README

# INSTALL INSTRUCTIONS #######################################################

# You need to have OCaml and OPAM installed on your system
# cf. http://opam.ocamlpro.com/doc/Quick_Install.html

# You need to have pdbset from CCP4 installed
# cf. http://www.ccp4.ac.uk/index.php

# compile Fragger and ranker_aa
./build.sh

# USAGE EXAMPLES #############################################################

# all tools have a -h or --help option, it is recommended to read the help
# message before really using any of the tools

# list your PDB files
find data/pdbs -regex '.*\.pdb$' > pdbs.txt

# clean the PDBs
mkdir -p cleaned
(
# CHANGE THE FOLLOWING LINE TO REFLECT YOUR CCP4 INSTALLATION
source /usr/local/src/ccp4/ccp4-6.3.0/setup-scripts/ccp4.setup-sh
cat pdbs.txt | xargs -L1 ./bin/pdb_filter.sh cleaned
)

# list your cleaned PDB files
find cleaned -regex '.*\.pdb$' > cleaned.txt

# create a "database"
./src/bb_atom_quads.native -i cleaned.txt -o fragments_DB

# prepare to generate all fragments of a given size
grep TER fragments_DB | awk '{print $2"_*"}' > all_ids

# generate all fragments of size 9
./src/get_frag.native -db fragments_DB -i all_ids -n 9 > fragments_9

# create an RMSD index
./src/query.native -db fragments_DB -i 01_A_0001:fragments_9 -o 01_A_0001.rmsds
# create another
./src/query.native -db fragments_DB -i 06_A_0049:fragments_9 -o 06_A_0049.rmsds
# we recommend at least 3 indices for large databases or as much as you have
# cores on your computer in case of parallel runs (-np option in query)
# as a rule of thumb, the reference fragments should be far from each others
# and at least two

# suppose you want to use 02_A_0045 as your query fragment
./src/get_frag.native -db fragments_DB -id 02_A_0045 -o 02_A_0045.pdb -n 9

# you can query with it now
./src/query.native -db fragments_DB -q 02_A_0045.pdb -d 0.2 -o results \
-idx 01_A_0001.rmsds,06_A_0049.rmsds

# Don't hesitate to contact us if you need any help to use the tool
# or find any bug.
#
# The authors,
# Francois Berenger, David Simoncini, Arnout Voet,
# Rojan Shrestha and Kam Zhang.