file:crd#

CHARMM card (CRD) file format with coordinates.

  • Technical Form Name: file:crd

  • Form Type: file

Added in version 1.0.0.

API documentation

  • Form adapter module: molsysmt.form.file_crd

Overview#

file:crd is a supported representation form in MolSysMT. CHARMM card (CRD) file format with coordinates.

Supported attributes#

The file:crd form container supports a total of 15 attributes:

Category

Subcategory / Level

Supported Attributes

Topological

Atom Level

atom_index, atom_name, atom_id, atom_type

Topological

Group Level

group_index, group_name, group_id, group_type

Topological

Element Counts

n_atoms, n_groups

Structural

Coordinates & Conformations

structure_id, coordinates, n_structures

Structural

Periodic Box

box

Structural

Trajectory Metadata

time

Structural

Other Attributes

atom_index, n_atoms

Implemented operations#

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

Function / Module

Description

extract()

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

copy()

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

add()

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

merge()

Merges multiple systems into a single combined file:crd 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:crd.

is_form()

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

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_crd:

Target Form

Form Type

API Documentation

file:crd

file

to_file_crd()

molsysmt.MolSys

class

to_molsysmt_MolSys()

molsysmt.Structures

class

to_molsysmt_Structures()

molsysmt.Topology

class

to_molsysmt_Topology()

openmm.CharmmCrdFile

class

to_openmm_CharmmCrdFile()

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: