AMDockVS¶

AMDockVS is a chemistry-focused desktop application and Python API for molecular import, preparation, QSAR, binding-site analysis, docking, and result inspection. It uses MolSuite for projects, task orchestration, executors, and data flow.

Install¶

AMDockVS requires Python 3.12. The MolSuite packages and PyMOL (the pymol-open-source alpha wheels, through ms_components) are installed automatically from PyPI, so no conda environment is needed:

python3.12 -m venv .venv
source .venv/bin/activate
pip install AMDockVS

Start the desktop application with:

amdockvs

The global selection¶

Right-click rows in a Ligands or Receptors table and choose Select to work on just those rows. The selection is global: there is one for ligands and one for receptors, and every table and tool of that role (Build, Docking Studio, including Preview & Run) works on it, whichever one it was made in. A tool that offers its own choice of what to work on, such as Diversity, uses the selection only under Current selection; any other choice there ignores it.

While a selection is active the status bar shows it, for example Ligands: 2 selected ✕, and the ID column of the table is marked as filtered. Nothing clears it for you: it survives preparing and docking, so a run can be repeated on the same rows. Click the status-bar entry to drop it and go back to the whole library.

Python API¶

The supported entry point is deliberately small:

from amdockvs import AMDockVSRuntime

runtime = AMDockVSRuntime()
try:
    project = runtime.create_or_open_project(
        name="screening",
        folder="./screening-project",
    )
    print(project)
finally:
    runtime.shutdown()

The runtime groups operations by domain:

Namespace	Responsibility
`runtime.loader`	Ligand and receptor import
`runtime.molecules`	Queries, scopes, filters, and saved sets
`runtime.chemistry`	Ligand and receptor preparation
`runtime.complexes`	Explicit receptor-ligand relationships
`runtime.qsar`	Activities, descriptors, models, and predictions
`runtime.binding_sites`	Manual sites and P2Rank predictions
`runtime.docking`	Preparation, grids, docking with Vina, QuickVina 2, gnina or AutoDock-GPU, and results
`runtime.diversity`	Clustering and representative selection
`runtime.tools`	External tools: status, install, repair

Continue with the API guide, copy a complete example, or browse the generated API reference.

License¶

AMDockVS is released under the MIT License.