1.15.2. Command Examples

It is the responsibility of the user, calling script, or calling software to ensure that the syntax rules are followed. In particular, not providing correct options, ignoring path information for either the program executable or input file(s), and not quoting file names containing spaces are typical sources of error.

The path to the ADMET Predictor executable is, in most cases:

C:\Program Files\Simulations Plus, Inc\ADMET_PredictorX.Y\ADMET_Predictor.exe

where X.Y represents the version number (e.g., 13.0).

Similarly, the path to the ADMET Modeler executable is:

C:\Program Files\Simulations Plus, Inc\ADMET_PredictorX.Y\ADMETModeler.exe

this is abbreviated admet_modeler in the examples below. ADMET Predictor 14 is the first version to contains an ADMET Modeler executable, so please let us know if you find any issues. The program takes a PRM and DAT files as the minimum input arguments. The DAT file must contain a column representing the dependent variable and all of the descriptor values. The DAT file can be created via the ADMET Predictor executable. The PRM file specifies all of the ADMET Modeler parameter. There are two examples PRM files in the ProgramData folder:

Demo2D-ExSol.prm
Demo2D-Low-logP.prm

These PRM files contain comments documenting each parameter. PRM files (and DAT files) are saved in ADMET Modeler project folders. Thus, one can use the ADMET Predictor and ADMET Modeler GUI to create PRM files that contain various options. Demo2D-ExSol.dat and Demo2D-Low-logP.dat files are also in the ProgramData directory. The Demo2D-ExSol files are examples of regression models and the Demo2D-Low-logP represent classification model examples.

If ADMETModeler.exe is run without arguments, then the GUI will be displayed, and the user will be prompted for a PRM file. If the user selects a PRM file that is inside an ADMET Modeler project folder, then the models in the folder will be displayed in the grid.

Option	Description
admet_predictor -h	Write the help message to the command line.
admet_predictor -t QMD -d 2D Demo2D.qmd or admet_predictor -t QMD Demo2D.qmd	Open 2D SMILES input Demo2D.qmd and store results in Demo2D.dat.
“C:\Program Files\Simulations Plus, Inc\ADMET Predictor12.0\admet_predictor” -t SDF -d 3D -u SDF “D:\My Files\My3DStructures.sdf”	Open 3D SDF input My3DStructures.sdf and store results in My3DStructures_ADMET_3D.sdf. Note: The program and the input file reside in different folders on different drives. Both paths contain spaces and must be quoted.
admet_predictor -t MOL -d 2D -u SDF “C:\Drawn Structures\str1.mol” “C:\Drawn Structures\str2.mol” “C:\Drawn Structures\str3.mol” “C:\Drawn Structures\str4.mol”	Open four 2D MOL structure files and store results in C:\Drawn Structures\str1_ADMET_2D.sdf.
admet_predictor -t SDF -m SIMFaFb -SimHIA_hia MyHIA.hia MyCompounds.sdf	Run the HTPK Fa/Fb workflow for compounds in MyCompounds.sdf and store the results in MyCompounds.dat. Both human and rat simulations will be performed, with parameters for the human simulations being obtained from the file MyHIA.hia. Rat simulations will use parameters from the default SimRIA.hia file.
admet_predictor -t SDF -d 3D -x MyCompounds.sdf	Similar to earlier examples, but excludes all out-of-scope predictions from the output. Warning: Excluded prediction values will be replaced by the “~” character; hence the processing script must be able to interpret these.
admet_predictor -t SDF -p 2.5 -i -d 3D Demo3D.sdf	Calculate descriptors, including ionization descriptors, and ADMET properties at pH 2.5. Results are saved in Demo3D.dat.
admet_predictor -t SDF -b 0 -k 10 -o -n -d 3D -u SDF Demo3D.sdf	Calculate descriptors and ADMET properties at pH 7.4, include aliphatic OH groups and aliphatic amides, skip negative pKa, skip molecules with more than 10 ionizable groups. Results are saved in Demo3D_ADMET_3D.sdf.
admet_predictor -t QMD -u RDF -z Demo2D.qmd	Calculate and save all predictions including pKa microstates in Demo2D_ADMET_2D.rdf.
admet_predictor -y -t QMD -g Demo2D.qmd	Calculate and save all predictions in Demo2D.dat and report predictions outside the chemical space of models in tab-delimited file Demo2D.ots. Also, save GastroPlus import files: Demo2D_DrugTable.txt and Demo2D_AcidBaseTable.txt.
admet_predictor -t QMD -x Demo2D.qmd	Save predictions in Demo2D.dat, excluding out-of-scope predictions.
admet_predictor -t SMI -n -w MC MyDrugCandidates.smi	Save pKa predictions only, including ionization of aliphatic amides, in MyDrugCandidates_ADMET_2D.sdf file using the Medicinal Chemist format.
admet_predictor -t SMI -u SDF -w PC -s 5 MyDrugCandidates.smi	Save ADMET and pKa predictions with microstate information in MyDrugCandidates_ADMET_2D.sdf file using the Physical Chemist format. Skip microstates contributing less than 5%.
admet_predictor -t SMI -p 6.9 -w CI MyDrugCandidates.smi	Save charge state predictions (only) at pH=6.9 in MyDrugCandidates_ADMET_2D.sdf file using the Cheminformatician format.
admet_modeler -p Demo2D-ExSol.prm -d Demo2D-ExSol.dat -o Demo2D-ExSol	Run ADMET Modeler executable to create regression models. The output directory is Demo2D-ExSol.
admet_modeler -p Demo2D-Low-logP.prm -d Demo2D-Low-logP.dat -o Demo2D-Low-logP -n No	Run ADMET Modeler executable to create classification models. The output directory is Demo2D-Low-logP and the negative class in “No”.