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Command Line Usage

The generation of conformations, ligand-based pharmacophores and the screening of molecule libraries can be called from the command line. The executables are located in the LigandScout installation directory.

Conformation Generation

Usage:

idbgen [Mandatory arguments] [Optional arguments] [Distribution arguments]

Mandatory arguments:
--input, -i {infile} input file (*.sdf, *.smi, *.mol2, *.ldb)
--output, -o {outfile} output file (*.ldb)
Optional arguments:
--help, -h {helptype} command line parameter help
   helptype:  all lists all arguments
  simple shows most important arguments
  distribution shows network arguments
  [param] displays detailed help for the argument '[param]'
--sysinfo system information
--log-file, -l {logfile} output file for logging-messages (default: stdout)
--confgen-type, -t {type} confgen type (default: omega-fast)
   type:  omega-fast omega high-throughput settings (25 confs)
  omega-best omega high-quality settings (500 confs)
  import import from input file
--multi-conf, -m {type} auto-sense conformations in SDF files (default: off)
   type:  name auto-sense by name comparison
  structure auto-sense by structure-hash comparison
--num-confs, -n {number} max. number of conformations to generate (default set by '--confgen-type' option)
--name-property, -p {propname} property for overriding molecule name
--omega-license, -z {file} omega license file (default: file specified by environment variable OE_LICENSE)
--hydrophob-threshold, -T {number} the minimal surface accessibility threshold for hydrophobicity (default: 0.25)
--error-file, -e {file} file that collects molecules where errors occurred (default: {OUTPUT_FILE}-failed.log)
--update-keep-old, -K update database and keep old entries
--update-drop-old, -R update database and drop old entries
--allow-duplicates, -A allow duplicates in the database (default: off)
--overwrite-existing, -O overwrite already existing molecules (default: off)
--num-processes, -b {#processes} number of processes to start (default: number of CPUs)
--first-index, -F {index} first molecule index to use (default: 1)
--last-index, -L {index} last molecule index to use (default: library-size)
--index-file, -I {file} file containing input molecule-indexes to use (default: all molecules)
--end-time, -E {time} task is stopped when end-time is reached (default: no time limit)
--process-time, -P {time} max amount of time this process is executed (default: no time limit)
--input-db, -D {file} input database (*.ldb) to use additionally to the input library.
--start-positions, -S {file} compound start positions file of the input library.
--exec-mode, -x {mode} the execution mode (default: multi)
   mode:  single only one CPU is used
  multi uses all CPUs/cores of this computer
  network uses computers in the network
Distribution options:
--host-list-file, -H {file} host list file (default: ${HOME}/.inteligand-data/ligandscout3/iworker-list.txt)
--comma-sep-hosts, -c {list} comma separated host list (HOST1:PORT1,HOST2:PORT2,...)
--network-interface, -N {name} network interface to use ('-N list' to list all available interfaces)
--verbosity, -v {loglevel} network logging verbosity (default: off)
   loglevel:  off no network log messages
  low network errors and warnings
  medium connection info messages are shown
  high high-level protocol messages
  highest debug (very verbose)
--kill-workers, -X kill iworkers when finished (default: off)

Ligand-based Pharmacophore Generation

Usage:

espresso [Mandatory arguments] [Optional arguments]

Mandatory arguments:
--training-set, -t {filen} input file containing the training-set (*.sdf, *.mol2, *.ldb, *.smi)
Optional arguments:
--input, -i {file} input file containing the training- and/or test-set (*.lsd)
--help, -h {helptype} command line parameter help
   helptype:  all lists all arguments
  simple shows most important arguments
  [param] displays detailed help for the argument '[param]'
--sysinfo system information
--quiet, -q suppress logging and info messages
--log-file, -l {logfile} output file for logging-messages (default: stdout)
--test-set, -s {file} input file containing the test-set (*.sdf, *.mol2, *.ldb, *.smi)
--pharmacophore, -p {file} output file containing the generated pharmacophore (*.pmz, *.pml)
--output, -o {file} output file for training-set ligands that were used for pharmacophore generation (*.sdf, *.mol2, *.ldb, *.smi, *.lsd)
--confgen-type, -c {type} confgen type (default: omega-fast)
--num-confs, -n {number} max. number of conformations to generate (default set by '--confgen-type' option)
--omega-license, -z {file} omega license file (default: file specified by environment variable OE_LICENSE)
--keep-confs, -y keep input conformations (default: override)
--disable-excluded-volumes, -x generate exclusion volumes from training-set
--pharmacophore-type, -g {type} the type of the pharmacophore to generate (default: merged)
   type:  shared shared feature pharmacophore
  merged merged feature pharmacophore
--scoring-function, -f {score} the function to use for scoring intermediate solutions and resulting pharmacophores (default: combo)
   score:  pharma_fit scores the number of matching pharmacophore features and the RMSD of the pharmacophore alignment
  fast_shape scores the atom van der Waals sphere overlap of the aligned training-set molecules
  shape scores the molecular shape similarity of the aligned training-set molecules based on a gauss function representation of the molecular volume
  combo scores the number of matching pharmacophore features, the RMSD of the pharmacophore alignment and the atom van der Waals sphere overlap of the aligned training-set molecules
--intermediate, -r {number} the number of intermediate alignment solutions to use (default: 10)
--tolerance, -e {number} the global feature tolerance scaling factor (default: 1.0)
--merged-omit, -m {number} max. omitted features for merged feature pharmacophores (default: 4)
--mark-optional-features, -k mark partially matching features as optional (default: enabled)
--optional-feature-t, -d {number} optional feature threshold (default: 10%)
--pharm-name-prefix, -u {prefix} name-prefix for resulting pharmacophore(s) (default: Model)

Virtual Screening

Usage:

iscreen [Mandatory arguments] [Optional arguments] [Distribution arguments]

Mandatory arguments:
--query, -q {file} query pharmacophore (*.pmz,*.pml)
--database, -d {file} database to screen (*.ldb)
--output, -o {file} hit list (*.sdf, *.ldb)
Optional arguments:
--help, -h {helptype} command line parameter help
   helptype:  all lists all arguments
  simple shows most important arguments
  distribution shows network arguments
  [param] displays detailed help for the argument '[param]'
--sysinfo system information
--log-file, -l {logfile} output file for logging-messages (default: stdout)
--disable-first-match-mode, -s all matching conformations are considered (default: only first matching)
--regex-file, -r file with regular expressions to select molecules from database.
--disable-exclusion-volumes, -e disable checking for exclusion volume clashes
--fragment-screening-mode, -f enable fragment screening mode
--allow-omit, -a maximum number of features to omit (default: 0)
--min-required, -m minimum number of required features (default: 3)
--first-index, -F {index} first molecule index to use (default: 1)
--last-index, -L {index} last molecule index to use (default: library-size)
--end-time, -E {time} task is stopped when end-time is reached (default: no time limit)
--process-time, -P {time} max amount of time this process is executed (default: no time limit)
--num-cores, -C {number} max amount of cores used by this process (default: all cores)
--timeout-cl, -T {time} execution time-out on compound level (default: disabled)
--exec-mode, -x {mode} the execution mode (default: multi)
   mode:  single only one CPU is used
  multi uses all CPUs/cores of this computer
  network uses computers in the network
Distribution options:
--host-list-file, -H {file} host list file (default: ${HOME}/.inteligand-data/ligandscout3/iworker-list.txt)
--comma-sep-hosts, -c {list} comma separated host list (HOST1:PORT1,HOST2:PORT2,...)
--network-interface, -N {name} network interface to use ('-N list' to list all available interfaces)
--verbosity, -v {loglevel} network logging verbosity (default: off)
   loglevel:  off no network log messages
  low network errors and warnings
  medium connection info messages are shown
  high high-level protocol messages
  highest debug (very verbose)
--kill-workers, -X kill iworkers when finished (default: off)

Networking: iworker

Usage:

iworker [Optional arguments]

Optional arguments:
--help, -h {helptype} command line parameter help
   helptype:  all lists all arguments
  simple shows most important arguments
  [param] displays detailed help for the argument '[param]'
--sysinfo system information
--log-file, -l {logfile} output file for logging-messages (default: stdout)
--auto-detection, -a enable auto-detection (default: off)
--max-parallel-tasks, -m {number} maximum number of parallel executed tasks (default: number of CPUs)
--max-load, -d {number} maximum cpu load (1-100) (default: disabled)
--network-interface, -N {name} network interface to use ('-N list' to list all available interfaces)
--port, -p {number} tcp server port to use (default:30000)
--verbosity, -v {loglevel} network logging verbosity (default: off)
   loglevel:  off no network log messages
  low network errors and warnings
  medium connection info messages are shown
  high high-level protocol messages
  highest debug (very verbose)

Retrieving Library Size

Usage:

libsize LIBRARY_FILE (*.smi, *.sdf, *.mol2, *.ldb)

Retrieving Database Information

Usage:

idbinfo [Mandatory arguments] [Optional arguments]

Mandatory arguments:
--dbase, -d {file} database to investigate (*.ldb)
Optional arguments:
--complete, -c perform complete analysis (takes long for large databases)
--help, -h command line parameter help
--sysinfo system information
--log-file, -l {logfile} output file for logging-messages (default: stdout)

Merging Databases

Usage:

idbmerger [Mandatory arguments] [Optional arguments] [LIBRARY_FILE (*.ldb) .. ]

Mandatory arguments:
--output, -o {outfile} output file (*.ldb)
Optional arguments:
--help, -h command line parameter help
--sysinfo system information
--allow-duplicates, -A allow duplicates in the database (default: off)

Retrieving Start Position File from Library

Usage:

libpos [Mandatory arguments]

Mandatory arguments:
--input, -i {infile} input file (*.sd, *.sdf, *.mol, *.smi)
--output, -o {outfile} output file (*.pos)
Optional arguments:
--help, -h command line parameter help
--sysinfo system information

Retrieving System ID

Usage:

ligandscout_sysid

LigandScout License Activation

Usage:

ligandscout_activate [Mandatory arguments] [Optional arguments]

Mandatory arguments:
--serial-number, -s {number} serial number
Optional arguments:
--help, -h command line parameter help
--sysinfo system information
--license-file, -f {file} license file
--proxy-address, -a {address} proxy address
--proxy-port, -p {number} proxy port
--proxy-user, -u {username} proxy username
--proxy-password, -w {username} proxy password

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Page designed & authored by G. Wolber

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