file:dcd#

Form adapter and capabilities for file:dcd.

  • Technical Form Name: file:dcd

  • Form Type: file

Added in version 1.0.0.

API documentation

  • Form adapter module: molsysmt.form.file_dcd

Overview#

file:dcd is a supported representation form in MolSysMT. Form adapter and capabilities for file:dcd.

Supported attributes#

The file:dcd form container supports a total of 9 attributes:

Category

Subcategory / Level

Supported Attributes

Topological

Element Counts

n_atoms

Structural

Coordinates & Conformations

structure_index, coordinates, n_structures

Structural

Periodic Box

box, box_shape, box_angles, box_lengths, box_volume

Structural

Other Attributes

n_atoms

Implemented operations#

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

Function / Module

Description

extract()

Extracts a subset of atoms, groups, or structures into a new file:dcd instance.

copy()

Creates an independent deep copy of the file:dcd object in memory.

add()

Adds elements from another system into an existing file:dcd instance.

merge()

Merges multiple systems into a single combined file:dcd 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.

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 file:dcd.

is_form()

Returns True if the provided object is an instance of file:dcd.

Note

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

Supported conversions#

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

Target Form

Form Type

API Documentation

file:dcd

file

to_file_dcd()

file:h5msm

file

to_file_h5msm()

mdtraj.DCDTrajectoryFile

class

to_mdtraj_DCDTrajectoryFile()

molsysmt.MolSys

class

to_molsysmt_MolSys()

molsysmt.Structures

class

to_molsysmt_Structures()

See also

Foundations & Object Architecture:

  • The Molecular System: The fundamental definition of a molecular system, forms, and attributes in MolSysMT.

  • MolSys: In-depth architectural guide on the native molsysmt.MolSys container.

  • Topology: Architectural specification of the native Topology object.

  • Structures: Architectural specification of the native Structures object.

Form Tools & Conversions: