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run_alphafold.sh
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run_alphafold.sh
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#!/bin/bash
# Description: AlphaFold non-docker version
# Author: Sanjay Kumar Srikakulam
# Modified by Bozitao Zhong
usage() {
echo ""
echo "Usage: $0 <OPTIONS>"
echo "Required Parameters:"
echo "-d <data_dir> Path to directory of supporting data"
echo "-o <output_dir> Path to a directory that will store the results."
echo "-p <model_preset> Model preset. Use monomer, monomer_ptm, monomer_casp14 or multimer models"
echo "-i <fasta_path> Path to a FASTA file containing query sequence(s)"
echo "Optional Parameters:"
echo "-t <max_template_date> Maximum template release date to consider (YYYY-MM-DD format). (default: 2020-12-01)"
echo "-b <benchmark> Run multiple JAX model evaluations to obtain a timing that excludes the compilation time (default: 'False')"
echo "-g <use_gpu> Enable NVIDIA runtime to run with GPUs (default: 'True')"
echo "-u <gpu_devices> Comma separated list of devices to pass to 'CUDA_VISIBLE_DEVICES' (default: 'all')"
echo "-c <db_preset> Choose database reduced_dbs or full_dbs (default: 'full_dbs')"
echo "-a <amber_relaxation> Skip AMBER refinemet for predicted structure (default: 'True' - Using AMBER)"
echo "-m <model_selection> Names of comma separated model names to use in prediction (default: All 5 models)"
echo "-r <recycling> Set cycles for recycling (default: '3')"
echo "-f <run_feature> Only run MSA and template search to generate feature file"
echo "Future Parameters (You cannot use them now):"
echo "-v <visualizaion> Automatic visualizaion of MSA, pLDDT, pTM of prediction results"
echo "-s <skip_msa> Skip MSA and template step, generate single sequence feature for ultimately fast prediction"
echo "-q <quick_mode> Quick mode. Use small BFD database, no templates"
echo "-k <is_prokaryote_list> Optional for multimer system, specifying true where the target complex is from a prokaryote"
echo "-e <random_seed> Set random seed"
echo "-l <precomputed_msas> Use precomputed MSAs"
echo ""
exit 1
}
while getopts ":d:o:p:i:t:u:c:m:r:bgravsqf" i; do
case "${i}" in
d)
data_dir=$OPTARG
;;
o)
output_dir=$OPTARG
;;
p)
model_preset=$OPTARG
;;
i)
fasta_path=$OPTARG
;;
t)
max_template_date=$OPTARG
;;
b)
benchmark=true
;;
g)
use_gpu=true
;;
u)
gpu_devices=$OPTARG
;;
c)
db_preset=$OPTARG
;;
a)
amber_relaxation=false
;;
m)
model_selection=$OPTARG
;;
v)
visualizaion=true
;;
s)
skip_msa=true
;;
q)
quick_mode=true
;;
r)
recycling=$OPTARG
;;
f)
run_feature=true
;;
esac
done
# Parse input and set defaults
if [[ "$data_dir" == "" || "$output_dir" == "" || "$model_preset" == "" || "$fasta_path" == "" ]] ; then
usage
fi
if [[ "$max_template_date" == "" ]] ; then
max_template_date="2020-12-01"
fi
if [[ "$benchmark" == "" ]] ; then
benchmark=false
fi
if [[ "$use_gpu" == "" ]] ; then
use_gpu=true
fi
if [[ "$gpu_devices" == "" ]] ; then
gpu_devices="0"
fi
if [[ "$db_preset" == "" ]] ; then
db_preset="full_dbs"
fi
if [[ "$amber_relaxation" == "" ]] ; then
amber_relaxation=true
fi
if [[ "$model_selection" == "" ]] ; then
model_selection=""
fi
if [[ "$visualizaion" == "" ]] ; then
visualizaion=false
fi
if [[ "$skip_msa" == "" ]] ; then
skip_msa=false
fi
if [[ "$quick_mode" == "" ]] ; then
quick_mode=false
fi
if [[ "$recycling" == "" ]] ; then
recycling=3
fi
if [[ "$run_feature" == "" ]] ; then
run_feature=false
fi
# This bash script looks for the run_alphafold.py script in its current working directory, if it does not exist then exits
#current_working_dir=$(pwd)
#alphafold_script="$current_working_dir/run_alphafold.py"
alphafold_script="$(readlink -f $(dirname $0))/run_alphafold.py"
if [ ! -f "$alphafold_script" ]; then
echo "Alphafold python script $alphafold_script does not exist."
exit 1
fi
# Export ENVIRONMENT variables and set CUDA devices for use
if [[ "$use_gpu" == true ]] ; then
export CUDA_VISIBLE_DEVICES=0
if [[ "$gpu_devices" ]] ; then
export CUDA_VISIBLE_DEVICES=$gpu_devices
fi
fi
export TF_FORCE_UNIFIED_MEMORY='1'
export XLA_PYTHON_CLIENT_MEM_FRACTION='4.0'
# Path and user config (change me if required)
bfd_database_path="$data_dir/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt"
small_bfd_database_path="$data_dir/small_bfd/bfd-first_non_consensus_sequences.fasta"
mgnify_database_path="$data_dir/mgnify/mgy_clusters_2018_12.fa"
template_mmcif_dir="$data_dir/pdb_mmcif/mmcif_files"
obsolete_pdbs_path="$data_dir/pdb_mmcif/obsolete.dat"
pdb70_database_path="$data_dir/pdb70/pdb70"
pdb_seqres_database_path="$data_dir/pdb_seqres/pdb_seqres.txt"
uniclust30_database_path="$data_dir/uniclust30/uniclust30_2018_08/uniclust30_2018_08"
uniref90_database_path="$data_dir/uniref90/uniref90.fasta"
uniprot_database_path="$data_dir/uniprot/uniprot.fasta"
if [[ "$db_preset" == "full_dbs" ]] ; then
small_bfd_database_path=""
fi
# Binary path (change me if required)
hhblits_binary_path=$(which hhblits)
hhsearch_binary_path=$(which hhsearch)
jackhmmer_binary_path=$(which jackhmmer)
kalign_binary_path=$(which kalign)
hmmsearch_binary_path=$(which hmmsearch)
hmmbuild_binary_path=$(which hmmbuild)
# Temporary
# Missing random_seed, is_prokaryote_list, use_precomputed_msas, amber_relaxation
if [[ "$model_preset" == "monomer" || "$model_preset" == "monomer_ptm" ]] ; then
pdb_seqres_database_path=""
uniprot_database_path=""
fi
if [[ "$model_preset" == "multimer" ]] ; then
pdb70_database_path=""
fi
# Run AlphaFold with required parameters
python $alphafold_script \
--fasta_paths=$fasta_path \
--model_names=$model_selection \
--data_dir=$data_dir \
--output_dir=$output_dir \
--jackhmmer_binary_path=$jackhmmer_binary_path \
--hhblits_binary_path=$hhblits_binary_path \
--hhsearch_binary_path=$hhsearch_binary_path \
--hmmsearch_binary_path=$hmmsearch_binary_path \
--hmmbuild_binary_path=$hmmbuild_binary_path \
--kalign_binary_path=$kalign_binary_path \
--uniref90_database_path=$uniref90_database_path \
--mgnify_database_path=$mgnify_database_path \
--bfd_database_path=$bfd_database_path \
--small_bfd_database_path=$small_bfd_database_path \
--uniclust30_database_path=$uniclust30_database_path \
--uniprot_database_path=$uniprot_database_path \
--pdb70_database_path=$pdb70_database_path \
--pdb_seqres_database_path=$pdb_seqres_database_path \
--template_mmcif_dir=$template_mmcif_dir \
--max_template_date=$max_template_date \
--obsolete_pdbs_path=$obsolete_pdbs_path \
--db_preset=$db_preset \
--model_preset=$model_preset \
--benchmark=$benchmark \
--amber_relaxation=$amber_relaxation \
--recycling=$recycling \
--run_feature=$run_feature \
--logtostderr