Items and Forms#

In MolSysMT, a fundamental distinction is made between a physical item and its data representation form:

Item: A concrete data container holding molecular information. An item can be a file path on disk (such as '181l.bcif.gz'), an in-memory Python object (such as an mdtraj.Trajectory instance), a web database identifier (such as '181L'), or a text string (such as an amino acid sequence).
Form: The standardized type tag or schema label that identifies how an item’s data is structured (such as 'file:bcif', 'molsysmt.MolSys', 'mdtraj.Trajectory', 'string:pdb_id').

Functions in MolSysMT inspect items dynamically to determine their form. You can query the form of any item using molsysmt.basic.get_form():

import molsysmt as msm

item = msm.systems['T4 lysozyme L99A']['181l.bcif.gz']
msm.get_form(item)

'file:bcif.gz'

Querying Supported Forms#

You can inspect all forms supported by your current environment using molsysmt.supported.forms(). Passing a specific form_type filters the catalog by category ('file', 'class', or 'string'):

# Query supported file forms
msm.supported.forms(form_type='file')

# Query supported Python class forms
msm.supported.forms(form_type='class')

# Query supported string forms
msm.supported.forms(form_type='string')

Catalog of Supported Forms#

The tables below provide the complete reference of supported forms categorized by representation type.

Files#

File forms represent molecular structures, topologies, or trajectories stored in disk files.

Form	Info
`file:bcif`
`file:bcif.gz`
`file:cif`
`file:cif.gz`
`file:crd`	CHARMM card (CRD) file format with coordinates.
`file:dcd`
`file:fasta`	FASTA sequence file format
`file:gro`	Gromacs gro file format
`file:h5`
`file:h5msm`
`file:inpcrd`	AMBER ASCII restart/inpcrd file format
`file:mdcrd`	AMBER MDCRD coordinate/trajectory file format
`file:mol2`
`file:molsys_yaml`	Human-authored declarative YAML molecular system file.
`file:pdb`	Protein Data Bank file format
`file:pir`	PIR/NBRF sequence file format
`file:prmtop`	AMBER parameter/topology file format
`file:psf`	CHARMM Protein Structure File (PSF).
`file:smi`	SMILES file format (.smi)
`file:structures_yaml`	Human-authored declarative YAML structures file.
`file:top`	GROMACS topology file format
`file:topology_yaml`	Human-authored declarative YAML topology file.
`file:trjpk`
`file:xtc`
`file:xyz`	MolSysMT ASCII XYZ coordinate file format
`file:xyznpy`	XYZ file format like saved with Numpy

Classes#

Class forms represent in-memory Python objects from third-party libraries (such as MDTraj, PyTraj, MDAnalysis, OpenMM, and ParmEd) as well as native MolSysMT classes.

Form	Info
`biopython.PDBStructure`
`biopython.Seq`
`biopython.SeqRecord`
`cupy_ndarray`
`MDAnalysis.AtomGroup`
`MDAnalysis.Topology`
`MDAnalysis.topology.PDBParser`
`MDAnalysis.Universe`
`mdtraj.AmberRestartFile`
`mdtraj.DCDTrajectoryFile`
`mdtraj.GroTrajectoryFile`
`mdtraj.HDF5TrajectoryFile`
`mdtraj.PDBTrajectoryFile`
`mdtraj.Topology`
`mdtraj.Trajectory`
`mdtraj.XTCTrajectoryFile`
`mmcif.PdbxContainers.DataContainer`
`molsysmt.CIFFileHandler`
`molsysmt.GROFileHandler`
`molsysmt.H5MSMFileHandler`
`molsysmt.MolecularMechanics`
`molsysmt.MolecularMechanicsDict`
`molsysmt.MolSys`
`molsysmt.MolSysBuilder`	Editable native molecular system builder.
`molsysmt.MolSysDict`	Declarative serializable molecular system dictionary.
`molsysmt.PDBFileHandler`
`molsysmt.Structures`
`molsysmt.StructuresDict`
`molsysmt.Topology`
`molsysmt.TopologyDict`	Declared, serializable topology representation.
`molsysmt.ViewerJSON`
`molsysviewer.MolSysView`	MolSysViewer visualization native object.
`networkx.Graph`
`nglview.NGLWidget`
`openff.Molecule`	OpenFF Toolkit Molecule
`openff.Topology`	OpenFF Toolkit Topology
`openmm.AmberInpcrdFile`
`openmm.AmberPrmtopFile`
`openmm.CharmmCrdFile`
`openmm.CharmmPsfFile`
`openmm.Context`
`openmm.GromacsGroFile`
`openmm.GromacsTopFile`
`openmm.Modeller`
`openmm.PDBFile`
`openmm.Simulation`
`openmm.State`
`openmm.System`
`openmm.Topology`
`parmed.GromacsTopologyFile`
`parmed.Structure`
`pdbfixer.PDBFixer`
`pytraj.Topology`
`pytraj.Trajectory`
`rdkit.Mol`
`XYZ`

Strings#

String forms represent character strings including web database accessions (such as 'pdb:id', 'uniprot:id'), raw record text (such as 'string:pdb_text'), and sequence strings (such as 'string:amino_acids_1').

Form	Info
`string:alphafold_id`
`string:amino_acids_1`
`string:amino_acids_3`
`string:pdb_id`
`string:pdb_text`	Protein Data Bank file format
`string:smiles`	SMILES (Simplified Molecular Input Line Entry System) string
`string:uniprot_id`	UniProt accession number string