Python API reference
These pages are generated from the package’s Python signatures and docstrings using Sphinx AutoAPI. Static parsing does not import the package, load molecular data, execute notebook cells, or start simulation tools.
Start with naming, build, export and workflows.design for the RDKit route;
analysis_contacts and trajectory_* for completed simulations. The
build_pha, pha_filepath_manager, build_single_PHA_systems, pha_melt_builder,
openmmscript_builder and sw_openmm modules expose additional database and MD
interfaces. Their presence in this reference does not remove external-tool or
input-data prerequisites. See current limits.
- iphasimulator
- Submodules
- iphasimulator.amber_complex
- iphasimulator.amber_solvation
- iphasimulator.analysis_contacts
- iphasimulator.build
- iphasimulator.build_pha
- iphasimulator.build_single_PHA_systems
- iphasimulator.charmmgui_import
- iphasimulator.conversion_amber_to_gromacs
- iphasimulator.docking_inputs
- iphasimulator.exceptions
- iphasimulator.export
- iphasimulator.monomers
- iphasimulator.naming
- iphasimulator.openmmscript_builder
- iphasimulator.parameterization_gaff2
- iphasimulator.pha_filepath_manager
- iphasimulator.pha_melt_builder
- iphasimulator.simulation_gromacs_runner
- iphasimulator.simulation_openmm_amber_runner
- iphasimulator.stereochemistry
- iphasimulator.sw_openmm
- iphasimulator.system_builder_packmol
- iphasimulator.trajectory_centering
- iphasimulator.trajectory_frame_extraction
- iphasimulator.trajectory_gromacs_merge
- iphasimulator.trajectory_gromacs_trjconv
- iphasimulator.trajectory_preprocessing
- iphasimulator.trajectory_processing
- iphasimulator.workflows
- Submodules
- iphasimulator.visualisation.visualiser
- iphasimulator.data.amber_openmm.run_openmm_md