alphafill.conf-dist.in

# Configuration file for alphafill
#
# First block of options is generic, used to locate data.
# Make sure the paths here are correct.

# Directory containing the mmCIF files for the PDB
pdb-dir=<NEEDS_TO_BE_CHANGED>/pdb-redo/

# The FastA file containing the PDB sequences
pdb-fasta=<NEEDS_TO_BE_CHANGED>/pdb-redo.fa

# File in CIF format describing the ligands and their modifications
ligands=@ALPHAFILL_DATA_DIR@/af-ligands.cif

# Directory containing the alphafilled data, only needed in the web server
# db-dir=<NEEDS_TO_BE_CHANGED>/af-filled/

# Number of threads to use, zero means all available cores
# threads=0

# ---------------------------------------------------------------------

# The options in the next block are meant to tweak the alphafill algorithm

# The minimal identity for a high scoring pair (note, value between 0 and 1)
# min-hsp-identity=0.25

# The minimal length of an alignment
# min-alignment-length=85

# The max distance to use to find neighbouring backbone atoms for the ligand
# in the AF structure
# max-ligand-to-backbone-distance=6

# The max distance between polymer atoms and ligand atoms used in calculating clash scores
# clash-distance-cutoff=4

# The centroids of two identical ligands should be at least this far apart to
# count as separate occurrences
# min-separation-distance=3.5

# ---------------------------------------------------------------------

# Options for the blast algorithm
# blast-report-limit=250
# blast-matrix=BLOSUM62
# blast-word-size=3
# blast-expect=10
# blast-no-filter=false
# blast-no-gapped=false
# blast-gap-open=11
# blast-gap-extend=1

# ---------------------------------------------------------------------

# The alphafill Postgresql database information
# A database is needed for a web server. The database
# must be created by an administrator and can be filled
# using the `alphafill rebuild-db` command.

# db-dbname=
# db-user=
# db-password=
# db-host=
# db-port=

# ---------------------------------------------------------------------

# The web server needs some more configuration

# Address to listen to
# address=127.0.0.1

# Port to listen to
# port=10342

# User to run as
# user=www-data

# Reverse proxy context (e.g. https://example.com/my-alphafill/ )
# context=

# Pattern for locating structure files
# structure-name-pattern=${db-dir}/${id:0:2}/AF-${id}-F${chunk}-filled_v${version}.cif.gz

# Pattern for locating metadata files
# metadata-name-pattern=${db-dir}/${id:0:2}/AF-${id}-F${chunk}-filled_v${version}.cif.json

# Pattern for locating PDB files
# pdb-name-pattern=${pdb-dir}/${id:1:2}/${id}/${id}_final.cif

# Template for links to pdb(-redo) entry
# db-link-template=https://pdb-redo.eu/db/${id}

# Directory for custom built entries
# custom-dir=/tmp/alphafill

# Location of the yasara executable, needed for optimising
# yasara=/opt/yasara/yasara