Files

MolSysMT supports a comprehensive set of disk file forms spanning native binary files, PDB/mmCIF structures, trajectory binaries, topological definitions, sequence files, and forcefield parameter files.

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Native

Native file formats are specifically engineered for high-performance storage, trajectory streaming, and lossy-free persistence. For complete format specifications and dataset layouts, see the [Native World Files Section].

Form Name	Extension	Description	Native Handler / Parser	Streaming Support
file:h5msm	.h5msm	Native HDF5 binary container	H5MSMFileHandler	Full Chunked & Iterative Streaming

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External

MolSysMT seamlessly reads, parses, and writes major third-party disk file formats across computational chemistry tools:

Form Name	Extension	Description	Native Handler / Parser	Streaming Support
file:pdb	.pdb	Protein Data Bank file	PDBFileHandler	Iterative Streaming (TopologyIterator, StructuresIterator)
file:cif	.cif / .mmcif	Macromolecular Crystallographic Info	CIFFileHandler	Iterative Streaming
file:cif_gz	.cif.gz	Gzipped mmCIF file	CIFFileHandler	Iterative Streaming
file:bcif	.bcif	Binary mmCIF file	Internal BCIF Parser	In-Memory Parsing
file:bcif_gz	.bcif.gz	Gzipped Binary mmCIF file	Internal BCIF Parser	In-Memory Parsing
file:gro	.gro	GROMACS structure file	GROFileHandler	Iterative Streaming
file:dcd	.dcd	CHARMM/NAMD binary trajectory	mdtraj_DCDTrajectoryFile	Bounded Chunked Streaming
file:xtc	.xtc	GROMACS compressed trajectory	mdtraj_XTCTrajectoryFile	Bounded Chunked Streaming
file:h5	.h5 / .trj.h5	MDTraj HDF5 trajectory	mdtraj_HDF5TrajectoryFile	Chunked Streaming
file:trjpk	.trjpk	Compressed trajectory package	Internal Parser	Bounded Streaming
file:mol2	.mol2	Tripos MOL2 chemical format	Third-Party Adapter	In-Memory Parsing
file:prmtop	.prmtop	AMBER topology file	openmm_AmberPrmtopFile	Full Topology Parsing
file:inpcrd	.inpcrd	AMBER coordinate file	openmm_AmberInpcrdFile	Full Coordinate Parsing
file:mdcrd	.mdcrd	AMBER trajectory coordinate file	Third-Party Adapter	Trajectory Parsing
file:top	.top	GROMACS topology file	openmm_GromacsTopFile	Full Topology Parsing
file:psf	.psf	CHARMM topology file	openmm_CharmmPsfFile	Full Topology Parsing
file:crd	.crd	CHARMM coordinate file	openmm_CharmmCrdFile	Full Coordinate Parsing
file:smi	.smi	SMILES chemical sequence file	Third-Party Adapter	In-Memory Parsing
file:fasta	.fasta / .fa	FASTA sequence alignment file	Internal Sequence Parser	Sequence Parsing
file:pir	.pir	PIR sequence alignment file	Internal Sequence Parser	Sequence Parsing
file:xyz	.xyz	Cartesian XYZ coordinate file	Third-Party Adapter	Coordinate Parsing
file:xyznpy	.xyz.npy	NumPy array XYZ trajectory file	Internal Parser	Array Parsing
file:sdf	.sdf	Structure-Data File (small molecules)	Third-Party Adapter	In-Memory Parsing
file:molsys_yaml	.molsys.yaml	Declarative system YAML specification	Internal YAML Parser	Declarative Parsing
file:topology_yaml	.topology.yaml	Declarative topology YAML specification	Internal YAML Parser	Declarative Parsing
file:structures_yaml	.structures.yaml	Declarative structures YAML specification	Internal YAML Parser	Declarative Parsing