molsysmt.native package

Submodules

molsysmt.native.file_tng module

class molsysmt.native.file_tng.TNGFile(filename=None, mode='read')

Bases: object

Placeholder handler for TNG trajectories.

molsysmt.native.file_xtc module

class molsysmt.native.file_xtc.XTCFile(filename=None, mode='read')

Bases: object

Placeholder handler for XTC trajectories.

molsysmt.native.gro_file_handler module

class molsysmt.native.gro_file_handler.GROAtomicCoordinateEntry

Bases: object

In-memory representation of a GRO coordinate entry.

class molsysmt.native.gro_file_handler.GROFileHandler(file, io_mode='r', closed=False, skip_digestion=False)

Bases: object

Handle reading and writing GRO coordinate files.

close()

Close the underlying file.

dump()

Serialize the current entry back to GRO format.

load()

Load and parse the current GRO entry.

molsysmt.native.gro_file_handler.parse(file)

Parse a GRO file-like object into a GROAtomicCoordinateEntry.

molsysmt.native.h5msm_file_handler module

class molsysmt.native.h5msm_file_handler.H5MSMFileHandler(filename, io_mode='r', creator='MolSysMT', compression='gzip', compression_opts=4, int_precision='single', float_precision='single', length_unit=None, time_unit=None, energy_unit=None, temperature_unit=None, charge_unit=None, mass_unit=None, closed=False, skip_digestion=False)

Bases: object

Lightweight handler for reading and writing h5msm files.

close()

Close the underlying HDF5 handle.

write_topology(topology, selection='all', syntax='MolSysMT')

Write a topology object into the file, converting if needed.

molsysmt.native.molecular_mechanics module

class molsysmt.native.molecular_mechanics.MolecularMechanics(forcefield=None, water_model=None, implicit_solvent=None, non_bonded_method=None, cutoff_distance=None, switch_distance=None, dispersion_correction=None, ewald_error_tolerance=None, constraints=None, flexible_constraints=None, rigid_water=None, hydrogen_mass=None, salt_concentration=None, kappa=None, solute_dielectric=None, solvent_dielectric=None, formal_charge=None, partial_charge=None)

Bases: object

Container for molecular mechanics force-field settings.

copy()

Create a deep copy of the MolecularMechanics object.

get_leap_parameters()

Get parameter names for LEaP-compatible force fields.

get_openmm_System_parameters()

Build the keyword dictionary for creating an OpenMM System.

get_openmm_forcefield_names()

Resolve OpenMM force field names for the configured options.

set_parameters(return_non_processed=False, **kwargs)

Standardize and set available parameters from keyword arguments.

to_dict()

Return a dictionary representation of the parameters.

to_openmm_ForceField()

Instantiate an OpenMM ForceField object.

molsysmt.native.molecular_mechanics_dict module

molsysmt.native.molsys module

class molsysmt.native.molsys.MolSys(n_atoms=0, n_groups=0, n_components=0, n_molecules=0, n_entities=0, n_chains=0, n_bonds=0, skip_digestion=False)

Bases: object

Container holding native topology, structures, and molecular mechanics data.

add(item, atom_indices='all', structure_indices='all', keep_ids=True, skip_digestion=False)

Append topology and structures from another MolSys.

add_missing_bonds(threshold='2 angstroms', selection='all', structure_indices=0, syntax='MolSysMT', engine='MolSysMT', with_templates=True, with_distances=True, skip_digestion=False)

Fill missing bonds inferred from the current coordinates.

append_structures(item, atom_indices='all', structure_indices='all', skip_digestion=False)

Append structures from another MolSys while aligning atom indices.

copy()

Deep-copy the MolSys.

extract(atom_indices='all', structure_indices='all', copy_if_all=True, skip_digestion=False)

Return a copy or subset of the molecular system.

get(element='system', selection='all', structure_indices='all', mask=None, syntax='MolSysMT', get_missing_bonds=True, output_type='values', skip_digestion=False, **kwargs)

Proxy to molsysmt.get() using this MolSys as input.

info(element='system', selection='all', syntax='MolSysMT', skip_digestion=False)

Return a text summary of the MolSys.

rebuild_atoms(redefine_ids=True, redefine_types=True)

Recompute atom ids/types from the present topology.

rebuild_chains(redefine_ids=True, redefine_types=True)

Recompute chain ids/types from the present topology.

rebuild_components(redefine_ids=True, redefine_types=True)

Recompute component ids/types from the present topology.

rebuild_entities(redefine_ids=True, redefine_types=True)

Recompute entity ids/types from the present topology.

rebuild_groups(redefine_ids=True, redefine_types=True)

Recompute group ids/types from the present topology.

rebuild_molecules(redefine_ids=True, redefine_types=True)

Recompute molecule ids/types from the present topology.

remove(atom_indices=None, structure_indices=None, copy_if_None=False, skip_digestion=False)

Remove atoms and/or structures by index and return the resulting MolSys.

to_form(to_form, skip_digestion=False, **kwargs)

Convert the MolSys to a target form.

molsysmt.native.pdb_atomic_coordinate_entry module

class molsysmt.native.pdb_atomic_coordinate_entry.AtomRecord

Bases: object

to_string(output='short_string')

class molsysmt.native.pdb_atomic_coordinate_entry.AuthorRecord

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.BookkeepingSection

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.CaveatRecord

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.CispepRecord

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.CompndRecord

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.ConectRecord

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.ConnectivityAnnotationSection

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.ConnectivitySection

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.CoordinateSection

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.Cryst1Record

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.CrystallographicAndCoordinateTransformationSection

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.Dbref1Dbref2Record

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.DbrefRecord

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.ExpdtaRecord

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.FormulRecord

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.HeaderRecord

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.HelixRecord

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.HetRecord

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.HetatmRecord

Bases: AtomRecord

class molsysmt.native.pdb_atomic_coordinate_entry.HeterogenSection

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.HetnamRecord

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.HetsynRecord

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.JrnlRecord

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.KeywdsRecord

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.LinkRecord

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.MasterRecord

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.MdltypRecord

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.MiscellaneousFeaturesSection

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.Model

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.ModresRecord

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.MtrixRecord

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.NummdlRecord

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.ObslteRecord

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.OrigxRecord

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.PDBAtomicCoordinateEntry

Bases: object

Aggregate of PDB record sections for atomic coordinate entries.

class molsysmt.native.pdb_atomic_coordinate_entry.PrimaryStructureSection

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.RemarkRecord

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.RevdatRecord

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.ScaleRecord

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.SecondaryStructureSection

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.SeqadvRecord

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.SeqresRecord

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.SheetRecord

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.SiteRecord

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.SourceRecord

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.SplitRecord

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.SprsdeRecord

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.SsbondRecord

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.TitleRecord

Bases: object

class molsysmt.native.pdb_atomic_coordinate_entry.TitleSection

Bases: object

molsysmt.native.pdb_file_handler module

class molsysmt.native.pdb_file_handler.PDBFileHandler(file, io_mode='r', closed=False, skip_digestion=False)

Bases: object

Handle reading and writing PDB coordinate files.

close()

Close the underlying file handle.

dump()

Serialize the current entry back to PDB format.

load()

Load and parse the PDB content.

molsysmt.native.pdb_file_handler.guess_format_version(file)

Return the PDB format version guessed from the file contents.

molsysmt.native.pdb_file_handler.parse_format33(file)

Parse a PDB file using the v3.3 specification.

molsysmt.native.simulation module

class molsysmt.native.simulation.Simulation(molecular_system=None, remove_cm_motion=True, integrator=None, temperature=None, collisions_rate=None, integration_timestep=None, initial_velocities_to_temperature=True, constraint_tolerance=1e-05, platform='CUDA', cuda_precision='mixed')

Bases: object

Container for simulation parameters used to build OpenMM objects.

copy()

Deep-copy the Simulation settings.

get_openmm_Context_parameters()

Return keyword arguments required to build an OpenMM Context.

get_openmm_Simulation_parameters()

Return keyword arguments required to build an OpenMM Simulation.

set_parameters(return_non_processed=False, **kwargs)

Standardize and set allowed parameters from keyword arguments.

to_dict()

Return a dictionary representation of the simulation parameters.

to_openmm_Context(molecular_system=None, selection='all', structure_indices='all')

Create an OpenMM Context from the current settings.

to_openmm_Integrator()

Build an OpenMM Integrator instance for the configured dynamics.

to_openmm_Platform()

Return the selected OpenMM Platform.

to_openmm_Simulation(molecular_system=None, selection='all', structure_indices='all')

Create an OpenMM Simulation from the current settings.

molsysmt.native.simulation_dict module

molsysmt.native.simulation_dict.is_simulation_dict(dictionary)

Return True if the dictionary only contains simulation parameter keys.

molsysmt.native.structures module

class molsysmt.native.structures.Structures(constant_time_step=False, time_step=None, constant_id_step=False, id_step=None, constant_box=False, structure_id=None, time=None, coordinates=None, velocities=None, box=None, b_factor=None, alternate_location=None, bioassembly=None, temperature=None, potential_energy=None, kinetic_energy=None, skip_digestion=False)

Bases: object

Storing per-structure data (coordinates, box, time, energies) for a molecular system.

add(item, atom_indices='all', structure_indices='all', skip_digestion=False)

Concatenate atomic data from another Structures object along the atom axis.

append(structure_id=None, time=None, coordinates=None, velocities=None, box=None, temperature=None, potential_energy=None, kinetic_energy=None, b_factor=None, alternate_location=None, atom_indices='all', structure_indices='all', skip_digestion=False)

Append one or more structures and associated metadata to this object.

append_structures(item, atom_indices='all', structure_indices='all', skip_digestion=False)

Append structures from another Structures object.

copy()

Returns a copy of the structures.

extract(atom_indices='all', structure_indices='all', copy_if_all=False, skip_digestion=False)

Returns a new Structures object with the specified atoms and/or structures.

Parameters:

• atom_indices (str or arraylike of int, default='all') – The indices of the extracted atoms.

• structure_indices (str or arraylike of int, default='all') – The indices of the extracted structures or frames.

Returns:

The new structures object with the extracted atoms and frames.

Return type:

Structures

get_n_structures()

molsysmt.native.structures_dict module

molsysmt.native.topology module

class molsysmt.native.topology.Atoms_DataFrame(n_atoms=0)

Bases: DataFrame

Pandas DataFrame wrapper storing atom-level topology fields.

class molsysmt.native.topology.Bonds_DataFrame(n_bonds=0)

Bases: DataFrame

Pandas DataFrame wrapper storing bond connectivity.

class molsysmt.native.topology.Chains_DataFrame(n_chains=0)

Bases: DataFrame

Pandas DataFrame wrapper storing chain-level fields.

class molsysmt.native.topology.Components_DataFrame(n_components=0)

Bases: DataFrame

Pandas DataFrame wrapper storing component-level fields.

class molsysmt.native.topology.Entities_DataFrame(n_entities=0)

Bases: DataFrame

Pandas DataFrame wrapper storing entity-level fields.

class molsysmt.native.topology.Groups_DataFrame(n_groups=0)

Bases: DataFrame

Pandas DataFrame wrapper storing group-level fields.

class molsysmt.native.topology.Molecules_DataFrame(n_molecules=0)

Bases: DataFrame

Pandas DataFrame wrapper storing molecule-level fields.

class molsysmt.native.topology.Topology(n_atoms=0, n_groups=0, n_components=0, n_molecules=0, n_entities=0, n_chains=0, n_bonds=0, skip_digestion=False)

Bases: object

Native topology container including atoms, groups, chains, and bonds.

add(item, atom_indices='all', keep_ids=True, skip_digestion=False)

Append another topology, offsetting indices as needed.

add_bonds(bonded_atom_pairs, skip_digestion=False)

Append new bonds given atom index pairs.

add_missing_bonds(selection='all', syntax='MolSysMT', skip_digestion=False)

Infer and add missing bonds using geometric templates.

compare(item, rule='equal', output_type='boolean', skip_digestion=False, **kwargs)

Compare topology content with another topology.

copy()

Return a deep copy of the topology tables.

extract(atom_indices='all', copy_if_all=False, skip_digestion=False)

Return a subset topology with the selected atoms and associated hierarchy.

get_atom_indices(**kwargs)

Select atom indices matching the provided hierarchical filters.

get_n_atoms()

get_n_bonds()

get_n_chains()

get_n_components()

get_n_entities()

get_n_groups()

get_n_molecules()

rebuild_atoms(redefine_ids=True, redefine_types=True)

Regenerate atom ids/types from names and current counts.

rebuild_chains(redefine_indices=True, redefine_ids=True, redefine_types=True, redefine_names=True)

Rebuild chain mapping and metadata.

rebuild_components(redefine_indices=True, redefine_ids=True, redefine_names=True, redefine_types=True)

Rebuild component mapping and metadata.

rebuild_entities(redefine_indices=True, redefine_ids=True, redefine_names=True, redefine_types=True)

Rebuild entity mapping and metadata.

rebuild_groups(redefine_ids=True, redefine_types=True)

Regenerate group ids/types from names and current counts.

rebuild_molecules(redefine_indices=True, redefine_ids=True, redefine_names=True, redefine_types=True, molecules_as_components=True)

Rebuild molecule mapping and metadata.

remove(atom_indices=None, copy_if_None=False, skip_digestion=False)

Remove atoms by index and return the resulting topology.

remove_bonds(bond_indices='all', skip_digestion=False)

Drop bonds by index.

reset_atoms(n_atoms=0)

Reset atoms table to a new size.

reset_bonds(n_bonds=0)

Reset bonds table to a new size.

reset_chains(n_chains=0)

Reset chains table to a new size.

reset_components(n_components=0)

Reset components table to a new size.

reset_entities(n_entities=0)

Reset entities table to a new size.

reset_groups(n_groups=0)

Reset groups table to a new size.

reset_molecules(n_molecules=0)

Reset molecules table to a new size.

molsysmt.native.trajectory_file module

class molsysmt.native.trajectory_file.TrajectoryFile(filepath=None, mode='read')

Bases: object

Unified interface to read various trajectory file formats.

copy()

Return a shallow copy of the trajectory handle.

read_frames(atom_indices='all', structure_indices='all')

Read selected frames and return IDs, time, coordinates, and box.

molsysmt.native.universal_json module

class molsysmt.native.universal_json.UniversalJSON(data=<factory>, compressed=False, compression='none', schema=<factory>)

Bases: object

Storing a general JSON representation of a molecular system (molsysmt.UniversalJSON).

The data dict follows a broad schema: - metadata: unitless descriptive fields. - topology: per-atom columns (ids, names, group/chain/entity ids, element symbols, charges). - bonds: atom_pairs (0-based) plus optional order. - coordinates: collections with structures, each holding coordinates (nm), optional time

(ps), and optional box (vectors v0, v1, v2 in nm).

• annotations: optional derived data.

compression/compressed control optional gzip serialization. Use to_dict(copy=True) for a JSON-compatible dict and copy() for deep copies.

Parameters:

• data (Dict[str, Any])

• compressed (bool)

• compression (Literal['none', 'gzip'])

• schema (Dict[str, str])

compressed: bool = False

compression: Literal['none', 'gzip'] = 'none'

copy()

Return a deep copy of the instance.

Return type:

UniversalJSON

data: Dict[str, Any]

dump(fp, *, indent=None, compression=None)

Write content to a file path or file-like as JSON (optionally gzipped).

Parameters:

• fp (str | TextIO)

• indent (int | None)

• compression (Literal['none', 'gzip'] | None)

Return type:

None

dumps(indent=None)

Return a JSON text representation.

Parameters:

indent (int | None)

Return type:

str

schema: Dict[str, str]

to_dict(copy=True)

Return the underlying JSON-compatible dict.

Parameters:

copy (bool)

Return type:

Dict[str, Any]

molsysmt.native.viewer_json module

class molsysmt.native.viewer_json.ViewerJSON(data=<factory>, compressed=False, compression='none', schema=<factory>)

Bases: object

Storing a minimal viewer-friendly JSON payload (molsysmt.ViewerJSON).

The underlying data dict follows the viewer schema:

• atoms: per-atom columns (ids/names/group/chain/entity ids, element symbol, optional charges). All ids/names are strings; charges are unitless integers.

• bonds: atom_pairs (0-based index pairs) and optional order.

• structures: list of structures with coordinates (nm), optional time (ps), and optional box with box vectors (v0, v1, v2 in nm).

compression/compressed control optional gzip serialization. Use to_dict(copy=True) to get a JSON-compatible dict and copy() for deep copies.

Parameters:

• data (Dict[str, Any])

• compressed (bool)

• compression (Literal['none', 'gzip'])

• schema (Dict[str, str])

compressed: bool = False

compression: Literal['none', 'gzip'] = 'none'

copy()

Return a deep copy of the instance.

Return type:

ViewerJSON

data: Dict[str, Any]

dump(fp, *, indent=None, compression=None)

Write content to a file path or file-like as JSON (optionally gzipped).

Parameters:

• fp (str | TextIO)

• indent (int | None)

• compression (Literal['none', 'gzip'] | None)

Return type:

None

dumps(indent=None)

Return a JSON text representation.

Parameters:

indent (int | None)

Return type:

str

schema: Dict[str, str]

to_dict(copy=True)

Return the underlying JSON-compatible dict.

Notes: - All values must be JSON types (dict, list, str, int, float, bool, None).

Parameters:

copy (bool)

Return type:

Dict[str, Any]

Module contents