file:pdb#

Protein Data Bank file format

  • Technical Form Name: file:pdb

  • Form Type: file

Added in version 1.0.0.

API documentation

  • Form adapter module: molsysmt.form.file_pdb

Overview#

file:pdb is a supported representation form in MolSysMT. Protein Data Bank file format

Supported attributes#

The file:pdb form container supports a total of 63 attributes:

Category

Subcategory / Level

Supported Attributes

Topological

Atom Level

atom_index, atom_name, atom_id, atom_type, formal_charge

Topological

Group Level

group_index, group_name, group_id, group_type

Topological

Component Level

component_index, component_name, component_id, component_type

Topological

Chain Level

chain_index, chain_name, chain_id, chain_type

Topological

Molecule Level

molecule_index, molecule_name, molecule_id, molecule_type

Topological

Entity Level

entity_index, entity_name, entity_id, entity_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

Crystallographic & Bioassembly

b_factor, alternate_location, occupancy, bioassembly, n_bioassemblies

Structural

Other Attributes

atom_index, n_atoms

Implemented operations#

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

Function / Module

Description

extract()

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

copy()

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

add()

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

merge()

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

is_form()

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

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_pdb:

Target Form

Form Type

API Documentation

MDAnalysis.Topology

class

to_MDAnalysis_Topology()

MDAnalysis.Universe

class

to_MDAnalysis_Universe()

MDAnalysis.topology.PDBParser

class

to_MDAnalysis_topology_PDBParser()

file:mol2

file

to_file_mol2()

file:pdb

file

to_file_pdb()

mdtraj.PDBTrajectoryFile

class

to_mdtraj_PDBTrajectoryFile()

mdtraj.Topology

class

to_mdtraj_Topology()

mdtraj.Trajectory

class

to_mdtraj_Trajectory()

molsysmt.MolSys

class

to_molsysmt_MolSys()

molsysmt.PDBFileHandler

class

to_molsysmt_PDBFileHandler()

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.PDBFile

class

to_openmm_PDBFile()

openmm.Simulation

class

to_openmm_Simulation()

openmm.System

class

to_openmm_System()

openmm.Topology

class

to_openmm_Topology()

parmed.Structure

class

to_parmed_Structure()

pdbfixer.PDBFixer

class

to_pdbfixer_PDBFixer()

pytraj.Topology

class

to_pytraj_Topology()

pytraj.Trajectory

class

to_pytraj_Trajectory()

string:pdb_text

string

to_string_pdb_text()

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: