1.15.1. Usage, Arguments and Options

-t <filetype>

Type of input data [SDF, RDF, MOL, QMD, or SMI].
This option is required.

-d <dimension>

Dimension of input data [2D (default) or 3D].

-u <filetype>

Type of the output file [DAT (default), TXT, SDF, or RDF]. Results are saved in *.dat, *.txt, *_ADMET_2D.sdf, or *_ADMET_2D.rdf files, respectively.

-m <module, ...>

Limit output to the specified combination of one or more modules separated by comma: PCB = Physico-chemical and Biopharmaceutical, MET = Metabolism, TRN = Transporters, TOX = Toxicity, DIL = DILIsym, SIMFaFb = Simulated percents absorbed and bioavailable, SIMDose = Simulated optimal dose, GLB = Global, USR = User models, DSC = Descriptors.

-g

Write GastroPlus Drug Table (in *_DrugTable.txt) and GastroPlus Acid/ Base Table (in *_AcidBaseTable.txt) using default settings.

-p <pH>

pH for pH-sensitive ADMET models [ default 7.4 ]. Either a numerical value, or title of an input column containing pH values, one per each compound.

-i

Also calculate ionization descriptors at the indicated pH. Note: -i must be used with -p, otherwise, it is ignored.
Warning: 
Use of this option invalidates ADMET predictions other than S+pKa!
Note: -i must be used with -p, ignored otherwise.

-a <upper-limit>

Exclude acidic pKa values above the <upper-limit>.

-b <lower-limit>

Exclude basic pKa values below the <lower-limit>.

-o

Include aliphatic -OH groups in S+pKa predictions..

-n

Include aliphatic amides in S+pKa predictions..

-c

Include carbon protonation in S+pKa predictions..

-k <num_igroups>

Skip molecules with more than <num_igroups> ionizable groups.

-h

Write usage information and quit. If operated in a batch mode the output goes to ADMETPredictorErrors.log file.

-r <risk oos penalty>

Out of scope penalty to apply to risk models. See manual for details.
Value must be between 0.0 and 1.0. If not specified a default value of 0.5 is used.

-x

Exclude predictions outside models’ applicability domains.. In these cases, predicted values are replaced by the "~" (tilde) character.

-y

Report predictions outside the applicability domain of models in a separate tab-delimited file (*.ots).
Also reports uncertainty predictions of models in separate tab-delimited file (*.unc).
May be invalidated by options -z and -w; see below.

-w <workflow>

Save pKa microstates in an SDF file *_ADMET_2D.sdf formatted in accordance with the given <workflow> argument: MC = Medicinal Chemist, PC = Physical Chemist, CI = Cheminformaticist, or CC = Computational Chemist. See User Manual. If option -u is SDF, then all ADMET predictions are also included in *_ADMET_2D.sdf. Other -u settings are nullified and cause option -y to be ignored. This option supersedes option -z.

-s <threshold>

Skip from the SDF output pKa microstates whose contributions are smaller than the given numeric <threshold>. Threshold must be given in %; its default value is 1. This option works only in connection with option -w.

-z

Save all predictions including pKa microstates in a separate RDF file (*_ADMET_2D.rdf) suitable for constructing the hierarchical tables in ISIS/Base™ databases. If option -u is RDF then all ADMET predictions are also included in *_ADMET_2D.rdf. Other -u settings are nullified and cause option -y to be ignored.

-N <threads>

Number of processors (threads) to use. If not specified the default value is 1.

-path <path>

optional path to non-default folder containing model files. If specified,this folder must exist.  Not supported on Linux.

-license <path>

optional path to Reprise license. Typical values are @localhost or port_num@xx.xx.xx.xx.  Not supported on Linux.

-out <basename>

optional basename for all output files. File extensions remain the same and any extension in the basename is ignored. The basename may also specify an output folder, e.g., C:\myFolder\myResults. Note that any specified folders must already exist.  If the basename ends with a forward or backward slash (e.g., C:\myFolder\myResults\), it will be interpreted as a folder name only, and the output filenames will be based on the name of the input file.

-cpt

Save Cp-time profiles containing time points and concentrations of an HTPK simulation run. This option requires specifying -m SIMDose or -m SIMFaFb or both to specify a simulation run. An optional numeric value following this flag can be used to limit the number of points output per Cp-time profile. A value >= 1 specifies the maximum number of points to output. A value between 0 and 1 specifies the fraction of points to output. In all cases, the first, last, and maximum value for each dosing interval is always output. The resulting file is named *_cpt.txt

-cpt+

Identical to -cpt, but saves three additional profiles representing amounts dissolved, absorbed and bioavailable.

-species

Limit HTPK simulations to the specified combination of one or more species separated by comma: hum=human, rat=rat, mou=mouse, dog=dog, mky=monkey.  For example, -species hum,mou will run both human and mouse.

-<SIM model>_hia <local hia file>

Specifies the use of a local hia file for an HTPK simulation overriding the default file.
<SIM model> must correspond to one of the following names: SimHIA, SimDOSE, SimRIA, SimDOSERat, SimMIA, SimDOSEMouse, SimDIA, SimDOSEDog, SimMKYIA or SimDOSEMonkey.
The local hia file must have the extension .hia. If .hia is not included in the name provided, it is automatically appended.
For example, -SimHIA_hia myHIAFile will use a local hia file named myHIAFile.hia for running a fixed dose human HTPK simulation. The option -m SIMFaFb is required, in this example, to trigger the running of the fixed dose HTPK simulation. Also note that the hia file contains the name of the acat file.
The program will look for this acat file in the same folder as the local hia file, and, if not found there, it will look in the user's <AppData> folder where all other model files are found. If not found in either location, this will trigger an error.

-<SIM model>_acat <local acat file>

Specifies the use of a local acat file for an HTPK simulation overriding the default acat file specified in the hia file.
<SIM model> follows the same naming conventions as for the _hia option. The local acat file may have any extension.
If no extension is provided, .inp is assumed. For example, -SimDOSERat_acat myACATfile will use a local acat file named myACATfile.inp to perform an HTPK dose optimization simulation for rat species. Note that one must also specify -m SIMDose to trigger the running of the dose optimization HTPK simulation.

-prm

Save a file indicating, for each compound, which values were used as inputs to an HTPK simulation. For each HTPK parameter (e.g., RefSolubility), a numeric value is listed along with a text value indicating the ADMET Predictor model or user-defined field that was the source of the value. The resulting file is named *_prm.txt

-pt

This “pass-through” option is used with SD file input to preserve as much of the original SD records as possible in the output SD file, including explicit hydrogens and stereo information.

-lc

Restrict license checkout to the ones included in a comma-separated list.  Allowed list elements are PCB, TRN, MET, TOX, SIM or DIL.  For example, -lc PCB,MET indicates that only the AP_PHYS_CHEM_BIOL and AP_METABOLISM licenses can be checked out.  If the -lc argument is used without any other arguments, ADMET Predictor will print current license usage information.

<file.txt>

When the first command-line argument is a filename with *.txt extension, ADMET Predictor runs a specialized workflow in which the various options are provided in the specified text file. These workflows are described in the subsequent Script File Workflows section.

-h, --help

Shows help message and then exits.

-v, --version

Shows version information and then exits.

-p, --prm <file>

Full path to .prm file.

-d, --dat <file>

Full path to .dat file.

-o, --output

Full path to output folder.

-k, --kohonen <file>

Full path to Kohonen map file.

-n, --negative <label>

Label of the negative class for binary classification models.

-c, --cpu <num>

Number of processors to use. Will use all processors, if the option is not specified.