diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2fb5707cc3c6e35bdd02906f715fd4502ce4fd39..57a5d76e751d4336e4926b2695530d98d99355be 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,12 @@
+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
=================================================================================
diff --git a/run_af2/bin/submit-af2 b/run_af2/bin/submit-af2
index 7d5b1d075d14991bf964d401dafeda682cf5bd0a..014b8b8ff3d4e094d4f0a4c77144c676bb668532 100755
--- a/run_af2/bin/submit-af2
+++ b/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
diff --git a/run_af2/src/run_af2/_shared.py b/run_af2/src/run_af2/_shared.py
index 5d7f22c75261a5320142ae8b6e69550fdc399616..27aa8e1ce24b726aa2b13e957b844950464e5797 100644
--- a/run_af2/src/run_af2/_shared.py
+++ b/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(
diff --git a/run_af2/src/run_af2/run_singularity.py b/run_af2/src/run_af2/run_singularity.py
index 5d87fa3b990016e6304fd932c54e442cb3aea9a5..de18bb1f407c9fbaa4bd69a1ee07fe4980e79679 100644
--- a/run_af2/src/run_af2/run_singularity.py
+++ b/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