Third-party Bridges#

MolSysMT does not want to replace the molecular ecosystem; it wants to unite it. We believe that researchers should be able to use the best tool for each task without wasting time on file conversion.

1. Target-aware conversion#

MolSysMT can “teleport” a molecular system into dozens of other libraries. Each bridge preserves the semantics represented by its documented contract; it does not pretend that every target can store the complete MolSysMT model. For example, an MDAnalysis Universe carries topology and structures, whereas an MDAnalysis Topology is topology-only.

2. Supported Embassies#

We provide native bridges to:

  • Simulators: OpenMM, AMBER (via TLeap), GROMACS.

  • Analysis Engines: MDAnalysis, MDTraj, BioPython.

  • Visualizers: NGLView, Py3Dmol.

  • Mathematics: NetworkX (Graphs), Pandas (DataFrames), Numpy.

3. Bi-directional Diplomacy#

In many cases, the bridge is bi-directional. You can load an MDAnalysis Universe, perform a selection with MolSysMT syntax, and materialize the selected atoms and frames as a new Universe or AtomGroup. AtomGroup conversions remain inside the group and do not reintroduce atoms from its parent Universe.

The MDAnalysis bridge preserves the caller’s active trajectory frame during reads. Coordinates, optional velocities, time, and triclinic boxes cross the boundary with explicit units. Arbitrary custom topology attributes, transformations, auxiliary readers, and analysis caches are outside this contractual scope. Use return_report=True when conversion losses must be inspected before accepting the result; every issue identifies its affected semantic scope as well as its attribute, kind, and reason. Preflight reporting is skipped when neither a report nor strict conversion is requested. Exhaustive reporting is a route-specific guarantee rather than a property inferred from the target form name. Native Structures, Topology, and composed MolSys conversions to their dictionary forms now have explicit profiles with complete declared-source coverage. Direct MolSys projections to native topology or structures, and StructuresDict projections to MolSys or native topology, also audit every declared source attribute. Strict mode therefore rejects a projection when it would discard a present domain. StructuresDict preserves optional temperature, potential-energy, and kinetic-energy series with their units; total energy is derived when both energy components are present. Converting a selected StructuresDict to MolSys or native Topology creates a topology with the same selected atom count as the structural atom axis.

The contractual chemistry and topology/mechanics bridges include RDKit, OpenFF Molecule and Topology, ParmEd Structure, SMILES/SMI, MOL2, and PSF. Rich object forms preserve the chemical fields they actually carry, while SMILES and SMI remain reduced graphs without coordinates or partial charges. OpenFF Topology does not fabricate a trajectory from independent molecule conformers. MOL2 preserves Tripos atom types, charges, coordinates, and ar/am bond semantics through an encapsulated parser backend; unsupported or multi-record input is rejected explicitly. PSF preserves CHARMM force-field atom types, partial charges, source IDs, and explicit connectivity, but it does not invent chemical bond orders or structures.