Structure#

Form adapter and capabilities for parmed.Structure.

Added in version 1.0.0.

API documentation

Overview#

parmed.Structure is a supported representation form in MolSysMT. Form adapter and capabilities for parmed.Structure.

The parmed.Structure form container supports a total of 59 attributes:

Category	Subcategory / Level	Supported Attributes
Topological	Atom Level	`atom_index`, `atom_name`, `atom_id`, `atom_type`, `formal_charge`, `atom_is_aromatic`
Topological	Group Level	`group_index`, `group_name`, `group_id`, `group_type`
Topological	Component Level	`component_index`
Topological	Chain Level	`chain_index`, `chain_name`, `chain_id`, `chain_type`
Topological	Molecule Level	`molecule_index`, `molecule_name`, `molecule_id`, `molecule_type`
Topological	Bonds & Connectivity	`connectivity_completeness`, `bond_index`, `bond_type`, `bond_order`, `fractional_bond_order`, `bond_is_aromatic`, `bond_evidence`, `bonded_atoms`, `inner_bonded_atoms`, `inner_bond_index`, `n_bonds`, `n_inner_bonds`
Topological	Element Counts	`n_atoms`, `n_groups`, `n_components`, `n_chains`, `n_molecules`, `n_entities`, `n_bonds`, `n_inner_bonds`, `n_amino_acids`, `n_nucleotides`, `n_ions`, `n_waters`, `n_small_molecules`, `n_peptides`, `n_proteins`, `n_dnas`, `n_rnas`, `n_lipids`, `n_polysaccharides`, `n_saccharides`
Structural	Coordinates & Conformations	`structure_index`, `coordinates`, `n_structures`
Structural	Periodic Box	`box`, `box_shape`, `box_angles`, `box_lengths`, `box_volume`
Structural	Crystallographic & Bioassembly	`b_factor`
Structural	Other Attributes	`atom_index`, `n_atoms`
Mechanical	Force Field Parameters	`partial_charge`

The form adapter module molsysmt.form.parmed_Structure implements the following functions and modules:

Function / Module	Description
`extract()`	Extracts a subset of atoms, groups, or structures into a new `parmed.Structure` instance.
`copy()`	Creates an independent deep copy of the `parmed.Structure` object in memory.
`add()`	Adds elements from another system into an existing `parmed.Structure` instance.
`merge()`	Merges multiple systems into a single combined `parmed.Structure` object.
`append_structures()`	Appends new coordinate frames or trajectories to the structures container.
`get_topological_attributes`	Module containing getters for topological attributes.
`get_structural_attributes`	Module containing getters for structural attributes.
`get_mechanical_attributes`	Module containing getters for mechanical attributes.
`set`	Module containing setters for updating coordinates, box dimensions, or attributes in-place.
`iterators`	Module providing iterators for streaming trajectory frames and structures.
`has_attribute()`	Checks whether a specific attribute name is supported by `parmed.Structure`.
`is_form()`	Returns `True` if the provided object is an instance of `parmed.Structure`.

Note

Each form adapter in MolSysMT implements only the specific functions that are meaningful for its data model.

The following table lists all direct conversion functions implemented in molsysmt.form.parmed_Structure:

Target Form	Form Type	API Documentation
`file:mol2`	`file`	`to_file_mol2()`
`file:pdb`	`file`	`to_file_pdb()`
`file:psf`	`file`	`to_file_psf()`
`mdtraj.Topology`	`class`	`to_mdtraj_Topology()`
`mdtraj.Trajectory`	`class`	`to_mdtraj_Trajectory()`
`molsysmt.MolSys`	`class`	`to_molsysmt_MolSys()`
`molsysmt.Structures`	`class`	`to_molsysmt_Structures()`
`molsysmt.Topology`	`class`	`to_molsysmt_Topology()`
`nglview.NGLWidget`	`class`	`to_nglview_NGLWidget()`
`openmm.Modeller`	`class`	`to_openmm_Modeller()`
`openmm.Topology`	`class`	`to_openmm_Topology()`
`parmed.GromacsTopologyFile`	`class`	`to_parmed_GromacsTopologyFile()`
`parmed.Structure`	`class`	`to_parmed_Structure()`