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.
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) |
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) |
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) |
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) |
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) |
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) |
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 |
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 |