Third-Party Bridges#

MolSysMT acts as a form-agnostic bridge across the Python structural biology ecosystem, enabling transparent conversion, query delegation, and topological synchronization between major computational chemistry packages.

Ecosystem Interoperability Architecture#

Soft dependencies in MolSysMT are managed centrally through lazy imports enforced by @dep_digest (molsysmt._depdigest). Optional third-party packages are never imported at top-level module load time. Instead, adapters dynamically detect package availability when a specific object form or file format is passed into API functions.

Supported Ecosystem Packages#

Comprehensive matrix of third-party packages bridged by MolSysMT, their target objects, and integration capabilities:

Library	Primary Data Objects	Bridge Capabilities	Dependency Tier
MDTraj	`mdtraj.Trajectory`, `mdtraj.Topology`	Coordinate array extraction, trajectory slicing, selection query translation, file format parsers (`dcd`, `xtc`, `h5`).	Soft Dependency
OpenMM	`openmm.Topology`, `openmm.System`, `openmm.Modeller`	Force field system creation, OpenMM state extraction, solvation modeling, simulation context bridge.	Soft Dependency
MDAnalysis	`MDAnalysis.Universe`, `MDAnalysis.AtomGroup`	Trajectory ensemble digestion, selection expression parsing, Universe extraction.	Soft Dependency
ParmEd	`parmed.Structure`, `parmed.gromacs.GromacsTopology`	Force field parameter editing, format conversion (`mol2`, `top`), molecular topology graph.	Soft Dependency
PyTraj	`pytraj.Trajectory`, `pytraj.Topology`	CPPTRAJ analysis acceleration, trajectory coordinate extraction.	Soft Dependency
BioPython	`Bio.PDB.Structure`, `Bio.Seq`, `Bio.SeqRecord`	Structural PDB hierarchy parsing, biological sequence alignment, FASTA/PIR parsing.	Soft Dependency
OpenFF	`openff.toolkit.topology.Molecule`, `Topology`	Small molecule stereochemistry, SMIRNOFF forcefield assignment.	Soft Dependency
RDKit	`rdkit.Chem.Mol`	Small molecule 2D/3D conformer generation, SMILES parsing (`string:smiles`, `file:smi`), graph topology.	Soft Dependency
PDBFixer	`pdbfixer.PDBFixer`	Protein structure fixing, missing heavy atom and residue rebuilding, terminal capping.	Soft Dependency
CuPy	`cupy.ndarray`	GPU-accelerated 3D coordinate array extraction and spatial transformations.	Soft Dependency
NetworkX	`networkx.Graph`	Covalent graph network analysis, component connectivity queries.	Hard Dependency

Bridge Operation Modes#

Interoperability bridge operations follow three execution patterns:

Pattern	Description	Primary API Methods
Zero-Copy View	Direct array pointer sharing for heavy 3D coordinate and trajectory arrays without memory duplication.	`msm.get(..., coordinates=True)`
Form Adapter Conversion	Lossless conversion between native MolSysMT objects and third-party classes.	`msm.convert(source, to_form=...)`
Delegated Querying	Transparent delegation of structural queries and selection syntax translation to underlying engines.	`msm.select(source, syntax=...)`

Third-Party Helper Extensions#

Beyond data conversion and selection translation, MolSysMT provides dedicated helper extensions in molsysmt.third_party designed to simplify and streamline workflows when working directly with external tools. Detailed, function-by-function tutorials for these extensions are provided in the User Guide > Tools > Third-Party section.

Extension Module	Target Software	Primary Helper Capabilities
`msm.third_party.nglview`	NGLView	Helper functions to manipulate NGLView representations (`show_as_cartoon`, `show_as_surface`), overlay 3D shapes (`add_arrows`, `add_cylinders`, `add_hbonds`), customize color schemes, and export HTML views.
`msm.third_party.openmm`	OpenMM	Helper functions to construct custom OpenMM forces (`add_harmonic_bond_force`, `pin_atoms`, region restraints) and specialized trajectory reporters (`H5MSMReporter`, `StructuresDictReporter`, `TQDMReporter`).
`msm.third_party.tleap`	AMBER LEaP	Helper wrappers to streamline system parameterization and LEaP script generation.