User needs to be in the docker
group, or use sudo
to run the script
./build.sh
or
sudo ./build.sh
Copy pharmer
to $SILCSBIODIR/programs
(needs write permission of the target folder)
./copy_pharmer.sh
or
sudo ./copy_pharmer.sh
The --help option will provide the following:
USAGE: pharmer [options] --cmd command [pharma, dbcreate, dbsearch, server]
OPTIONS:
-bloom-large=<uint> - Number of bits for coarse discretization fingerprint.
-bloom-small=<uint> - Number of bits for fine discretization fingerprint.
-cmd=<string> - command [pharma, dbcreate, dbsearch, server]
-dbdir=<string> - database directory(s)
-extra-info - Output additional molecular properties. Slower.
-file-partition - Partion database slices based on files
-help - Display available options (--help-hidden for more)
-in=<string> - input file(s)
-logdir=<string> - log directory for server
-max-hits=<n> - return at most n results
-max-orient=<n> - return at most n orientations of each conformation
-max-rmsd=<number> - maximum allowed RMSD; default max allowed by query
-max-weight=<uint> - maximum allowed molecular weight
-nthreads=<n> - utilize n threads; default 1
-out=<string> - output file
-pharmaspec=<string> - pharmacophore specification
-port=<uint> - port for server to listen on
-print - print results
-q - quiet; suppress informational messages
-reduceconfs=<n> - return at most n conformations for each molecule
-separate-weight - Segregate database based on molecular weight
-show-query - print query points
-sort-rmsd - Sort results by RMSD.
-unweighted-rmsd - Compute minimal RMSD without radius weights