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executable file
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###########################This is an option file####################################
################################tools option#########################################
# hhblits program path
hhblits_program = /opt/conda/bin/hhblits
# hhfilter program path
hhfilter_program = /opt/conda/bin/hhfilter
# hhmake program path
hhmake_program = /opt/conda/bin/hhmake
# hhalign program path
hhalign_program = /opt/conda/bin/hhalign
# jackhmmer program path
jackhmmer_program = /opt/conda/bin/jackhmmer
# hhsearch program path
hhsearch_program = /app/MULTICOM3/tools/hhsuite-3.2.0/bin/hhsearch
# deepmsa2 program path
deepmsa2_program = /app/MULTICOM3/tools/deepmsa/hhsuite2/scripts/build_MSA2.py
# tmalign program path
tmalign_program = /app/MULTICOM3/tools/tmalign/TMalign
# mmalign program path
mmalign_program = /app/MULTICOM3/tools/mmalign/MMalign
# dockq program
dockq_program = /app/MULTICOM3/tools/DockQ/DockQ.py
# qscore program
qscore_program = /app/MULTICOM3/tools/pairwiseQA/q_score
# tmscore program
tmscore_program = /app/MULTICOM3/tools/tmscore/TMscore
################################MSA generation tool###########################
colabfold_search_program = /app/MULTICOM3/tools/colabfold/search.py
colabfold_split_msas_program = /app/MULTICOM3/tools/colabfold/split_msas.py
colabfold_databases = INSTALLDIR_DATABASES/colabfold
mmseq_program = /opt/conda/bin/mmseqs
################################QA option#####################################
#########################Customized alphafold program###########################
# alphafold environment directory
alphafold_env_dir = /opt/conda/bin/
# alphafold database directory
alphafold_database_dir = AFDB_DIR
# alphafold program path
alphafold_program_dir = /app/MULTICOM3/tools/alphafold-v2.3.2/
# alphafold tertiary structure prediction script
alphafold_program = run_alphafold_custom.py
# alphafold tertiary structure prediction script
alphafold_multimer_program = run_alphafold_multimer_custom.py
# alphafold tertiary structure prediction script
alphafold_default_program = run_alphafold_pre.py
# AlphaFold2 parameters
monomer_num_ensemble = 1
monomer_num_recycle = 3
num_monomer_predictions_per_model = 1
monomer_model_preset = monomer
# AlphaFold-Multimer parameters
multimer_num_ensemble = 1
multimer_num_recycle = 3
num_multimer_predictions_per_model = 5
multimer_model_preset = multimer
# Common parameters
alphafold_benchmark = True
use_gpu_relax = True
# ALL, BEST, NONE
models_to_relax = ALL
max_template_date = 2024-06-01
pdb_release_date_file = INSTALLDIR_DATABASES/pdb_release_date_filtered.csv
######################Monomer template search option#################################
foldseek_program = /app/MULTICOM3/tools/foldseek/bin/foldseek
foldseek_pdb_database = /app/MULTICOM3/tools/foldseek/databases/complex
foldseek_pdb_database_dir = INSTALLDIR_DATABASES/pdb_complex/pdb
foldseek_af_database = /app/MULTICOM3/tools/foldseek/databases/af_db
foldseek_af_database_dir = INSTALLDIR_DATABASES/af_pdbs
################################databases option#####################################
bfd_database = AFDB_DIR/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt
mgnify_database = AFDB_DIR/mgnify/mgy_clusters_2022_05.fa
metaclust_database = INSTALLDIR_DATABASES/Metaclust_2018_06/metaclust_50
img_database = INSTALLDIR_DATABASES/img/img_new.fasta
###########################Complex alignment generation option#######################
###########################UNIPROT TO PDB database option############################
# uniclust database
uniclust_db = INSTALLDIR_DATABASES/uniclust30_2018_08/uniclust30_2018_08
# uniref database
uniref_db = AFDB_DIR/uniref30/UniRef30_2021_03
uniref90_fasta = AFDB_DIR/uniref90/uniref90.fasta
uniprot_fasta = AFDB_DIR/uniprot/uniprot.fasta
###########################UNIPROT TO PDB database option############################
uniprot2pdb_mapping_file = INSTALLDIR_DATABASES/uniprot2pdb/uniprot2pdb.map
complexes_list = INSTALLDIR_DATABASES/uniprot2pdb/complexes_cm.list
###########################STRING database option####################################
string2uniprot_map = INSTALLDIR_DATABASES/string/string2uniprot.map
#######################End of Complex alignment generation option###################
###########################Complex template search option###########################
###########################Sequence and structure based template search option####################
pdb70_hhsuite_database = AFDB_DIR/pdb70/pdb70
pdb70_hhsuite_cluster_tsv = AFDB_DIR/pdb70/pdb70_clu.tsv
pdb_seqs_dir = AFDB_DIR/pdb_seqres/pdb_seqs
pdb_sort90_hhsuite_database = INSTALLDIR_DATABASES/pdb_sort90/hhsuitedb3
pdb_sort90_hhsuite_cluster_tsv = INSTALLDIR_DATABASES/pdb_sort90/sort90_clust
pdb_sort90_atom_dir = INSTALLDIR_DATABASES/pdb_sort90/pdb
pdb_sort90_hmm_dir =INSTALLDIR_DATABASES/pdb_sort90/hmm
complex_sort90_hhsuite_database = INSTALLDIR_DATABASES/pdb_complex/hhsuitedb3
complex_sort90_hhsuite_cluster_tsv = INSTALLDIR_DATABASES/pdb_complex/sort90_clust
complex_sort90_atom_dir = INSTALLDIR_DATABASES/pdb_complex/pdb
complex_sort90_hmm_dir = INSTALLDIR_DATABASES/pdb_complex/hmm
#######################End of Complex alignment generation option###################