Alphafold/2.1.1 with multimer support!

Includes syntax changes. See https://intranet.psi.ch/en/bio/alphafold

MX/alphafold/README.md

@@ -23,7 +23,7 @@ conda install -y -c bioconda hmmer==3.3.2 hhsuite==3.3.0 kalign2==2.04
 
 pip install absl-py==0.13.0 biopython==1.79 chex==0.0.7 dm-haiku==0.0.4 \
     dm-tree==0.1.6 immutabledict==2.0.0 jax==0.2.14 ml-collections==0.1.0 \
-    numpy==1.19.5 scipy==1.7.0 tensorflow==2.5.0
+    numpy==1.19.5 scipy==1.7.0 tensorflow==2.5.0 pandas==1.3.4
 pip install --upgrade jax jaxlib==0.1.69+cuda111 \
     -f https://storage.googleapis.com/jax-releases/jax_releases.html
 ```
@@ -54,7 +54,7 @@ GWSTELEKHREELKEFLKKEGITNVEIRIDNGRLEVRVEGGTERLKRFLEELRQKLEKKGYTVDIKIE
 EOF
 
 module use MX unstable
-module load alphafold/2.0.1
-sbatch $ALPHAFOLD_DIR/bin/submit_merlin.sh query.fasta
+module load alphafold/2.1.1
+sbatch alphafold_merlin.sh query.fasta
 ```
 

MX/alphafold/bin/alphafold_merlin.sh

+#!/bin/bash
+#SBATCH -p gpu
+#SBATCH -J alphafold
+#SBATCH -M gmerlin6
+#SBATCH --gpus=1
+#SBATCH -n 1
+#SBATCH -c 10
+
+# Alphafold submission script for the merlin cluster
+# Usage: sbatch [slurm_opts] alphafold_merlin.sh [options] fasta_file
+#
+# OPTIONS
+# All alphafold options are set automatically, but can be overwritten.
+# Some common options:
+#
+# --max_template_date=YYYY-MM-DD (default: today)
+# --output_dir (default: current directory
+# --helpfull List all options
+#
+# 2021-12-22 Spencer Bliven, D.Ozerov
+#
+
+export ALPHAFOLD_DATA=/data/project/bio/shared/alphafold/versions/latest
+module purge
+module use MX unstable
+module load alphafold/2.1.1
+conda activate "${ALPHAFOLD_ENV:?"Error: ALPHAFOLD_ENV not set. Try 'module use MX unstable; module load alphafold'"}"
+
+echo "hostname=$(hostname)"
+echo "python=$(which python)"
+echo "ALPHAFOLD_DATA=$(realpath "$ALPHAFOLD_DATA")"
+
+python "${ALPHAFOLD_DIR:?Error loading module}/bin/alphafold_runner.py" -v 0 "$@"
+

MX/alphafold/bin/alphafold_ra.sh

+#!/bin/bash
+#SBATCH -p gpu-week
+#SBATCH -t 2-00:00:00
+#SBATCH -J alphafold
+#SBATCH --gres=gpu:1
+#SBATCH -J alphafold
+#SBATCH -n 1
+#SBATCH -c 10
+
+# Alphafold submission script for the merlin cluster
+# Usage: sbatch [slurm_opts] alphafold_merlin.sh [options] fasta_file
+#
+# OPTIONS
+# All alphafold options are set automatically, but can be overwritten.
+# Some common options:
+#
+# --max_template_date=YYYY-MM-DD    (default: today)
+# --output_dir                      (default: current directory)
+# --helpfull                        List all options
+#
+# 2021-12-22 Spencer Bliven, D.Ozerov
+#
+
+export ALPHAFOLD_DATA=/das/work/common/opt/alphafold/data_2.1.1/versions/latest
+
+# Need at least rc6 to see alphafold
+PMODULES_VERSION=1.0.0rc10;
+source /opt/psi/config/profile.bash;
+
+module --version
+
+module purge
+module use MX unstable Programming
+module load alphafold/2.1.1
+conda activate "${ALPHAFOLD_ENV:?"Error: ALPHAFOLD_ENV not set. Try 'module use MX unstable; module load alphafold'"}"
+
+echo "hostname=$(hostname)"
+echo "python=$(which python)"
+echo "ALPHAFOLD_DATA=$(realpath "$ALPHAFOLD_DATA")"
+
+python "${ALPHAFOLD_DIR:?Error loading module}/bin/alphafold_runner.py" -v 0 "$@"
+

MX/alphafold/bin/alphafold_runner.py

+#!/usr/bin/env python
+"""
+Wrapper script for Alphafold 2, with automatic setting of common options
+
+usage: python alphafold_runner.py [alphafold options] input.fa
+"""
+import sys
+import os
+import importlib
+import subprocess
+import logging
+import argparse
+from datetime import date
+from pathlib import Path
+from typing import Union
+from absl import app
+from absl.flags import FLAGS
+from absl import logging
+
+def import_alphafold():
+    "Import run_alphafold.py from ALPHAFOLD_HOME"
+    home = os.environ.get('ALPHAFOLD_HOME', str(Path(__file__).parent.resolve("../alphafold")))
+    sys.path.append(home)
+    try:
+        return importlib.import_module("run_alphafold")
+    except ImportError:
+        sys.stderr.write(f"Unable to find run_alphafold.py\n")
+        sys.stderr.write(f"path:{', '.join(sys.path)}")
+        sys.exit(1)
+af =  import_alphafold()
+
+def multi_fasta(fasta_path):
+    entries = 0
+    with open(fasta_path, 'r') as fasta:
+        for line in fasta:
+            if line and line[0] == '>':
+                entries += 1
+                if entries > 1:
+                    return True
+    return False
+
+
+def guess_model_preset(fasta_paths):
+    if any(multi_fasta(f) for f in fasta_paths):
+        logging.info("Input appears to be multimer")
+        return "multimer"
+    logging.info("Input appears to be monomer")
+    return "monomer"
+
+
+def main(argv):
+    """Set some option defaults and then call alphafold's main method
+
+    Most alphafold options have defaults set automatically:
+
+    - database files are set from the ALPHAFOLD_DATA variable or the --data_dir option
+      (assuming the versioned layout, which differs slightly from the default)
+    - `--model_preset` is set to either monomer or multimer depending on the number of sequences in the fasta file
+    - `--max_template_date` defaults to the current date
+    """
+
+
+    if len(argv) > 2:
+        raise app.UsageError('Too many command-line arguments.')
+
+    # Accept positional fasta_paths
+    if len(argv) > 1:
+        if FLAGS["fasta_paths"].present:
+            raise app.UsageError("Both the --fasta_paths option and a fasta file argument were given")
+        FLAGS["fasta_paths"].parse(argv[1])
+    elif not FLAGS.fasta_paths:
+        raise app.UsageError("No fasta file specified")
+
+    # Database flags
+    if FLAGS["data_dir"].present:
+        data_dir = FLAGS.data_dir
+    elif "ALPHAFOLD_DATA" in os.environ:
+        data_dir = os.environ["ALPHAFOLD_DATA"]
+        logging.info(f"Using ALPHAFOLD_DATA={data_dir}")
+        FLAGS['data_dir'].value = data_dir
+    else:
+        raise app.UsageError("Specify --data_dir or set ALPHAFOLD_DATA")
+
+    if not FLAGS["model_preset"].present:
+        FLAGS.model_preset = guess_model_preset(FLAGS.fasta_paths)
+
+    use_small_bfd = FLAGS.db_preset == 'reduced_dbs'
+
+    if use_small_bfd:
+        if not FLAGS.small_bfd_database_path:
+            FLAGS.small_bfd_database_path = os.path.join(data_dir, "small_bfd", "bfd-first_non_concensus_sequences.fasta")
+    else:
+        if not FLAGS.bfd_database_path:
+            FLAGS.bfd_database_path = os.path.join(data_dir, "bfd", "bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt")
+        if not FLAGS.uniclust30_database_path:
+            FLAGS.uniclust30_database_path = os.path.join(data_dir, "uniclust30", "uniclust30_2018_08")
+
+    run_multimer_system = 'multimer' in FLAGS.model_preset
+
+    if run_multimer_system:
+        if not FLAGS.pdb_seqres_database_path:
+            FLAGS.pdb_seqres_database_path = os.path.join(data_dir, "pdb", "pdb_seqres.txt")
+        if not FLAGS.uniprot_database_path:
+            FLAGS.uniprot_database_path = os.path.join(data_dir, "uniprot", "uniprot.fasta")
+    else:
+        if not FLAGS.pdb70_database_path:
+            FLAGS.pdb70_database_path = os.path.join(data_dir, "pdb70", "pdb70")
+
+    if not FLAGS.mgnify_database_path:
+        FLAGS.mgnify_database_path = os.path.join(data_dir, "mgnify", "mgy_clusters_2018_12.fa")
+    if not FLAGS.obsolete_pdbs_path:
+        FLAGS.obsolete_pdbs_path = os.path.join(data_dir, "pdb", "obsolete.dat")
+    if not FLAGS.template_mmcif_dir:
+        FLAGS.template_mmcif_dir = os.path.join(data_dir, "pdb", "mmcif_files")
+    if not FLAGS.uniref90_database_path:
+        FLAGS.uniref90_database_path = os.path.join(data_dir, "uniprot", "uniref90.fasta")
+
+    if not FLAGS.output_dir:
+        FLAGS.output_dir = os.getcwd()
+
+    if not FLAGS.max_template_date:
+        FLAGS["max_template_date"].parse(date.today().isoformat())
+
+    af.main(argv[0:1])
+
+
+if __name__ == "__main__":
+    app.run(main)
+

MX/alphafold/bin/submit_merlin.sh

-#!/bin/bash
-#SBATCH -p gpu
-#SBATCH -J alphafold
-#SBATCH -M gmerlin6
-#SBATCH --gpus=1
-#SBATCH -n 1
-#SBATCH -c 10
-
-# Alphafold submission script for the merlin cluster
-# Usage: sbatch [slurm_opts] $ALPHAFOLD_DIR/bin/submit_merlin.sh fasta_file [max_template_date]
-#
-# Output will be in the same directory as the fasta_file.
-# Slurm logs will be in the current directory.
-#
-# 2021-08-09 Spencer Bliven, D.Ozerov
-#
-
-export ALPHAFOLD_DATA=/data/project/bio/shared/alphafold
-module purge
-module use MX unstable
-module load alphafold/ALPHAFOLD_VERSION
-
-exec "${ALPHAFOLD_DIR:?Error loading module}/bin/submit.sh" "$@"

MX/alphafold/bin/submit_ra.sh

-#!/bin/bash
-#SBATCH -p day
-#SBATCH -t 1-00:00:00
-#SBATCH -J alphafold
-#SBATCH -n 1
-#SBATCH -c 10
-
-# Alphafold submission script for the ra cluster
-# Usage: sbatch [slurm_opts] $ALPHAFOLD_DIR/bin/submit_merlin.sh fasta_file [max_template_date]
-#
-# Output will be in the same directory as the fasta_file.
-# Slurm logs will be in the current directory.
-#
-# 2021-08-09 Spencer Bliven, D.Ozerov
-#
-
-export ALPHAFOLD_DATA=/das/work/common/opt/alphafold/data
-
-# Need at least rc6 to see alphafold
-PMODULES_VERSION=1.0.0rc10;
-source /opt/psi/config/profile.bash;
-
-module --version
-
-module purge
-module use MX unstable Programming
-module load alphafold/ALPHAFOLD_VERSION
-module list
-
-exec "${ALPHAFOLD_DIR:?Error loading module}/bin/submit.sh" "$@"

MX/alphafold/build

@@ -27,14 +27,12 @@ pbuild::install() {
     fi
 
     git clone --depth=1 -b "$BRANCH" https://github.com/deepmind/alphafold.git "$ALPHAFOLD_HOME" || return $?
+
     if ! [ -f "$ALPHAFOLD_HOME/alphafold/common/stereo_chemical_props.txt" ]; then
-        wget -q -P "$ALPHAFOLD_HOME/alphafold/common/" \
-            --no-check-certificate `# wget root certs are old` \
+
+        curl -fLsS -o "$ALPHAFOLD_HOME/alphafold/common/stereo_chemical_props.txt" \
             https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt
     fi
-    wget -O "$ALPHAFOLD_HOME/run_alphafold.sh" \
-        https://raw.githubusercontent.com/kalininalab/alphafold_non_docker/main/run_alphafold.sh
-    chmod +x "$ALPHAFOLD_HOME/run_alphafold.sh"
 
     cp -r "$BUILDBLOCK_DIR/bin" "$PREFIX/"
     sed -i "s/ALPHAFOLD_VERSION/$V/g" "$PREFIX/bin/"*

MX/alphafold/files/variants

 alphafold/2.0.0-b88f8da	unstable	anaconda/2019.07 b:gcc/10.3.0 cuda/11.0.3
 alphafold/2.0.1	stable	anaconda/2019.07 b:gcc/10.3.0 cuda/11.0.3
+alphafold/2.1.1	unstable	anaconda/2019.07 b:gcc/10.3.0 cuda/11.0.3