molsysmt.native package

Submodules

molsysmt.native.cif_file_handler module

class molsysmt.native.cif_file_handler.CIFFileHandler(filename, io_mode='r', closed=False)

Bases: object

close()

parse()

molsysmt.native.file_tng module

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

Bases: object

molsysmt.native.file_xtc module

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

Bases: object

molsysmt.native.gro_file_handler module

class molsysmt.native.gro_file_handler.GROAtomicCoordinateEntry

Bases: object

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

Bases: object

close()

dump()

load()

molsysmt.native.gro_file_handler.parse(file)

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

close()

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

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

copy()

get_leap_parameters()

get_openmm_System_parameters()

get_openmm_forcefield_names()

set_parameters(return_non_processed=False, **kwargs)

to_dict()

to_openmm_ForceField()

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

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

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

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

copy()

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

rebuild_atoms(redefine_ids=True, redefine_types=True)

rebuild_chains(redefine_ids=True, redefine_types=True)

rebuild_components(redefine_ids=True, redefine_types=True)

rebuild_entities(redefine_ids=True, redefine_types=True)

rebuild_groups(redefine_ids=True, redefine_types=True)

rebuild_molecules(redefine_ids=True, redefine_types=True)

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

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

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

close()

dump()

load()

molsysmt.native.pdb_file_handler.guess_format_version(file)

molsysmt.native.pdb_file_handler.parse_format33(file)

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

copy()

get_openmm_Context_parameters()

get_openmm_Simulation_parameters()

set_parameters(return_non_processed=False, **kwargs)

to_dict()

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

to_openmm_Integrator()

to_openmm_Platform()

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

molsysmt.native.simulation_dict module

molsysmt.native.simulation_dict.is_simulation_dict(dictionary)

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

Class to store the trajectory data of a molecular system

box

The box of the molecular system in nanometers.

Type:

pint.Quantity of shape (n_structures, 3, 3)

coordinates

The coordinates of the trajectory for each frame.

Type:

pint.Quantity of shape (n_structures, n_atoms, 3)

velocities

The velocities of the trajectory for each frame.

Type:

pint.Quantity of shape (n_structures, n_atoms, 3)

n_atoms

Number of atoms in the trajectory.

Type:

int

n_structures

Number of structures or frames in the trajectory.

Type:

int

time

The times of the trajectory in picoseconds.

Type:

pint.Quantity of shape (n_structures, )

id

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

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 structures or frames to this object.

boxpint.Quantity of shape (n_structures, 3, 3)

The box of the structures

coordinatespint.Quantity of shape (n_structures, n_atoms, 3)

The coordinates of the trajectory for each frame of it in nanometers.

timepint.Quantity of shape (n_structures, )

The times of the trajectory in picoseconds

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

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

molsysmt.native.structures_dict module

molsysmt.native.topology module

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

Bases: DataFrame

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

Bases: DataFrame

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

Bases: DataFrame

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

Bases: DataFrame

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

Bases: DataFrame

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

Bases: DataFrame

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

Bases: DataFrame

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

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

add_bonds(bonded_atom_pairs, skip_digestion=False)

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

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

copy()

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

rebuild_atoms(redefine_ids=True, redefine_types=True)

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

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

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

rebuild_groups(redefine_ids=True, redefine_types=True)

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

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

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

reset_atoms(n_atoms=0)

reset_bonds(n_bonds=0)

reset_chains(n_chains=0)

reset_components(n_components=0)

reset_entities(n_entities=0)

reset_groups(n_groups=0)

reset_molecules(n_molecules=0)

molsysmt.native.trajectory_file module

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

Bases: object

copy()

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

Module contents