libconfig_af.py

#!/usr/bin/env python

import os

jackhmmer_binary_path = "/home/huhlim/apps/hmmer/current/bin/jackhmmer"
hhblits_binary_path = "/home/huhlim/apps/hhsuite/current/bin/hhblits"
hhsearch_binary_path = "/home/huhlim/apps/hhsuite/current/bin/hhsearch"
kalign_binary_path = "/home/huhlim/conda/envs/af2/bin/kalign"
hmmsearch_binary_path = "/home/huhlim/apps/hmmer/current/bin/hmmsearch"
hmmbuild_binary_path = "/home/huhlim/apps/hmmer/current/bin/hmmbuild"

data_dir = "/feig/s1/huhlim/db/AlphaFold"

# Path to the Uniref90 database for use by JackHMMER.
uniref90_database_path = os.path.join(data_dir, "uniref90", "uniref90.fasta")

# Path to the MGnify database for use by JackHMMER.
mgnify_database_path = os.path.join(data_dir, "mgnify", "mgy_clusters.fa")

# Path to the BFD database for use by HHblits.
bfd_database_path = os.path.join(
    data_dir, "bfd", "bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt"
)
small_bfd_database_path = os.path.join(
    data_dir, "small_bfd", "bfd-first_non_consensus_sequences.fasta"
)

# Path to the UniRef30 database for use by HHblits.
uniref30_database_path = os.path.join(data_dir, "uniclust30", "uc30")

# Path to the UniProt database for used by JackHMMer.
uniprot_database_path = os.path.join(data_dir, "uniprot", "uniprot.fasta")

# Path to the PDB70 database for use by HHsearch.
pdb70_database_path = os.path.join(data_dir, "pdb70", "pdb70")

# Path to the PDB seqres database for use by hmmsearch.
pdb_seqres_database_path = os.path.join(data_dir, "pdb_seqres", "pdb_seqres.txt")

# Path to a directory with template mmCIF structures, each named <pdb_id>.cif')
template_mmcif_dir = os.path.join(data_dir, "pdb_mmcif", "mmcif_files")

# Path to a file mapping obsolete PDB IDs to their replacements.
obsolete_pdbs_path = os.path.join(data_dir, "pdb_mmcif", "obsolete.dat")

max_template_date = "2099-12-31"

os.environ["NVIDIA_VISIBLE_DEVICES"] = os.getenv("CUDA_VISIBLE_DEVICES", "")
os.environ["TF_FORCE_UNIFIED_MEMORY"] = "1"
os.environ["XLA_PYTHON_CLIENT_MEM_FRACTION"] = "4.0"
if os.getenv("CUDA_VISIBLE_DEVICES", "") == "":
    os.environ["JAX_PLATFORM_NAME"] = "cpu"
    os.environ["CUDA_VISIBLE_DEVICES"] = "-1"

N_PROC = int(os.getenv("SLURM_CPUS_PER_TASK", 8))

model_names = [
    "model_1",
    "model_2",
    "model_3",
    "model_4",
    "model_5",
]