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 | |