Add arguments needed for model_preset multimer

CHANGELOG.md

+Changes in Release 2.0.0
+=================================================================================
+
+* `run_af2` Python package:
+  * Prepare to run AF2 pipeline 2.1
+  * rename command line options `--pdb70_database_path` and
+    `--obsolete_pdbs_path` to `--pdb70-database-path` and `--obsolete-pdbs-path`
+
+
 Changes in Release 1.0.5
 =================================================================================
 

run_af2/bin/submit-af2

@@ -28,7 +28,8 @@
 if test $# -lt 2; then
     echo "usage: submit-af2 [--use-gpu]"
     echo "                  [--db-preset {reduced_dbs,full_dbs}]"
-    echo "                  [model-preset {monomer,monomer_casp14,monomer_ptm,multimer}]"
+    echo "                  [--model-preset {monomer,monomer_casp14,monomer_ptm,multimer}]"
+    echo "                  [--is-prokaryote-list <bool>,<bool>,...]"
     echo "                  [--max-template-date YYYY-MM-DD]"
     echo "                  <OUTPUT DIR> <FASTA FILE> [<FASTA FILE> ...]"
     exit 1
@@ -36,9 +37,9 @@ fi
 
 # There are only two non-positional arguments, simply loop over candidates.
 # This should be turned into switch..case if argument extension goes on.
-SLURM_AF_PARAMS="--exclude=lii[02-28]"
+SLURM_AF_PARAMS="" #"--exclude=lii[02-28]"
 AF_PIPELINE_PARAM=""
-for i in 1 2 3 4; do
+for i in 1 2 3 4 5; do
     if test x"${1}" = x"--use-gpu"; then
         shift
         SLURM_AF_PARAMS="--partition=a100,rtx8000 --gres=gpu:1"
@@ -54,6 +55,12 @@ for i in 1 2 3 4; do
               else if test x"${1}" = x"--model-preset"; then
                        shift
                        AF_PIPELINE_PARAM="${AF_PIPELINE_PARAM} --model-preset ${1}"
+                       shift
+                   else if test x"${1}" = x"--is-prokaryote-list"; then
+                            shift
+                            AF_PIPELINE_PARAM="${AF_PIPELINE_PARAM} --is-prokaryote-list ${1}"
+                            shift
+                       fi
                    fi
               fi
          fi

run_af2/src/run_af2/_shared.py

@@ -14,8 +14,8 @@ functionality to be external, we should create a proper module for that.
 # copies of the Software, and to permit persons to whom the Software is
 # furnished to do so, subject to the following conditions:
 #
-# The above copyright notice and this permission notice shall be included in all
-# copies or substantial portions of the Software.
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
 #
 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
@@ -110,6 +110,16 @@ def parse_af2_arguments(parser):
         + "AF2 pipeline.",
         default="monomer",
     )
+    af2_group.add_argument(
+        "-i",
+        "--is-prokaryote-list",
+        type=str,
+        help="For the multimer model, declare sequences to by prokaryotic or "
+        + "not. Goes by true/ false, needs to be listed for every input FASTA "
+        + "as a list.",
+        metavar="<true|false>,<true|false>,...",
+        default=None,
+    )
     af2_group.add_argument(
         "--version",
         action="version",
@@ -161,12 +171,26 @@ def parse_af2_arguments(parser):
         default=None,
     )
     af2_group.add_argument(
-        "--pdb70_database_path",
+        "--uniprot-database-path",
+        type=str,
+        help="Path to the UniProt database, for the JackHMMer call.",
+        metavar="<PATH>",
+        default=None,
+    )
+    af2_group.add_argument(
+        "--pdb70-database-path",
         type=str,
         help="Path to the PDB70 database, prefix for the HHsearch call.",
         metavar="<PATH/ PREFIX>",
         default=None,
     )
+    af2_group.add_argument(
+        "--pdb-seqres-database-path",
+        type=str,
+        help="Path to the PDB seqres database, for the hhmsearch call.",
+        metavar="<PATH>",
+        default=None,
+    )
     af2_group.add_argument(
         "--template-mmcif-dir",
         type=str,
@@ -175,7 +199,7 @@ def parse_af2_arguments(parser):
         default=None,
     )
     af2_group.add_argument(
-        "--obsolete_pdbs_path",
+        "--obsolete-pdbs-path",
         type=str,
         help="File mapping obsoleted PDB entries to their replacements.",
         metavar="<File>",
@@ -200,6 +224,26 @@ def parse_af2_arguments(parser):
                 flush=True,
             )
 
+    # check that model_preset settings go along with databases
+    if opts.model_preset == "multimer":
+        if opts.pdb70_database_path is not None:
+            print(
+                f"WARNING: '--model-preset {opts.model_preset}' disables use "
+                + "of '--pdb70_database_path'.",
+                file=sys.stderr,
+                flush=True,
+            )
+
+    # check that --is-prokaryote-list has as many values as sequence files
+    if opts.is_prokaryote_list is not None:
+        if opts.is_prokaryote_list.count(",") + 1 != len(opts.fasta_files):
+            print(
+                "Number of values for '--is-prokaryote-list' does not match "
+                + "the number of FASTA files. Aborting.",
+                file=sys.stderr,
+            )
+            sys.exit(1)
+
     if opts.singularity_image is not None:
         if not os.path.exists(opts.singularity_image):
             print(

run_af2/src/run_af2/run_singularity.py

@@ -116,6 +116,7 @@ def _assemble_singularity_call(  # pylint: disable=too-many-arguments
     use_gpu,
     db_preset,
     model_preset,
+    is_prokaryote_list,
     data_paths,
 ):
     """Assemble the command to run AF2 from the Singularity image."""
@@ -151,6 +152,9 @@ def _assemble_singularity_call(  # pylint: disable=too-many-arguments
             "--logtostderr",
         ]
     )
+    if is_prokaryote_list is not None:
+        snglrty_cmd.append(f"--is_prokaryote_list={is_prokaryote_list}")
+
     for flag, path in data_paths.items():
         snglrty_cmd.append(f"--{flag}={path}")
 
@@ -189,6 +193,7 @@ def run_af2_singularity_image(  # pylint: disable=too-many-arguments
     use_gpu=False,
     db_preset="full_dbs",
     model_preset="monomer",
+    is_prokaryote_list=None,
     af2_image_file=None,
     # "/export/soft/singularity-containers/alphafold",
     af2_image_dir="/scicore/home/schwede/GROUP/alphafold_data/",
@@ -205,7 +210,11 @@ def run_af2_singularity_image(  # pylint: disable=too-many-arguments
     + "frozen_210812T135116/bfd-first_non_consensus_sequences.fasta",
     uniclust30_database_path="/scicore/data/managed/Uniclust/"
     + "frozen_181015T170110/uniclust30_2018_08/uniclust30_2018_08",
+    uniprot_database_path="/scicore/home/schwede/scicore/home/schwede/GROUP/"
+    + "alphafold_data/uniprot/uniprot.fasta",
     pdb70_database_path="/scicore/data/managed/PDB70/frozen_210805T142857/pdb70",
+    pdb_seqres_database_path="/scicore/home/schwede/scicore/home/schwede/GROUP/"
+    + "alphafold_data/pdb_seqres/pdb_seqres.txt",
     template_mmcif_dir="/scicore/data/managed/PDB/latest/data/structures/all/"
     + "mmcif_files/",
     obsolete_pdbs_path="/scicore/data/managed/PDB/latest/data/status/"
@@ -240,6 +249,11 @@ def run_af2_singularity_image(  # pylint: disable=too-many-arguments
     :param model_preset: Model configuration - corresponds to the model_preset
                          parameter in AF2.
     :type model_preset: :class:`str`
+    :param is_prokaryote_list: For the multimer model, mark sequences as
+                               prokaryotic. Corresponds to the
+                               is_prokaryote_list parameter in AF2.
+    :type is_prokaryote_list: :class:`str` like needed by AF2, e.g.
+                              "true,false,true"
     :param af2_image_file: Declare a Singularity image to run the AF2 pipeline
                            from. If None, an image from af2_image_dir will be
                            used.
@@ -276,8 +290,17 @@ def run_af2_singularity_image(  # pylint: disable=too-many-arguments
     :param uniclust30_database_path: Uniclust30 database prefix. Corresponds to
                                      uniclust30_database_path in AF2.
     :type uniclust30_database_path: :class:`str`
+    :param uniprot_database_path: UniProt sequence file. Corresponds to
+                                  uniprot_database_path in AF2. Needed for
+                                  model_preset == multimer.
+    :type uniprot_database_path: :class:`str`
     :param pdb70_database_path: PDB70 database prefix. Corresponds to
-                                pdb70_database_path in AF2.
+                                pdb70_database_path in AF2. Will be disabled if
+                                model_preset == multimer.
+    :param pdb_seqres_database_path: PDB seqres file. Corresponds to
+                                     pdb_seqres_database_path in AF2. Needed for
+                                     model_preset == multimer.
+    :type pdb_seqres_database_path: :class:`str`
     :type pdb70_database_path: :class:`str`
     :param template_mmcif_dir: Path to the template structures. Corresponds to
                                template_mmcif_dir in AF2.
@@ -303,7 +326,7 @@ def run_af2_singularity_image(  # pylint: disable=too-many-arguments
         )
     if model_preset not in _shared.MODEL_PRESET_CHOICES:
         raise ValueError(
-            f"model_reset {model_preset} not allowed, known "
+            f"model_preset {model_preset} not allowed, known "
             + f"values: {', '.join(_shared.MODEL_PRESET_CHOICES)}"
         )
 
@@ -321,6 +344,10 @@ def run_af2_singularity_image(  # pylint: disable=too-many-arguments
         data_paths["uniclust30_database_path"] = uniclust30_database_path
     elif db_preset == "reduced_dbs":
         data_paths["small_bfd_database_path"] = small_bfd_database_path
+    if model_preset == "multimer":
+        del data_paths["pdb70_database_path"]
+        data_paths["pdb_seqres_database_path"] = pdb_seqres_database_path
+        data_paths["uniprot_database_path"] = uniprot_database_path
 
     # Collect bind mountpoints for singularity, mountpoints for input data plus
     # adjusting input file paths, deal with the output directory.
@@ -348,6 +375,7 @@ def run_af2_singularity_image(  # pylint: disable=too-many-arguments
         use_gpu,
         db_preset,
         model_preset,
+        is_prokaryote_list,
         data_paths,
     )
 
@@ -396,8 +424,12 @@ def main():
         data_paths["small_bfd_database_path"] = opts.bfd_database_path
     if opts.uniclust30_database_path is not None:
         data_paths["uniclust30_database_path"] = opts.uniclust30_database_path
+    if opts.uniprot_database_path is not None:
+        data_paths["uniprot_database_path"] = opts.uniprot_database_path
     if opts.pdb70_database_path is not None:
         data_paths["pdb70_database_path"] = opts.pdb70_database_path
+    if opts.pdb_seqres_database_path is not None:
+        data_paths["pdb_seqres_database_path"] = opts.pdb_seqres_database_path
     if opts.template_mmcif_dir is not None:
         data_paths["template_mmcif_dir"] = opts.template_mmcif_dir
     if opts.obsolete_pdbs_path is not None:
@@ -411,6 +443,7 @@ def main():
             opts.use_gpu,
             opts.db_preset,
             opts.model_preset,
+            opts.is_prokaryote_list,
             af2_image_file=opts.singularity_image,
             **data_paths,
         )
@@ -422,4 +455,5 @@ def main():
 #  LocalWords:  AlphaFold Slurm sciCORE param FASTA Basenames RuntimeException
 #  LocalWords:  str dir snglrty tmpdir tmp argparse os ArgumentParser metavar
 #  LocalWords:  RawDescriptionHelpFormatter nargs getenv startswith ValueError
-#  LocalWords:  RuntimeError bfd BFD dbs
+#  LocalWords:  RuntimeError bfd BFD dbs mgnify HHblits uniclust Uniclust pdb
+#  LocalWords:  multimer seqres uniprot