PDBFixer#

Form adapter and capabilities for pdbfixer.PDBFixer.

  • Technical Form Name: pdbfixer.PDBFixer

  • Form Type: class

Added in version 1.0.0.

API documentation

  • Form adapter module: molsysmt.form.pdbfixer_PDBFixer

Overview#

pdbfixer.PDBFixer is a supported representation form in MolSysMT. Form adapter and capabilities for pdbfixer.PDBFixer.

Supported attributes#

The pdbfixer.PDBFixer form container supports a total of 48 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

Component Level

component_index, component_type

Topological

Chain Level

chain_index, chain_id

Topological

Molecule Level

molecule_index, molecule_type

Topological

Bonds & Connectivity

bond_index, 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, structure_id, coordinates, n_structures

Structural

Periodic Box

box, box_shape, box_angles, box_lengths, box_volume

Structural

Trajectory Metadata

time

Structural

Other Attributes

atom_index, n_atoms

Implemented operations#

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

Function / Module

Description

extract()

Extracts a subset of atoms, groups, or structures into a new pdbfixer.PDBFixer instance.

copy()

Creates an independent deep copy of the pdbfixer.PDBFixer object in memory.

add()

Adds elements from another system into an existing pdbfixer.PDBFixer instance.

merge()

Merges multiple systems into a single combined pdbfixer.PDBFixer 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 pdbfixer.PDBFixer.

is_form()

Returns True if the provided object is an instance of pdbfixer.PDBFixer.

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.pdbfixer_PDBFixer:

Target Form

Form Type

API Documentation

biopython.Seq

class

to_biopython_Seq()

biopython.SeqRecord

class

to_biopython_SeqRecord()

file:pdb

file

to_file_pdb()

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()

pdbfixer.PDBFixer

class

to_pdbfixer_PDBFixer()

string:amino_acids_1

string

to_string_amino_acids_1()

string:amino_acids_3

string

to_string_amino_acids_3()

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: