+
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+RUN_GRID_SEARCH_ACTL="${RUN_GRID_SEARCH_ACTL:-$SCRIPT_DIR/run_grid_search_actl.sh}"
+
+show_help() {
+    cat << 'EOF'
+Usage: run_all_models_mdc_actl.sh [OPTIONS]
+
+Options:
+  --boltz2-xrd    Run Boltz2 with X-ray diffraction (GPUs 0,1)
+  --boltz2-md     Run Boltz2 with MD (GPUs 2,3)
+  --rf3           Run RosettaFold3 (GPUs 4,5)
+  --protenix      Run Protenix (GPUs 6,7)
+  --all           Run all models (default if no args)
+  --help          Show this help message
+
+Environment overrides:
+  DATA_DIR       Input directory containing proteins.csv
+  RESULTS_DIR    Output directory
+  MSA_CACHE_DIR  MSA cache directory
+  PROTEINS_CSV   Explicit proteins CSV path
+EOF
+}
+
+DATA_DIR="${DATA_DIR:-/mnt/diffuse-private/raw/sampleworks/initial_dataset_40}"
+RESULTS_DIR="${RESULTS_DIR:-${HOME}/sampleworks-exp/grid_search_results}"
+MSA_CACHE_DIR="${MSA_CACHE_DIR:-${HOME}/sampleworks-exp/msa_cache}"
+PROTEINS_CSV="${PROTEINS_CSV:-$DATA_DIR/proteins.csv}"
+
+RUN_BOLTZ2_XRD=false
+RUN_BOLTZ2_MD=false
+RUN_RF3=false
+RUN_PROTENIX=false
+
+if [[ $# -eq 0 ]]; then
+    RUN_BOLTZ2_XRD=true
+    RUN_BOLTZ2_MD=true
+    RUN_RF3=true
+    RUN_PROTENIX=true
+else
+    while [[ $# -gt 0 ]]; do
+        case "$1" in
+            --boltz2-xrd|--boltz-xrd|--boltz2_xrd) RUN_BOLTZ2_XRD=true ;;
+            --boltz2-md|--boltz-md|--boltz2_md) RUN_BOLTZ2_MD=true ;;
+            --rf3|--rosettafold3|--rosettafold) RUN_RF3=true ;;
+            --protenix) RUN_PROTENIX=true ;;
+            --all) RUN_BOLTZ2_XRD=true; RUN_BOLTZ2_MD=true; RUN_RF3=true; RUN_PROTENIX=true ;;
+            --help|-h) show_help; exit 0 ;;
+            *) echo "Unknown option: $1" >&2; echo "Use --help for usage." >&2; exit 1 ;;
+        esac
+        shift
+    done
+fi
+
+if [[ ! -f "$PROTEINS_CSV" ]]; then
+    echo "Error: proteins CSV not found: $PROTEINS_CSV" >&2
+    exit 1
+fi
+
+mkdir -p "$RESULTS_DIR" "$MSA_CACHE_DIR"
+
+echo "=========================================="
+echo "Starting selected model grid searches natively"
+echo "Data: $DATA_DIR"
+echo "Proteins CSV: $PROTEINS_CSV"
+echo "Results: $RESULTS_DIR"
+echo "MSA Cache: $MSA_CACHE_DIR"
+echo "Models to run:"
+[[ "$RUN_BOLTZ2_XRD" == true ]] && echo "  - Boltz2 X-ray (GPUs 0,1)"
+[[ "$RUN_BOLTZ2_MD" == true ]] && echo "  - Boltz2 MD (GPUs 2,3)"
+[[ "$RUN_RF3" == true ]] && echo "  - RosettaFold3 (GPUs 4,5)"
+[[ "$RUN_PROTENIX" == true ]] && echo "  - Protenix (GPUs 6,7)"
+echo "=========================================="
+
+PIDS=()
+NAMES=()
+
+start_grid_search() {
+    local name="$1"
+    local gpu_devices="$2"
+    local log_file="$3"
+    shift 3
+
+    echo "[$(date)] Starting $name on GPUs $gpu_devices"
+    CUDA_VISIBLE_DEVICES="$gpu_devices" "$RUN_GRID_SEARCH_ACTL" "$@" 2>&1 | tee "$log_file" &
+    PIDS+=("$!")
+    NAMES+=("$name")
+    echo "[$(date)] $name job started (PID: ${PIDS[-1]})"
+}
+
+if [[ "$RUN_BOLTZ2_XRD" == true ]]; then
+    start_grid_search "Boltz2 X-ray" "0,1" "$RESULTS_DIR/boltz2_xrd_run.log" \
+        --model boltz2 --method "X-RAY DIFFRACTION" --proteins "$PROTEINS_CSV" \
+        --scalers pure_guidance --partial-diffusion-step 120 --ensemble-sizes "8" \
+        --gradient-weights "0.1 0.2 0.5" --gradient-normalization --augmentation \
+        --align-to-input --output-dir "$RESULTS_DIR"
+fi
+
+if [[ "$RUN_BOLTZ2_MD" == true ]]; then
+    start_grid_search "Boltz2 MD" "2,3" "$RESULTS_DIR/boltz2_md_run.log" \
+        --model boltz2 --method "MD" --proteins "$PROTEINS_CSV" \
+        --scalers pure_guidance --partial-diffusion-step 120 --ensemble-sizes "8" \
+        --gradient-weights "0.1 0.2 0.5" --gradient-normalization --augmentation \
+        --align-to-input --output-dir "$RESULTS_DIR"
+fi
+
+if [[ "$RUN_RF3" == true ]]; then
+    start_grid_search "RosettaFold3" "4,5" "$RESULTS_DIR/rf3_run.log" \
+        --model rf3 --proteins "$PROTEINS_CSV" --scalers pure_guidance \
+        --ensemble-sizes "8" --gradient-weights "0.01 0.02 0.05" \
+        --gradient-normalization --augmentation --align-to-input --output-dir "$RESULTS_DIR"
+fi
+
+if [[ "$RUN_PROTENIX" == true ]]; then
+    start_grid_search "Protenix" "6,7" "$RESULTS_DIR/protenix_run.log" \
+        --model protenix --proteins "$PROTEINS_CSV" --scalers pure_guidance \
+        --partial-diffusion-step 120 --ensemble-sizes "8" --gradient-weights "0.1 0.2 0.5" \
+        --gradient-normalization --augmentation --align-to-input --output-dir "$RESULTS_DIR"
+fi
+
+if [[ ${#PIDS[@]} -eq 0 ]]; then
+    echo "No models selected to run." >&2
+    exit 1
+fi
+
+echo "Waiting for ${#PIDS[@]} jobs: ${PIDS[*]}"
+failed=0
+for index in "${!PIDS[@]}"; do
+    if wait "${PIDS[$index]}"; then
+        echo "[$(date)] ${NAMES[$index]} completed successfully"
+    else
+        status=$?
+        echo "[$(date)] ${NAMES[$index]} failed with exit code $status" >&2
+        failed=1
+    fi
+done
+
+exit "$failed"
diff --git a/run_grid_search_actl.sh b/run_grid_search_actl.sh
new file mode 100755
index 00000000..64e2bd95
--- /dev/null
+++ b/run_grid_search_actl.sh
@@ -0,0 +1,180 @@
+#!/bin/bash
+# Run Sampleworks grid search natively inside the current ACTL/Kubernetes container.
+
+set -euo pipefail
+
+show_help() {
+    cat << 'EOF'
+Run Sampleworks run_grid_search.py inside the already-running container.
+
+Usage:
+  run_grid_search_actl.sh [-e ENV] [run_grid_search.py args...]
+  run_grid_search_actl.sh --params /data/input/params.json --output-dir /data/results
+  run_grid_search_actl.sh --model rf3 --proteins /data/input/proteins.csv --output-dir /data/results
+
+Options:
+  -e, --env ENV   Pixi environment to use: boltz, protenix, or rf3.
+                  If omitted, inferred from --model/--models or --params.
+  -h, --help      Show this help message.
+
+This script must be run from inside the Sampleworks image. It never starts Docker.
+EOF
+}
+
+infer_env_from_model() {
+    case "$1" in
+        boltz1|boltz2) echo "boltz" ;;
+        protenix) echo "protenix" ;;
+        rf3) echo "rf3" ;;
+        *) echo "Error: unknown model '$1'. Expected boltz1, boltz2, protenix, or rf3." >&2; exit 1 ;;
+    esac
+}
+
+infer_env_from_params() {
+    pixi run -e boltz python - "$1" << 'PY'
+import json
+import sys
+
+with open(sys.argv[1]) as handle:
+    params = json.load(handle)
+
+if isinstance(params, dict) and isinstance(params.get("params_json"), dict):
+    params = params["params_json"]
+
+def model_value(value):
+    if value is None:
+        return None
+    if isinstance(value, dict):
+        return model_value(value.get("name") or value.get("type") or value.get("model"))
+    if isinstance(value, list):
+        if len(value) != 1:
+            raise SystemExit("Sampleworks params mode supports exactly one model")
+        return str(value[0])
+    return str(value)
+
+model = model_value(params.get("model"))
+models = params.get("models")
+if models is not None:
+    if isinstance(models, str):
+        models = models.split()
+    if not isinstance(models, list) or len(models) != 1:
+        raise SystemExit("Sampleworks params mode supports exactly one model")
+    if model is not None and str(models[0]) != model:
+        raise SystemExit("Sampleworks params JSON defines conflicting model and models values")
+    model = str(models[0])
+
+model_section = params.get("model_config") or params.get("model_settings")
+if isinstance(model_section, dict):
+    nested_model = model_value(
+        model_section.get("name") or model_section.get("type") or model_section.get("model")
+    )
+    if nested_model is not None:
+        if model is not None and nested_model != model:
+            raise SystemExit("Sampleworks params JSON defines conflicting nested model value")
+        model = nested_model
+
+if model in ("boltz1", "boltz2"):
+    print("boltz")
+elif model == "protenix":
+    print("protenix")
+elif model == "rf3":
+    print("rf3")
+else:
+    raise SystemExit("params JSON must include model: boltz1, boltz2, protenix, or rf3")
+PY
+}
+
+ENV_NAME=""
+ARGS=()
+MODEL=""
+PARAMS_FILE=""
+PROTEINS_FILE=""
+
+while [[ $# -gt 0 ]]; do
+    case "$1" in
+        -h|--help)
+            show_help
+            exit 0
+            ;;
+        -e|--env)
+            if [[ -z "${2:-}" || "${2:-}" == -* ]]; then
+                echo "Error: $1 requires an environment name: boltz, protenix, or rf3" >&2
+                exit 1
+            fi
+            ENV_NAME="$2"
+            shift 2
+            ;;
+        --model|--models)
+            if [[ -z "${2:-}" || "${2:-}" == -* ]]; then
+                echo "Error: $1 requires a model value" >&2
+                exit 1
+            fi
+            MODEL="$2"
+            ARGS+=("$1" "$2")
+            shift 2
+            ;;
+        --params)
+            if [[ -z "${2:-}" || "${2:-}" == -* ]]; then
+                echo "Error: --params requires a JSON file path" >&2
+                exit 1
+            fi
+            PARAMS_FILE="$2"
+            ARGS+=("$1" "$2")
+            shift 2
+            ;;
+        --proteins)
+            if [[ -z "${2:-}" || "${2:-}" == -* ]]; then
+                echo "Error: --proteins requires a CSV file path" >&2
+                exit 1
+            fi
+            PROTEINS_FILE="$2"
+            ARGS+=("$1" "$2")
+            shift 2
+            ;;
+        run_grid_search.py|/app/run_grid_search.py)
+            shift
+            ;;
+        *)
+            ARGS+=("$1")
+            shift
+            ;;
+    esac
+done
+
+if [[ ${#ARGS[@]} -eq 0 ]]; then
+    show_help >&2
+    exit 1
+fi
+
+if [[ -n "$PARAMS_FILE" ]]; then
+    if [[ ! -f "$PARAMS_FILE" ]]; then
+        echo "Error: params JSON not found: $PARAMS_FILE" >&2
+        exit 1
+    fi
+elif [[ -n "$PROTEINS_FILE" ]]; then
+    if [[ ! -f "$PROTEINS_FILE" ]]; then
+        echo "Error: proteins CSV not found: $PROTEINS_FILE" >&2
+        exit 1
+    fi
+else
+    echo "Error: pass --proteins <csv> or --params <json>" >&2
+    exit 1
+fi
+
+if [[ -z "$ENV_NAME" ]]; then
+    if [[ -n "$MODEL" ]]; then
+        ENV_NAME="$(infer_env_from_model "$MODEL")"
+    elif [[ -n "$PARAMS_FILE" ]]; then
+        ENV_NAME="$(infer_env_from_params "$PARAMS_FILE")"
+    else
+        echo "Error: unable to infer pixi env. Pass -e boltz, -e protenix, or -e rf3." >&2
+        exit 1
+    fi
+fi
+
+case "$ENV_NAME" in
+    boltz|protenix|rf3) ;;
+    *) echo "Error: invalid pixi environment '$ENV_NAME'. Expected boltz, protenix, or rf3." >&2; exit 1 ;;
+esac
+
+exec pixi run -e "$ENV_NAME" python /app/run_grid_search.py "${ARGS[@]}"
diff --git a/run_protenix_mini_tiny_actl.sh b/run_protenix_mini_tiny_actl.sh
new file mode 100755
index 00000000..d8cf6a52
--- /dev/null
+++ b/run_protenix_mini_tiny_actl.sh
@@ -0,0 +1,86 @@
+#!/bin/bash
+# Run Protenix tiny and mini grid searches inside the current container.
+
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+RUN_GRID_SEARCH_ACTL="${RUN_GRID_SEARCH_ACTL:-$SCRIPT_DIR/run_grid_search_actl.sh}"
+
+if [[ "${1:-}" == "-h" || "${1:-}" == "--help" ]]; then
+    cat << 'EOF'
+Usage: run_protenix_mini_tiny_actl.sh
+
+Environment overrides:
+  DATA_DIR, MSA_CACHE_DIR, TINY_RESULTS_DIR, MINI_RESULTS_DIR, PROTEINS_CSV
+  TINY_GPU_DEVICES, MINI_GPU_DEVICES, PROTENIX_TINY_CHECKPOINT, PROTENIX_MINI_CHECKPOINT
+EOF
+    exit 0
+fi
+
+DATA_DIR="${DATA_DIR:-/mnt/diffuse-private/raw/sampleworks/initial_dataset_40_occ_sweeps}"
+MSA_CACHE_DIR="${MSA_CACHE_DIR:-/data/sampleworks-exp/msa_cache}"
+TINY_RESULTS_DIR="${TINY_RESULTS_DIR:-${RESULTS_DIR:-/data/sampleworks-exp/occ_sweep/grid_search_results_protenix_tiny}}"
+MINI_RESULTS_DIR="${MINI_RESULTS_DIR:-${RESULTS_DIR:-/data/sampleworks-exp/occ_sweep/grid_search_results_protenix_mini}}"
+PROTEINS_CSV="${PROTEINS_CSV:-$DATA_DIR/proteins.csv}"
+TINY_GPU_DEVICES="${TINY_GPU_DEVICES:-2,3}"
+MINI_GPU_DEVICES="${MINI_GPU_DEVICES:-6,7}"
+PROTENIX_TINY_CHECKPOINT="${PROTENIX_TINY_CHECKPOINT:-/extra_checkpoints/protenix_tiny_default_v0.5.0.pt}"
+PROTENIX_MINI_CHECKPOINT="${PROTENIX_MINI_CHECKPOINT:-/extra_checkpoints/protenix_mini_default_v0.5.0.pt}"
+
+if [[ ! -f "$PROTEINS_CSV" ]]; then
+    echo "Error: proteins CSV not found: $PROTEINS_CSV" >&2
+    exit 1
+fi
+if [[ ! -f "$PROTENIX_TINY_CHECKPOINT" ]]; then
+    echo "Error: Protenix tiny checkpoint not found: $PROTENIX_TINY_CHECKPOINT" >&2
+    exit 1
+fi
+if [[ ! -f "$PROTENIX_MINI_CHECKPOINT" ]]; then
+    echo "Error: Protenix mini checkpoint not found: $PROTENIX_MINI_CHECKPOINT" >&2
+    exit 1
+fi
+
+mkdir -p "$TINY_RESULTS_DIR" "$MINI_RESULTS_DIR" "$MSA_CACHE_DIR"
+
+PIDS=()
+NAMES=()
+
+start_protenix() {
+    local name="$1"
+    local gpu_devices="$2"
+    local checkpoint="$3"
+    local output_dir="$4"
+    local log_file="$5"
+
+    echo "[$(date)] Starting $name on GPUs $gpu_devices"
+    CUDA_VISIBLE_DEVICES="$gpu_devices" "$RUN_GRID_SEARCH_ACTL" \
+        --model protenix \
+        --proteins "$PROTEINS_CSV" \
+        --model-checkpoint "$checkpoint" \
+        --scalers pure_guidance \
+        --partial-diffusion-step 120 \
+        --ensemble-sizes "8" \
+        --gradient-weights "0.0 0.05 0.1 0.2 0.35 0.5" \
+        --gradient-normalization --augmentation --align-to-input \
+        --output-dir "$output_dir" \
+        2>&1 | tee "$log_file" &
+    PIDS+=("$!")
+    NAMES+=("$name")
+    echo "[$(date)] $name job started (PID: ${PIDS[-1]})"
+}
+
+start_protenix "Protenix tiny" "$TINY_GPU_DEVICES" "$PROTENIX_TINY_CHECKPOINT" "$TINY_RESULTS_DIR" "$TINY_RESULTS_DIR/protenix_tiny_run.log"
+start_protenix "Protenix mini" "$MINI_GPU_DEVICES" "$PROTENIX_MINI_CHECKPOINT" "$MINI_RESULTS_DIR" "$MINI_RESULTS_DIR/protenix_mini_run.log"
+
+failed=0
+for index in "${!PIDS[@]}"; do
+    if wait "${PIDS[$index]}"; then
+        echo "[$(date)] ${NAMES[$index]} completed successfully"
+    else
+        status=$?
+        echo "[$(date)] ${NAMES[$index]} failed with exit code $status" >&2
+        failed=1
+    fi
+done
+
+exit "$failed"
diff --git a/run_rf3_partial_actl.sh b/run_rf3_partial_actl.sh
new file mode 100755
index 00000000..975eb5fa
--- /dev/null
+++ b/run_rf3_partial_actl.sh
@@ -0,0 +1,49 @@
+#!/bin/bash
+# Run RF3 partial-diffusion grid search inside the current container.
+
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+RUN_GRID_SEARCH_ACTL="${RUN_GRID_SEARCH_ACTL:-$SCRIPT_DIR/run_grid_search_actl.sh}"
+
+if [[ "${1:-}" == "-h" || "${1:-}" == "--help" ]]; then
+    cat << 'EOF'
+Usage: run_rf3_partial_actl.sh
+
+Environment overrides:
+  DATA_DIR       Input directory containing proteins.csv
+  RESULTS_DIR    Output directory
+  MSA_CACHE_DIR  MSA cache directory
+  PROTEINS_CSV   Explicit proteins CSV path
+  GPU_DEVICES    CUDA_VISIBLE_DEVICES value
+EOF
+    exit 0
+fi
+
+DATA_DIR="${DATA_DIR:-/mnt/diffuse-private/raw/sampleworks/initial_dataset_40}"
+RESULTS_DIR="${RESULTS_DIR:-${HOME}/sampleworks-exp/grid_search_results_rf3_partial}"
+MSA_CACHE_DIR="${MSA_CACHE_DIR:-${HOME}/sampleworks-exp/msa_cache}"
+PROTEINS_CSV="${PROTEINS_CSV:-$DATA_DIR/proteins.csv}"
+GPU_DEVICES="${GPU_DEVICES:-4,5}"
+
+if [[ ! -f "$PROTEINS_CSV" ]]; then
+    echo "Error: proteins CSV not found: $PROTEINS_CSV" >&2
+    exit 1
+fi
+
+mkdir -p "$RESULTS_DIR" "$MSA_CACHE_DIR"
+
+echo "[$(date)] Starting RF3 partial run on GPUs $GPU_DEVICES"
+CUDA_VISIBLE_DEVICES="$GPU_DEVICES" "$RUN_GRID_SEARCH_ACTL" \
+    --model rf3 \
+    --proteins "$PROTEINS_CSV" \
+    --scalers pure_guidance \
+    --partial-diffusion-step 120 \
+    --ensemble-sizes "8" \
+    --gradient-weights "0.01 0.02 0.05" \
+    --gradient-normalization --augmentation --align-to-input \
+    --output-dir "$RESULTS_DIR" \
+    --model-checkpoint "${RF3_CHECKPOINT:-/checkpoints/rf3_foundry_01_24_latest.ckpt}" \
+    2>&1 | tee "$RESULTS_DIR/rf3_partial_run.log"
+
+echo "[$(date)] RF3 job completed."
diff --git a/run_rf3_partial_fixed_actl.sh b/run_rf3_partial_fixed_actl.sh
new file mode 100755
index 00000000..70aeab83
--- /dev/null
+++ b/run_rf3_partial_fixed_actl.sh
@@ -0,0 +1,44 @@
+#!/bin/bash
+# Run RF3 partial occ-sweep grid search inside the current container.
+
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+RUN_GRID_SEARCH_ACTL="${RUN_GRID_SEARCH_ACTL:-$SCRIPT_DIR/run_grid_search_actl.sh}"
+
+if [[ "${1:-}" == "-h" || "${1:-}" == "--help" ]]; then
+    cat << 'EOF'
+Usage: run_rf3_partial_fixed_actl.sh
+
+Environment overrides: DATA_DIR, RESULTS_DIR, MSA_CACHE_DIR, PROTEINS_CSV, GPU_DEVICES, RF3_CHECKPOINT
+EOF
+    exit 0
+fi
+
+DATA_DIR="${DATA_DIR:-/mnt/diffuse-private/raw/sampleworks/initial_dataset_40_occ_sweeps}"
+RESULTS_DIR="${RESULTS_DIR:-${HOME}/sampleworks-exp/occ_sweep/grid_search_results}"
+MSA_CACHE_DIR="${MSA_CACHE_DIR:-${HOME}/sampleworks-exp/msa_cache}"
+PROTEINS_CSV="${PROTEINS_CSV:-$DATA_DIR/proteins.csv}"
+GPU_DEVICES="${GPU_DEVICES:-4}"
+
+if [[ ! -f "$PROTEINS_CSV" ]]; then
+    echo "Error: proteins CSV not found: $PROTEINS_CSV" >&2
+    exit 1
+fi
+
+mkdir -p "$RESULTS_DIR" "$MSA_CACHE_DIR"
+
+echo "[$(date)] Starting RF3 occ-sweep partial run on GPUs $GPU_DEVICES"
+CUDA_VISIBLE_DEVICES="$GPU_DEVICES" "$RUN_GRID_SEARCH_ACTL" \
+    --model rf3 \
+    --proteins "$PROTEINS_CSV" \
+    --scalers pure_guidance \
+    --partial-diffusion-step 120 \
+    --ensemble-sizes "8" \
+    --gradient-weights "0.0 0.005 0.01 0.02 0.035 0.05 0.1" \
+    --gradient-normalization --augmentation --align-to-input \
+    --output-dir "$RESULTS_DIR" \
+    --model-checkpoint "${RF3_CHECKPOINT:-/checkpoints/rf3_foundry_01_24_latest.ckpt}" \
+    2>&1 | tee "$RESULTS_DIR/rf3_partial_run_occ_sweep.log"
+
+echo "[$(date)] RF3 job completed."
diff --git a/run_rf3_protenix_mdc_actl.sh b/run_rf3_protenix_mdc_actl.sh
new file mode 100755
index 00000000..5179458b
--- /dev/null
+++ b/run_rf3_protenix_mdc_actl.sh
@@ -0,0 +1,73 @@
+#!/bin/bash
+# Run RF3 and Protenix grid searches inside the current container.
+
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+RUN_GRID_SEARCH_ACTL="${RUN_GRID_SEARCH_ACTL:-$SCRIPT_DIR/run_grid_search_actl.sh}"
+
+if [[ "${1:-}" == "-h" || "${1:-}" == "--help" ]]; then
+    cat << 'EOF'
+Usage: run_rf3_protenix_mdc_actl.sh
+
+Environment overrides: DATA_DIR, RESULTS_DIR, MSA_CACHE_DIR, PROTEINS_CSV, RF3_GPU_DEVICES, PROTENIX_GPU_DEVICES
+EOF
+    exit 0
+fi
+
+DATA_DIR="${DATA_DIR:-/mnt/diffuse-private/raw/sampleworks/initial_dataset_40_occ_sweeps}"
+RESULTS_DIR="${RESULTS_DIR:-${HOME}/sampleworks-exp/occ_sweep/grid_search_results}"
+MSA_CACHE_DIR="${MSA_CACHE_DIR:-${HOME}/sampleworks-exp/msa_cache}"
+PROTEINS_CSV="${PROTEINS_CSV:-$DATA_DIR/proteins.csv}"
+RF3_GPU_DEVICES="${RF3_GPU_DEVICES:-0,1,2,3}"
+PROTENIX_GPU_DEVICES="${PROTENIX_GPU_DEVICES:-4,5,6,7}"
+
+if [[ ! -f "$PROTEINS_CSV" ]]; then
+    echo "Error: proteins CSV not found: $PROTEINS_CSV" >&2
+    exit 1
+fi
+
+mkdir -p "$RESULTS_DIR" "$MSA_CACHE_DIR"
+
+PIDS=()
+NAMES=()
+
+echo "[$(date)] Starting RF3 on GPUs $RF3_GPU_DEVICES"
+CUDA_VISIBLE_DEVICES="$RF3_GPU_DEVICES" "$RUN_GRID_SEARCH_ACTL" \
+    --model rf3 \
+    --proteins "$PROTEINS_CSV" \
+    --scalers pure_guidance \
+    --ensemble-sizes "8" \
+    --gradient-weights "0.0 0.01 0.02 0.05 0.1" \
+    --gradient-normalization --augmentation --align-to-input \
+    --output-dir "$RESULTS_DIR" \
+    2>&1 | tee "$RESULTS_DIR/rf3_run.log" &
+PIDS+=("$!")
+NAMES+=("RF3")
+
+echo "[$(date)] Starting Protenix on GPUs $PROTENIX_GPU_DEVICES"
+CUDA_VISIBLE_DEVICES="$PROTENIX_GPU_DEVICES" "$RUN_GRID_SEARCH_ACTL" \
+    --model protenix \
+    --proteins "$PROTEINS_CSV" \
+    --scalers pure_guidance \
+    --partial-diffusion-step 120 \
+    --ensemble-sizes "8" \
+    --gradient-weights "0.0 0.1 0.2 0.5" \
+    --gradient-normalization --augmentation --align-to-input \
+    --output-dir "$RESULTS_DIR" \
+    2>&1 | tee "$RESULTS_DIR/protenix_run.log" &
+PIDS+=("$!")
+NAMES+=("Protenix")
+
+failed=0
+for index in "${!PIDS[@]}"; do
+    if wait "${PIDS[$index]}"; then
+        echo "[$(date)] ${NAMES[$index]} completed successfully"
+    else
+        status=$?
+        echo "[$(date)] ${NAMES[$index]} failed with exit code $status" >&2
+        failed=1
+    fi
+done
+
+exit "$failed"