Classes#

MolSysMT provides a form-agnostic architecture capable of digesting, querying, and converting data across a broad matrix of in-memory object classes from native data structures to major third-party libraries in the Python structural biology ecosystem.

Native#

Native MolSysMT objects are engineered for high-performance indexing, zero-loss serialization, and fast spatial queries. For detailed technical specifications, internal schemas, and attributes of each native class, see the [Native World Classes Section].

Class	Description
`molsysmt.MolSys`	Primary unified molecular system container composing topology, structures, and mechanics contracts.
`molsysmt.MolSysBuilder`	Editable native staging container for incremental system assembly and structural modifications.
`molsysmt.MolSysDict`	Declarative, serializable dictionary representation of a complete molecular system.
`molsysmt.Topology`	Native topological graph managing atom inventories, residue groups, and chemical state attributes.
`molsysmt.TopologyDict`	Declarative, serializable dictionary representation of molecular topology.
`molsysmt.Structures`	Native 3D coordinate, periodic cell box, and trajectory frame container.
`molsysmt.StructuresDict`	Declarative, serializable dictionary representation of structural and trajectory data.
`molsysmt.MolecularMechanics`	Native molecular mechanics object managing force field terms, partial charges, and masses.
`molsysmt.MolecularMechanicsDict`	Declarative, serializable dictionary representation of molecular mechanics parameters.
`molsysmt.ViewerJSON`	Lightweight, JSON-serializable graphics schema for 3D visualization.

External#

MolSysMT seamlessly digests and converts object instances from major ecosystem packages:

Class	Library	Description
`mdtraj.Trajectory`	MDTraj	Full 3D coordinate and box trajectory ensemble.
`mdtraj.Topology`	MDTraj	Topological atom and residue hierarchy.
`mdtraj.DCDTrajectoryFile`	MDTraj	DCD file object handle.
`mdtraj.HDF5TrajectoryFile`	MDTraj	HDF5 trajectory file handle. A filtered `msm.extract()` call without an output filename returns an in-memory `mdtraj.Trajectory` and preserves the reader cursor.
`mdtraj.XTCTrajectoryFile`	MDTraj	XTC compressed trajectory file handle.
`mdtraj.PDBTrajectoryFile`	MDTraj	PDB trajectory file handle.
`mdtraj.GroTrajectoryFile`	MDTraj	GRO trajectory file handle.
`mdtraj.AmberRestartFile`	MDTraj	AMBER restart file handle.
`openmm.Topology`	OpenMM	Molecular topology object representation.
`openmm.System`	OpenMM	Physical forcefield system and force terms object.
`openmm.State`	OpenMM	Thermodynamic state holding coordinates, velocities, and energies.
`openmm.Modeller`	OpenMM	Structural editing, residue addition, and solvation object.
`openmm.Simulation`	OpenMM	OpenMM simulation context and integrator workspace.
`openmm.Context`	OpenMM	Low-level OpenMM execution context handle.
`openmm.app.PDBFile`	OpenMM	OpenMM PDB file object representation.
`openmm.app.AmberPrmtopFile`	OpenMM	OpenMM AMBER topology file object.
`openmm.app.AmberInpcrdFile`	OpenMM	OpenMM AMBER coordinate file object.
`openmm.app.CharmmCrdFile`	OpenMM	OpenMM CHARMM coordinate file object.
`openmm.app.CharmmPsfFile`	OpenMM	OpenMM CHARMM topology file object.
`openmm.app.GromacsGroFile`	OpenMM	OpenMM GROMACS coordinate file object.
`openmm.app.GromacsTopFile`	OpenMM	OpenMM GROMACS topology file object.
`MDAnalysis.Universe`	MDAnalysis	Core trajectory and topology container object.
`MDAnalysis.AtomGroup`	MDAnalysis	Atom selection subset group.
`MDAnalysis.Topology`	MDAnalysis	MDAnalysis topology object.
`parmed.Structure`	ParmEd	Unified molecular topology, coordinate, and forcefield structure.
`parmed.gromacs.GromacsTopologyFile`	ParmEd	GROMACS topology file object representation.
`pytraj.Trajectory`	PyTraj	Trajectory container object representation.
`pytraj.Topology`	PyTraj	Topology container object representation.
`openff.toolkit.topology.Molecule`	OpenFF	Small molecule graph with stereochemistry and charges.
`openff.toolkit.topology.Topology`	OpenFF	OpenFF molecular system topology.
`pdbfixer.PDBFixer`	PDBFixer	Protein structure fixing and atom rebuilding tool.
`Bio.PDB.Structure.Structure`	BioPython	Structural PDB hierarchy object.
`Bio.Seq.Seq`	BioPython	Biological sequence object.
`Bio.SeqRecord.SeqRecord`	BioPython	Sequence record with metadata annotations.
`networkx.Graph`	NetworkX	Covalent graph network topology representation.
`rdkit.Chem.Mol`	RDKit	Small molecule topology and 3D conformers representation.
`cupy.ndarray`	CuPy	GPU-accelerated array coordinates.
`mmcif.PdbxContainers.DataContainer`	mmCIF	Raw mmCIF DataContainer representation.
`molsysviewer.MolSysView`	MolSysViewer	Native 3D WebGL viewer widget object.
`XYZ`	PyUnitWizard / NumPy	Raw 3D coordinate Quantity array (`puw.Quantity`) with length units (`nm`).
`nglview.NGLWidget`	NGLView	NGLView 3D widget object.