1.15.3. Script File Workflows
Additional functionality is available by running a command invoking one of the scripts from CmdLineScripts folder in the local user directory, and supplying a structure file as an input. The following script files are available.
ms_generate_analogs.txt - generates structural analogs of molecules from an input file
ms_generate_classes.txt - generates classes using the structures from an input file
ms_generate_keys.txt - generates keys (descriptors) using the structures from an input file
ms_generate_pairs.txt - generates matched molecular pairs using the structures from an input file
ms_generate_metabolites.txt - generates metabolites for molecules contained in an input file
ms_transform_compounds.txt - transforms compounds contained in an input file using user-defined rules
ms_generate_tautomers.txt - generates tautomers for molecules contained in an input file
ms_solubility_profile.txt - generates a solubility versus pH profile for each molecule contained in an input file
ms_logd_profile.txt - generates a logD versus pH profile for each molecule contained in an input file
ms_generate_atomprop_images.txt - generates image files for specified atomic properties
ms_generate_pka_images.txt - generates images and chart data from the pKa Microstates Display
ms_generate_mol_images.txt - generates images of individual molecules, with options for atom/substructure highlighting
ms_generate_ssa_images.txt - generates images from the Structure Sensitivity Analysis display
ms_match_pka.txt - generates tab-delimited file with optimally matched observed and predicted pKa
ms_run_AIDD.txt - performs an AIDD compound optimization run
ms_generate_3d.txt - generates 3D conformers for molecules from an input file
ms_mmff_energies.txt - computes MMFF94s energies of molecules from a 3D input file
ms_mmff_minimize.txt - performs MMFF94s energy minimization of molecules from a 3D input file
ms_align3d.txt - performs rigid alignment of molecules from a 3D input file
ms_create_3dtemplates.txt - creates 3D ring-system templates for use with 3D conformer generation
ms_query_compounds.txt - select molecules from an input file using a query
ms_add_query_attributes.txt - adds query-based attributes to molecules contained in an input file
ms_add_mcda_attributes.txt - adds attributes based on Multi-Criteria Decision Analysis (MCDA) to molecules contained in an input file
ms_create_3ddb.txt - creates a 3D conformer database
ms_export_3ddb.txt - exports an existing 3D conformer database to an SD file
ms_find_3dmatches.txt - computes 3D similarity scores between 3D reference and database conformers
ms_perform_simpsa.txt - performs an HTPK parameter sensitivity analysis for one or more compounds
Each script file is self documenting and contains a number of parameters that should be modified prior to use, preferably using a copy of the file. To utilize the file it is sufficient to specify its name as the single command-line argument. It is also possible to override parameters from the file using parameter name/value pairs on the command line, in the form "-name value".
For example, the file ms_generate_metabolites.txt has a parameter called structureFile, which defines the input file containing structures for which metabolites will be generated. To specify this parameter on the command line, you could use:
ADMET_Predictor.exe ms_generate_metabolites.txt -structureFile MyFile.sdf
This allows you to specify on the command line those parameters that tend to change from run to run, while leaving the other parameters defined in the file. Note that parameters should not be removed from the script files even if you plan to override them; ADMET Predictor uses the script files to obtain the list of all necessary parameters for a given workflow.
If any errors occur during an operation, an appropriate message will be written to the log file specified in the script file. An error message may also be visible in the console window. By default, no popup message windows will appear. If you would like to see error messages in a popup window, you can include "popups" as one of the command-line parameters.
In order to see the list of available script-file parameters, you can use the -p command-line option. This flag should be placed after the name of the script file. For example:
ADMET_Predictor.exe ms_generate_metabolites.txt -p
Another option available in several workflows is -apel_path, allowing users to specify the location of the ADMET Predictor error log file.