Seq#

Form adapter and capabilities for biopython.Seq.

  • Technical Form Name: biopython.Seq

  • Form Type: class

Added in version 1.0.0.

API documentation

  • Form adapter module: molsysmt.form.biopython_Seq

Overview#

biopython.Seq is a supported representation form in MolSysMT. Form adapter and capabilities for biopython.Seq.

Supported attributes#

The biopython.Seq form container supports a total of 2 attributes:

Category

Subcategory / Level

Supported Attributes

Topological

Group Level

group_index, group_name

Implemented operations#

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

Function / Module

Description

extract()

Extracts a subset of atoms, groups, or structures into a new biopython.Seq instance.

copy()

Creates an independent deep copy of the biopython.Seq object in memory.

add()

Adds elements from another system into an existing biopython.Seq instance.

merge()

Merges multiple systems into a single combined biopython.Seq object.

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 biopython.Seq.

is_form()

Returns True if the provided object is an instance of biopython.Seq.

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.biopython_Seq:

Target Form

Form Type

API Documentation

biopython.Seq

class

to_biopython_Seq()

biopython.SeqRecord

class

to_biopython_SeqRecord()

file:fasta

file

to_file_fasta()

file:pir

file

to_file_pir()

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: